@article {pmid33639345, year = {2021}, author = {Zhang, X and Wen, K and Ding, D and Liu, J and Lei, Z and Chen, X and Ye, G and Zhang, J and Shen, H and Yan, C and Dong, S and Huang, Q and Lin, Y}, title = {Size-dependent adverse effects of microplastics on intestinal microbiota and metabolic homeostasis in the marine medaka (Oryzias melastigma).}, journal = {Environment international}, volume = {151}, number = {}, pages = {106452}, doi = {10.1016/j.envint.2021.106452}, pmid = {33639345}, issn = {1873-6750}, abstract = {Microplastic (MP) is an emerging environmental pollutant and exposure to MPs has been associated with numerous adverse health outcomes in both wild and laboratory animals. The toxicity of MPs depends on concentration, exposure time, chemical composition and size distribution, but the impacts of particle size remain inconclusive yet. In this study, adult marine medaka (Oryzias melastigma) were exposed to different size of polystyrene MPs (PS-MPs) with concentration of 10 mg/L for 60 days and the growth performance, lipid metabolism, immune parameters and gut microbiome were determined. Results indicated that particle size is a dominant factor causing lipid metabolism disorders and hepatic toxicity in PS-MPs-exposed fish. The bodyweight, adipocyte size and hepatic lipid contents were significantly increased in 200 μm PS-MPs-exposed fish, while 2 and 10 μm PS-MPs-exposed fish exhibited liver injury principally manifested asthepresence oflittlefibrosis and inflammation. Given that larger particles could not enter the circulatory system, the impacts of PS-MPs on intestinal microbial biota homeostasis were further investigated. The results not only showed the characterization of gut microbial communities in Oryzias melastigma, but also indicated that microbial diversity and composition were altered in gut of fish exposed to PS-MPs, in particular 200 μm PS-MPs. The differentially abundant bacterial taxa in PS-MPs-exposed fish mainly belonged to the phylum Verrucomicrobia, Firmicutes and Fusobacteria. And furthermore, increased abundance of Verrucomicrobia and Firmicutes/Bacteroidetes ratio and decreased Fusobacteria were correlated with the increased bodyweight. Intestinal microbiome should play a critical role in regulating host lipid metabolism in fish exposed to lager size of PS-MPs.}, }
@article {pmid33639341, year = {2021}, author = {Constance, LA and Thissen, JB and Jaing, CJ and McLoughlin, KS and Rowland, RRR and Serão, NVL and Cino-Ozuna, AG and Niederwerder, MC}, title = {Gut microbiome associations with outcome following co-infection with porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2) in pigs immunized with a PRRS modified live virus vaccine.}, journal = {Veterinary microbiology}, volume = {254}, number = {}, pages = {109018}, doi = {10.1016/j.vetmic.2021.109018}, pmid = {33639341}, issn = {1873-2542}, abstract = {Porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2) are two of the most significant pathogens affecting swine. Co-infections are common and result in respiratory disease and reduced weight gain in growing pigs. Although PRRS modified live virus (MLV) vaccines are widely used to decrease PRRS-associated losses, they are generally considered inadequate for disease control. The gut microbiome provides an alternative strategy to enhance vaccine efficacy and improve PRRS control. The objective of this study was to identify gut microbiome characteristics associated with improved outcome in pigs immunized with a PRRS MLV and co-challenged with PRRSV and PCV2b. Twenty-eight days after vaccination and prior to co-challenge, fecal samples were collected from an experimental population of 50 nursery pigs. At 42 days post-challenge, 20 pigs were retrospectively identified as having high or low growth outcomes during the post-challenge period. Gut microbiomes of the two outcome groups were compared using the Lawrence Livermore Microbial Detection Array (LLMDA) and 16S rDNA sequencing. High growth outcomes were associated with several gut microbiome characteristics, such as increased bacterial diversity, increased Bacteroides pectinophilus, decreased Mycoplasmataceae species diversity, higher Firmicutes:Bacteroidetes ratios, increased relative abundance of the phylum Spirochaetes, reduced relative abundance of the family Lachnospiraceae, and increased Lachnospiraceae species C6A11 and P6B14. Overall, this study identifies gut microbiomes associated with improved outcomes in PRRS vaccinated pigs following a polymicrobial respiratory challenge and provides evidence towards the gut microbiome playing a role in PRRS vaccine efficacy.}, }
@article {pmid33639178, year = {2021}, author = {Troyer, EA and Kohn, JN and Ecklu-Mensah, G and Aleti, G and Rosenberg, DR and Hong, S}, title = {Searching for host immune-microbiome mechanisms in obsessive-compulsive disorder: A narrative literature review and future directions.}, journal = {Neuroscience and biobehavioral reviews}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.neubiorev.2021.02.034}, pmid = {33639178}, issn = {1873-7528}, abstract = {Obsessive-compulsive disorder (OCD) is disabling and often treatment-refractory. Host immunity and gut microbiota have bidirectional communication with each other and with the brain. Perturbations to this axis have been implicated in neuropsychiatric disorders, but immune-microbiome signaling in OCD is relatively underexplored. We review support for further pursuing such investigations in OCD, including: 1) gut microbiota has been associated with OCD, but causal pathogenic mechanisms remain unclear; 2) early environmental risk factors for OCD overlap with critical periods of immune-microbiome development; 3) OCD is associated with increased risk of immune-mediated disorders and changes in immune parameters, which are separately associated with the microbiome; and 4) gut microbiome manipulations in animal models are associated with changes in immunity and some obsessive-compulsive symptoms. Theoretical pathogenic mechanisms could include microbiota programming of cytokine production, promotion of expansion and trafficking of peripheral immune cells to the CNS, and regulation of microglial function. Immune-microbiome signaling in OCD requires further exploration, and may offer novel insights into pathogenic mechanisms and potential treatment targets for this disabling disorder.}, }
@article {pmid33639033, year = {2021}, author = {Shanahan, ER and McMaster, JJ and Staudacher, HM}, title = {Conducting research on diet-microbiome interactions: A review of current challenges, essential methodological principles, and recommendations for best practice in study design.}, journal = {Journal of human nutrition and dietetics : the official journal of the British Dietetic Association}, volume = {}, number = {}, pages = {}, doi = {10.1111/jhn.12868}, pmid = {33639033}, issn = {1365-277X}, support = {//William Arthur Martin à Beckett Cancer Research Trust (Australia)/ ; //Alfred Deakin Postdoctoral Research Fellowship/ ; }, abstract = {Diet is one of the strongest modulators of the gut microbiome. However, the complexity of the interactions between diet and the microbial community emphasises the need for a robust study design and continued methodological development. This review aims to summarise considerations for conducting high-quality diet-microbiome research, outline key challenges unique to the field, and provide advice for addressing these in a practical manner useful to dietitians, microbiologists, gastroenterologists and other diet-microbiome researchers. Searches of databases and references from relevant articles were conducted using the primary search terms 'diet', 'diet intervention', 'dietary analysis', 'microbiome' and 'microbiota', alone or in combination. Publications were considered relevant if they addressed methods for diet and/or microbiome research, or were a human study relevant to diet-microbiome interactions. Best-practice design in diet-microbiome research requires appropriate consideration of the study population and careful choice of trial design and data collection methodology. Ongoing challenges include the collection of dietary data that accurately reflects intake at a timescale relevant to microbial community structure and metabolism, measurement of nutrients in foods pertinent to microbes, improving ability to measure and understand microbial metabolic and functional properties, adequately powering studies, and the considered analysis of multivariate compositional datasets. Collaboration across the disciplines of nutrition science and microbiology is crucial for high-quality diet-microbiome research. Improvements in our understanding of the interaction between nutrient intake and microbial metabolism, as well as continued methodological innovation, will facilitate development of effective evidence-based personalised dietary treatments.}, }
@article {pmid33639022, year = {2021}, author = {Říhová, J and Batani, G and Rodríguez-Ruano, SM and Martinů, J and Vácha, F and Nováková, E and Hypša, V}, title = {A new symbiotic lineage related to Neisseria and Snodgrassella arises from the dynamic and diverse microbiomes in sucking lice.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.15866}, pmid = {33639022}, issn = {1365-294X}, abstract = {The phylogenetic diversity of symbiotic bacteria in sucking lice suggests that lice have a complex history of symbiont acquisition, loss, and replacement throughout their evolution. These processes have resulted in the establishment of different, phylogenetically distant bacteria as obligate mutualists in different louse groups. By combining metagenomics and amplicon screening across several populations of three louse species (members of the genera Polyplax and Hoplopleura) we describe a novel louse symbiont lineage related to Neisseria and Snodgrassella, and show its independent origin in the two louse genera. While the genomes of these symbionts are highly similar, their respective distributions and status within lice microbiomes indicate that they have different functions and history. In Hoplopleura acanthopus, the Neisseriaceae-related bacterium is a dominant obligate symbiont present across several host populations. In contrast, the Polyplax microbiomes are dominated by the obligate symbiont Legionella polyplacis, with the Neisseriaceae-related bacterium co-occurring only in some samples and with much lower abundance. The results thus support the view that compared to other exclusively blood feeding insects, Anoplura possess a unique capacity to acquire symbionts from diverse groups of bacteria.}, }
@article {pmid33638901, year = {2021}, author = {Shah, AS and Wakelin, SA and Moot, DJ and Blond, C and Laugraud, A and Ridgway, HJ}, title = {Trifolium repens and T. subterraneum modify their nodule microbiome in response to soil pH.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jam.15050}, pmid = {33638901}, issn = {1365-2672}, abstract = {AIMS: The influence of soil edaphic factors on recruitment and composition of bacteria in the legume nodule is unknown. Typically, low (acidic) pH soils have a negative effect on the plant-rhizobia symbiosis and thereby reduce clover growth. However, the specific relationship between soil pH and the ecology of rhizobia is unknown, in either their free-living or nodule-inhabiting states. We used New Zealand pasture systems with soils of different pH, and white (WC) and subterranean (SC) clovers, to examine the relationship between soil pH and the diversity of bacteria that inhabit the nodules.<br><br>METHODS AND RESULTS: Amplicon sequencing (16S rRNA) assessed the bacterial community in 5,299 nodules recovered from both legume species grown in 47 soils of different edaphic (including pH) properties. Fewer nodules were formed on both clovers at low soil pH. As expected, rhizobia comprised ~ 92% of the total reads in both clovers, however 28 non-rhizobia genera were also present. Soil pH influenced the community structure of bacteria within the nodule, and this was more evident in non-Rhizobium taxa than Rhizobium. Host strongly influenced the diversity of bacteria in the nodules. The alpha diversity of nodule microbiome in SC nodules was higher than in WC nodules and SC nodules also harbored a higher relative abundance of non-Rhizobium bacteria than WC. Beta diversity of Rhizobium and non-Rhizobium bacteria was influenced more by clover species rather than edaphic factors.<br><br>CONCLUSIONS: The results indicate that these clover species modified their nodule biomes in response to pH-stress.<br><br>The non-Rhizobium bacteria may have some functional significance (such as improved clover persistence in low pH soils) in legume nodules.}, }
@article {pmid33637779, year = {2021}, author = {Han, Z and Thuy-Boun, PS and Pfeiffer, W and Vartabedian, VF and Torkamani, A and Teijaro, JR and Wolan, DW}, title = {Identification of an N-acetylneuraminic acid-presenting bacteria isolated from a human microbiome.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {4763}, pmid = {33637779}, issn = {2045-2322}, support = {CTSA/TR/NCATS NIH HHS/United States ; R21 AI139744/AI/NIAID NIH HHS/United States ; }, abstract = {N-Acetylneuraminic acid is the most abundant sialic acid (SA) in humans and is expressed as the terminal sugar on intestinal mucus glycans. Several pathogenic bacteria harvest and display host SA on their own surfaces to evade Siglec-mediated host immunity. While previous studies have identified bacterial enzymes associated with SA catabolism, no reported methods permit the selective labeling, tracking, and quantitation of SA-presenting microbes within complex multi-microbial systems. We combined metabolic labeling, click chemistry, 16S rRNA gene, and whole-genome sequencing to track and identify SA-presenting microbes from a cultured human fecal microbiome. We isolated a new strain of Escherichia coli that incorporates SA onto its own surface and encodes for the nanT, neuA, and neuS genes necessary for harvesting and presenting SA. Our method is applicable to the identification of SA-presenting bacteria from human, animal, and environmental microbiomes, as well as providing an entry point for the investigation of surface-expressed SA-associated structures.}, }
@article {pmid33637740, year = {2021}, author = {Goyal, A and Wang, T and Dubinkina, V and Maslov, S}, title = {Ecology-guided prediction of cross-feeding interactions in the human gut microbiome.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {1335}, pmid = {33637740}, issn = {2041-1723}, support = {GBMF4513//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; }, abstract = {Understanding a complex microbial ecosystem such as the human gut microbiome requires information about both microbial species and the metabolites they produce and secrete. These metabolites are exchanged via a large network of cross-feeding interactions, and are crucial for predicting the functional state of the microbiome. However, till date, we only have information for a part of this network, limited by experimental throughput. Here, we propose an ecology-based computational method, GutCP, using which we predict hundreds of new experimentally untested cross-feeding interactions in the human gut microbiome. GutCP utilizes a mechanistic model of the gut microbiome with the explicit exchange of metabolites and their effects on the growth of microbial species. To build GutCP, we combine metagenomic and metabolomic measurements from the gut microbiome with optimization techniques from machine learning. Close to 65% of the cross-feeding interactions predicted by GutCP are supported by evidence from genome annotations, which we provide for experimental testing. Our method has the potential to greatly improve existing models of the human gut microbiome, as well as our ability to predict the metabolic profile of the gut.}, }
@article {pmid33637574, year = {2021}, author = {Loftie-Eaton, W and Crabtree, A and Perry, D and Millstein, J and Baytosh, J and Stalder, T and Robison, BD and Forney, LJ and Top, EM}, title = {Contagious Antibiotic Resistance: Plasmid Transfer Among Bacterial Residents of the Zebrafish Gut.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02735-20}, pmid = {33637574}, issn = {1098-5336}, abstract = {By characterizing the trajectories of antibiotic resistance gene transfer in bacterial communities such as the gut microbiome, we will better understand the factors that influence this spread of resistance. Our aim was to investigate the host network of a multi-drug resistance broad-host-range plasmid in the culturable gut microbiome of zebrafish. This was done through in vitro and in vivo conjugation experiments with Escherichia coli as donor of the plasmid pB10::gfp When this donor was mixed with the extracted gut microbiome, only transconjugants of Aeromonas veronii were detected. In separate matings between the same donor and four prominent isolates from the gut microbiome, the plasmid transferred to two of these four isolates, A. veronii andPlesiomonas shigelloides, but not to Shewanella putrefaciens and Vibrio mimicus When these A. veronii andP. shigelloides transconjugants were the donors in matings with the same four isolates, the plasmid now also transferred from A. veronii to S. putrefaciensP. shigelloides was unable to donate the plasmid and V. mimicus was unable to acquire it. Finally, when the E. coli donor was added in vivo to zebrafish through their food, plasmid transfer was observed in the gut but only to Achromobacter sp., a rare member of the gut microbiome. This work shows that the success of plasmid-mediated antibiotic resistance spread in a gut microbiome depends on the donor-recipient species combinations and therefore their spatial arrangement. It also suggests that rare gut microbiome members should not be ignored as potential reservoirs of multi-drug resistance plasmids from food.Importance:To understand how antibiotic resistance plasmids end up in human pathogens it is crucial to learn how, where and when they are transferred and maintained in members of bacterial communities such as the gut microbiome. To gain insight into the network of plasmid-mediated antibiotic resistance sharing in the gut microbiome, we investigated the transferability and maintenance of a multi-drug resistance plasmid among the culturable bacteria of the zebrafish gut. We show that the success of plasmid-mediated antibiotic resistance spread in a gut microbiome can depend on which species are involved, as some are important nodes in the plasmid-host network and others dead-ends. Our findings also suggest that rare gut microbiome members should not be ignored as potential reservoirs of multi-drug resistance plasmids from food.}, }
@article {pmid33637572, year = {2021}, author = {Wang, Z and Chen, Z and Kowalchuk, GA and Xu, Z and Fu, X and Kuramae, EE}, title = {Succession of the Resident Soil Microbial Community in Response to Periodic Inoculations.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.00046-21}, pmid = {33637572}, issn = {1098-5336}, abstract = {To maintain the beneficial effects of microbial inoculants on plant and soil, repeated inoculation represents a promising option. Until now, the impacts of one-off inoculation on the native microbiome have been explored, but it remains unclear how long and to what extent the periodic inoculations would affect the succession of the resident microbiome in bulk soil. Here we examined the dynamic responses of plant growth, soil functions and resident bacterial community in the bulk soil to periodic inoculations of phosphate-solubilizing and N2-fixing bacteria alone or in combination. Compared to single-strain inoculation, co-inoculation better stimulated plant growth and soil nutrients. However, the benefits from inoculants did not increase with repeated inoculations and were not maintained after transplanting to a different site. In response to microbial inoculants, three patterns of shifts in bacterial composition were observed - fold increased, fold decreased, and resilience. The periodic inoculations impacted the succession course of resident bacterial communities in bulk soil, mainly driven by changes in soil pH and nitrate, resulting in the development of three main cluster types throughout the investigation. The single and mixed inoculants transiently modulated the variation in the resident community in association with soil pH and C/N, but finally the community established and showed resilience to following inoculations. Consequently, the necessity of repeated inoculations should be reconsidered, and while the different microbial inoculants showed distinct impacts on resident microbiome succession, communities ultimately exhibited resilience.IMPORTANCEIntroducing beneficial microbes to the plant-soil system is an environmentally friendly approach to improve crop yield and soil environment. Numerous studies have attempted to reveal the impacts of inoculation on rhizosphere microbiome. However, little is known about the effectiveness of periodic inoculations on soil functioning. In addition, the impact persistence of repeated inoculations on the native community remains unclear. Here, we track the succession traits of resident microbiome in the bulk soil across a growing season and identify the taxa clusters that diversely respond to periodic inoculation. Crucially, we compare the development of resident community composition with and without inoculation, thus providing new insight into understanding the interactions between resident microbes and intruders. Finally, we conclude that initial inoculation plays a more important role in influencing the whole system, and the native microbial community exhibits traits of resilience, but no resistance, to the subsequent inoculations.}, }
@article {pmid33637135, year = {2021}, author = {Kaushal, R and Peng, L and Singh, SK and Zhang, M and Zhang, X and Vílchez, JI and Wang, Z and He, D and Yang, Y and Lv, S and Xu, Z and Morcillo, RJL and Wang, W and Huang, W and Paré, PW and Song, CP and Zhu, JK and Liu, R and Zhong, W and Ma, P and Zhang, H}, title = {Dicer-like proteins influence Arabidopsis root microbiota independent of RNA-directed DNA methylation.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {57}, pmid = {33637135}, issn = {2049-2618}, abstract = {BACKGROUND: Plants are naturally associated with root microbiota, which are microbial communities influential to host fitness. Thus, it is important to understand how plants control root microbiota. Epigenetic factors regulate the readouts of genetic information and consequently many essential biological processes. However, it has been elusive whether RNA-directed DNA methylation (RdDM) affects root microbiota assembly.<br><br>RESULTS: By applying 16S rRNA gene sequencing, we investigated root microbiota of Arabidopsis mutants defective in the canonical RdDM pathway, including dcl234 that harbors triple mutation in the Dicer-like proteins DCL3, DCL2, and DCL4, which produce small RNAs for RdDM. Alpha diversity analysis showed reductions in microbe richness from the soil to roots, reflecting the selectivity of plants on root-associated bacteria. The dcl234 triple mutation significantly decreases the levels of Aeromonadaceae and Pseudomonadaceae, while it increases the abundance of many other bacteria families in the root microbiota. However, mutants of the other examined key players in the canonical RdDM pathway showed similar microbiota as Col-0, indicating that the DCL proteins affect root microbiota in an RdDM-independent manner. Subsequently gene analysis by shotgun sequencing of root microbiome indicated a selective pressure on microbial resistance to plant defense in the dcl234 mutant. Consistent with the altered plant-microbe interactions, dcl234 displayed altered characters, including the mRNA and sRNA transcriptomes that jointly highlighted altered cell wall organization and up-regulated defense, the decreased cellulose and callose deposition in root xylem, and the restructured profile of root exudates that supported the alterations in gene expression and cell wall modifications.<br><br>CONCLUSION: Our findings demonstrate an important role of the DCL proteins in influencing root microbiota through integrated regulation of plant defense, cell wall compositions, and root exudates. Our results also demonstrate that the canonical RdDM is dispensable for Arabidopsis root microbiota. These findings not only establish a connection between root microbiota and plant epigenetic factors but also highlight the complexity of plant regulation of root microbiota. Video abstract.}, }
@article {pmid33637088, year = {2021}, author = {Li, F and Ye, J and Shao, C and Zhong, B}, title = {Compositional alterations of gut microbiota in nonalcoholic fatty liver disease patients: a systematic review and Meta-analysis.}, journal = {Lipids in health and disease}, volume = {20}, number = {1}, pages = {22}, pmid = {33637088}, issn = {1476-511X}, support = {81870404, 81670518, 81170392//National Natural Science Foundation of China/ ; 201604020155//Special Project on the Integration of Industry, Education and Research of Guangzhou, China/ ; 2013B021800290, 2014A020212118, 2017A020215015//Science and Technology Program of Guangdong province, China/ ; A2019496//Medical Scientific Research Foundation of Guangdong Province/ ; }, abstract = {BACKGROUND: Although imbalanced intestinal flora contributes to the pathogenesis of nonalcoholic fatty liver disease (NAFLD), conflicting results have been obtained for patient-derived microbiome composition analyses. A meta-analysis was performed to summarize the characteristics of intestinal microbiota at the species level in NAFLD patients.<br><br>METHODS: Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) Statement, a completed search (last update: December 30, 2020) of databases was performed to identify eligible case-control studies detecting gut microbiota in NAFLD patients. The meta-analysis results are presented as the standard mean difference (SMD) and 95% confidence interval (CI). Bias controls were evaluated with the Newcastle-Ottawa Scale (NOS), funnel plot analysis, and Egger's and Begg's tests.<br><br>RESULTS: Fifteen studies (NOS score range: 6-8) that detected the gut microbiota in the stools of 1265 individuals (577 NAFLD patients and 688 controls) were included. It was found that Escherichia, Prevotella and Streptococcus (SMD = 1.55 [95% CI: 0.57, 2.54], 1.89 [95% CI: 0.02, 3.76] and 1.33 [95% CI: 0.62, 2.05], respectively) exhibited increased abundance while Coprococcus, Faecalibacterium and Ruminococcus (SMD = - 1.75 [95% CI: - 3.13, - 0.37], - 9.84 [95% CI: - 13.21, - 6.47] and - 1.84 [95% CI, - 2.41, - 1.27], respectively) exhibited decreased abundance in the NAFLD patients compared with healthy controls. No differences in the abundance of Bacteroides, Bifidobacterium, Blautia, Clostridium, Dorea, Lactobacillus, Parabacteroides or Roseburia were confirmed between the NAFLD patients and healthy controls.<br><br>CONCLUSIONS: This meta-analysis revealed that changes in the abundance of Escherichia, Prevotella, Streptococcus, Coprococcus, Faecalibacterium and Ruminococcus were the universal intestinal bacterial signature of NAFLD.}, }
@article {pmid33636766, year = {2021}, author = {Yan, X and Chen, X and Tian, X and Qiu, Y and Wang, J and Yu, G and Dong, N and Feng, J and Xie, J and Nalesnik, M and Niu, R and Xiao, B and Song, G and Quinones, S and Ren, X}, title = {Co-exposure to inorganic arsenic and fluoride prominently disrupts gut microbiota equilibrium and induces adverse cardiovascular effects in offspring rats.}, journal = {The Science of the total environment}, volume = {767}, number = {}, pages = {144924}, doi = {10.1016/j.scitotenv.2020.144924}, pmid = {33636766}, issn = {1879-1026}, abstract = {Co-exposure to inorganic arsenic (iAs) and fluoride (F-) and their collective actions on cardiovascular systems have been recognized as a global public health concern. Emerging studies suggest an association between the perturbation of gut bacterial microbiota and adverse cardiovascular effects (CVEs), both of which are the consequence of iAs and F- exposure in human and experimental animals. The aim of this study was to fill the gap of understanding the relationship among co-exposure to iAs and F-, gut microbiota perturbation, and adverse CVEs. We systematically assessed cardiac morphology and functions (blood pressure, echocardiogram, and electrocardiogram), and generated gut microbiota profiles using 16S rRNA gene sequencing on rats exposed to iAs (50 mg/L NaAsO2), F- (100 mg/L NaF) or combined iAs and F- (50 mg/L NaAsO2 + 100 mg/L NaF), in utero and during early postnatal periods (postnatal day 90). Correlation analysis was then performed to examine relationship between significantly altered microbiota and cardiac performance indices. Our results showed that co-exposure to iAs and F- resulted in more prominent effects in CVEs and perturbation of gut microbiota profiles, compared to iAs or F- treatment alone. Furthermore, nine bacterial genera (Adlercreutzia, Clostridium sensu stricto 1, Coprococcus 3, Romboutsia, [Bacteroides] Pectinophilus group, Lachnospiraceae NC2004 group, Desulfovibrio, and two unidentified genera in Muribaculaceae and Ruminococcaceae family), which differed significantly in relative abundance between control and iAs and F- co-exposure group, were strongly correlated with the higher risk of CVEs (correlation coefficient = 0.70-0.88, p < 0.05). Collectively, these results suggest that co-exposure to iAs and F- poses a higher risk of CVEs, and the part of the mode of action is potentially through inducing gut microbiota disruption, and the strong correlations between them indicate a high potential for the development of novel microbiome-based biomarkers of iAs and/or F- associated CVEs.}, }
@article {pmid33636759, year = {2021}, author = {Zhu, H and Teng, Y and Wang, X and Zhao, L and Ren, W and Luo, Y and Christie, P}, title = {Changes in clover rhizosphere microbial community and diazotrophs in mercury-contaminated soils.}, journal = {The Science of the total environment}, volume = {767}, number = {}, pages = {145473}, doi = {10.1016/j.scitotenv.2021.145473}, pmid = {33636759}, issn = {1879-1026}, abstract = {Little is known about the response of the soil microbiome (including bacteria in the rhizosphere of legumes such as clover) to mercury (Hg) despite the toxicity of Hg to soil microorganisms. Here, Hg-contaminated soils collected from Guizhou province, southwest China, were divided into three groups according to their Hg contents and were planted with clover. High-throughput sequencing of bacterial 16S rRNA and nitrogenase (nifH) genes and quantitative polymerase chain reaction (qPCR) were used to study the response of bacteria and diazotrophs to soil Hg stress and the effects of Hg on the abundance of functional genes in rhizosphere soils. High concentrations of soil Hg decreased bacterial community abundance and diversity and increased the abundance and diversity of nitrogen-fixing bacteria. LEfSe analysis indicates that Rhizobium was a biomarker at sites with high soil Hg contents and the co-occurrence network results indicate a positive relationship between the abundance of the dominant module (from the co-occurrence network analysis) of Rhizobiaceae and soil Hg concentration. Structural equation modeling (SEM) indicates that the Hg content in the clover shoots (ShootHg) was negatively correlated with the abundance of the mercury reductase (merA) gene (r = -0.26, P < 0.05) and the organomercury lyase (merB) gene (r = -0.23, P < 0.05) in rhizosphere soils. Moreover, correlation analysis and SEM indicate that soil total nitrogen (TN), nitrate‑nitrogen (NO3-N), soil organic matter (SOM), and available molybdenum (Mo) contents were also important factors affecting the structure of the microbial community and the abundance of functional genes. The results provide a basis for further study of the mechanism(s) by which microorganisms may impart tolerance of clover to Hg in contaminated soils.}, }
@article {pmid33636479, year = {2021}, author = {Basic, M and Bolsega, S and Smoczek, A and Gläsner, J and Hiergeist, A and Eberl, C and Stecher, B and Gessner, A and Bleich, A}, title = {Monitoring and contamination incidence of gnotobiotic experiments performed in microisolator cages.}, journal = {International journal of medical microbiology : IJMM}, volume = {311}, number = {3}, pages = {151482}, doi = {10.1016/j.ijmm.2021.151482}, pmid = {33636479}, issn = {1618-0607}, abstract = {With the increased interest in the microbiome research, gnotobiotic animals and techniques emerged again as valuable tools to investigate functional effects of host-microbe and microbe-microbe interactions. The increased demand for gnotobiotic experiments has resulted in the greater need for housing systems for short-term maintenance of gnotobiotic animals. During the last six years, the gnotobiotic facility of the Hannover Medical School has worked intensively with different housing systems for gnotobiotic animals. Here, we report our experience in handling, contamination incidence, and monitoring strategies that we apply for controlling gnotobiotic experiments. From our experience, the risk of introducing contaminants to animals housed in microisolator cages is higher than in isolators. However, with strict operating protocols, the contamination rate in these systems can be minimized. In addition to spore-forming bacteria and fungi from the environment, spore-forming bacteria from defined bacterial communities used in experiments represent the major risk for contamination of gnotobiotic experiments performed in microisolator cages. The presence/absence of contaminants in germ-free animals can be easily monitored by preparation of wet mounts and Gram staining of fecal samples. Contaminants in animals colonized with specific microorganisms need to be tracked with methods such as next-generation sequencing. However, when using PCR-based methods it is important to consider that relatively small amounts of bacterial DNA detected likely originates from food, bedding, or reagents and is not to be interpreted as true contamination.}, }
@article {pmid33636133, year = {2021}, author = {Desai, P and Janova, H and White, JP and Reynoso, GV and Hickman, HD and Baldridge, MT and Urban, JF and Stappenbeck, TS and Thackray, LB and Diamond, MS}, title = {Enteric helminth coinfection enhances host susceptibility to neurotropic flaviviruses via a tuft cell-IL-4 receptor signaling axis.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2021.01.051}, pmid = {33636133}, issn = {1097-4172}, abstract = {Although enteric helminth infections modulate immunity to mucosal pathogens, their effects on systemic microbes remain less established. Here, we observe increased mortality in mice coinfected with the enteric helminth Heligmosomoides polygyrus bakeri (Hpb) and West Nile virus (WNV). This enhanced susceptibility is associated with altered gut morphology and transit, translocation of commensal bacteria, impaired WNV-specific T cell responses, and increased virus infection in the gastrointestinal tract and central nervous system. These outcomes were due to type 2 immune skewing, because coinfection in Stat6-/- mice rescues mortality, treatment of helminth-free WNV-infected mice with interleukin (IL)-4 mirrors coinfection, and IL-4 receptor signaling in intestinal epithelial cells mediates the susceptibility phenotypes. Moreover, tuft cell-deficient mice show improved outcomes with coinfection, whereas treatment of helminth-free mice with tuft cell-derived cytokine IL-25 or ligand succinate worsens WNV disease. Thus, helminth activation of tuft cell-IL-4-receptor circuits in the gut exacerbates infection and disease of a neurotropic flavivirus.}, }
@article {pmid33635583, year = {2021}, author = {Jin, J and Spenkelink, A and Beekmann, K and Baccaro, M and Xing, F and Rietjens, IMCM}, title = {Species Differences in in vitro and Estimated in vivo Kinetics for Intestinal Microbiota Mediated Metabolism of Acetyl- deoxynivalenols.}, journal = {Molecular nutrition &amp; food research}, volume = {}, number = {}, pages = {e2001085}, doi = {10.1002/mnfr.202001085}, pmid = {33635583}, issn = {1613-4133}, abstract = {SCOPE: Deoxynivalenol (DON) and its acetylated derivatives 3-acetyl-DON (3-Ac-DON) and 15-acetyl-DON (15-Ac-DON) are important mycotoxins of concern in the modern food chain.<br><br>METHODS AND RESULTS: The present study reveals that the rate of de-acetylation in in vitro anaerobic fecal incubations decreased in the order rat > mouse > human > pig for 3-Ac-DON, and mouse > human > rat > pig for 15-Ac-DON. The ratio between the de-acetylation rate of 3-Ac-DON and 15-Ac-DON varied with the species. Scaling of the kinetic parameters to the in vivo situation resulted in catalytic efficiencies decreasing in the order human > rat > pig > mouse for 3-Ac-DON and human > pig > rat > mouse for 15-Ac-DON. The results obtained indicate that in mice 3-Ac-DON can be fully deconjugated while 15-Ac-DON cannot. In rats, pigs and humans, both 3-Ac-DON and 15-Ac-DON can be totally transformed by gut fecal microbiota during the estimated intestinal residence time. A correlation analysis between the deacetylation rate and the relative abundance of the microbiome suggests Lachnospiraceae may be involved in the deacetylation process.<br><br>CONCLUSION: It is concluded that interspecies differences in deacetylation of acetylated DONs exist but that in risk assessment assumption of complete intestinal deconjugation provides an adequate approach. This article is protected by copyright. All rights reserved.}, }
@article {pmid33635417, year = {2021}, author = {Zhao, L and Yang, L and Guo, Y and Xiao, J and Zhang, J and Xu, S}, title = {New Insights into Stroke Prevention and Treatment: Gut Microbiome.}, journal = {Cellular and molecular neurobiology}, volume = {}, number = {}, pages = {}, pmid = {33635417}, issn = {1573-6830}, support = {81774059//the National Natural Science Foundation of China/ ; 19JCZDJC37100//Natural Science Foundation of Tianjin Municipal Science and Technology Commission/ ; }, abstract = {Stroke, a lethal neurological disease, accounts for a grave economic burden on society. Despite extensive basic and clinical studies on stroke prevention, a precise effective treatment approach for stroke at this stage remains unavailable. The majority of our body's gut microbiota plays a vital role in food digestion, immune regulation, and nervous system development, which is highly associated with the development of some diseases. Multiple clinical studies have documented variation in the composition of gut microbiota between stroke patients and healthy counterparts. Moreover, the intervention of intestinal symbiotic microorganisms via several mechanisms plays an active role in stroke prognosis. In the prevention and treatment of stroke, the gut microbiota gives off a seductive glow, this is a promising therapeutic target. This paper summarizes the current knowledge of stroke and gut microbiota, and systematically describes the possible mechanisms of interaction between stroke and gut microbiota, the relationship between stroke-related risk factors and gut microbiota, and the treatment of gut flora using microorganisms. Thus, it could valuably elucidate the correlation of gut microbiota with stroke incidence, providing stroke researchers with a new strategy for stroke prevention and treatment by regulating gut microbiota.}, }
@article {pmid33634901, year = {2021}, author = {Aliakbari, A and Zemb, O and Billon, Y and Barilly, C and Ahn, I and Riquet, J and Gilbert, H}, title = {Genetic relationships between feed efficiency and gut microbiome in pig lines selected for residual feed intake.}, journal = {Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie}, volume = {}, number = {}, pages = {}, doi = {10.1111/jbg.12539}, pmid = {33634901}, issn = {1439-0388}, support = {16-CE20-0003//Agence Nationale de la Recherche/ ; }, abstract = {This study aimed to evaluate the genetic relationship between faecal microbial composition and five feed efficiency (FE) and production traits, residual feed intake (RFI), feed conversion ratio (FCR), daily feed intake (DFI), average daily gain (ADG) and backfat thickness (BFT). A total of 588 samples from two experimental pig lines developed by divergent selection for RFI were sequenced for the 16 rRNA hypervariable V3-V4 region. The 75 genera with less than 20% zero values (97% of the counts) and two α-diversity indexes were analysed. Line comparison of the microbiota traits and estimations of heritability (h2) and genetic correlations (rg) were analysed. A non-metric multidimensional scaling showed line differences between genera. The α-diversity indexes were higher in the LRFI line than in the HRFI line (p < .01), with h2 estimates of 0.19 ± 0.08 (Shannon) and 0.12 ± 0.06 (Simpson). Forty-eight genera had a significant h2 (>0.125). The rg of the α-diversities indexes with production traits were negative. Some rg of genera belonging to the Lachnospiraceae, Ruminococcaceae, Prevotellaceae, Lactobacillaceae, Streptococcaceae, Rikenellaceae and Desulfovibrionaceae families significantly differed from zero (p < .05) with FE traits, RFI (3), DFI (7) and BFT (11). These results suggest that a sizable part of the variability of the gut microbial community is under genetic control and has genetic relationships with FE, including diversity indicators. It offers promising perspectives for selection for feed efficiency using gut microbiome composition in pigs.}, }
@article {pmid33634824, year = {2021}, author = {Zhou, F and He, K and Li, Q and Chapkin, RS and Ni, Y}, title = {Bayesian biclustering for microbial metagenomic sequencing data via multinomial matrix factorization.}, journal = {Biostatistics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/biostatistics/kxab002}, pmid = {33634824}, issn = {1468-4357}, abstract = {High-throughput sequencing technology provides unprecedented opportunities to quantitatively explore human gut microbiome and its relation to diseases. Microbiome data are compositional, sparse, noisy, and heterogeneous, which pose serious challenges for statistical modeling. We propose an identifiable Bayesian multinomial matrix factorization model to infer overlapping clusters on both microbes and hosts. The proposed method represents the observed over-dispersed zero-inflated count matrix as Dirichlet-multinomial mixtures on which latent cluster structures are built hierarchically. Under the Bayesian framework, the number of clusters is automatically determined and available information from a taxonomic rank tree of microbes is naturally incorporated, which greatly improves the interpretability of our findings. We demonstrate the utility of the proposed approach by comparing to alternative methods in simulations. An application to a human gut microbiome data set involving patients with inflammatory bowel disease reveals interesting clusters, which contain bacteria families Bacteroidaceae, Bifidobacteriaceae, Enterobacteriaceae, Fusobacteriaceae, Lachnospiraceae, Ruminococcaceae, Pasteurellaceae, and Porphyromonadaceae that are known to be related to the inflammatory bowel disease and its subtypes according to biological literature. Our findings can help generate potential hypotheses for future investigation of the heterogeneity of the human gut microbiome.}, }
@article {pmid33634334, year = {2021}, author = {Srivastava, A and Mishra, S and Verma, D}, title = {Characterization of Oral Bacterial Composition of Adult Smokeless Tobacco Users from Healthy Indians Using 16S rDNA Analysis.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33634334}, issn = {1432-184X}, support = {SB/YS/LS-102/2014//Science and Engineering Research Board/ ; F 30-442/2018/BSR//University Grants Commission/ ; }, abstract = {The present investigation is aiming to report the oral bacterial composition of smokeless tobacco (SLT) users and to determine the influence of SLT products on the healthy Indian population. With the aid of the V3 hypervariable region of the 16S rRNA gene, a total of 8,080,889 high-quality reads were clustered into 15 phyla and 180 genera in the oral cavity of the SLT users. Comparative analysis revealed a more diverse microbiome where two phyla and sixteen genera were significantly different among the SLT users as compared to the control group (p-value < 0.05). The prevalence of Fusobacteria-, Porphyromonas-, Desulfobulbus-, Enterococcus-, and Parvimonas-like genera among SLT users indicates altered bacterial communities among SLT users. Besides, the depletion of health-compatible bacteria such as Lactobacillus and Haemophilus also suggests poor oral health. Here, the majority of the altered genera belong to Gram-negative anaerobes that have been reported for assisting biofilm formation that leads in the progression of several oral diseases. The PICRUSt analysis further supports the hypothesis where a significant increase in the count of the genes involved in the metabolism of nitrogen, amino acids, and nicotinate/nicotinamide was observed among tobacco chewers. Moreover, this study has a high significance in Indian prospects where the SLT consumers are prevalent but we are deficient in information on their oral microbiome.}, }
@article {pmid33634320, year = {2021}, author = {Zorba, M and Melidou, A and Patsatsi, A and Poulopoulos, A and Gioula, G and Kolokotronis, A and Minti, F}, title = {The role of oral microbiome in pemphigus vulgaris.}, journal = {Archives of microbiology}, volume = {}, number = {}, pages = {}, pmid = {33634320}, issn = {1432-072X}, abstract = {While the impact of oral microbiome dysbiosis on autoimmune diseases has been partially investigated, its role on bullous diseases like Pemphigus Vulgaris (PV) is a totally unexplored field. This study aims to present the composition and relative abundance of microbial communities in both healthy individuals and patients with oral PV lesions. Ion Torrent was used to apply deep sequencing of the bacterial 16S rRNA gene to oral smear samples of 15 healthy subjects and 15 patients. The results showed that the most dominant phyla were Firmicutes (55.88% controls-c vs 61.27% patients-p, p value = 0.002), Proteobacteria (9.17%c vs 12.33%p, p value = 0.007) and Fusobacteria (3.39%c vs 4.09%p, p value = 0.03). Alpha diversity showed a significant difference in the number of genera between patients and controls (p value = 0.04). Beta diversity showed statistical differences in the microbial community composition between two groups. Fusobacterium nucleatum, Gemella haemolysans and Parvimonas micra were statistically abundant in patients. We noticed the characteristic fetor coming out of oral PV lesions. Most of anaerobic bacteria responsible for oral halitosis are periopathogenic. Though, only F. nucleatum and P. micra were differentially abundant in our patients. Especially, F. nucleatum has been reported many times as responsible for bad breath. Furthermore, Streptococcus salivarius and Rothia mucilaginosa, species mostly associated with clean breath, were found in relative abundance in the healthy group. Consequently, the distinct malodor observed in PV patients might be attributed either to the abundance of F. nucleatum and P. micra and/or to the lower levels of S. salivarius and R. mucilanginosa in oral lesions.}, }
@article {pmid33634319, year = {2021}, author = {Rahman, S and Kortman, GAM and Boekhorst, J and Lee, P and Khan, MR and Ahmed, F}, title = {Effect of low-iron micronutrient powder (MNP) on the composition of gut microbiota of Bangladeshi children in a high-iron groundwater setting: a randomized controlled trial.}, journal = {European journal of nutrition}, volume = {}, number = {}, pages = {}, pmid = {33634319}, issn = {1436-6215}, abstract = {PURPOSE: Adverse effects of iron fortification/supplements such as Micronutrient Powder (MNP) on gut microbiota have previously been found in infection-prone African settings. This study examined the adversaries of a low-iron MNP compared with the standard MNP on the composition of gut microbiota in Bangladeshi children exposed to a high concentration of iron from potable groundwater.<br><br>METHODS: A randomized controlled trial was conducted in 2- to 5-year-old children, drinking groundwater with a high concentration of iron (≥ 2 mg/L). Children were randomized to receive one sachet per day of either standard MNP (12.5 mg iron) or low-iron MNP (5 mg iron), for 2 months. A sub-sample of 53 children was considered for paired assessment of the gut microbiome by 16S rRNA amplicon sequencing.<br><br>RESULTS: At baseline, the gut microbiota consisted of Bifidobacteriaceae (15.6%), Prevotellaceae (12.2%), Lactobacillaceae (3.6%), Clostridiaceae (4.1%) and Enterobacteriaceae (2.8%). Overall, there was no significant treatment effect of the low-iron MNP compared to the standard MNP. However, an apparent treatment effect was observed in children with a relative adult-like microbiota, with a higher relative abundance of potentially pathogenic Enterobacteriaceae after receiving the standard MNP compared to the low-iron MNP. This effect, however, was statistically non-significant (p = 0.07).<br><br>CONCLUSION: In Bangladeshi children drinking iron-rich groundwater, a low-iron MNP supplementation did not have a significant impact on their gut microbiota profile/composition compared to the standard MNP. The trial registration number is ISRCTN60058115; Date of registration 03/07/2019; retrospectively registered.}, }
@article {pmid33633723, year = {2020}, author = {Gorlé, N and Bauwens, E and Haesebrouck, F and Smet, A and Vandenbroucke, RE}, title = {Helicobacter and the Potential Role in Neurological Disorders: There Is More Than Helicobacter pylori.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {584165}, doi = {10.3389/fimmu.2020.584165}, pmid = {33633723}, issn = {1664-3224}, abstract = {Trillions of symbiotic microbial cells colonize our body, of which the larger part is present in the human gut. These microbes play an essential role in our health and a shift in the microbiome is linked to several diseases. Recent studies also suggest a link between changes in gut microbiota and neurological disorders. Gut microbiota can communicate with the brain via several routes, together called the microbiome-gut-brain axis: the neuronal route, the endocrine route, the metabolic route and the immunological route. Helicobacter is a genus of Gram-negative bacteria colonizing the stomach, intestine and liver. Several papers show the role of H. pylori in the development and progression of neurological disorders, while hardly anything is known about other Helicobacter species and the brain. We recently reported a high prevalence of H. suis in patients with Parkinson's disease and showed an effect of a gastric H. suis infection on the mouse brain homeostasis. Here, we discuss the potential role of H. suis in neurological disorders and how it may affect the brain via the microbiome-gut-brain axis.}, }
@article {pmid33633704, year = {2021}, author = {Shi, W and Su, G and Li, M and Wang, B and Lin, R and Yang, Y and Wei, T and Zhou, B and Gao, Z}, title = {Distribution of Bacterial Endophytes in the Non-lesion Tissues of Potato and Their Response to Potato Common Scab.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {616013}, doi = {10.3389/fmicb.2021.616013}, pmid = {33633704}, issn = {1664-302X}, abstract = {The response of plant endophytes to disease within infected tissues has been well demonstrated, but the corresponding response of endophytes in non-lesion tissues remains unclear. Here, we studied the composition and distribution of bacterial endophytes in potato roots (RE), stems (SE), and tubers (TE), and explored the response of endophytes in non-lesion tissues to potato common scab (PCS), which is a soil-borne disease caused by pathogenic Streptomyces and results in serious losses to the global economy every year. Via high-throughput sequencing, it was seen that the composition of endophytes in roots, stems, and tubers had significant differences (P < 0.05) and the distribution of the bacterial communities illustrated a gradient from soil to root to tuber/stem. PCS significantly reduced bacterial endophytes α-diversity indexes, including ACE and the number of observed operational taxonomic units (OTUs), of RE without significantly reducing the indexes of SE and TE. No significant effect on the composition of endophytes were caused by PCS in roots, tubers, or stems between high PCS severity (H) and low PCS severity (L) infections at the community level, but PCS did have a substantial impact on the relative abundance of several specific endophytes. Rhizobium and Sphingopyxis were significantly enriched in root endophytes with low PCS severity (REL); Delftia and Ochrobactrum were significantly enriched in stem endophytes with low PCS severity (SEL); Pedobacter, Delftia, and Asticcacaulis were significantly enriched in tuber endophytes with high PCS severity (TEH). OTU62, a potential PCS pathogen in this study, was capable of colonizing potato tubers, roots, and stems with few or no symptoms present. Co-occurrence networks showed that the number of correlations to OTU62 was higher than average in these three tissue types, suggesting the importance of OTU62 in endophytic communities. This study clarified the distribution and composition of potato endophytes in tubers, roots, and stems, and demonstrated the response of endophytes in non-lesion tissues to PCS.}, }
@article {pmid33633246, year = {2021}, author = {Kang, L and Li, P and Wang, D and Wang, T and Hao, D and Qu, X}, title = {Alterations in intestinal microbiota diversity, composition, and function in patients with sarcopenia.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {4628}, pmid = {33633246}, issn = {2045-2322}, support = {CIFMS #2017-I2M-3-008//Chinese Academy of Medical Sciences/ ; 2018YFC2002100//National Key Research and Development Program of China/ ; 2018YFC2002104//National Key Research and Development Program of China,China/ ; }, abstract = {16S rRNA sequencing of human fecal samples has been tremendously successful in identifying microbiome changes associated with both aging and disease. A number of studies have described microbial alterations corresponding to physical frailty and nursing home residence among aging individuals. A gut-muscle axis through which the microbiome influences skeletal muscle growth/function has been hypothesized. However, the microbiome has yet to be examined in sarcopenia. Here, we collected fecal samples of 60 healthy controls (CON) and 27 sarcopenic (Case)/possibly sarcopenic (preCase) individuals and analyzed the intestinal microbiota using 16S rRNA sequencing. We observed an overall reduction in microbial diversity in Case and preCase samples. The genera Lachnospira, Fusicantenibacter, Roseburia, Eubacterium, and Lachnoclostridium-known butyrate producers-were significantly less abundant in Case and preCase subjects while Lactobacillus was more abundant. Functional pathways underrepresented in Case subjects included numerous transporters and phenylalanine, tyrosine, and tryptophan biosynthesis suggesting that protein processing and nutrient transport may be impaired. In contrast, lipopolysaccharide biosynthesis was overrepresented in Case and PreCase subjects suggesting that sarcopenia is associated with a pro-inflammatory metagenome. These analyses demonstrate structural and functional alterations in the intestinal microbiota that may contribute to loss of skeletal muscle mass and function in sarcopenia.}, }
@article {pmid33633180, year = {2021}, author = {Mishima, Y and Osaki, T and Shimada, A and Kamiya, S and Hasegawa-Ishii, S}, title = {Sex-dependent differences in the gut microbiota following chronic nasal inflammation in adult mice.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {4640}, pmid = {33633180}, issn = {2045-2322}, support = {19K17870//the Grant-in-Aid for Scientific Research KAKENHI/ ; 18K07395//the Grant-in-Aid for Scientific Research KAKENHI/ ; }, abstract = {A growing body of evidence suggests a relationship between olfactory dysfunction and the pathogenesis of mental disorders. Our previous studies indicated that chronic nasal inflammation caused loss of olfactory sensory neurons and gross atrophy of the olfactory bulb, which may lead to olfactory dysfunction. Simultaneously, increasing numbers of reports have elucidated the importance of gut microbiota to maintain brain function and that dysbiosis may be associated with neuropsychiatric disorders. Here we examined whether chronic nasal inflammation perturbed gut microbiota and whether there were sex differences in this pattern. Eight-week-old C57BL/6 mice repeatedly received bilateral nasal administration of lipopolysaccharide (LPS) 3 times/week to cause chronic nasal inflammation or saline as a control. At 9 weeks, cecal feces were used for 16S metagenomic analysis and whole blood and fresh tissue of spleen were used for ELISA analyses. Microbiome analysis demonstrated a remarkable change of the gut microbiota in male mice with chronic nasal inflammation which was different from that in female mice. In both mice, systemic inflammation did not occur. This has shown for the first time that chronic nasal inflammation correlates with sex-dependent changes in the gut microbiota. The detailed mechanism and potential alteration to brain functions await further studies.}, }
@article {pmid33633172, year = {2021}, author = {Carrieri, AP and Haiminen, N and Maudsley-Barton, S and Gardiner, LJ and Murphy, B and Mayes, AE and Paterson, S and Grimshaw, S and Winn, M and Shand, C and Hadjidoukas, P and Rowe, WPM and Hawkins, S and MacGuire-Flanagan, A and Tazzioli, J and Kenny, JG and Parida, L and Hoptroff, M and Pyzer-Knapp, EO}, title = {Explainable AI reveals changes in skin microbiome composition linked to phenotypic differences.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {4565}, pmid = {33633172}, issn = {2045-2322}, abstract = {Alterations in the human microbiome have been observed in a variety of conditions such as asthma, gingivitis, dermatitis and cancer, and much remains to be learned about the links between the microbiome and human health. The fusion of artificial intelligence with rich microbiome datasets can offer an improved understanding of the microbiome's role in human health. To gain actionable insights it is essential to consider both the predictive power and the transparency of the models by providing explanations for the predictions. We combine the collection of leg skin microbiome samples from two healthy cohorts of women with the application of an explainable artificial intelligence (EAI) approach that provides accurate predictions of phenotypes with explanations. The explanations are expressed in terms of variations in the relative abundance of key microbes that drive the predictions. We predict skin hydration, subject's age, pre/post-menopausal status and smoking status from the leg skin microbiome. The changes in microbial composition linked to skin hydration can accelerate the development of personalized treatments for healthy skin, while those associated with age may offer insights into the skin aging process. The leg microbiome signatures associated with smoking and menopausal status are consistent with previous findings from oral/respiratory tract microbiomes and vaginal/gut microbiomes respectively. This suggests that easily accessible microbiome samples could be used to investigate health-related phenotypes, offering potential for non-invasive diagnosis and condition monitoring. Our EAI approach sets the stage for new work focused on understanding the complex relationships between microbial communities and phenotypes. Our approach can be applied to predict any condition from microbiome samples and has the potential to accelerate the development of microbiome-based personalized therapeutics and non-invasive diagnostics.}, }
@article {pmid33633159, year = {2021}, author = {Kundu, P and Torres, ERS and Stagaman, K and Kasschau, K and Okhovat, M and Holden, S and Ward, S and Nevonen, KA and Davis, BA and Saito, T and Saido, TC and Carbone, L and Sharpton, TJ and Raber, J}, title = {Integrated analysis of behavioral, epigenetic, and gut microbiome analyses in AppNL-G-F, AppNL-F, and wild type mice.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {4678}, pmid = {33633159}, issn = {2045-2322}, support = {R56 AG057495-01/GF/NIH HHS/United States ; T32 AG055378/GF/NIH HHS/United States ; R01 ES030226/GF/NIH HHS/United States ; RF1 AG059088/GF/NIH HHS/United States ; }, abstract = {Epigenetic mechanisms occurring in the brain as well as alterations in the gut microbiome composition might contribute to Alzheimer's disease (AD). Human amyloid precursor protein knock-in (KI) mice contain the Swedish and Iberian mutations (AppNL-F) or those two and also the Arctic mutation (AppNL-G-F). In this study, we assessed whether behavioral and cognitive performance in 6-month-old AppNL-F, AppNL-G-F, and C57BL/6J wild-type (WT) mice was associated with the gut microbiome, and whether the genotype modulates this association. The genotype effects observed in behavioral tests were test-dependent. The biodiversity and composition of the gut microbiome linked to various aspects of mouse behavioral and cognitive performance but differences in genotype modulated these relationships. These genotype-dependent associations include members of the Lachnospiraceae and Ruminococcaceae families. In a subset of female mice, we assessed DNA methylation in the hippocampus and investigated whether alterations in hippocampal DNA methylation were associated with the gut microbiome. Among other differentially methylated regions, we identified a 1 Kb region that overlapped ing 3'UTR of the Tomm40 gene and the promoter region of the Apoe gene that and was significantly more methylated in the hippocampus of AppNL-G-F than WT mice. The integrated gut microbiome hippocampal DNA methylation analysis revealed a positive relationship between amplicon sequence variants (ASVs) within the Lachnospiraceae family and methylation at the Apoe gene. Hence, these microbes may elicit an impact on AD-relevant behavioral and cognitive performance via epigenetic changes in AD-susceptibility genes in neural tissue or that such changes in the epigenome can elicit alterations in intestinal physiology that affect the growth of these taxa in the gut microbiome.}, }
@article {pmid33632860, year = {2021}, author = {Babalola, OO and Molefe, RR and Amoo, AE}, title = {Metagenome Assembly and Metagenome-Assembled Genome Sequences from the Rhizosphere of Maize Plants in Mafikeng, South Africa.}, journal = {Microbiology resource announcements}, volume = {10}, number = {8}, pages = {}, pmid = {33632860}, issn = {2576-098X}, abstract = {The rhizosphere microbiome plays an essential role in enhancing the growth of plants, raising the need for comprehension of their metabolic abilities. Here, we investigated rhizospheric and bulk soils of maize plants in Mafikeng, South Africa. Metagenome-assembled genomes containing plant growth-promoting genes were reconstructed.}, }
@article {pmid33632634, year = {2021}, author = {Severance, EG and Leister, F and Lea, A and Yang, S and Dickerson, F and Yolken, RH}, title = {Complement C4 associations with altered microbial biomarkers exemplify gene-by-environment interactions in schizophrenia.}, journal = {Schizophrenia research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.schres.2021.02.001}, pmid = {33632634}, issn = {1573-2509}, abstract = {Schizophrenia is a complex brain disorder with genetic and environmental factors contributing to its etiology. Complement C4 genes are schizophrenia susceptibility loci and are activated in response to infections and gut microbiome imbalances. We hypothesize that C4 genetic susceptibility predisposes individuals to neuropathological effects from pathogen exposures or a microbiome in dysbiosis. In 214 individuals with schizophrenia and 123 non-psychiatric controls, we examined C4 gene copy number and haplotype groups for associations with schizophrenia and microbial plasma biomarkers. C4A copy number and haplotypes containing HERV-K insertions (C4A-long; C4AL-C4AL) conferred elevated odds ratios for schizophrenia diagnoses (OR 1.58-2.56, p < 0.0001), while C4B-short (C4BS) haplogroups conferred decreased odds (OR 0.43, p < 0.0001). Haplogroup-microbe combinations showed extensive associations with schizophrenia including C4AL with Candida albicans IgG (OR 2.16, p < 0.0005), C4AL-C4BL with cytomegalovirus (CMV) IgG (OR 1.79, p < 0.008), C4BS with lipopolysaccharide-binding protein (LBP) (OR 1.18, p < 0.0001), and C4AL-C4AL with Toxoplasma gondii IgG (OR = 17.67, p < 0.0001). In controls, only one haplogroup-microbe combination was significant: C4BS with CMV IgG (OR 0.52, p < 0.02). In schizophrenia only, LBP and CMV IgG levels were inversely correlated with C4A and C4S copy numbers, respectively (R2 = 0.13-0.16, p < 0.0001). C4 haplogroups were associated with altered scores of cognitive functioning in both cases and controls and with psychiatric symptom scores in schizophrenia. Our findings link complement C4 genes with a susceptibility to infections and a dysbiotic microbiome in schizophrenia. These results support immune system mechanisms by which gene-environmental interactions may be operative in schizophrenia.}, }
@article {pmid33632307, year = {2021}, author = {Hu, S and Png, E and Gowans, M and Ong, DEH and de Sessions, PF and Song, J and Nagarajan, N}, title = {Ectopic gut colonization: a metagenomic study of the oral and gut microbiome in Crohn's disease.}, journal = {Gut pathogens}, volume = {13}, number = {1}, pages = {13}, pmid = {33632307}, issn = {1757-4749}, support = {Start up grant: Exploring the oral microbiome in Crohn's disease//National University of Singapore/ ; }, abstract = {BACKGROUND: This study aims to characterize, the gut and oral microbiome in Asian subjects with Crohn's disease (CD) using whole genome shotgun sequencing, thereby allowing for strain-level comparison.<br><br>METHODS: A case-control study with age, sex and ethnicity matched healthy controls was conducted. CD subjects were limited to well-controlled patients without oral manifestations. Fecal and saliva samples were collected for characterization of gut and oral microbiome respectively. Microbial DNA were extracted, libraries prepared and sequenced reads profiled. Taxonomic diversity, taxonomic association, strain typing and microbial gene pathway analyses were conducted.<br><br>RESULTS: The study recruited 25 subjects with CD and 25 healthy controls. The oral microbe Streptococcus salivarius was found to be enriched and of concordant strains in the gut and oral microbiome of Crohn's disease subjects. This was more likely in CD subjects with higher Crohn's Disease Activity Index (184.3 ± 2.9 vs 67.1 ± 82.5, p = 0.012) and active disease status (Diarrhoea/abdominal pain/blood-in-stool/fever and fatigue) (p = 0.016). Gut species found to be significantly depleted in CD compared to control (Relative abundance: Median[Range]) include: Faecalibacterium prausnitzii (0.03[0.00-4.56] vs 13.69[5.32-18.71], p = 0.010), Roseburia inulinivorans (0.00[0.00-0.03] vs 0.21[0.01-0.53], p = 0.010) and Alistipes senegalensis (0.00[0.00-0.00] vs 0.00[0.00-0.02], p = 0.029). While Clostridium nexile (0.00[0.00-0.12] vs 0.00[0.00-0.00], p = 0.038) and Ruminococcus gnavus (0.43[0.02-0.33] vs 0.00[0.00-0.13], p = 0.043) were found to be enriched. C. nexile enrichment was not found in CD subjects of European descent. Microbial arginine (Linear-discriminant-analysis: 3.162, p = 0.001) and isoprene (Linear-discriminant-analysis: 3.058, p < 0.001) pathways were found at a higher relative abundance level in gut microbiome of Crohn's disease.<br><br>CONCLUSIONS: There was evidence of ectopic gut colonization by oral bacteria, especially during the active phase of CD. Previously studied gut microbial differences were detected, in addition to novel associations which could have resulted from geographical/ethnic differences to subjects of European descent. Differences in microbial pathways provide possible targets for microbiome modification.}, }
@article {pmid33632296, year = {2021}, author = {Chhibber-Goel, J and Gopinathan, S and Sharma, A}, title = {Interplay between severities of COVID-19 and the gut microbiome: implications of bacterial co-infections?.}, journal = {Gut pathogens}, volume = {13}, number = {1}, pages = {14}, pmid = {33632296}, issn = {1757-4749}, support = {BT/PR30603/BIC/101/1104/2018//Department of Biotechnology, Government of India/ ; }, abstract = {COVID-19 is an acute respiratory distress syndrome and is often accompanied by gastrointestinal symptoms. The SARS-CoV-2 has been traced not only in nasopharyngeal and mid-nasal swabs but also in stool and rectal swabs of COVID-19 patients. The gut microbiota is important for an effective immune response as it ensures that unfavorable immune reactions in lungs and other vital organs are regulated. The human gut-lung microbiota interplay provides a framework for therapies in the treatment and management of several pulmonary diseases and infections. Here, we have collated data from COVID-19 studies, which suggest that bacterial co-infections as well as the gut-lung cross talk may be important players in COVID-19 disease prognosis. Our analyses suggests a role of gut microbiome in pathogen infections as well as in an array of excessive immune reactions during and post COVID-19 infection recovery period.}, }
@article {pmid33632119, year = {2021}, author = {Ksiezarek, M and Ugarcina-Perovic, S and Rocha, J and Grosso, F and Peixe, L}, title = {Long-term stability of the urogenital microbiota of asymptomatic European women.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {64}, pmid = {33632119}, issn = {1471-2180}, support = {UID/Multi/04378/2019//Fundação para a Ciência e a Tecnologia/ ; UIDB/04378/2020//Fundação para a Ciência e a Tecnologia/ ; SFRH/BD/132497/2017//Fundação para a Ciência e a Tecnologia/ ; UID/MULTI/04378/2013//Fundação para a Ciência e a Tecnologia/ ; DL57/2016/CP1346/CT0034//Fundação para a Ciência e a Tecnologia/ ; UIDP/04378/2020//Fundação para a Ciência e a Tecnologia/ ; NORTH-01-0145-FEDER-000024//Comissão de Coordenação e Desenvolvimento Regional do Norte/ ; }, abstract = {BACKGROUND: To date, information on healthy female urinary microbiota is available mostly at genus level and at one time point. However, profound species-level characterization of healthy urinary microbiome and its stability over time are essential for further correct interpretation of its role in healthy urogenital tract. In this study, we investigated female urogenital microbiome (FUM) at two timepoints (within 2.5-year interval) in young asymptomatic European women. We used culturomics with accurate isolates' identification (MALDI-TOF MS and gene markers sequencing) to understand species stability within healthy FUM.<br><br>RESULTS: Extended culturomics of voided midstream urine sample pairs revealed a mean Shannon diversity index of 1.25 and mean of 19 species/sample (range 5-39 species; total of 115 species; 1830 isolates). High overall species variability between individuals was captured by beta diversity and a variety of community structure types, with the largest cluster characterized by Lactobacillus crispatus, often in combination with Gardnerella vaginalis or Gardnerella genomospecies 3. Significant FUM composition differences, related to Finegoldia magna and Streptococcus anginosus, according to smoking status were found. A high species variability within individuals (Shannon index SD > 0.5 in 7 out of 10 sample pairs) with a mean of 29% of shared species (range 9.1-41.7%) was observed. Moreover, 4 out of 10 sample pairs clustered in the same community structure type. The stable FUM sample pairs presented high abundance of Lactobacillus crispatus, Streptococcus agalactiae or Lactobacillus paragasseri and Bifidobacterium spp.. Moreover, Gardnerella vaginalis, Gardnerella genomospecies 3 or Gardnerella swidsinskii were often maintained within individuals in high abundance.<br><br>CONCLUSIONS: Shift in species composition at two distant timepoints was frequently observed among urogenital microbiome of European asymptomatic women. This suggests possible interchange of particular species in healthy FUM and the existence of multiple health-associated FUM compositions in certain individuals. Additionally, we provided additional evidence on resilience of particular bacterial communities and identified certain species more prone to persist in urogenital tract. This study revealed important details on the FUM composition complexity relevant for studies aiming to understand microbiota role in the urogenital tract health and for identification of eubiotic and dysbiotic FUM.}, }
@article {pmid33631782, year = {2021}, author = {Vieira-Baptista, P and Grincevičienė, Š and Oliveira, C and Fonseca-Moutinho, J and Cherey, F and Stockdale, CK}, title = {The International Society for the Study of Vulvovaginal Disease Vaginal Wet Mount Microscopy Guidelines: How to Perform, Applications, and Interpretation.}, journal = {Journal of lower genital tract disease}, volume = {}, number = {}, pages = {}, doi = {10.1097/LGT.0000000000000595}, pmid = {33631782}, issn = {1526-0976}, abstract = {OBJECTIVES: The aims of the study were to assess the available literature concerning the indications, performance, technique, and classification of wet mount microscopy (WMM) and to establish evidence-based recommendations.<br><br>METHODS: Literature review from the main scientific databases was performed by the ad hoc &quot;Vaginitis and Microbiome Committee&quot; of the International Society for the Study of Vulvovaginal Disease. The document was approved by the executive council and membership of the International Society for the Study of Vulvovaginal Disease.<br><br>RESULTS: Available data are limited and usually of low level of evidence. Nevertheless, it shows that WMM is capable of reducing misdiagnosis, overtreatment, and undertreatment of vaginal conditions. It has an excellent performance for the diagnosis of bacterial vaginosis and variable performance for trichomoniasis and candidiasis. It is the gold standard for aerobic vaginitis/desquamative inflammatory vaginitis. Currently, there is no recommendation to use WMM in the screening of asymptomatic women.The use of phase contrast is recommended to improve performance and reproducibility. Sampling location, devices, and technique have an impact on the results.Available scoring and classification scores have significant limitations.<br><br>CONCLUSIONS: Wet mount microscopy is a point-of-care, inexpensive, and fast technique that, with practice, can be mastered by office clinicians. It should be considered a basic skill in the curricula of gynecology and obstetrics residencies. Recommendations are provided on sampling, reading, and scoring.}, }
@article {pmid33631565, year = {2021}, author = {Sadeq, SA and Mills, RIL and Beckerman, AP}, title = {The microbiome mediates the interaction between predation and heavy metals.}, journal = {The Science of the total environment}, volume = {775}, number = {}, pages = {145144}, doi = {10.1016/j.scitotenv.2021.145144}, pmid = {33631565}, issn = {1879-1026}, abstract = {Gut microbiota communities are fundamental ecological components in the aquatic food web. Their potential to mediate how organisms respond to multiple environmental stressors remains understudied. Here we explored how manipulations of the gut microbiome of Daphnia pulex, a keystone species in aquatic communities, influenced life history (size at maturity, age at maturity, somatic growth rate and clutch size), morphology (induced defence) and body condition (lipid status deposits) responses to combined anthropogenic (copper) and natural (predation risk) stress. Data from a factorial experiment revealed that the effect of predation risk on traits was often mediated by copper (predation risk and copper interact). These patterns align with theory linking predation risk and copper contamination via digestive physiology. We also found that each stressor, and their combination, was associated with the same community composition of the D. pulex microbiome. However, antibiotic manipulation of the microbiome reversed 7/12 the trait responses across life history, morphology and body condition. This was associated with dramatically different communities to control conditions, with clear and unique patterns of microbiome community composition for each stressor and their combination. Our study revealed that microbiome community composition is highly correlated with the response of organisms to multiple, simultaneous stressors.}, }
@article {pmid33631103, year = {2021}, author = {Khanna, S}, title = {A defined microbiome therapeutic prevents recurrent Clostridioides difficile.}, journal = {The lancet. Gastroenterology &amp; hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/S2468-1253(21)00011-X}, pmid = {33631103}, issn = {2468-1253}, }
@article {pmid33631098, year = {2021}, author = {Suzuki, T and Salzano, A and Israr, MZ}, title = {Targeting the gut microbiome in coronary artery disease.}, journal = {American heart journal}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ahj.2021.02.017}, pmid = {33631098}, issn = {1097-6744}, }
@article {pmid33630979, year = {2021}, author = {Deng, L and Wojciech, L and Gascoigne, NRJ and Peng, G and Tan, KSW}, title = {New insights into the interactions between Blastocystis, the gut microbiota, and host immunity.}, journal = {PLoS pathogens}, volume = {17}, number = {2}, pages = {e1009253}, doi = {10.1371/journal.ppat.1009253}, pmid = {33630979}, issn = {1553-7374}, abstract = {The human gut microbiota is a diverse and complex ecosystem that is involved in beneficial physiological functions as well as disease pathogenesis. Blastocystis is a common protistan parasite and is increasingly recognized as an important component of the gut microbiota. The correlations between Blastocystis and other communities of intestinal microbiota have been investigated, and, to a lesser extent, the role of this parasite in maintaining the host immunological homeostasis. Despite recent studies suggesting that Blastocystis decreases the abundance of beneficial bacteria, most reports indicate that Blastocystis is a common component of the healthy gut microbiome. This review covers recent finding on the potential interactions between Blastocystis and the gut microbiota communities and its roles in regulating host immune responses.}, }
@article {pmid33630889, year = {2021}, author = {Thomas, S and Dunn, CD and Campbell, LJ and Strand, DW and Vezina, CM and Bjorling, DE and Penniston, KL and Li, L and Ricke, WA and Goldberg, TL}, title = {A multi-omic investigation of male lower urinary tract symptoms: Potential role for JC virus.}, journal = {PloS one}, volume = {16}, number = {2}, pages = {e0246266}, doi = {10.1371/journal.pone.0246266}, pmid = {33630889}, issn = {1932-6203}, abstract = {Male lower urinary tract symptoms (LUTS) comprise a common syndrome of aging that negatively impacts quality of life. The etiology of LUTS is multifactorial, involving benign prostatic hyperplasia, smooth muscle and neurologic dysfunction, inflammation, sexually transmitted infections, fibrosis, and potentially dysbiosis, but this aspect remains poorly explored. We investigated whether the presence of infectious agents in urine might be associated with LUTS by combining next-generation DNA sequencing for virus discovery, microbiome analysis for characterization of bacterial communities, and mass spectrometry-based metabolomics. In urine from 29 LUTS cases and 9 controls from Wisconsin, we found a statistically significant association between a diagnosis of LUTS and the presence of JC virus (JCV), a common neurotropic human polyomavirus (Polyomaviridae, Betapolyomavirus) linked to severe neurologic disease in rare cases. This association (based on metagenomics) was not borne out when specific polymerase chain reaction (PCR) testing was applied to this set of samples, likely due to the greater sensitivity of PCR. Interestingly, urine metabolomics analysis identified dysregulation of metabolites associated with key LUTS processes. Microbiome analysis found no evidence of microbial community dysbiosis in LUTS cases, but JCV-positive samples contained more Anaerococcus species, which are involved in polymicrobial infections of the urinary tract. Neither age nor body mass index were significantly associated with the presence of urinary JCV-in the initial group or in an additional, regionally distinct group. These data provide preliminary support the hypothesis that viruses such as JCV may play a role in the development or progression of LUTS, together with other infectious agents and host metabolic responses.}, }
@article {pmid33630874, year = {2021}, author = {Aya, V and Flórez, A and Perez, L and Ramírez, JD}, title = {Association between physical activity and changes in intestinal microbiota composition: A systematic review.}, journal = {PloS one}, volume = {16}, number = {2}, pages = {e0247039}, doi = {10.1371/journal.pone.0247039}, pmid = {33630874}, issn = {1932-6203}, abstract = {INTRODUCTION: The intestinal microbiota comprises bacteria, fungi, archaea, protists, helminths and viruses that symbiotically inhabit the digestive system. To date, research has provided limited data on the possible association between an active lifestyle and a healthy composition of human microbiota. This review was aimed to summarize the results of human studies comparing the microbiome of healthy individuals with different physical activity amounts.<br><br>METHODS: We searched Medline/Ovid, NIH/PubMed, and Academic Search Complete between August-October 2020. Inclusion criteria comprised: (a) cross-sectional studies focused on comparing gut microbiome among subjects with different physical activity levels; (b) studies describing human gut microbiome responses to any type of exercise stimulus; (c) studies containing healthy adult women and men. We excluded studies containing diet modifications, probiotic or prebiotic consumption, as well as studies focused on diabetes, hypertension, cancer, hormonal dysfunction. Methodological quality and risk of bias for each study were assessed using the Risk Of Bias In Non-randomized Studies-of Interventions tool. The results from cross-sectional and longitudinal studies are shown independently.<br><br>RESULTS: A total of 17 articles were eligible for inclusion: ten cross-sectional and seven longitudinal studies. Main outcomes vary significantly according to physical activity amounts in longitudinal studies. We identified discrete changes in diversity indexes and relative abundance of certain bacteria in active people.<br><br>CONCLUSION: As literature in this field is rapidly growing, it is important that studies incorporate diverse methods to evaluate other aspects related to active lifestyles such as sleep and dietary patterns. Exploration of other groups such as viruses, archaea and parasites may lead to a better understanding of gut microbiota adaptation to physical activity and sports and its potentially beneficial effects on host metabolism and endurance.}, }
@article {pmid33630830, year = {2021}, author = {Ras, V and Botha, G and Aron, S and Lennard, K and Allali, I and Claassen-Weitz, S and Mwaikono, KS and Kennedy, D and Holmes, JR and Rendon, G and Panji, S and Fields, CJ and Mulder, N}, title = {Using a multiple-delivery-mode training approach to develop local capacity and infrastructure for advanced bioinformatics in Africa.}, journal = {PLoS computational biology}, volume = {17}, number = {2}, pages = {e1008640}, doi = {10.1371/journal.pcbi.1008640}, pmid = {33630830}, issn = {1553-7358}, abstract = {With more microbiome studies being conducted by African-based research groups, there is an increasing demand for knowledge and skills in the design and analysis of microbiome studies and data. However, high-quality bioinformatics courses are often impeded by differences in computational environments, complicated software stacks, numerous dependencies, and versions of bioinformatics tools along with a lack of local computational infrastructure and expertise. To address this, H3ABioNet developed a 16S rRNA Microbiome Intermediate Bioinformatics Training course, extending its remote classroom model. The course was developed alongside experienced microbiome researchers, bioinformaticians, and systems administrators, who identified key topics to address. Development of containerised workflows has previously been undertaken by H3ABioNet, and Singularity containers were used here to enable the deployment of a standard replicable software stack across different hosting sites. The pilot ran successfully in 2019 across 23 sites registered in 11 African countries, with more than 200 participants formally enrolled and 106 volunteer staff for onsite support. The pulling, running, and testing of the containers, software, and analyses on various clusters were performed prior to the start of the course by hosting classrooms. The containers allowed the replication of analyses and results across all participating classrooms running a cluster and remained available posttraining ensuring analyses could be repeated on real data. Participants thus received the opportunity to analyse their own data, while local staff were trained and supported by experienced experts, increasing local capacity for ongoing research support. This provides a model for delivering topic-specific bioinformatics courses across Africa and other remote/low-resourced regions which overcomes barriers such as inadequate infrastructures, geographical distance, and access to expertise and educational materials.}, }
@article {pmid33630786, year = {2021}, author = {Roddy, GW}, title = {Metabolic syndrome and the aging retina.}, journal = {Current opinion in ophthalmology}, volume = {}, number = {}, pages = {}, doi = {10.1097/ICU.0000000000000747}, pmid = {33630786}, issn = {1531-7021}, abstract = {PURPOSE OF REVIEW: This review explores metabolic syndrome (MetS) as a risk factor that accelerates aging in retinal neurons and may contribute to the neurodegeneration seen in glaucomatous optic neuropathy (GON) and age-related macular degeneration (AMD).<br><br>RECENT FINDINGS: Both animal model experiments and epidemiologic studies suggest that metabolic stress may lead to aberrant regulation of a number of cellular pathways that ultimately lead to premature aging of the cell, including those of a neuronal lineage.<br><br>SUMMARY: GON and AMD are each leading causes of irreversible blindness worldwide. Aging is a significant risk factor in the specific retinal neuron loss that is seen with each condition. Though aging at a cellular level is difficult to define, there are many mechanistic modifiers of aging. Metabolic-related stresses induce inflammation, oxidative stress, mitochondrial dysfunction, endoplasmic reticulum stress, alterations to the unfolded protein response, defects in autophagy, alterations to the microbiome, and deposition of advanced glycation end products that can all hasten the aging process. Due to the number of variables related to metabolic health, defining criteria to enable the study of risk factors at a population level is challenging. MetS is a definable constellation of related metabolic risk factors that includes enlarged waist circumference, dyslipidemia, systemic hypertension, and hyperglycemia. MetS has been associated with both GON and AMD and may contribute to disease onset and/or progression in each disease.}, }
@article {pmid33630385, year = {2021}, author = {Mowat, AM}, title = {Historical Perspective: Metchnikoff and the intestinal microbiome.}, journal = {Journal of leukocyte biology}, volume = {109}, number = {3}, pages = {513-517}, doi = {10.1002/JLB.4RI0920-599}, pmid = {33630385}, issn = {1938-3673}, abstract = {Metchnikoff's essay, Intestinal Bacteriotherapy, was written when the study of microbiology was still in its infancy and few intestinal diseases had been ascribed to a specific bacterial infection. Metchnikoff offered perceptive ideas that have become standard in today's science. This Historical Perspectives commentary examines how Metchnikoff's article influenced our field. An accompanying editorial by Siamon Gordon explores this topic further and describes the relevance of Metchnikoff's work to the current Covid-19 infection. We also include a translation of this fundamental article by Metchnikoff, as presented by Claudine Neyen.}, }
@article {pmid33630191, year = {2021}, author = {Li, XJ and Wang, M and Xue, Y and Duan, D and Li, C and Ye, J and Han, X and Qiao, R and Wang, K and Li, XL}, title = {Characterization and comparison of the bacterial community between complete intensive and extensive feeding patterns in pigs.}, journal = {AMB Express}, volume = {11}, number = {1}, pages = {32}, pmid = {33630191}, issn = {2191-0855}, support = {S2012-06-G03//Pig Industry Technology System Innovation Team Project of Henan Province/ ; }, abstract = {To investigate and compare the gut microbiota structures in complete intensive feeding pattern (CP) and extensive feeding pattern (EP) groups, a total of 20 pigs were divided into two groups and fed the same diet. The fecal microbial composition was profiled using 16S rRNA gene sequencing. Our results showed that seventeen predominant genera were present in each pig sample and constituted the phylogenetic core of the microbiota at the class level. The abundance of most of the core microbial flora were significantly higher in the CP group than in the EP group (P < 0.05), while the abundance of Gammaproteobacteria was significantly lower in the CP group than in the EP group (P < 0.05). The CP group had significantly greater community diversity, richness, and evenness than the EP group (P < 0.05). Functional prediction analysis indicated that intestinal microbial species potentially led to faster growth and an increased fat accumulation capacity in the CP group; however, disease resistance was weaker in the CP group than in the EP group. In conclusion, EP pigs have a wider range of activity and better animal welfare than CP pigs, which helps reduce the occurrence of diseases and neurological symptoms. To explore the effect of intestinal flora on disease resistance in pigs at the molecular level, Coprococcus, which is a key gut bacterium in the intestine, was selected for isolation and purification and cocultured with intestinal epithelial cells. qPCR was performed to determine the effect of Coprococcus on SLA-DRB gene expression in intestinal epithelial cells. The results showed that Coprococcus enhanced SLA-DRB gene expression in intestinal epithelial cells. The results provide useful reference data for further study on the relationship between intestinal flora and pig disease resistance.}, }
@article {pmid33629964, year = {2021}, author = {Li, G and Li, W and Song, B and Wang, C and Shen, Q and Li, B and Tang, D and Xu, C and Geng, H and Gao, Y and Wang, G and Wu, H and Zhang, Z and Xu, X and Zhou, P and Wei, Z and He, X and Cao, Y}, title = {Differences in the Gut Microbiome of Women With and Without Hypoactive Sexual Desire Disorder: Case Control Study.}, journal = {Journal of medical Internet research}, volume = {23}, number = {2}, pages = {e25342}, doi = {10.2196/25342}, pmid = {33629964}, issn = {1438-8871}, abstract = {BACKGROUND: The gut microbiome is receiving considerable attention as a potentially modifiable risk factor and therapeutic target for numerous mental and neurological diseases.<br><br>OBJECTIVE: This study aimed to explore and assess the difference in the composition of gut microbes and fecal metabolites between women with hypoactive sexual desire disorder (HSDD) and healthy controls.<br><br>METHODS: We employed an online recruitment method to enroll &quot;hard-to-reach&quot; HSDD populations. After a stringent diagnostic and exclusion process based on DSM-IV criteria, fecal samples collected from 24 women with HSDD and 22 age-matched, healthy controls underwent microbiome analysis using 16S ribosomal RNA gene sequencing and metabolome analysis using untargeted liquid chromatography-mass spectrometry.<br><br>RESULTS: We found a decreased abundance of Ruminococcaceae and increased abundance of Bifidobacterium and Lactobacillus among women with HSDD. Fecal samples from women with HSDD showed significantly altered metabolic signatures compared with healthy controls. The abundance of Bifidobacterium, Lactobacillus, and several fecal metabolites correlated negatively with the sexual desire score, while the number of Ruminococcaceae correlated positively with the sexual desire score in all subjects.<br><br>CONCLUSIONS: Our analysis of fecal samples from women with HSDD and healthy controls identified significantly different gut microbes and metabolic signatures. These preliminary findings could be useful for developing strategies to adjust the level of human sexual desire by modifying gut microbiota.<br><br>TRIAL REGISTRATION: Chinese Clinical Trial Registry ChiCTR1800020321; http://www.chictr.org.cn/showproj.aspx?proj=34267.}, }
@article {pmid33629947, year = {2021}, author = {Mores, CR and Price, TK and Wolff, B and Halverson, T and Limeira, R and Brubaker, L and Mueller, ER and Putonti, C and Wolfe, AJ}, title = {Genomic relatedness and clinical significance of Streptococcus mitis strains isolated from the urogenital tract of sexual partners.}, journal = {Microbial genomics}, volume = {}, number = {}, pages = {}, doi = {10.1099/mgen.0.000535}, pmid = {33629947}, issn = {2057-5858}, abstract = {Research into the lower urinary tract (LUT) microbiota has primarily focused on its relationship to LUT symptoms (LUTS), taking snapshots of these communities in individuals with and without LUTS. While certain bacterial taxa have been associated with LUTS, or the lack thereof, the temporal dynamics of this community were largely unknown. Recently, we conducted a longitudinal study and found that vaginal intercourse resulted in a shift in species richness and diversity within the LUT microbiota. This is particularly relevant as frequent vaginal intercourse is a major risk factor for urinary tract infection (UTI) in premenopausal women (Aydin et al. Int Urogynecol J 2015;26:795-804). To further investigate the relationship between vaginal intercourse and LUT microbiota, here we present the results of a 3 week study in which daily urogenital specimens were collected from a female participant and her male sexual partner. Consistent with our previous findings, the LUT microbiota changed after vaginal intercourse, most notably a high abundance of Streptococcus mitis was observed post-coitus. We isolated and sequenced S. mitis from both sexual partners finding that: (i) the S. mitis isolates from the female partner's urogenital tract were genomically similar throughout the duration of the study, and (ii) they were related to one isolate from the male partner's oral cavity collected at the end of the study, suggesting transmission between the two individuals. We hypothesize that blooms in S. mitis after vaginal intercourse may play a role in coitus-related UTI. We found that a S. mitis isolate, in contrast to a Lactobacillus jensenii isolate displaced after vaginal intercourse, cannot inhibit the growth of uropathogenic Escherichia coli. Thus, this bloom in S. mitis may provide a window of opportunity for a uropathogen to colonize the LUT.}, }
@article {pmid33629812, year = {2021}, author = {Langley, BO and Ryan, JJ and Hanes, D and Phipps, J and Stack, E and Metz, TO and Stevens, JF and Bradley, R}, title = {Xanthohumol Microbiome and Signature in Healthy Adults (the XMaS Trial): Safety and Tolerability Results of a Phase I Triple-Masked, Placebo-Controlled Clinical Trial.}, journal = {Molecular nutrition &amp; food research}, volume = {}, number = {}, pages = {e2001170}, doi = {10.1002/mnfr.202001170}, pmid = {33629812}, issn = {1613-4133}, abstract = {SCOPE: Xanthohumol, a prenylflavonoid from hops, has been extensively studied preclinically but has undergone limited research in human subjects. A triple-masked, placebo-controlled phase I clinical trial was conducted to examine the safety and tolerability of xanthohumol.<br><br>METHODS AND RESULTS: Thirty healthy volunteers were randomized to 24 mg/day xanthohumol (99.8% pure) or placebo for eightweeks. Comprehensive metabolic panels, complete blood counts, body weight, vital signs, and health-related quality of life questionnaires were assessed every two weeks. Participants were interviewed for adverse events (AEs) throughout the trial. Thirteen of 14 (93%) and 14 of 16 (88%) participants completed the trial in the placebo and xanthohumol groups, respectively. There were no withdrawals due to AEs. There were no clinically relevant, between-group differences in laboratory biomarkers, body weight, vital signs, or health-related quality of life. There were no severe or FDA-defined serious AEs, but non-serious AEs were documented in both the placebo (n = 42) and xanthohumol (n = 58) groups.<br><br>CONCLUSION: Over an eight-week period, 24 mg daily xanthohumol was safe and well-tolerated by healthy adults. This article is protected by copyright. All rights reserved.}, }
@article {pmid33629787, year = {2021}, author = {Wang, Q and Guo, A and Sheng, M and Zhou, H}, title = {The changes of respiratory microbiome between mild and severe.}, journal = {Microbiology and immunology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1348-0421.12881}, pmid = {33629787}, issn = {1348-0421}, abstract = {Due to the increased number of patients who suffer from asthma, the mechanism of this disease has caught much attention to public and to find a cure for this disease is urgent. Changed abundance of microbiome has been proven to play an important role in the genesis and development of asthma. In this study, the abundance and the function of microbiome are studied. We found that there are significant changes in the component and the function of microbiome when the asthma was changed from mild to severe. This study would help us to better understand the relationship between asthma and the respiratory microbiome. This article is protected by copyright. All rights reserved.}, }
@article {pmid33629669, year = {2021}, author = {Jiang, J and Chu, C and Wu, C and Wang, C and Zhang, C and Li, T and Zhai, Q and Yu, L and Tian, F and Chen, W}, title = {Efficacy of probiotics in multiple sclerosis: a systematic review of preclinical trials and meta-analysis of randomized controlled trials.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d0fo03203d}, pmid = {33629669}, issn = {2042-650X}, abstract = {Preliminary evidence shows the potential role of probiotics in ameliorating multiple sclerosis (MS); however, the effects of probiotics on MS remain unclear. Therefore, the aim of this study was to evaluate the efficacy of probiotics on multiple sclerosis by systematically reviewing the preclinical trials (animal trials) and performing meta-analysis of randomized controlled trials. PubMed, Web of Science, Cochrane central of randomized clinical trials, EMBASE, Clinical Trials, and a search engine Google Scholar were systematically searched and manually screened updated to November 2020, resulting in eligible 3 randomized controlled trials (RCTs) and 22 preclinical studies. Meta-analysis of RCTs enrolling 173 patients with MS receiving probiotics revealed significant beneficial effects of probiotic supplementation on mental health (expanded disability status scale scores: standardized mean difference [SMD] = -1.22; I2 = 92%; 95% CI, -2.40 to -0.03, P = 0.04; Beck depression inventory total scores: SMD = -1.58; I2 = 94%; 95% CI, -3.03 to -0.12; P = 0.03; general health questionnaire scores: SMD = -0.71; I2 = 0%; 95% CI, -1.02 to -0.40; P < 0.00001; depression anxiety and stress scale scores: SMD = -0.72; I2 = 0%; 95% CI, -1.12 to -0.33; P = 0.0003), with very low certainty of evidence. In addition, probiotic intake markedly improved insulin resistance and inflammatory and oxidative stress markers. Preclinical studies have shown that probiotic consumption reduces the incidence and severity of MS, delays MS progression (15 studies), and improves motor impairment (3 studies) with favorable alterations of immune and inflammatory markers (20 studies) and intestinal microbiome compositions (4 studies) in MS. These results indicated that probiotics may have beneficial effects on the prevention and treatment of multiple sclerosis.}, }
@article {pmid33629663, year = {2021}, author = {Moore, MJ and Rowles, TK and Fauquier, DA and Baker, JD and Biedron, I and Durban, JW and Hamilton, PK and Henry, AG and Knowlton, AR and McLellan, WA and Miller, CA and Pace, RM and Pettis, HM and Raverty, S and Rolland, RM and Schick, RS and Sharp, SM and Smith, CR and Thomas, L and der Hoop, JMV and Ziccardi, MH}, title = {REVIEW: Assessing North Atlantic right whale health: threats, and development of tools critical for conservation of the species.}, journal = {Diseases of aquatic organisms}, volume = {143}, number = {}, pages = {205-226}, doi = {10.3354/dao03578}, pmid = {33629663}, issn = {0177-5103}, abstract = {Whaling has decimated North Atlantic right whales Eubalaena glacialis (NARW) since the 11th century and southern right whales E. australis (SRW) since the 19th century. Today, NARWs are Critically Endangered and decreasing, whereas SRWs are recovering. We review NARW health assessment literature, NARW Consortium databases, and efforts and limitations to monitor individual and species health, survival, and fecundity. Photographs are used to track individual movement and external signs of health such as evidence of vessel and entanglement trauma. Post-mortem examinations establish cause of death and determine organ pathology. Photogrammetry is used to assess growth rates and body condition. Samples of blow, skin, blubber, baleen and feces quantify hormones that provide information on stress, reproduction, and nutrition, identify microbiome changes, and assess evidence of infection. We also discuss models of the population consequences of multiple stressors, including the connection between human activities (e.g. entanglement) and health. Lethal and sublethal vessel and entanglement trauma have been identified as major threats to the species. There is a clear and immediate need for expanding trauma reduction measures. Beyond these major concerns, further study is needed to evaluate the impact of other stressors, such as pathogens, microbiome changes, and algal and industrial toxins, on NARW reproductive success and health. Current and new health assessment tools should be developed and used to monitor the effectiveness of management measures and will help determine whether they are sufficient for a substantive species recovery.}, }
@article {pmid33629659, year = {2021}, author = {Jung, J and Gillevet, PM and Sikaroodi, M and Andrews, J and Song, B and Shields, JD}, title = {Comparative study of the hemolymph microbiome between live and recently dead American lobsters Homarus americanus.}, journal = {Diseases of aquatic organisms}, volume = {143}, number = {}, pages = {147-158}, doi = {10.3354/dao03568}, pmid = {33629659}, issn = {0177-5103}, abstract = {Lobsters and other crustaceans do not have sterile hemolymph. Despite this, little is known about the microbiome in the hemolymph of the lobster Homarus americanus. The purpose of this study was to characterize the hemolymph microbiome in lobsters. The lobsters were part of a larger study on the effect of temperature on epizootic shell disease, and several died during the course of the study, providing an opportunity to examine differences in the microbiomes between live and recently dead (1-24 h) animals. The hemolymph microbiomes of live lobsters was different from those in dead animals and both were different from the tank microbiome in which the animals had been held. The microbiomes of live lobsters were more diverse and had a different suite of bacteria than those from dead animals. The dominant taxa in live lobsters belonged to Flavobacteriaceae and Rhodobacteraceae, whereas Vibrionaceae and Enterobacteriaceae were predominant in the dead lobsters. Although aquarium microbiomes overlapped with the hemolymph microbiomes, there was less overlap and lower abundance of taxa in comparison with hemolymph from live lobsters. Previous studies reporting bacteria in the digestive tract of lobsters suggested that Vibrionaceae and Enterobacteriaceae had invaded the hemolymph via the gut. Our study suggests that hemolymph bacteria abundant in live lobsters do not originate from the tank milieu and comprise a rich, natural, or native background of bacterial constituents.}, }
@article {pmid33629506, year = {2021}, author = {Benítez-Páez, A and Hess, AL and Krautbauer, S and Liebisch, G and Christensen, L and Hjorth, MF and Larsen, TM and Sanz, Y}, title = {Sex, Food, and the Gut Microbiota: Disparate Response to Caloric Restriction Diet with Fibre Supplementation in Women and Men.}, journal = {Molecular nutrition &amp; food research}, volume = {}, number = {}, pages = {e2000996}, doi = {10.1002/mnfr.202000996}, pmid = {33629506}, issn = {1613-4133}, abstract = {SCOPE: Dietary-based strategies are regularly explored in controlled clinical trials to provide cost-effective therapies to tackle obesity and its comorbidities. We present a complementary analysis based on a multivariate multi-omics approach of a caloric restriction intervention with fibre supplementation to unveil synergic effects on body weight control, lipid metabolism, and gut microbiota.<br><br>METHODS AND RESULTS: We explored faecal BAs and SCFAs, plasma BAs, and faecal shotgun metagenomics on 80 overweight participants of a 12-week caloric restriction clinical trial (-500 kcal/day) randomly allocated into fibre (10 g/day inulin + 10 g/day resistant maltodextrin) or placebo (maltodextrin) supplementation groups. The multi-omic data integration analysis (sparse PLS-DA method) uncovered the benefits of the fibre supplementation and/or the CRD (e.g., increase of Parabacteroides distasonis and faecal propionate), showing sex-specific effects on either adiposity and fasting insulin; effects thought to be linked to changes of specific gut microbiota species, functional genes, and bacterially produced metabolites like SCFAs and secondary BAs.<br><br>CONCLUSIONS: Our study has identified diet-microbe-host interactions helping to design personalised interventions. It also suggests that sex perspective should be considered routinely in future studies on dietary interventions efficacy. All in all, we uncovered that our dietary intervention was more beneficial for women than men. This article is protected by copyright. All rights reserved.}, }
@article {pmid33628982, year = {2020}, author = {Mahmoudi, E and Rezaie, J}, title = {Isolation of different fungi from the skin of patients with seborrheic dermatitis.}, journal = {Current medical mycology}, volume = {6}, number = {2}, pages = {49-51}, doi = {10.18502/CMM.6.2.2841}, pmid = {33628982}, issn = {2423-3439}, abstract = {Background and Purpose: Seborrheic dermatitis (SD) is characterized by erythematous inflammatory patches that mostly appear in the sebaceous gland-rich skin areas. In addition to the key role of Malassezia species in SD, its contribution to other fungal microbiota has been recently addressed in the literature. Regarding this, the present study was conducted to identify and determine the fungal species associated with the incidence of SD.<br><br>Materials and Methods: For the purpose of the study, fungal microbiome in scaling samples were collected from SD lesions and then analyzed based on the DNA sequencing of ITS regions.<br><br>Results: In addition to Malassezia, several fungal species were detected in the samples collected from the SD lesions. According to the results, 15.5%, 13.3%, and 6.7% of the isolates were identified as Candida parapsilosis, Cryptococcus albidus var. albidus/ Rhodotorula mucilaginosa, and Penicillium polonicum, respectively.<br><br>Conclusion: Based on the obtained results, C. parapsilosis was the most prevalent non-Malassezia species isolated from SD lesions. Our results provided basic information about a specific fungal population accounting for the incidence of SD.}, }
@article {pmid33628766, year = {2021}, author = {Zhou, M and Zhao, J}, title = {A Review on the Health Effects of Pesticides Based on Host Gut Microbiome and Metabolomics.}, journal = {Frontiers in molecular biosciences}, volume = {8}, number = {}, pages = {632955}, doi = {10.3389/fmolb.2021.632955}, pmid = {33628766}, issn = {2296-889X}, abstract = {Due to their large number of applications, the pesticides pose potential toxicity risks to the non-target organisms. In recent years, the studies on the toxic effects of pesticides on non-target organisms, based on their gut microbiome and metabolome, have been continuously reported. As a dense and diverse microbial community, the gut microbiota in the mammalian gut plays a key role in the maintenance of host metabolic homeostasis. The imbalance in the gut microbiota of host is closely associated with the disturbance in the host's metabolic profile. A comprehensive analysis of the changes in the gut microbiota and metabolic profile of host will help in understanding the internal mechanism of pesticide-induced toxic effects. This study reviewed the composition and function of the gut microbiota of host, as well as the analysis methods and applications of metabolomics. Importantly, the latest research on the toxic effects of the exposure of pesticide to host was reviewed on the basis of changes in their gut microbiota and metabolic profile.}, }
@article {pmid33628398, year = {2021}, author = {Chung, M and Zhao, N and Meier, R and Koestler, DC and Wu, G and de Castillo, E and Paster, BJ and Charpentier, K and Izard, J and Kelsey, KT and Michaud, DS}, title = {Comparisons of oral, intestinal, and pancreatic bacterial microbiomes in patients with pancreatic cancer and other gastrointestinal diseases.}, journal = {Journal of oral microbiology}, volume = {13}, number = {1}, pages = {1887680}, doi = {10.1080/20002297.2021.1887680}, pmid = {33628398}, issn = {2000-2297}, abstract = {Background: Oral microbiota is believed to play important roles in systemic diseases, including cancer. Methods: We collected oral samples (tongue, buccal, supragingival, and saliva) and pancreatic tissue or intestinal samples from 52 subjects, and characterized 16S rRNA genes using high-throughput DNA sequencing. Results: Bray-Curtis plot showed clear separations between bacterial communities in the oral cavity and those in intestinal and pancreatic tissue samples. PERMANOVA tests indicated that bacterial communities from buccal samples were similar to supragingival and saliva samples, and pancreatic duct samples were similar to pancreatic tumor samples, but all other samples were significantly different from each other. A total of 73 unique Amplicon Sequence Variants (ASVs) were shared between oral and pancreatic or intestinal samples. Only four ASVs showed significant concordance, and two specific bacterial species (Gemella morbillorum and Fusobacterium nucleatum subsp. vincentii) showed consistent presence or absence patterns between oral and intestinal or pancreatic samples, after adjusting for within-subject correlation and disease status. Lastly, microbial co-abundance analyses showed distinct strain-level cluster patterns among microbiome members in buccal, saliva, duodenum, jejunum, and pancreatic tumor samples. Conclusions: Our findings indicate that oral, intestinal, and pancreatic bacterial microbiomes overlap but exhibit distinct co-abundance patterns in patients with pancreatic cancer and other gastrointestinal diseases.}, }
@article {pmid33628361, year = {2021}, author = {Du, D and Tang, W and Zhou, C and Sun, X and Wei, Z and Zhong, J and Huang, Z}, title = {Fecal Microbiota Transplantation Is a Promising Method to Restore Gut Microbiota Dysbiosis and Relieve Neurological Deficits after Traumatic Brain Injury.}, journal = {Oxidative medicine and cellular longevity}, volume = {2021}, number = {}, pages = {5816837}, doi = {10.1155/2021/5816837}, pmid = {33628361}, issn = {1942-0994}, abstract = {Background: Traumatic brain injury (TBI) can induce persistent fluctuation in the gut microbiota makeup and abundance. The present study is aimed at determining whether fecal microbiota transplantation (FMT) can rescue microbiota changes and ameliorate neurological deficits after TBI in rats.<br><br>Methods: A controlled cortical impact (CCI) model was used to simulate TBI in male Sprague-Dawley rats, and FMT was performed for 7 consecutive days. 16S ribosomal RNA (rRNA) sequencing of fecal samples was performed to analyze the effects of FMT on gut microbiota. Modified neurological severity score and Morris water maze were used to evaluate neurobehavioral functions. Metabolomics was used to screen differential metabolites from the rat serum and ipsilateral brains. The oxidative stress indices were measured in the brain.<br><br>Results: TBI induced significance changes in the gut microbiome, including the alpha- and beta-bacterial diversity, as well as the microbiome composition at 8 days after TBI. On the other hand, FMT could rescue these changes and relieve neurological deficits after TBI. Metabolomics results showed that the level of trimethylamine (TMA) in feces and the level of trimethylamine N-oxide (TMAO) in the ipsilateral brain and serum was increased after TBI, while FMT decreased TMA levels in the feces, and TMAO levels in the ipsilateral brain and serum. Antioxidant enzyme methionine sulfoxide reductase A (MsrA) in the ipsilateral hippocampus was decreased after TBI but increased after FMT. In addition, FMT elevated SOD and CAT activities and GSH/GSSG ratio and diminished ROS, GSSG, and MDA levels in the ipsilateral hippocampus after TBI.<br><br>Conclusions: FMT can restore gut microbiota dysbiosis and relieve neurological deficits possibly through the TMA-TMAO-MsrA signaling pathway after TBI.}, }
@article {pmid33628167, year = {2020}, author = {Al-Asmakh, M and Sohail, MU and Al-Jamal, O and Shoair, BM and Al-Baniali, AY and Bouabidi, S and Nasr, S and Bawadi, H}, title = {The Effects of Gum Acacia on the Composition of the Gut Microbiome and Plasma Levels of Short-Chain Fatty Acids in a Rat Model of Chronic Kidney Disease.}, journal = {Frontiers in pharmacology}, volume = {11}, number = {}, pages = {569402}, doi = {10.3389/fphar.2020.569402}, pmid = {33628167}, issn = {1663-9812}, abstract = {Chronic kidney disease (CKD) may be fatal for its victims and is an important long-term public health problem. The complicated medical procedures and diet restrictions to which patients with CKD are subjected alter the gut microbiome in an adverse manner, favoring over-accumulation of proteolytic bacteria that produce ammonia and other toxic substances. The present study aimed to investigate the effect of GA on 1) the composition of the gut microbiome and 2) on plasma levels of short-chain fatty acids. Male Wister rats were divided into four groups (six each) and treated for 4 weeks based on the following: control, dietary adenine (0.75%, w/w) to induce CKD, GA in the drinking water (15%, w/v), and both adenine and GA. At the end of the treatment period, plasma, urine, and fecal samples were collected for determination of several biochemical indicators of renal function and plasma levels of short-chain fatty acids (SCFAs) as well as characterization of the gut microbiome. Dietary adenine induced the typical signs of CKD, i.e., loss of body weight and impairment of renal function, while GA alleviated these effects. The intestine of the rats with CKD contained an elevated abundance of pathogenic Proteobacteria, Actinobacteria, and Verrucomicrobia but lowered proportions of Lactobacillaceae belonging to the Firmicutes phylum. Plasma levels of propionate and butyrate were lowered by dietary adenine and restored by GA. A negative association (Spearman's p-value ≤ 0.01, r ≤ 0.5) was observed between Firmicutes and plasma creatinine, urea, urine N-acetyl-beta-D-glucosaminidase (NAG) and albumin. Phylum Proteobacteria on the other hand was positively associated with these markers while Phylum Bacteroidetes was positively associated with plasma SCFAs. In conclusion, the adverse changes in the composition of the gut microbiome, plasma levels of SCFAs, and biochemical indicators of renal function observed in the rats with CKD induced by dietary adenine were mitigated by GA. These findings are indicative of a link between uremia and the composition of the microbiome in connection with this disease. Dietary administration of GA to patients with CKD may improve their renal function via modulating the composition of their microbiome-a finding that certainly warrants further investigation.}, }
@article {pmid33628152, year = {2021}, author = {Mukhtar, I and Anwar, H and Mirza, OA and Ali, Q and Ijaz, MU and Hume, M and Prabhala, BK and Iftikhar, A and Hussain, G and Sohail, MU and Khan, KUR}, title = {Sulpiride Serves, a Substrate for the Gut Microbiome.}, journal = {Dose-response : a publication of International Hormesis Society}, volume = {19}, number = {1}, pages = {1559325820987943}, doi = {10.1177/1559325820987943}, pmid = {33628152}, issn = {1559-3258}, abstract = {In the contemporary research world, the intestinal microbiome is now envisioned as a new body organ. Recently, the gut microbiome represents a new drug target in the gut, since various orthologues of intestinal drug transporters are also found present in the microbiome that lines the small intestine of the host. Owing to this, absorbance of sulpiride by the gut microbiome in an in vivo albino rats model was assessed after the oral administration with a single dose of 20mg/kg b.w. The rats were subsequently sacrificed at 2, 3, 4, 5 and 6 hours post oral administration to collect the gut microbial mass pellet. The drug absorbance by the gut microbiome was determined by pursuing the microbial lysate through RP-HPLC-UV. Total absorbance of sulpiride by the whole gut microbiome and drug absorbance per milligram of microbial pellet were found significantly higher at 4 hours post-administration as compared to all other groups. These results affirm the hypothesis that the structural homology between membrane transporters of the gut microbiome and intestinal epithelium of the host might play an important role in drug absorbance by gut microbes in an in vivo condition.}, }
@article {pmid33627969, year = {2021}, author = {Gupta, R and Anand, G and Gaur, R and Yadav, D}, title = {Plant-microbiome interactions for sustainable agriculture: a review.}, journal = {Physiology and molecular biology of plants : an international journal of functional plant biology}, volume = {27}, number = {1}, pages = {165-179}, doi = {10.1007/s12298-021-00927-1}, pmid = {33627969}, issn = {0971-5894}, abstract = {Plant-microbiome interactions are significant determinant for plant growth, fitness and productivity. Depending upon the specific habitat, plants' microbial communities are classified as the rhizo-, phyllo-, and endospheric regions. Understanding the plant microbiome interactions could provide an opportunity to develop strategies for sustainable agricultural practices. There is a necessity to decipher the complex structural and functional diversity within plant microbiomes to reveal its immense potential in agriculture. The plant microbiota harbors enormous microbial communities that defy analytical methodologies to study dynamics underlying plant microbiome interactions. Findings based on conventional approaches have ignored many beneficial microbial strains, which creates a serious gap in understanding the microbial communications along with the genetic adaptations, which favors their association with host plant. The new era of next generation sequencing techniques and modern cost-effective high-throughput molecular approaches can decipher microbial community composition and function. In this review, we have presented the overview of the various compartments of plants, approaches to allow the access to microbiome and factors that influence microbial community composition and function. Next, we summarize how plant microbiome interactions modulate host beneficial properties particularly nutrient acquisition and defense, along with future agricultural applications.<br><br>Supplementary Information: The online version contains supplementary material available at. 10.1007/s12298-021-00927-1.}, }
@article {pmid33627867, year = {2021}, author = {Rao, C and Coyte, KZ and Bainter, W and Geha, RS and Martin, CR and Rakoff-Nahoum, S}, title = {Multi-kingdom ecological drivers of microbiota assembly in preterm infants.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {33627867}, issn = {1476-4687}, abstract = {The gut microbiota of preterm infants develops predictably1-7, with pioneer species colonizing the gut after birth, followed by an ordered succession of microorganisms. The gut microbiota is vital to the health of preterm infants8,9, but the forces that shape these predictable dynamics of microbiome assembly are unknown. The environment, the host and interactions between microorganisms all potentially shape the dynamics of the microbiota, but in such a complex ecosystem, identifying the specific role of any individual factor is challenging10-14. Here we use multi-kingdom absolute abundance quantification, ecological modelling and experimental validation to address this challenge. We quantify the absolute dynamics of bacteria, fungi and archaea in a longitudinal cohort of 178 preterm infants. We uncover microbial blooms and extinctions, and show that there is an inverse correlation between bacterial and fungal loads in the infant gut. We infer computationally and demonstrate experimentally in vitro and in vivo that predictable assembly dynamics may be driven by directed, context-dependent interactions between specific microorganisms. Mirroring the dynamics of macroscopic ecosystems15-17, a late-arriving member of the microbiome, Klebsiella, exploits the pioneer microorganism, Staphylococcus, to gain a foothold within the gut. Notably, we find that interactions between different kingdoms can influence assembly, with a single fungal species-Candida albicans-inhibiting multiple dominant genera of gut bacteria. Our work reveals the centrality of simple microbe-microbe interactions in shaping host-associated microbiota, which is critical both for our understanding of microbiota ecology and for targeted microbiota interventions.}, }
@article {pmid33627698, year = {2021}, author = {Mason, CJ and Hoover, K and Felton, GW}, title = {Effects of maize (Zea mays) genotypes and microbial sources in shaping fall armyworm (Spodoptera frugiperda) gut bacterial communities.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {4429}, pmid = {33627698}, issn = {2045-2322}, support = {2018-67012-27979//USDA/ ; 2017-67013-26596//USDA/ ; }, abstract = {Plants can have fundamental roles in shaping bacterial communities associated with insect herbivores. For larval lepidopterans (caterpillars), diet has been shown to be a driving force shaping gut microbial communities, where the gut microbiome of insects feeding on different plant species and genotypes can vary in composition and diversity. In this study, we aimed to better understand the roles of plant genotypes, sources of microbiota, and the host gut environment in structuring bacterial communities. We used multiple maize genotypes and fall armyworm (Spodoptera frugiperda) larvae as models to parse these drivers. We performed a series of experiments using axenic larvae that received a mixed microbial community prepared from frass from larvae that consumed field-grown maize. The new larval recipients were then provided different maize genotypes that were gamma-irradiated to minimize bacteria coming from the plant during feeding. For field-collected maize, there were no differences in community structure, but we did observe differences in gut community membership. In the controlled experiment, the microbial inoculation source, plant genotype, and their interactions impacted the membership and structure of gut bacterial communities. Compared to axenic larvae, fall armyworm larvae that received frass inoculum experienced reduced growth. Our results document the role of microbial sources and plant genotypes in contributing to variation in gut bacterial communities in herbivorous larvae. While more research is needed to shed light on the mechanisms driving this variation, these results provide a method for incorporating greater gut bacterial community complexity into laboratory-reared larvae.}, }
@article {pmid33627633, year = {2021}, author = {Kwee, LC and Ilkayeva, O and Muehlbauer, MJ and Bihlmeyer, N and Wolfe, B and Purnell, JQ and Xavier Pi-Sunyer, F and Chen, H and Bahnson, J and Newgard, CB and Shah, SH and Laferrère, B}, title = {Metabolites and diabetes remission after weight loss.}, journal = {Nutrition &amp; diabetes}, volume = {11}, number = {1}, pages = {10}, pmid = {33627633}, issn = {2044-4052}, support = {NIH R01 DK108580//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; R01 DK108580/DK/NIDDK NIH HHS/United States ; R01 DK108580/DK/NIDDK NIH HHS/United States ; R01 DK108580/DK/NIDDK NIH HHS/United States ; 5U01DK057178//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; 5U01DK057136//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; 5U01DK057136//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; R01 DK108580/DK/NIDDK NIH HHS/United States ; 5U01DK057178//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; }, abstract = {There is marked heterogeneity in the response to weight loss interventions with regards to weight loss amount and metabolic improvement. We sought to identify biomarkers predictive of type 2 diabetes remission and amount of weight loss in individuals with severe obesity enrolled in the Longitudinal Assessment of Bariatric Surgery (LABS) and the Look AHEAD (Action for Health in Diabetes) studies. Targeted mass spectrometry-based profiling of 135 metabolites was performed in pre-intervention blood samples using a nested design for diabetes remission over five years (n = 93 LABS, n = 80 Look AHEAD; n = 87 remitters), and for extremes of weight loss at five years (n = 151 LABS; n = 75 with high weight loss). Principal components analysis (PCA) was used for dimensionality reduction, with PCA-derived metabolite factors tested for association with both diabetes remission and weight loss. Metabolic markers were tested for incremental improvement to clinical models, including the DiaRem score. Two metabolite factors were associated with diabetes remission: one primarily composed of branched chain amino acids (BCAA) and tyrosine (odds ratio (95% confidence interval) [OR (95% CI)] = 1.4 [1.0-1.9], p = 0.045), and one with betaine and choline (OR [95% CI] = 0.7 [0.5-0.9], p = 0.02).These results were not significant after adjustment for multiple tests. Inclusion of these two factors in clinical models yielded modest improvements in model fit and performance: in a constructed clinical model, the C-statistic improved from 0.87 to 0.90 (p = 0.02), while the net reclassification index showed improvement in prediction compared to the DiaRem score (NRI = 0.26, p = 0.0013). No metabolite factors associated with weight loss at five years. Baseline levels of metabolites in the BCAA and trimethylamine-N-oxide (TMAO)-microbiome-related pathways are independently and incrementally associated with sustained diabetes remission after weight loss interventions in individuals with severe obesity. These metabolites could serve as clinically useful biomarkers to identify individuals who will benefit the most from weight loss interventions.}, }
@article {pmid33627512, year = {2021}, author = {Abellan-Schneyder, I and Matchado, MS and Reitmeier, S and Sommer, A and Sewald, Z and Baumbach, J and List, M and Neuhaus, K}, title = {Primer, Pipelines, Parameters: Issues in 16S rRNA Gene Sequencing.}, journal = {mSphere}, volume = {6}, number = {1}, pages = {}, pmid = {33627512}, issn = {2379-5042}, abstract = {Short-amplicon 16S rRNA gene sequencing is currently the method of choice for studies investigating microbiomes. However, comparative studies on differences in procedures are scarce. We sequenced human stool samples and mock communities with increasing complexity using a variety of commonly used protocols. Short amplicons targeting different variable regions (V-regions) or ranges thereof (V1-V2, V1-V3, V3-V4, V4, V4-V5, V6-V8, and V7-V9) were investigated for differences in the composition outcome due to primer choices. Next, the influence of clustering (operational taxonomic units [OTUs], zero-radius OTUs [zOTUs], and amplicon sequence variants [ASVs]), different databases (GreenGenes, the Ribosomal Database Project, Silva, the genomic-based 16S rRNA Database, and The All-Species Living Tree), and bioinformatic settings on taxonomic assignment were also investigated. We present a systematic comparison across all typically used V-regions using well-established primers. While it is known that the primer choice has a significant influence on the resulting microbial composition, we show that microbial profiles generated using different primer pairs need independent validation of performance. Further, comparing data sets across V-regions using different databases might be misleading due to differences in nomenclature (e.g., Enterorhabdus versus Adlercreutzia) and varying precisions in classification down to genus level. Overall, specific but important taxa are not picked up by certain primer pairs (e.g., Bacteroidetes is missed using primers 515F-944R) or due to the database used (e.g., Acetatifactor in GreenGenes and the genomic-based 16S rRNA Database). We found that appropriate truncation of amplicons is essential and different truncated-length combinations should be tested for each study. Finally, specific mock communities of sufficient and adequate complexity are highly recommended.IMPORTANCE In 16S rRNA gene sequencing, certain bacterial genera were found to be underrepresented or even missing in taxonomic profiles when using unsuitable primer combinations, outdated reference databases, or inadequate pipeline settings. Concerning the last, quality thresholds as well as bioinformatic settings (i.e., clustering approach, analysis pipeline, and specific adjustments such as truncation) are responsible for a number of observed differences between studies. Conclusions drawn by comparing one data set to another (e.g., between publications) appear to be problematic and require independent cross-validation using matching V-regions and uniform data processing. Therefore, we highlight the importance of a thought-out study design including sufficiently complex mock standards and appropriate V-region choice for the sample of interest. The use of processing pipelines and parameters must be tested beforehand.}, }
@article {pmid33627510, year = {2021}, author = {Zhu, J and Ren, H and Zhong, H and Li, X and Zou, Y and Han, M and Li, M and Madsen, L and Kristiansen, K and Xiao, L}, title = {An Expanded Gene Catalog of Mouse Gut Metagenomes.}, journal = {mSphere}, volume = {6}, number = {1}, pages = {}, pmid = {33627510}, issn = {2379-5042}, abstract = {High-quality and comprehensive reference gene catalogs are essential for metagenomic research. The rather low diversity of samples used to construct existing catalogs of the mouse gut metagenome limits the numbers of identified genes in existing catalogs. We therefore established an expanded catalog of genes in the mouse gut metagenome (EMGC) containing >5.8 million genes by integrating 88 newly sequenced samples, 86 mouse gut-related bacterial genomes, and 3 existing gene catalogs. EMGC increases the number of nonredundant genes by more than 1 million genes compared to the so-far most extensive catalog. More than 60% of the genes in EMGC were assigned to Bacteria, with 54.20% being assigned to a phylum and 35.33% to a genus, while 30.39% were annotated at the KEGG orthology level. Nine hundred two metagenomic species (MGS) assigned to 122 taxa are identified based on the EMGC. The EMGC-based analysis of samples from groups of mice originating from different animal providers, housing laboratories, and genetic strains substantiated that diet is a major contributor to differences in composition and functional potential of the gut microbiota irrespective of differences in environment and genetic background. We envisage that EMGC will serve as a valuable reference data set for future metagenomic studies in mice.IMPORTANCE We established an expanded gene catalog of the mouse gut metagenome not only to increase the sample size compared to that in existing catalogs but also to provide a more comprehensive reference data set of the mouse gut microbiome for bioinformatic analysis. The expanded gene catalog comprises more than 5.8 million unique genes, as well as a wide range of taxonomic and functional information. Particularly, the analysis of metagenomic species with the expanded gene catalog reveals a great novelty of mouse gut-inhabiting microbial species. We envisage that the expanded gene catalog of the mouse gut metagenome will serve as a valuable bioinformatic resource for future gut metagenomic studies in mice.}, }
@article {pmid33627505, year = {2021}, author = {Fordyce, AJ and Ainsworth, TD and Leggat, W}, title = {Light Capture, Skeletal Morphology, and the Biomass of Corals' Boring Endoliths.}, journal = {mSphere}, volume = {6}, number = {1}, pages = {}, pmid = {33627505}, issn = {2379-5042}, abstract = {There is a growing interest in the endolithic microbial biofilms inhabiting skeletons of living corals because of their contribution to coral reef bioerosion and the reputed benefits they provide to live coral hosts. Here, we sought to identify possible correlations between coral interspecific patterns in skeletal morphology and variability in the biomass of, and chlorophyll concentrations within, the endolithic biofilm. We measured five morphological characteristics of five coral species and the biomasses/chlorophyll concentrations of their endolithic microbiome, and we compare interspecific patterns in these variables. We propose that the specific density of a coral's skeleton and its capacity for capturing and scattering incident light are the main correlates of endolithic microbial biomass. Our data suggest that the correlation between light capture and endolithic biomass is likely influenced by how the green microalgae (obligatory microborers) respond to skeletal variability. These results demonstrate that coral species differ significantly in their endolithic microbial biomass and that their skeletal structure could be used to predict these interspecific differences. Further exploring how and why the endolithic microbiome varies between coral species is vital in defining the role of these microbes on coral reefs, both now and in the future.IMPORTANCE Microbial communities living inside the skeletons of living corals play a variety of important roles within the coral meta-organism, both symbiotic and parasitic. Properly contextualizing the contribution of these enigmatic microbes to the life history of coral reefs requires knowledge of how these endolithic biofilms vary between coral species. To this effect, we measured differences in the morphology of five coral species and correlate these with variability in the biomass of the skeletal biofilms. We found that the density of the skeleton and its capacity to trap incoming light, as opposed to scattering it back into the surrounding water, both significantly correlated with skeletal microbial biomass. These patterns are likely driven by how dominant green microalgae in the endolithic niche, such as Ostreobium spp., are responding to the skeletal morphology. This study highlights that the structure of a coral's skeleton could be used to predict the biomass of its resident endolithic biofilm.}, }
@article {pmid33627470, year = {2021}, author = {Putnam, HM}, title = {Avenues of reef-building coral acclimatization in response to rapid environmental change.}, journal = {The Journal of experimental biology}, volume = {224}, number = {Pt Suppl 1}, pages = {}, doi = {10.1242/jeb.239319}, pmid = {33627470}, issn = {1477-9145}, abstract = {The swiftly changing climate presents a challenge to organismal fitness by creating a mismatch between the current environment and phenotypes adapted to historic conditions. Acclimatory mechanisms may be especially crucial for sessile benthic marine taxa, such as reef-building corals, where climate change factors including ocean acidification and increasing temperature elicit strong negative physiological responses such as bleaching, disease and mortality. Here, within the context of multiple stressors threatening marine organisms, I describe the wealth of metaorganism response mechanisms to rapid ocean change and the ontogenetic shifts in organism interactions with the environment that can generate plasticity. I then highlight the need to consider the interactions of rapid and evolutionary responses in an adaptive (epi)genetic continuum. Building on the definitions of these mechanisms and continuum, I also present how the interplay of the microbiome, epigenetics and parental effects creates additional avenues for rapid acclimatization. To consider under what conditions epigenetic inheritance has a more substantial role, I propose investigation into the offset of timing of gametogenesis leading to different environmental integration times between eggs and sperm and the consequences of this for gamete epigenetic compatibility. Collectively, non-genetic, yet heritable phenotypic plasticity will have significant ecological and evolutionary implications for sessile marine organism persistence under rapid climate change. As such, reef-building corals present ideal and time-sensitive models for further development of our understanding of adaptive feedback loops in a multi-player (epi)genetic continuum.}, }
@article {pmid33627367, year = {2021}, author = {Fukuda, T and Bouchi, R and Takeuchi, T and Amo-Shiinoki, K and Kudo, A and Tanaka, S and Tanabe, M and Akashi, T and Hirayama, K and Odamaki, T and Igarashi, M and Kimura, I and Tanabe, K and Tanizawa, Y and Yamada, T and Ogawa, Y}, title = {Importance of Intestinal Environment and Cellular Plasticity of Islets in the Development of Postpancreatectomy Diabetes.}, journal = {Diabetes care}, volume = {}, number = {}, pages = {}, doi = {10.2337/dc20-0864}, pmid = {33627367}, issn = {1935-5548}, abstract = {OBJECTIVE: To elucidate the pathogenesis of postpancreatectomy diabetes mellitus (PPDM).<br><br>RESEARCH DESIGN AND METHODS: Forty-eight patients without diabetes undergoing either pancreatoduodenectomy (PD) (n = 20) or distal pancreatectomy (DP) (n = 28) were included. A 75-g oral glucose tolerance test was performed every 6 months. Microbiome composition and short-chain fatty acids (SCFAs) in feces were examined before and 6 months after surgery. The association of histological characteristics of the resected pancreas with PPDM was examined.<br><br>RESULTS: During follow-up (median 3.19 years), 2 of 20 PD patients and 16 of 28 DP patients developed PPDM. Proteobacteria relative abundance, plasma glucagon-like peptide 1 (GLP-1), and fecal butyrate levels increased only after PD. Postsurgical butyrate levels were correlated with postsurgical GLP-1 levels. With no significant difference in the volume of the resected pancreas between the surgical procedures, both β-cell and α-cell areas in the resected pancreas were significantly higher in DP patients than in PD patients. In DP patients, the progressors to diabetes showed preexisting insulin resistance compared with nonprogressors, and both increased α- and β-cell areas were predictors of PPDM. Furthermore, in DP patients, α-cell and β-cell areas were associated with ALDH1A3 expression in islets.<br><br>CONCLUSIONS: We postulate that a greater removal of β-cells contributes to the development of PPDM after DP. Islet expansion along with preexisting insulin resistance is associated with high cellular plasticity, which may predict the development of PPDM after DP. In contrast, PD is associated with alterations of gut microbiome and increases in SCFA production and GLP-1 secretion, possibly protecting against PPDM development.}, }
@article {pmid33626996, year = {2021}, author = {Singha, LP and Pandey, P}, title = {Rhizosphere assisted bioengineering approaches for the mitigation of petroleum hydrocarbons contamination in soil.}, journal = {Critical reviews in biotechnology}, volume = {}, number = {}, pages = {1-26}, doi = {10.1080/07388551.2021.1888066}, pmid = {33626996}, issn = {1549-7801}, abstract = {The high demand for petroleum oil has led to hydrocarbon contamination in soil, including agricultural lands, and many other ecosystems across the globe. Physical and chemical treatments are effective strategies for the removal of high contamination levels and are useful for small areas, although with concerns of cost-effectiveness. Alternatively, several bacteria belonging to the Phylum: Proteobacteria, Bacteroidetes, Actinobacteria, Nocardioides, or Firmicutes are used for biodegradation of different hydrocarbons - aliphatic, polyaromatic hydrocarbons (PAH), and asphaltenes in the oil-contaminated soil. The rhizoremediation strategy with plant-microbe interactions has prospects to achieve the desired result in the field conditions. However, adequate biostimulation, and bioaugmentation with the suitable plant-microbe combination, and efficiency under a toxic environment needs to be evaluated. Modifying the microbiomes to achieve better biodegradation of contaminants is an upcoming strategy popularly known as microbiome engineering. In this review, rhizoremediation for the successful removal of the hydrocarbons have been critically discussed, with challenges for making it a feasible technology.HIGHLIGHTSPetroleum hydrocarbon contamination has increased around the globe.Rhizoremediation has the potential for the mitigation of pollutants from the contaminated sites.An accurate and detailed analysis of the physio-chemical and climatic conditions of the contaminated sites must be focused on.The suitable plant and bacteria, with other major considerations, may be employed for in-situ remediation.The appropriate data should be obtained using the omics approach to help toward the success of the rhizoremediation strategy.}, }
@article {pmid33626428, year = {2021}, author = {Hong, S and Cha, KH and Kwon, DY and Son, YJ and Kim, SM and Choi, JH and Yoo, G and Nho, CW}, title = {Agastache rugosa ethanol extract suppresses bone loss via induction of osteoblast differentiation with alteration of gut microbiota.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {84}, number = {}, pages = {153517}, doi = {10.1016/j.phymed.2021.153517}, pmid = {33626428}, issn = {1618-095X}, abstract = {PURPOSE: Osteoporosis is a metabolic skeletal disease characterized by bone loss and an increased risk of fractures. This study aimed to investigate the therapeutic effect of Agastache rugosa on postmenopausal osteoporosis and elucidate its mechanisms in modulating the bone status.<br><br>METHODS AND RESULTS: In the osteoblast differentiation process with MC3T3-E1 pre-osteoblasts, ethanol extract of Agastache rugosa (EEAR) and its compounds increased the expression of the proteins and genes of the osteoblast differentiation-related markers such as Runt-related transcription factor 2 (RUNX2) and β-catenin along with the elevation of calcium deposits. An ovariectomized mouse model was utilized to determine the impact of EEAR extract on postmenopausal osteoporosis. Twelve weeks of AR treatment suppressed the loss of bone strength, which was observed through micro-computed tomography. AR elevated osteogenic markers in the bone marrow cells, and collagen type 1 alpha 1 in the distal femoral bone. The results of the 16S rRNA gene sequencing analysis of cecal gut microbiomes demonstrated that AR reversed the ovariectomy-induced changes in the gut microbiomes.<br><br>CONCLUSION: Ethanol extract of Agastache rugosa has a therapeutic effect on postmenopausal osteoporosis via bone morphogenic protein, transforming growth factor β, and Wnt signaling pathway. It also increases the diversity of gut microbiota. Therefore, these data suggest that EEAR could be a potential candidate to treat postmenopausal osteoporosis.}, }
@article {pmid33626417, year = {2021}, author = {Andersen, VD and Jensen, MS and Munk, P and Vigre, H}, title = {Robustness in quantifying the abundance of antimicrobial resistance genes in pooled faeces samples from batches of slaughter pigs using metagenomics analysis.}, journal = {Journal of global antimicrobial resistance}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jgar.2021.02.005}, pmid = {33626417}, issn = {2213-7173}, abstract = {OBJECTIVES: With the continued spread of antimicrobial resistance in animals, it is important to assess its occurrence throughout a microbiome quantitatively in order to evaluate significantly affecting factors e.g. antimicrobial usage. Metagenomics methods makes it possible to measure the abundance of antimicrobial resistance genes in complex samples such as pooled faeces samples from batches of slaughter pigs. This study was performed to determine; the random error in antimicrobial resistance in pooled samples from batches pigs at slaughter, and the measurement error from the metagenomics processes.<br><br>METHODS: In four farms, two pooled samples were obtained from a batch of slaughter pigs by two individual samplers, each pooled sample was hereafter processed twice. Hierarchically clustered heatmaps were applied to evaluate dissimilarities between samples. The coefficient of variation was used to calculate the percentage difference between samples from the same farm.<br><br>RESULTS: The results of the analysis revealed that it was not possible to quantitatively separate the variation arising from sampling and metagenomics processes. They both contributed to the overall measurement error of antimicrobial resistance in batches of slaughter pigs.<br><br>CONCLUSIONS: Sampling of single pigs in 30 randomly selected pig pens within the farms provides a composition representative for frequently occurring antimicrobial resistance genes present within the farms, while rare genes were not dispersed in a similar manner. Aggregating the resistance abundance at gene family or antimicrobial class level will reduce the apparent variation originating from errors in sampling and metagenomics processing.}, }
@article {pmid33626128, year = {2021}, author = {Kiousi, DE and Rathosi, M and Tsifintaris, M and Chondrou, P and Galanis, A}, title = {Pro-biomics: Omics Technologies To Unravel the Role of Probiotics in Health and Disease.}, journal = {Advances in nutrition (Bethesda, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1093/advances/nmab014}, pmid = {33626128}, issn = {2156-5376}, abstract = {The comprehensive characterization of probiotic action has flourished during the past few decades, alongside the evolution of high-throughput, multiomics platforms. The integration of these platforms into probiotic animal and human studies has provided valuable insights into the holistic effects of probiotic supplementation on intestinal and extraintestinal diseases. Indeed, these methodologies have informed about global molecular changes induced in the host and residing commensals at multiple levels, providing a bulk of metagenomic, transcriptomic, proteomic, and metabolomic data. The meaningful interpretation of generated data remains a challenge; however, the maturation of the field of systems biology and artificial intelligence has supported analysis of results. In this review article, we present current literature on the use of multiomics approaches in probiotic studies, we discuss current trends in probiotic research, and examine the possibility of tailor-made probiotic supplementation. Lastly, we delve deeper into newer technologies that have been developed in the last few years, such as single-cell multiomics analyses, and provide future directions for the maximization of probiotic efficacy.}, }
@article {pmid33626077, year = {2021}, author = {Valencia-Giraldo, SM and Niño-Castro, A and López-Peña, A and Trejos-Vidal, D and Correa-Bueno, O and Montoya-Lerma, J}, title = {Immunity and survival response of Atta cephalotes (Hymenoptera: Myrmicinae) workers to Metarhizium anisopliae infection: Potential role of their associated microbiota.}, journal = {PloS one}, volume = {16}, number = {2}, pages = {e0247545}, doi = {10.1371/journal.pone.0247545}, pmid = {33626077}, issn = {1932-6203}, abstract = {Leaf-cutting ants of the genera Atta and Acromyrmex are at constant risk of epizootics due to their dense living conditions and frequent social interactions between genetically related individuals. To help mitigate the risk of epizootics, these ants display individual and collective immune responses, including associations with symbiotic bacteria that can enhance their resistance to pathogenic infections. For example, Acromyrmex spp. harbor actinobacteria that control infection by Escovopsis in their fungal gardens. Although Atta spp. do not maintain symbiosis with protective actinobacteria, the evidence suggests that these insects are colonized by bacterial microbiota that may play a role in their defense against pathogens. The potential role of the bacterial microbiome of Atta workers in enhancing host immunity remains unexplored. We evaluated multiple parameters of the individual immunity of Atta cephalotes (Linnaeus, 1758) workers, including hemocyte count, encapsulation response, and the antimicrobial activity of the hemolymph in the presence or absence of bacterial microbiota. Experiments were performed on ants reared under standard conditions as well as on ants previously exposed to the entomopathogenic fungus Metharrizium anisopliae. Furthermore, the effects of the presence/absence of bacteria on the survival of workers exposed to M. anisopliae were evaluated. The bacterial microbiota associated with A. cephalotes workers does not modulate the number of hemocytes under control conditions or under conditions of exposure to the fungal pathogen. In addition, infection by M. anisopliae, but not microbiota, increases the encapsulation response. Similarly, the exposure of workers to this fungus led to increased hemolymph antimicrobial activity. Conversely, the removal of bacterial microbiota did not have a significant impact on the survival of workers with M. anisopliae. Our results suggest that the bacterial microbiota associated with the cuticle of A. cephalotes workers does not play a role as a modulator of innate immunity, either at baseline or after exposure to the entomopathogen M. anisopliae. Further, upon infection, workers rely on mechanisms of humoral immunity to respond to this threat. Overall, our findings indicate that the bacterial microbiota associated with A. cephalotes workers does not play a defensive role.}, }
@article {pmid33625549, year = {2021}, author = {Qaiyum, Z and Lim, M and Inman, RD}, title = {The gut-joint axis in spondyloarthritis: immunological, microbial, and clinical insights.}, journal = {Seminars in immunopathology}, volume = {}, number = {}, pages = {}, pmid = {33625549}, issn = {1863-2300}, support = {159671/CAPMC/CIHR/Canada ; }, abstract = {The strong genetic and clinical overlaps between spondyloarthritis (SpA) and inflammatory bowel disease (IBD) have placed much needed focus on the gut-joint axis of inflammation in SpA, leading to three key hypotheses that attempt to unravel this complex relationship. The arthritogenic peptide hypothesis and the aberrant cellular trafficking hypothesis have been put forth to rationalize the manner by which the innate and adaptive immune systems cooperate and converge during SpA pathogenesis. The bacterial dysbiosis hypothesis discusses how changes in the microbiome lead to architectural and immunological consequences in SpA. These theories are not mutually exclusive, but can provide an explanation as to why subclinical gut inflammation may sometimes precede joint inflammation in SpA patients, thereby implying a causal relationship. Such investigations will be important in informing therapeutic decisions which may be common to both SpA and IBD. However, these hypotheses can also offer insights for a coincident inflammatory relationship between the gut and the joint, particularly when assessing the immunological players involved. Insights from understanding how these systems might affect the gut and joint differently will be equally imperative to address where the therapeutic differences lie between the two diseases. Collectively, this knowledge has practical implications in predicting the likelihood of IBD development in SpA or presence of coincident SpA-IBD, uncovering novel therapeutic targets, and redesigning currently approved treatments. It is evident that a multidisciplinary approach between the rheumatology and gastroenterology fields cannot be ignored, when it comes to the care of SpA patients at risk of IBD or vice versa.}, }
@article {pmid33624438, year = {2021}, author = {McCann, JR and Bihlmeyer, NA and Roche, K and Catherine, C and Jawahar, J and Kwee, LC and Younge, NE and Silverman, J and Ilkayeva, O and Sarria, C and Zizzi, A and Wootton, J and Poppe, L and Anderson, P and Arlotto, M and Wei, Z and Granek, JA and Valdivia, RH and David, LA and Dressman, HK and Newgard, CB and Shah, SH and Seed, PC and Rawls, JF and Armstrong, SC}, title = {The Pediatric Obesity Microbiome and Metabolism Study (POMMS): Methods, Baseline Data, and Early Insights.}, journal = {Obesity (Silver Spring, Md.)}, volume = {29}, number = {3}, pages = {569-578}, doi = {10.1002/oby.23081}, pmid = {33624438}, issn = {1930-739X}, support = {17SFRN33670990//American Heart Association/ ; R24-DK110492/DK/NIDDK NIH HHS/United States ; }, abstract = {OBJECTIVE: The purpose of this study was to establish a biorepository of clinical, metabolomic, and microbiome samples from adolescents with obesity as they undergo lifestyle modification.<br><br>METHODS: A total of 223 adolescents aged 10 to 18 years with BMI ≥95th percentile were enrolled, along with 71 healthy weight participants. Clinical data, fasting serum, and fecal samples were collected at repeated intervals over 6 months. Herein, the study design, data collection methods, and interim analysis-including targeted serum metabolite measurements and fecal 16S ribosomal RNA gene amplicon sequencing among adolescents with obesity (n = 27) and healthy weight controls (n = 27)-are presented.<br><br>RESULTS: Adolescents with obesity have higher serum alanine aminotransferase, C-reactive protein, and glycated hemoglobin, and they have lower high-density lipoprotein cholesterol when compared with healthy weight controls. Metabolomics revealed differences in branched-chain amino acid-related metabolites. Also observed was a differential abundance of specific microbial taxa and lower species diversity among adolescents with obesity when compared with the healthy weight group.<br><br>CONCLUSIONS: The Pediatric Metabolism and Microbiome Study (POMMS) biorepository is available as a shared resource. Early findings suggest evidence of a metabolic signature of obesity unique to adolescents, along with confirmation of previously reported findings that describe metabolic and microbiome markers of obesity.}, }
@article {pmid33624266, year = {2021}, author = {Whon, TW and Shin, NR and Kim, JY and Roh, SW}, title = {Omics in gut microbiome analysis.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {59}, number = {3}, pages = {292-297}, pmid = {33624266}, issn = {1976-3794}, abstract = {Our understanding of the interactions between microbial communities and their niche in the host gut has improved owing to recent advances in environmental microbial genomics. Integration of metagenomic and metataxonomic sequencing data with other omics data to study the gut microbiome has become increasingly common, but downstream analysis after data integration and interpretation of complex omics data remain challenging. Here, we review studies that have explored the gut microbiome signature using omics approaches, including metagenomics, metataxonomics, metatranscriptomics, and metabolomics. We further discuss recent analytics programs to analyze and integrate multi-omics datasets and further utilization of omics data with other advanced techniques, such as adaptive immune receptor repertoire sequencing, microbial culturomics, and machine learning, to evaluate important microbiome characteristics in the gut.}, }
@article {pmid33624265, year = {2021}, author = {Choi, K and Khan, R and Lee, SW}, title = {Dissection of plant microbiota and plant-microbiome interactions.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {59}, number = {3}, pages = {281-291}, pmid = {33624265}, issn = {1976-3794}, abstract = {Plants rooted in soil have intimate associations with a diverse array of soil microorganisms. While the microbial diversity of soil is enormous, the predominant bacterial phyla associated with plants include Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Verrucomicrobia. Plants supply nutrient niches for microbes, and microbes support plant functions such as plant growth, development, and stress tolerance. The interdependent interaction between the host plant and its microbes sculpts the plant microbiota. Plant and microbiome interactions are a good model system for understanding the traits in eukaryotic organisms from a holobiont perspective. The holobiont concept of plants, as a consequence of co-evolution of plant host and microbiota, treats plants as a discrete ecological unit assembled with their microbiota. Dissection of plant-microbiome interactions is highly complicated; however, some reductionist approaches are useful, such as the synthetic community method in a gnotobiotic system. Deciphering the interactions between plant and microbiome by this reductionist approach could lead to better elucidation of the functions of microbiota in plants. In addition, analysis of microbial communities' interactions would further enhance our understanding of coordinated plant microbiota functions. Ultimately, better understanding of plantmicrobiome interactions could be translated to improvements in plant productivity.}, }
@article {pmid33624262, year = {2021}, author = {Cho, JC}, title = {Omics-based microbiome analysis in microbial ecology: from sequences to information.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {59}, number = {3}, pages = {229-232}, pmid = {33624262}, issn = {1976-3794}, abstract = {Microbial ecology is the study of microorganisms present in nature. It particularly focuses on microbial interactions with any biota and with surrounding environments. Microbial ecology is entering its golden age with innovative multi-omics methods triggered by next-generation sequencing technologies. However, the extraction of ecologically relevant information from ever-increasing omics data remains one of the most challenging tasks in microbial ecology. This special issue includes 11 review articles that provide an overview of the state of the art of omics-based approaches in the field of microbial ecology, with particular emphasis on the interpretation of omics data, environmental pollution tracking, interactions in microbiomes, and viral ecology.}, }
@article {pmid33622857, year = {2021}, author = {Vangay, P and Burgin, J and Johnston, A and Beck, KL and Berrios, DC and Blumberg, K and Canon, S and Chain, P and Chandonia, JM and Christianson, D and Costes, SV and Damerow, J and Duncan, WD and Dundore-Arias, JP and Fagnan, K and Galazka, JM and Gibbons, SM and Hays, D and Hervey, J and Hu, B and Hurwitz, BL and Jaiswal, P and Joachimiak, MP and Kinkel, L and Ladau, J and Martin, SL and McCue, LA and Miller, K and Mouncey, N and Mungall, C and Pafilis, E and Reddy, TBK and Richardson, L and Roux, S and Shaffer, JP and Sundaramurthi, JC and Thompson, LR and Timme, RE and Zheng, J and Wood-Charlson, EM and Eloe-Fadrosh, EA}, title = {Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities.}, journal = {mSystems}, volume = {6}, number = {1}, pages = {}, pmid = {33622857}, issn = {2379-5077}, abstract = {Microbiome samples are inherently defined by the environment in which they are found. Therefore, data that provide context and enable interpretation of measurements produced from biological samples, often referred to as metadata, are critical. Important contributions have been made in the development of community-driven metadata standards; however, these standards have not been uniformly embraced by the microbiome research community. To understand how these standards are being adopted, or the barriers to adoption, across research domains, institutions, and funding agencies, the National Microbiome Data Collaborative (NMDC) hosted a workshop in October 2019. This report provides a summary of discussions that took place throughout the workshop, as well as outcomes of the working groups initiated at the workshop.}, }
@article {pmid33622856, year = {2021}, author = {Kleine Bardenhorst, S and Berger, T and Klawonn, F and Vital, M and Karch, A and Rübsamen, N}, title = {Data Analysis Strategies for Microbiome Studies in Human Populations-a Systematic Review of Current Practice.}, journal = {mSystems}, volume = {6}, number = {1}, pages = {}, pmid = {33622856}, issn = {2379-5077}, abstract = {Reproducibility is a major issue in microbiome studies, which is partly caused by missing consensus about data analysis strategies. The complex nature of microbiome data, which are high-dimensional, zero-inflated, and compositional, makes them challenging to analyze, as they often violate assumptions of classic statistical methods. With advances in human microbiome research, research questions and study designs increase in complexity so that more sophisticated data analysis concepts are applied. To improve current practice of the analysis of microbiome studies, it is important to understand what kind of research questions are asked and which tools are used to answer these questions. We conducted a systematic literature review considering all publications focusing on the analysis of human microbiome data from June 2018 to June 2019. Of 1,444 studies screened, 419 fulfilled the inclusion criteria. Information about research questions, study designs, and analysis strategies were extracted. The results confirmed the expected shift to more advanced research questions, as one-third of the studies analyzed clustered data. Although heterogeneity in the methods used was found at any stage of the analysis process, it was largest for differential abundance testing. Especially if the underlying data structure was clustered, we identified a lack of use of methods that appropriately addressed the underlying data structure while taking into account additional dependencies in the data. Our results confirm considerable heterogeneity in analysis strategies among microbiome studies; increasingly complex research questions require better guidance for analysis strategies.IMPORTANCE The human microbiome has emerged as an important factor in the development of health and disease. Growing interest in this topic has led to an increasing number of studies investigating the human microbiome using high-throughput sequencing methods. However, the development of suitable analytical methods for analyzing microbiome data has not kept pace with the rapid progression in the field. It is crucial to understand current practice to identify the scope for development. Our results highlight the need for an extensive evaluation of the strengths and shortcomings of existing methods in order to guide the choice of proper analysis strategies. We have identified where new methods could be designed to address more advanced research questions while taking into account the complex structure of the data.}, }
@article {pmid33622853, year = {2021}, author = {Shi, Z and Lei, H and Chen, G and Yuan, P and Cao, Z and Ser, HL and Zhu, X and Wu, F and Liu, C and Dong, M and Song, Y and Guo, Y and Chen, C and Hu, K and Zhu, Y and Zeng, XA and Zhou, J and Lu, Y and Patterson, AD and Zhang, L}, title = {Impaired Intestinal Akkermansia muciniphila and Aryl Hydrocarbon Receptor Ligands Contribute to Nonalcoholic Fatty Liver Disease in Mice.}, journal = {mSystems}, volume = {6}, number = {1}, pages = {}, pmid = {33622853}, issn = {2379-5077}, abstract = {Noncaloric artificial sweeteners (NAS) are extensively introduced into commonly consumed drinks and foods worldwide. However, data on the health effects of NAS consumption remain elusive. Saccharin and sucralose have been shown to pass through the human gastrointestinal tract without undergoing absorption and metabolism and directly encounter the gut microbiota community. Here, we aimed to identify a novel mechanism linking intestinal Akkermansia muciniphila and the aryl hydrocarbon receptor (AHR) to saccharin/sucralose-induced nonalcoholic fatty liver disease (NAFLD) in mice. Saccharin/sucralose consumption altered the gut microbial community structure, with significant depletion of A. muciniphila abundance in the cecal contents of mice, resulting in disruption of intestinal permeability and a high level of serum lipopolysaccharide, which likely contributed to systemic inflammation and caused NAFLD in mice. Saccharin/sucralose also markedly decreased microbiota-derived AHR ligands and colonic AHR expression, which are closely associated with many metabolic syndromes. Metformin or fructo-oligosaccharide supplementation significantly restored A. muciniphila and AHR ligands in sucralose-consuming mice, consequently ameliorating NAFLD.IMPORTANCE Our findings indicate that the gut-liver signaling axis contributes to saccharin/sucralose consumption-induced NAFLD. Supplementation with metformin or fructo-oligosaccharide is a potential therapeutic strategy for NAFLD treatment. In addition, we also developed a new nutritional strategy by using a natural sweetener (neohesperidin dihydrochalcone [NHDC]) as a substitute for NAS and free sugars.}, }
@article {pmid33622403, year = {2021}, author = {Holland-Moritz, H and Stuart, JEM and Lewis, LR and Miller, SN and Mack, MC and Ponciano, JM and McDaniel, SF and Fierer, N}, title = {The bacterial communities of Alaskan mosses and their contributions to N2-fixation.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {53}, pmid = {33622403}, issn = {2049-2618}, support = {DEB 1542609//National Science Foundation (US)/ ; }, abstract = {BACKGROUND: Mosses in high-latitude ecosystems harbor diverse bacterial taxa, including N2-fixers which are key contributors to nitrogen dynamics in these systems. Yet the relative importance of moss host species, and environmental factors, in structuring these microbial communities and their N2-fixing potential remains unclear. We studied 26 boreal and tundra moss species across 24 sites in Alaska, USA, from 61 to 69° N. We used cultivation-independent approaches to characterize the variation in moss-associated bacterial communities as a function of host species identity and site characteristics. We also measured N2-fixation rates via 15N2 isotopic enrichment and identified potential N2-fixing bacteria using available literature and genomic information.<br><br>RESULTS: Host species identity and host evolutionary history were both highly predictive of moss microbiome composition, highlighting strong phylogenetic coherence in these microbial communities. Although less important, light availability and temperature also influenced composition of the moss microbiome. Finally, we identified putative N2-fixing bacteria specific to some moss hosts, including potential N2-fixing bacteria outside well-studied cyanobacterial clades.<br><br>CONCLUSIONS: The strong effect of host identity on moss-associated bacterial communities demonstrates mosses' utility for understanding plant-microbe interactions in non-leguminous systems. Our work also highlights the likely importance of novel bacterial taxa to N2-fixation in high-latitude ecosystems. Video Abstract.}, }
@article {pmid33622400, year = {2021}, author = {Kang, Y and Lin, S and Ma, X and Che, Y and Chen, Y and Wan, T and Zhang, D and Shao, J and Xu, J and Xu, Y and Lou, Y and Zheng, M}, title = {Strain heterogeneity, cooccurrence network, taxonomic composition and functional profile of the healthy ocular surface microbiome.}, journal = {Eye and vision (London, England)}, volume = {8}, number = {1}, pages = {6}, pmid = {33622400}, issn = {2326-0254}, support = {2018ZX10201001//National Major Science and Technology Projects of China/ ; }, abstract = {BACKGROUND: There is growing evidence indicating that the microbial communities that dwell on the human ocular surface are crucially important for ocular surface health and disease. Little is known about interspecies interactions, functional profiles, and strain heterogeneity across individuals in healthy ocular surface microbiomes.<br><br>METHODS: To comprehensively characterize the strain heterogeneity, cooccurrence network, taxonomic composition and functional profile of the healthy ocular surface microbiome, we performed shotgun metagenomics sequencing on ocular surface mucosal membrane swabs of 17 healthy volunteers.<br><br>RESULTS: The healthy ocular surface microbiome was classified into 12 phyla, 70 genera, and 140 species. The number of species in each healthy ocular surface microbiome ranged from 6 to 47, indicating differences in microbial diversity among individuals. The species with high relative abundances and high positivity rates were Streptococcus pyogenes, Staphylococcus epidermidis, Propionibacterium acnes, Corynebacterium accolens, and Enhydrobacter aerosaccus. A correlation network analysis revealed a competitive interaction of Staphylococcus epidermidis with Streptococcus pyogenes in ocular surface microbial ecosystems. Staphylococcus epidermidis and Streptococcus pyogenes revealed phylogenetic diversity among different individuals. At the functional level, the pathways related to transcription were the most abundant. We also found that there were abundant lipid and amino acid metabolism pathways in the healthy ocular surface microbiome.<br><br>CONCLUSION: This study explored the strain heterogeneity, cooccurrence network, taxonomic composition, and functional profile of the healthy ocular surface microbiome. These findings have important significance for the future development of probiotic-based eye therapeutic drugs.}, }
@article {pmid33621916, year = {2021}, author = {Xiong, W and Jousset, A and Li, R and Delgado-Baquerizo, M and Bahram, M and Logares, R and Wilden, B and de Groot, GA and Amacker, N and Kowalchuk, GA and Shen, Q and Geisen, S}, title = {A global overview of the trophic structure within microbiomes across ecosystems.}, journal = {Environment international}, volume = {151}, number = {}, pages = {106438}, doi = {10.1016/j.envint.2021.106438}, pmid = {33621916}, issn = {1873-6750}, abstract = {The colossal project of mapping the microbiome on Earth is rapidly advancing, with a focus on individual microbial groups. However, a global assessment of the associations between predatory protists and their bacterial prey is still missing at a cross-ecosystem level. This knowledge is critical to better understand the importance of top-down links in structuring microbiomes. Here, we examined 38 sequence-based datasets of paired bacterial and protistan taxa, covering 3,178 samples from diverse habitats including freshwater, marine and soils. We show that community profiles of protists and bacteria strongly correlated across and within habitats, with trophic microbiome structures fundamentally differing across habitats. Soils hosted the most heterogenous and diverse microbiomes. Protist communities were dominated by predators in soils and phototrophs in aquatic environments. This led to changes in the ratio of total protists to bacteria richness, which was highest in marine, while that of predatory protists to bacteria was highest in soils. Taxon richness and relative abundance of predatory protists positively correlated with bacterial richness in marine habitats. These links differed between soils, predatory protist richness and the relative abundance of predatory protists positively correlated with bacterial richness in forest and grassland soils, but not in agricultural soils. Our results suggested that anthropogenic pressure affects higher trophic levels more than lower ones leading to a decoupled trophic structure in microbiomes. Together, our cumulative overview of microbiome patterns of bacteria and protists at the global scale revealed major patterns and differences of the trophic structure of microbiomes across Earth's habitats, and show that anthropogenic factors might have negative effects on the trophic structure within microbiomes. Furthermore, the increased impact of anthropogenic factors on especially higher trophic levels suggests that often-observed reduced ecosystem functions in anthropogenic systems might be partly attributed to a reduction of trophic complexity.}, }
@article {pmid33621653, year = {2021}, author = {Bloom, PP and Luévano, JM and Miller, KJ and Chung, RT}, title = {Deep stool microbiome analysis in cirrhosis reveals an association between short-chain fatty acids and hepatic encephalopathy.}, journal = {Annals of hepatology}, volume = {}, number = {}, pages = {100333}, doi = {10.1016/j.aohep.2021.100333}, pmid = {33621653}, issn = {1665-2681}, abstract = {INTRODUCTION AND OBJECTIVES: Hepatic encephalopathy (HE) is a complication of cirrhosis linked to the microbiome. We aimed to characterize the fecal microbiome of patients with prior and future overt HE, and explore the relationship between fecal species, short-chain fatty acids (SCFAs) and ammonia on HE pathogenesis.<br><br>MATERIALS AND METHODS: Consecutive inpatients and outpatients with cirrhosis were recruited. A single stool sample was collected and underwent shallow shotgun sequencing, and SCFA and ammonia quantification. Patients were followed until the end of the study period. Prior and new overt HE was diagnosed by the treating hepatologist.<br><br>RESULTS: Forty-nine patients with cirrhosis, mean MELD-Na 20 (SD = 9) and 33 (67%) with a history of OHE provided a stool sample. Over a median 85 days of follow up (interquartile range 34 to 181 days), 16 developed an OHE episode. Eight fecal bacterial species were associated with a history of OHE, and no species predicted future OHE. Bacterial species positively associated with SCFA content were inversely related to cirrhosis disease severity. Patients with a history of OHE had lower concentrations of 6 fecal SCFAs. Fecal ammonia concentrations were similar between those with and without a history of OHE (273 μmol/g ± 214 vs. 327 ± 234, P = 0.43).<br><br>CONCLUSIONS: We found 8 fecal species and 6 SCFAs linked to OHE. Many of the species inversely linked to OHE also have an association with SCFA production. Further work is needed to detail this relationship and to develop targeted interventions to treat HE.}, }
@article {pmid33621451, year = {2021}, author = {Delseny, M}, title = {Genus Variovorax is a key player in the root microbiome.}, journal = {Comptes rendus biologies}, volume = {343}, number = {3}, pages = {221-222}, doi = {10.5802/crbiol.28}, pmid = {33621451}, issn = {1768-3238}, }
@article {pmid33621444, year = {2021}, author = {Pierson, M and Merley, A and Hamilton, SE}, title = {Generating Mice with Diverse Microbial Experience.}, journal = {Current protocols}, volume = {1}, number = {2}, pages = {e53}, doi = {10.1002/cpz1.53}, pmid = {33621444}, issn = {2691-1299}, support = {AI116678/NH/NIH HHS/United States ; }, abstract = {Laboratory strains of mice are typically housed in specific pathogen-free facilities to minimize exposure to microbes. This method encourages uniformity in responses to experimentally induced parameters and reduces loss of animals, allowing for the survival and study of immunodeficient mice. However, the restrictions also limit physiologic relevance to humans, who are exposed to numerous microbes from birth. Recent evidence from several groups has demonstrated that exposure of laboratory mice to commensal and pathogenic microbes normally found in wild or pet store mice can dramatically impact the cellular makeup and function of the immune system. This article outlines procedures for exposing laboratory strains of mice to the diverse array of microbes typically found in pet store mice. Suggested methods for characterization of the immune system following this exposure are also described. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Cohousing laboratory strains of mice with pet store mice Support Protocol: Antibody staining of circulating immune cells and analysis by flow cytometry Basic Protocol 2: Exposure of laboratory strains of mice to fomite bedding.}, }
@article {pmid33621265, year = {2021}, author = {Day, JA and Diener, C and Otwell, AE and Tams, KE and Bebout, B and Detweiler, AM and Lee, MD and Scott, MT and Ta, W and Ha, M and Carreon, SA and Tong, K and Ali, AA and Gibbons, SM and Baliga, NS}, title = {Lettuce (Lactuca sativa) productivity influenced by microbial inocula under nitrogen-limited conditions in aquaponics.}, journal = {PloS one}, volume = {16}, number = {2}, pages = {e0247534}, doi = {10.1371/journal.pone.0247534}, pmid = {33621265}, issn = {1932-6203}, abstract = {The demand for food will outpace productivity of conventional agriculture due to projected growth of the human population, concomitant with shrinkage of arable land, increasing scarcity of freshwater, and a rapidly changing climate. While aquaponics has potential to sustainably supplement food production with minimal environmental impact, there is a need to better characterize the complex interplay between the various components (fish, plant, microbiome) of these systems to optimize scale up and productivity. Here, we investigated how the commonly-implemented practice of continued microbial community transfer from pre-existing systems might promote or impede productivity of aquaponics. Specifically, we monitored plant growth phenotypes, water chemistry, and microbiome composition of rhizospheres, biofilters, and fish feces over 61-days of lettuce (Lactuca sativa var. crispa) growth in nitrogen-limited aquaponic systems inoculated with bacteria that were either commercially sourced or originating from a pre-existing aquaponic system. Lettuce above- and below-ground growth were significantly reduced across replicates treated with a pre-existing aquaponic system inoculum when compared to replicates treated with a commercial inoculum. Reduced productivity was associated with enrichment in specific bacterial genera in plant roots, including Pseudomonas, following inoculum transfer from pre-existing systems. Increased productivity was associated with enrichment of nitrogen-fixing Rahnella in roots of plants treated with the commercial inoculum. Thus, we show that inoculation from a pre-existing system, rather than from a commercial inoculum, is associated with lower yields. Further work will be necessary to test the putative mechanisms involved.}, }
@article {pmid33620148, year = {2021}, author = {Cao, Y and Liu, Y and Dong, Q and Wang, T and Niu, C}, title = {Alterations in the gut microbiome and metabolic profile in rats acclimated to high environmental temperature.}, journal = {Microbial biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1751-7915.13772}, pmid = {33620148}, issn = {1751-7915}, support = {81901914//National Natural Science Foundation of China/ ; BWS17J031//Tianjin Institute of Environmental and Operational Medicine/ ; }, abstract = {Heat acclimation (HA) is the best strategy to improve heat stress tolerance by inducing positive physiological adaptations. Evidence indicates that the gut microbiome plays a fundamental role in the development of HA, and modulation of gut microbiota can improve tolerance to heat exposure and decrease the risks of heat illness. In this study, for the first time, we applied 16S rRNA gene sequencing and untargeted liquid chromatography-mass spectrometry (LC-MS) metabolomics to explore variations in the gut microbiome and faecal metabolic profiles in rats after HA. The gut microbiota of HA subjects exhibited higher diversity and richer microbes. HA altered the gut microbiota composition with significant increases in the genera Lactobacillus (a major probiotic) and Oscillospira alongside significant decreases in the genera Blautia and Allobaculum. The faecal metabolome was also significantly changed after HA, and among the 13 perturbed metabolites, (S)-AL 8810 and celastrol were increased. Moreover, the two increased genera were positively correlated with the two upregulated metabolites and negatively correlated with the other 11 downregulated metabolites, while the correlations between the two decreased genera and the upregulated/downregulated metabolites were completely contrary. In summary, both the structure of the gut microbiome community and the faecal metabolome were improved after 28 days of HA. These findings provide novel insights regarding the improvement of the gut microbiome and its functions as a potential mechanism by which HA confers protection against heat stress.}, }
@article {pmid33620078, year = {2021}, author = {Sheh, A}, title = {The Gastrointestinal Microbiota of the Common Marmoset (Callithrix jacchus).}, journal = {ILAR journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ilar/ilaa025}, pmid = {33620078}, issn = {1930-6180}, abstract = {The microbiota is heavily involved in both health and disease pathogenesis, but defining a normal, healthy microbiota in the common marmoset has been challenging. The aim of this review was to systematically review recent literature involving the gastrointestinal microbiome of common marmosets in health and disease. Twelve sources were included in this review. The gut microbiome composition was reviewed across institutions worldwide, and taxonomic shifts between healthy individuals were described. Unlike the human gut microbiome, which is dominated by Firmicutes and Bacteroidetes, the marmoset gut microbiome shows great plasticity across institutions, with 5 different phyla described as dominant in different healthy cohorts. Genera shared across institutions include Anaerobiospirillum, Bacteroides, Bifidobacterium, Collinsella, Fusobacterium, Megamonas, Megasphaera, Phascolarctobacterium, and Prevotella. Shifts in the abundance of Prevotella or Bifidobacterium or invasion by pathogens like Clostridium perfringens may be associated with disease. Changes in microbial composition have been described in healthy and diseased marmosets, but factors influencing the severe changes in microbial composition have not been established. Multi-institutional, prospective, and longitudinal studies that utilize multiple testing methodologies are required to determine sources of variability in the reporting of marmoset microbiomes. Furthermore, methods of microbial manipulation, whether by diet, enrichment, fecal microbiome transplantation, etc, need to be established to modulate and maintain robust and resilient microbiome communities in marmoset colonies and reduce the incidence of idiopathic gastrointestinal disease.}, }
@article {pmid33619554, year = {2021}, author = {Nakayasu, M and Ohno, K and Takamatsu, K and Aoki, Y and Yamazaki, S and Takase, H and Shoji, T and Yazaki, K and Sugiyama, A}, title = {Tomato roots secrete tomatine to modulate the bacterial assemblage of the rhizosphere.}, journal = {Plant physiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/plphys/kiab069}, pmid = {33619554}, issn = {1532-2548}, abstract = {Saponins are a group of plant specialized metabolites which are widely distributed in angiosperm plants and have various biological activities. The present study focused on α-tomatine, a major saponin present in tissues of tomato (Solanum lycopersicum) plants. α-Tomatine is responsible for defense against plant pathogens and herbivores, but its biological function in the rhizosphere remains unknown. Secretion of tomatine was higher at the early growth than the green-fruit stage in hydroponically grown plants, and the concentration of tomatine in the rhizosphere of field-grown plants was higher than that of the bulk soil at all growth stages. The effects of tomatine and its aglycone tomatidine on the bacterial communities in the soil were evaluated in vitro, revealing that both compounds influenced the microbiome in a concentration-dependent manner. Numerous bacterial families were influenced in tomatine/tomatidine-treated soil as well as in the tomato rhizosphere. Sphingomonadaceae species, which are commonly observed and enriched in tomato rhizospheres in the fields, were also enriched in tomatine- and tomatidine-treated soils. Moreover, a jasmonate-responsive ETHYLENE RESPONSE FACTOR 4 mutant associated with low tomatine production caused the root-associated bacterial communities to change with a reduced abundance of Sphingomonadaceae. Taken together, our results highlight the role of tomatine in shaping the bacterial communities of the rhizosphere and suggest additional functions of tomatine in belowground biological communication.}, }
@article {pmid33619379, year = {2021}, author = {Wilmanski, T and Diener, C and Rappaport, N and Patwardhan, S and Wiedrick, J and Lapidus, J and Earls, JC and Zimmer, A and Glusman, G and Robinson, M and Yurkovich, JT and Kado, DM and Cauley, JA and Zmuda, J and Lane, NE and Magis, AT and Lovejoy, JC and Hood, L and Gibbons, SM and Orwoll, ES and Price, ND}, title = {Gut microbiome pattern reflects healthy ageing and predicts survival in humans.}, journal = {Nature metabolism}, volume = {3}, number = {2}, pages = {274-286}, pmid = {33619379}, issn = {2522-5812}, support = {2U19AG023122-11A1//U.S. Department of Health &amp; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; 2U19AG023122-11A1//U.S. Department of Health &amp; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; 5U19AG023122-13//U.S. Department of Health &amp; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; 5U19AG023122-13//U.S. Department of Health &amp; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; 5U19AG023122-13//U.S. Department of Health &amp; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; 5U19AG023122-13//U.S. Department of Health &amp; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; AG042124//U.S. Department of Health &amp; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; 5U19AG023122-13//U.S. Department of Health &amp; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; 2U19AG023122-11A1//U.S. Department of Health &amp; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; }, abstract = {The gut microbiome has important effects on human health, yet its importance in human ageing remains unclear. In the present study, we demonstrate that, starting in mid-to-late adulthood, gut microbiomes become increasingly unique to individuals with age. We leverage three independent cohorts comprising over 9,000 individuals and find that compositional uniqueness is strongly associated with microbially produced amino acid derivatives circulating in the bloodstream. In older age (over ~80 years), healthy individuals show continued microbial drift towards a unique compositional state, whereas this drift is absent in less healthy individuals. The identified microbiome pattern of healthy ageing is characterized by a depletion of core genera found across most humans, primarily Bacteroides. Retaining a high Bacteroides dominance into older age, or having a low gut microbiome uniqueness measure, predicts decreased survival in a 4-year follow-up. Our analysis identifies increasing compositional uniqueness of the gut microbiome as a component of healthy ageing, which is characterized by distinct microbial metabolic outputs in the blood.}, }
@article {pmid33618307, year = {2021}, author = {Bello, A and Wang, B and Zhao, Y and Yang, W and Ogundeji, A and Deng, L and Egbeagu, UU and Yu, S and Zhao, L and Li, D and Xu, X}, title = {Composted biochar affects structural dynamics, function and co-occurrence network patterns of fungi community.}, journal = {The Science of the total environment}, volume = {775}, number = {}, pages = {145672}, doi = {10.1016/j.scitotenv.2021.145672}, pmid = {33618307}, issn = {1879-1026}, abstract = {A few researchers have reported enhancing soil physicochemical properties and reducing greenhouse gas emission using biochar-compost mixture as an alternative method to address soil fertility, soil degradation and climate change. However, information about its effects on soil microbiome has rarely been studied. This investigation was on the impact of a combined biochar-compost application on soil physicochemical variables, fungal community composition, function and network patterns in maize at seedling stage (SS), reproductive stage (RS), and maturity stage (MS). The experimental design consists of five treatments: control (CNT), compost (CMP), composted biochar (CMB), compost fortified with biochar (CFWB), biochar (BCH). The results showed that CFWB, CMB, and CMP increased fungal diversity indices (Shannon, Sobs, and Chao) at the RS and MS stages respectively, compared to BCH and CNT. Distance-based redundancy analysis (db-RDA) at genus level indicated that the pH, available nitrogen, and soil organic matter at SS; available phosphorus at RS; Mg, Mn, Fe, and Zn at MS significantly and positively affected the fungi community. Based on the Linear discriminant analysis (LDA) and effect size (LEfSe) analysis, the results revealed that only Cystofilobasidiaceae and Guehomyces were the MS biomarkers; and significantly enriched in CFWB. FUNGuild analysis indicated that organic amendments (CFWB, CMB, CMP, and BCH) suppressed the abundance of plant pathogenic fungi (Edenia and Waitea) compared to CNT. Network analysis showed that CFWB and CMB had a high niche overlap and cross-feeding in their networks compared to other treatments. However, CMP network had more positive links with Saprotroph, Pathotroph-Saprotroph-Symbiotroph, Pathotroph and Pathotroph-Symbiotroph compared with other treatments. This study showed that applying biochar, compost and a mixture of both, positively affected soil fungal communities plus co-occurrence network pattern in a single cropping season. Thus, their application as soil amendments may improve the soil fungi ecosystem, soil health and quality and mitigate climate change.}, }
@article {pmid33618184, year = {2021}, author = {Sharma, P}, title = {Efficiency of bacteria and bacterial assisted phytoremediation of heavy metals: An update.}, journal = {Bioresource technology}, volume = {328}, number = {}, pages = {124835}, doi = {10.1016/j.biortech.2021.124835}, pmid = {33618184}, issn = {1873-2976}, abstract = {The aim of this review to address the plant-associated bacteria to enhance the phytoremediation efficiency of the heavy metals from polluted sites and it is also highlighted advances for the application in wastewater treatment. Plant-associated bacteria have potential to encourage the plant growth and resistance under stress conditions. Such bacteria could enhance plant growth by controlling growth hormone, nutrition security, producing siderophore, secondary metabolites, and improving the antioxidant enzymes system. This review also explores the concepts and applications of bacteria assisted phytoremediation, addressing aspects that affect phytoremediation and pathways for restoration. Significant review issues relating to production and application of bacteria for improvement of bioremediation were established and presented for possible future research. Bacteria assisted phytoremediation is cost-effective strategy and metal sequestration mechanism that hold high metal biosorption capacities. This also takes into consideration the current state of technology implementations and proposals for prospective clean-up studies.}, }
@article {pmid33617049, year = {2020}, author = {Visseren, T and Fuhler, GM and Erler, NS and Nossent, YRA and Metselaar, HJ and IJzermans, JNM and Darwish Murad, S and Peppelenbosch, MP}, title = {Recurrence of primary sclerosing cholangitis after liver transplantation is associated with specific changes in the gut microbiome pretransplant - a pilot study.}, journal = {Transplant international : official journal of the European Society for Organ Transplantation}, volume = {33}, number = {11}, pages = {1424-1436}, doi = {10.1111/tri.13692}, pmid = {33617049}, issn = {1432-2277}, abstract = {Primary sclerosing cholangitis (PSC) is a common indication for liver transplantation (LT). Up to 25% of patients experience recurrence of PSC (rPSC) after LT, which is associated with significant morbidity and mortality. To date, it is not possible to predict which patients are at risk for rPSC. The aetiology of PSC is complex and is speculated to involve translocation of intestinal bacteria to the liver, because of its frequent co-occurrence with inflammatory bowel diseases (IBD). Here, we investigate whether the mucosal intestinal microbiome of PSC patients (n = 97) at time of first LT can identify those patients who will develop rPSC. 16S gene sequencing of bacterial DNA isolated from formalin-fixed paraffin-embedded biopsies showed that PSC patients with Crohn's disease (n = 15) have a reduced microbial diversity and that inflammation of the mucosa is associated with beta-diversity changes and feature differences. No differences in alpha- or beta diversity were observed between patients with rPSC (n = 14) and without rPSC (n = 83). However, many over-represented bacterial features were detected in patients with rPSC, while surprisingly, those without recurrence of disease were characterized by an increased presence of the Gammaproteobacteria Shigella. This pilot study warrants further investigation into bacterial differences between rPSC and non-rPSC patients.}, }
@article {pmid33617025, year = {2021}, author = {Lu, H and Yan, X and Zhu, B and Zhang, L and Feng, X and Piao, M and Huang, B and Wang, X and Zhang, H and Wang, Q and Meng, H}, title = {The occurrence of peri-implant mucositis associated with the shift of submucosal microbiome in patients with a history of periodontitis during the first two years.}, journal = {Journal of clinical periodontology}, volume = {48}, number = {3}, pages = {441-454}, doi = {10.1111/jcpe.13410}, pmid = {33617025}, issn = {1600-051X}, support = {81570980//National Natural Science Foundation of China/ ; 81870773//National Natural Science Foundation of China/ ; }, abstract = {AIM: To investigate the dynamic changes of peri-implant microbiome in patients with a history of periodontitis and to construct a microbial prediction model.<br><br>MATERIALS AND METHODS: The prospective study was performed at one month (T1), one year (T2) and two years (T3) after restoration. Clinical examinations [probing depth (PD), bleeding on probing (BOP), suppuration (SUP)], radiographic examinations and sample collection were conducted at three timepoints. Peri-implant sulcular fluid (PISF) was collected and analysed by 16S rRNA gene sequencing. Generalized linear mixed model (GLMM) was used to identify differences.<br><br>RESULTS: Totally, 168 subjects were assessed for eligibility. Twenty-two patients were recruited in the longitudinal study. Eventually, 67 PISF samples from 24 implants of 12 patients were collected and analysed. Peri-implant microbiome showed increasing diversity and complexity over time. Disease-associated genera Porphyromonas, Tannerella, Treponema and Prevotella dramatically increased from T1 to T3. The prediction model for clinical suppuration at T1 showed a high accuracy of 90%.<br><br>CONCLUSION: The dysbiosis of peri-implant microbiome increased with time during the two-year observation in patients with a history of periodontitis. Genera of Porphyromonas, Tannerella, Treponema and Prevotella were biomarkers of peri-implant mucositis. Microbiota at the early stage could predict subsequent microbial dysbiosis and clinical suppuration.}, }
@article {pmid33616993, year = {2021}, author = {Youn, GS and Suk, KT}, title = {Editorial: microbiome modulation by rifaximin in severe alcoholic hepatitis.}, journal = {Alimentary pharmacology &amp; therapeutics}, volume = {53}, number = {4}, pages = {561-562}, doi = {10.1111/apt.16218}, pmid = {33616993}, issn = {1365-2036}, support = {NRF-2020R1A6A1A03043026//National Research Foundation of Korea (NRF)/ ; //Ministry of Education, Science and Technology/ ; }, }
@article {pmid33616876, year = {2021}, author = {Waeijen-Smit, K and Houben-Wilke, S and DiGiandomenico, A and Gehrmann, U and Franssen, FME}, title = {Unmet needs in the management of exacerbations of chronic obstructive pulmonary disease.}, journal = {Internal and emergency medicine}, volume = {}, number = {}, pages = {}, pmid = {33616876}, issn = {1970-9366}, support = {LSHI19003//AstraZeneca/ ; LSHI19003//Dutch Top Sector Life Sciences and Health Topconsortia for Knowledge and Innovation/ ; }, abstract = {Exacerbations of chronic obstructive pulmonary disease (COPD) are episodes of acute worsening of respiratory symptoms that require additional therapy. These events play a pivotal role in the natural course of the disease and are associated with a progressive decline in lung function, reduced health status, a low physical activity level, tremendous health care costs, and increased mortality. Although most exacerbations have an infectious origin, the underlying mechanisms are heterogeneous and specific predictors of their occurrence in individual patients are currently unknown. Accurate prediction and early diagnosis of exacerbations is essential to develop novel targets for prevention and personalized treatments to reduce the impact of these events. Several potential biomarkers have previously been studied, these however lack specificity, accuracy and do not add value to the available clinical predictors. At present, microbial composition and host-microbiome interactions in the lung are increasingly recognized for their role in affecting the susceptibility to exacerbations, and may steer towards a novel direction in the management of COPD exacerbations. This narrative review describes the current challenges and unmet needs in the management of acute exacerbations of COPD. Exacerbation triggers, biological clusters, current treatment strategies, and their limitations, previously studied biomarkers and prediction tools, the lung microbiome and its role in COPD exacerbations as well as future directions are discussed.}, }
@article {pmid33616663, year = {2021}, author = {DeMerle, KM and Kennedy, JN and Peck Palmer, OM and Brant, E and Chang, CH and Dickson, RP and Huang, DT and Angus, DC and Seymour, CW}, title = {Feasibility of Embedding a Scalable, Virtually Enabled Biorepository in the Electronic Health Record for Precision Medicine.}, journal = {JAMA network open}, volume = {4}, number = {2}, pages = {e2037739}, doi = {10.1001/jamanetworkopen.2020.37739}, pmid = {33616663}, issn = {2574-3805}, abstract = {Importance: A cornerstone of precision medicine is the identification and use of biomarkers that help subtype patients for targeted treatment. Such an approach requires the development and subsequent interrogation of large-scale biobanks linked to well-annotated clinical data. Traditional means of creating these data-linked biobanks are costly and lengthy, especially in acute conditions that require time-sensitive clinical data and biospecimens.<br><br>Objectives: To develop a virtually enabled biorepository and electronic health record (EHR)-embedded, scalable cohort for precision medicine (VESPRE) and compare the feasibility, enrollment, and costs of VESPRE with those of a traditional study design in acute care.<br><br>In a prospective cohort study, the EHR-embedded screening alert was generated for 3428 patients, and 2199 patients (64%) were eligible and screened. Of these, 1027 patients (30%) were enrolled. VESPRE was developed for regulatory compliance, feasibility, internal validity, and cost in a prospective cohort of 1027 patients (aged ≥18 years) with sepsis-3 within 6 hours of presentation to the emergency department. The VESPRE infrastructure included (1) automated EHR screening, (2) remnant blood collection for creation of a virtually enabled biorepository, and (3) automated clinical data abstraction. The study was conducted at an academic institution in southwestern Pennsylvania from October 17, 2017, to June 6, 2019.<br><br>Main Outcomes and Measures: Regulatory compliance, enrollment, internal validity of automated screening, biorepository acquisition, and costs.<br><br>Results: Of the 1027 patients enrolled in the study, 549 were included in the proof-of-concept analysis (305 [56%] men); median (SD) age was 59 (17) years. VESPRE collected 12 963 remnant blood and urine samples and demonstrated adequate feasibility for clinical, biomarker, and microbiome analyses. Over the 20-month test, the total cost beyond the existing operations infrastructure was $39 417.50 ($14 880.00 project management, $22 717.50 laboratory supplies/staff, and $1820.00 data management)-approximately $39 per enrolled patient vs $239 per patient for a traditional cohort study.<br><br>Conclusions and Relevance: Results of this study suggest that, in a large US health system that collects data using a common EHR platform and centralized laboratory system, VESPRE, a large-scale, inexpensive EHR-embedded infrastructure for precision medicine can be used. Tested in the sepsis setting, VESPRE appeared to capture a high proportion of eligible patients at low incremental cost.}, }
@article {pmid33616233, year = {2021}, author = {Gabryszewski, SJ and Dudley, J and Grundmeier, RW and Hill, DA}, title = {Early-life environmental exposures associate with individual and cumulative allergic morbidity.}, journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology}, volume = {}, number = {}, pages = {}, doi = {10.1111/pai.13486}, pmid = {33616233}, issn = {1399-3038}, abstract = {Several early-life environmental factors have been associated with altered risk for the development and/or severity of individual allergic conditions. These include exposures implicated in the modulation of the microbiome, such as infant delivery mode, diet, and exposure to antibiotics and antacids. The impact of these early-life factors on allergic multimorbidity remains unknown. To address this knowledge gap, we used electronic medical records for a birth cohort of 158,510 children to track development of atopic dermatitis (AD), IgE-mediated food allergy (IgE-FA), asthma, and allergic rhinitis (AR) in individual children over time. We measured hazard ratios (HRs), adjusted for birth year, race, ethnicity, sex, and insurance payer type, to assess how development of both individual and multiple allergic conditions is influenced by birth mode, feeding practice during the first year of life, or exposure to antibiotics and/or antacids during the first six months of life. We found that vaginal delivery (VD; HR 0.89, 0.83, 0.84, 0.79 for at least 1, 2, 3, 4 conditions, respectively; p≤0.001) and exclusive breastmilk (BM) feeding (HR 0.74, 0.75, 0.89, for at least 1, 2, 3 conditions, respectively; p≤0.001) are associated with reduced cumulative allergic burden, while antibiotic exposure (HR 1.40, 1.44, 1.48, 1.63 for at least 1, 2, 3, 4 conditions, respectively; p≤0.001) and antacid exposure (HR 1.26, 1.35, 1.32 for at least 1, 2, 3 conditions, respectively; p≤0.001) are associated with increased cumulative allergic burden during childhood. This work expands our understanding of how a child's early-life environment may influence their risk of allergy development and progression.}, }
@article {pmid33616007, year = {2021}, author = {Hartman, JH and Widmayer, SJ and Bergemann, CM and King, DE and Morton, KS and Romersi, RF and Jameson, LE and Leung, MCK and Andersen, EC and Taubert, S and Meyer, JN}, title = {Xenobiotic metabolism and transport in Caenorhabditis elegans.}, journal = {Journal of toxicology and environmental health. Part B, Critical reviews}, volume = {}, number = {}, pages = {1-44}, doi = {10.1080/10937404.2021.1884921}, pmid = {33616007}, issn = {1521-6950}, abstract = {Caenorhabditis elegans has emerged as a major model in biomedical and environmental toxicology. Numerous papers on toxicology and pharmacology in C. elegans have been published, and this species has now been adopted by investigators in academic toxicology, pharmacology, and drug discovery labs. C. elegans has also attracted the interest of governmental regulatory agencies charged with evaluating the safety of chemicals. However, a major, fundamental aspect of toxicological science remains underdeveloped in C. elegans: xenobiotic metabolism and transport processes that are critical to understanding toxicokinetics and toxicodynamics, and extrapolation to other species. The aim of this review was to initially briefly describe the history and trajectory of the use of C. elegans in toxicological and pharmacological studies. Subsequently, physical barriers to chemical uptake and the role of the worm microbiome in xenobiotic transformation were described. Then a review of what is and is not known regarding the classic Phase I, Phase II, and Phase III processes was performed. In addition, the following were discussed (1) regulation of xenobiotic metabolism; (2) review of published toxicokinetics for specific chemicals; and (3) genetic diversity of these processes in C. elegans. Finally, worm xenobiotic transport and metabolism was placed in an evolutionary context; key areas for future research highlighted; and implications for extrapolating C. elegans toxicity results to other species discussed.}, }
@article {pmid33615992, year = {2021}, author = {Pham, VT and Fehlbaum, S and Seifert, N and Richard, N and Bruins, MJ and Sybesma, W and Rehman, A and Steinert, RE}, title = {Effects of colon-targeted vitamins on the composition and metabolic activity of the human gut microbiome- a pilot study.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1-20}, doi = {10.1080/19490976.2021.1875774}, pmid = {33615992}, issn = {1949-0984}, abstract = {An increasing body of evidence has shown that gut microbiota imbalances are linked to diseases. Currently, the possibility of regulating gut microbiota to reverse these perturbations by developing novel therapeutic and preventive strategies is being extensively investigated. The modulatory effect of vitamins on the gut microbiome and related host health benefits remain largely unclear. We investigated the effects of colon-delivered vitamins A, B2, C, D, and E on the gut microbiota using a human clinical study and batch fermentation experiments, in combination with cell models for the assessment of barrier and immune functions. Vitamins C, B2, and D may modulate the human gut microbiome in terms of metabolic activity and bacterial composition. The most distinct effect was that of vitamin C, which significantly increased microbial alpha diversity and fecal short-chain fatty acids compared to the placebo. The remaining vitamins tested showed similar effects on microbial diversity, composition, and/or metabolic activity in vitro, but in varying degrees. Here, we showed that vitamins may modulate the human gut microbiome. Follow-up studies investigating targeted delivery of vitamins to the colon may help clarify the clinical significance of this novel concept for treating and preventing dysbiotic microbiota-related human diseases. Trial registration: ClinicalTrials.gov, NCT03668964. Registered 13 September 2018 - Retrospectively registered, https://clinicaltrials.gov/ct2/show/NCT03668964.}, }
@article {pmid33615984, year = {2021}, author = {Coker, JK and Moyne, O and Rodionov, DA and Zengler, K}, title = {Carbohydrates great and small, from dietary fiber to sialic acids: How glycans influence the gut microbiome and affect human health.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1-18}, doi = {10.1080/19490976.2020.1869502}, pmid = {33615984}, issn = {1949-0984}, abstract = {Gut microbiome composition depends heavily upon diet and has strong ties to human health. Dietary carbohydrates shape the gut microbiome by providing a potent nutrient source for particular microbes. This review explores how dietary carbohydrates in general, including individual monosaccharides and complex polysaccharides, influence the gut microbiome with subsequent effects on host health and disease. In particular, the effects of sialic acids, a prominent and influential class of monosaccharides, are discussed. Complex plant carbohydrates, such as dietary fiber, generally promote microbial production of compounds beneficial to the host while preventing degradation of host carbohydrates from colonic mucus. In contrast, simple and easily digestible sugars such as glucose are often associated with adverse effects on health and the microbiome. The monosaccharide class of sialic acids exerts a powerful but nuanced effect on gut microbiota. Sialic acid consumption (in monosaccharide form, or as part of human milk oligosaccharides or certain animal-based foods) drives the growth of organisms with sialic acid metabolism capabilities. Minor chemical modifications of Neu5Ac, the most common form of sialic acid, can alter these effects. All aspects of carbohydrate composition are therefore relevant to consider when designing dietary therapeutic strategies to alter the gut microbiome.}, }
@article {pmid33615652, year = {2021}, author = {Mancabelli, L and Tarracchini, C and Milani, C and Lugli, GA and Fontana, F and Turroni, F and van Sinderen, D and Ventura, M}, title = {Vaginotypes of the human vaginal microbiome.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.15441}, pmid = {33615652}, issn = {1462-2920}, abstract = {The human vaginal environment harbors a community of bacteria that plays an important role in maintaining vaginal health and in protecting this environment from various urogenital infections. This bacterial population, also known as vaginal microbiota, has been demonstrated to be dominated by members of the Lactobacillus genus. Several studies employing 16S rRNA gene-based amplicon sequencing have classified the vaginal microbiota into five distinct Community State Types (CSTs) or vaginotypes. To deepen our understanding of the vaginal microbiota we performed an in-depth meta-analysis of 1312 publicly available data sets concerning healthy vaginal microbiome information obtained by metagenomics sequencing. The analysis confirmed the predominance of taxa belonging to the Lactobacillus genus, followed by members of the genera Gardnerella, Vibrio and Atopobium. Moreover, the statistical robustness offered by this meta-analysis allowed us to disentangle the species-level composition of dominant and accessory taxa constituting each vaginotype and to revisit and refine the previously proposed CST classification. In addition, a functional characterization of the metagenomic datasets revealed particular genetic features associated with each assigned vaginotype. This article is protected by copyright. All rights reserved.}, }
@article {pmid33615594, year = {2021}, author = {Holmes, TH}, title = {Rigorous quantification of bacterial richness in ticks: A case study.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.15816}, pmid = {33615594}, issn = {1365-294X}, support = {//Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine/ ; //Human Immune Monitoring Center, Stanford University School of Medicine/ ; }, abstract = {Kwan et al. (2017) published an informative study comparing results obtained by next-generation sequencing (NGS) of mean bacterial genera richness among different life stages, male and female adults, and rearing conditions (field vs. laboratory) for Ixodes pacificus. The current paper examines Kwan et al. (2017) as a case study to provide guidance on statistical design and analysis for estimation of richness, derived from next generation sequencing technology, of the bacterial microbiome in field-collected I. pacificus. Suggestions are provided to further strengthen quantification of microbiome richness in studies in ticks, with focus on sampling design. In-depth treatment is provided of the relative merits of estimating mean richness versus median richness. Research on microbiome diversity in ticks can be made quantitatively rigorous; although, more research on methods is needed.}, }
@article {pmid33615460, year = {2020}, author = {Loss, M and Thompson, KG and Agostinho-Hunt, A and James, GA and Mongodin, EF and Rosenthal, I and Cheng, N and Leung, S and Chien, AL and Kang, S}, title = {Noninflammatory comedones have greater diversity in microbiome and are more prone to biofilm formation than inflammatory lesions of acne vulgaris.}, journal = {International journal of dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1111/ijd.15308}, pmid = {33615460}, issn = {1365-4632}, support = {//Provost Young Investigator Fund of the Johns Hopkins Department of Dermatology/ ; //American Acne and Rosacea Society/ ; //University of Maryland School of Medicine/ ; }, abstract = {BACKGROUND: The ability of Cutibacterium acnes strains to form biofilms has been correlated with their virulence.<br><br>OBJECTIVE: This study examined biofilm and skin microbiota in acne patients in order to understand their role in the development of acne lesions.<br><br>METHODS: Thin sections of punch biopsy specimens of (i) uninflamed comedones, (ii) inflammatory lesions, and (iii) uninvolved adjacent skin of acne patients were examined. Epiflourescence and confocal laser scanning microscopy were used for biofilm detection, and pyrosequencing with taxonomic classification of 16s rRNA gene amplicons was used for microbiota analysis.<br><br>RESULTS: Of the 39 skin specimens from patients with mild-moderate acne (n = 13) that were studied, nine (23%) contained biofilm. Among these specimens, biofilm was most frequently detected in comedones (55.6%) and less frequently in inflammatory papules (22.2%) and uninvolved skin (22.2%). Comedones demonstrated the highest mean alpha diversity of all the lesion subtypes. The relative abundance of Staphylococcus was significantly higher in comedones (11.400% ± 12.242%) compared to uninvolved skin (0.073% ± 0.185%, P = 0.024).<br><br>CONCLUSIONS: The microenvironment of the comedone differs from that of inflammatory lesions and unaffected skin. The increased frequency of biofilm in comedones may account for the lack of host inflammatory response to these lesions.}, }
@article {pmid33615021, year = {2019}, author = {Fuse, N and Sakurai-Yageta, M and Katsuoka, F and Danjoh, I and Shimizu, R and Tamiya, G and Nagami, F and Kawame, H and Higuchi, S and Kinoshita, K and Kure, S and Yamamoto, M}, title = {Establishment of Integrated Biobank for Precision Medicine and Personalized Healthcare: The Tohoku Medical Megabank Project.}, journal = {JMA journal}, volume = {2}, number = {2}, pages = {113-122}, doi = {10.31662/jmaj.2019-0014}, pmid = {33615021}, issn = {2433-3298}, abstract = {The Tohoku Medical Megabank (TMM) project was established to provide creative reconstruction of the Tohoku area that suffered from a huge earthquake and ensuing tsunami (the Great East Japan Earthquake, GEJE). TMM aims to establish two large-scale genome cohorts and an integrated biobank managing biospecimen and related information. It supports community medicine by establishing next-generation medical systems through a combination of the prospective genome cohort studies with a total of 150,000 participants and genomic medicine. The strategies for genome analyses in TMM are to develop an elaborate genome reference panel by means of high-fidelity Japanese whole-genome sequence, to design custom single nucleotide polymorphism (SNP) arrays based on the reference panel, and to obtain genotype data for all the TMM cohort participants subsequently. Disease-associated genomic information and omics data, including metabolomics and microbiome analysis, provide an essential platform for precision medicine and personalized healthcare (PHC). Ethical, legal, and social issues (ELSI) and education are important for implementing genomic medicine. The major considerations of ELSI regarding each participant of the cohort studies are the respect for the autonomy and the protection of privacies. Moreover, developing and provide human resources not only for the TMM project but also for the social implementation of precision medicine and PHC is required. We started a pilot study of the return of genomic results for familial hypercholesterolemia (FH) as a target disease. TMM aims to establish solid platforms that support precision medicine and PHC based on the genomic and omics information and environmental and lifestyle factors of the individuals, which is one of the most advanced medical care beyond the evidenced-based medicine in the near future.}, }
@article {pmid33614931, year = {2021}, author = {Lambert, PA and Gill, AL and Gill, SR and Allen, PD and Man, LX}, title = {Microbiomics of irrigation with xylitol or Lactococcus lactis in chronic rhinosinusitis.}, journal = {Laryngoscope investigative otolaryngology}, volume = {6}, number = {1}, pages = {64-70}, doi = {10.1002/lio2.524}, pmid = {33614931}, issn = {2378-8038}, abstract = {Objective: Topical sinonasal rinse therapies may alter the local microbiome and improve disease control in chronic rhinosinusitis (CRS). The objective of this study was to examine microbiome changes in post-surgical CRS patients when rinsing with commercially available products containing xylitol or Lactococcus lactis.<br><br>Methods: A crossover-type protocol with a washout period was designed. Swab samples from anterior ethmoid cavities of CRS patients were collected prospectively at baseline. Subjects were provided packets containing either L. lactis W136 or xylitol in non-blinded fashion and instructed to add it to their rinse bottles daily for 28 days, after which another swab was taken. A saline wash-out period was completed and a third swab taken. A final 28-day regimen of the opposite product was followed by a final swab. DNA extraction and sequencing of the 16S rRNA gene allowed for global microbiome analysis.<br><br>Results: We enrolled 25 subjects with CRS and 10 controls resulting in 70 adequate samples. Increased detection of Lactococcus was observed after use of L. lactis. No significant trends in alpha or beta diversity as a result of treatment were observed. SNOT-22 score did not change significantly following treatment with xylitol, L. lactis, or saline.<br><br>Conclusion: We did not detect any major clinical or microbiome-level effect due to treatment with two topical rinse products. Further research is needed to elucidate their clinical utility and possible probiotic effect.<br><br>Level of Evidence: 3.}, }
@article {pmid33614758, year = {2020}, author = {Dunislawska, A and Herosimczyk, A and Lepczynski, A and Slama, P and Slawinska, A and Bednarczyk, M and Siwek, M}, title = {Molecular Response in Intestinal and Immune Tissues to in Ovo Administration of Inulin and the Combination of Inulin and Lactobacillus lactis Subsp. cremoris.}, journal = {Frontiers in veterinary science}, volume = {7}, number = {}, pages = {632476}, doi = {10.3389/fvets.2020.632476}, pmid = {33614758}, issn = {2297-1769}, abstract = {Intestinal microbiota are a key factor in maintaining good health and production results in chickens. They play an important role in the stimulation of immune responses, as well as in metabolic processes and nutrient digestion. Bioactive substances such as prebiotics, probiotics, or a combination of the two (synbiotic) can effectively stimulate intestinal microbiota and therefore replace antibiotic growth promoters. Intestinal microbiota might be stimulated at the early stage of embryo development in ovo. The aim of the study was to analyze the expression of genes related to energy metabolism and immune response after the administration of inulin and a synbiotic, in which lactic acid bacteria were combined with inulin in the intestines and immune tissues of chicken broilers. The experiment was performed on male broiler chickens. Eggs were incubated for 21 days in a commercial hatchery. On day 12 of egg incubation, inulin as a prebiotic and inulin with Lactobacillus lactis subsp. cremoris as a synbiotic were delivered to the egg chamber. The control group was injected with physiological saline. On day 35 post-hatching, birds from each group were randomly selected and sacrificed. Tissues (spleen, cecal tonsils, and large intestine) were collected and intended for RNA isolation. The gene panel (ABCG8, HNF4A, ACOX2, APBB1IP, BRSK2, APOA1, and IRS2) was selected based on the microarray dataset and biological functions of genes related to the energy metabolism and immune responses. Isolated RNA was analyzed using the RT-qPCR method, and the relative gene expression was calculated. In our experiment, distinct effects of prebiotics and synbiotics following in ovo delivery were manifested in all analyzed tissues, with the lowest number of genes with altered expression shown in the large intestines of broilers. The results demonstrated that prebiotics or synbiotics provide a potent stimulation of gene expression in the spleen and cecal tonsils of broiler chickens. The overall number of gene expression levels and the magnitude of their changes in the spleen and cecal tonsils were higher in the group of synbiotic chickens compared to the prebiotic group.}, }
@article {pmid33614273, year = {2021}, author = {Hu, Z and Tong, Q and Chang, J and Yu, J and Li, S and Niu, H and Ma, D}, title = {Gut bacterial communities in the freshwater snail Planorbella trivolvis and their modification by a non-herbivorous diet.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e10716}, doi = {10.7717/peerj.10716}, pmid = {33614273}, issn = {2167-8359}, abstract = {The freshwater pulmonate snail Planorbella trivolvis is a common species in various bodies of water but is not native to China. Planorbella trivolvis usually live on diets with high fiber content, such as water grasses, algae and fallen leaves. These snails can attach to the wall of a water tank or to water grass and can be transported overseas to China through the ornamental fish trade. There are few studies investigating the intestinal microbiota of freshwater snails. In this study, using culture-independent molecular analysis, we assessed for the first time the complexity of bacterial communities in the intestines of reared snails. The intestinal microbiota in the snails fed different diets, that is, herbivorous feed (HV) with high cellulose and non-herbivorous feed (NHV) with low cellulose, were analyzed by Illumina sequencing. The results showed that the NHV-based diet significantly increased the body mass, shell diameter and specific growth rate of the snails after 60 days of rearing (P < 0.05). Histological experiments showed that the fat droplets in the epithelium columnar cells of the intestines of the NHV snails increased, and the cilia on these cells fell off. The sequencing results identified 486 and 195 OTUs in HV and NHV, respectively. Lots of bacteria were not reported previously in snails. The intestinal microbiota diversity index (Shannon, Simpson, Ace and Chao) in the NHV snails was significantly lower than that in the HV snails. The gut microbiota in the HV snails were predominantly Proteobacteria (52.97%) and Bacteroidetes (28.75%), while the gut microbiota in NHV snails were predominantly Proteobacteria (95.23%). At the genus level, Cloacibacterium (24.60%), Pseudomonas (4.47%), OM6ON (6.12%), and Rhodobacter (5.79%) were observed to be abundant in HV snails. However, Aeromonas (85.4%) was determined to be predominant in NHV snails. Functional prediction of the gut microbiome in snails by PICRUSt demonstrated a significant difference between the two groups, and the HV snails exhibited higher lignocellulose enzyme activity than did the NHV snails. This study represents a first step in characterizing the gut microbiota of the freshwater snail. Most of these microbes can process plant biomass and digest cellulose and lignocellulose, and the enzymes of these bacteria may have potential biotechnological applications in a variety of industrial processes.}, }
@article {pmid33614006, year = {2021}, author = {Vu, JP and Vasquez, MF and Feng, Z and Lombardo, K and Haagensen, S and Bozinovic, G}, title = {Relative genetic diversity of the rare and endangered Agave shawii ssp. shawii and associated soil microbes within a southern California ecological preserve.}, journal = {Ecology and evolution}, volume = {11}, number = {4}, pages = {1829-1842}, doi = {10.1002/ece3.7172}, pmid = {33614006}, issn = {2045-7758}, abstract = {Shaw's Agave (Agave shawii ssp. shawii) is an endangered maritime succulent growing along the coast of California and northern Baja California. The population inhabiting Point Loma Peninsula has a complicated history of transplantation without documentation. The low effective population size in California prompted agave transplanting from the U.S. Naval Base site (NB) to Cabrillo National Monument (CNM). Since 2008, there are no agave sprouts identified on the CNM site, and concerns have been raised about the genetic diversity of this population. We sequenced two barcoding loci, rbcL and matK, of 27 individual plants from 5 geographically distinct populations, including 12 individuals from California (NB and CNM). Phylogenetic analysis revealed the three US and two Mexican agave populations are closely related and have similar genetic variation at the two barcoding regions, suggesting the Point Loma agave population is not clonal. Agave-associated soil microbes used significantly more carbon sources in CNM soil samples than in NB soil likely due to higher pH and moisture content; meanwhile, soil type and soil chemistry analysis including phosphorus, nitrate nitrogen, organic matter, and metals revealed significant correlations between microbial diversity and base saturation (p < 0.05, r2 = 0.3676), lime buffer capacity (p < 0.01, r2 = 0.7055), equilibrium lime buffer capacity (p < 0.01, r2 = 0.7142), and zinc (p < 0.01, r2 = 0.7136). Soil microbiome analysis within the CNM population revealed overall expected richness (H' = 5.647-6.982) for Agave species, while the diversity range (1 - D = 0.003392-0.014108) suggests relatively low diversity marked by high individual variation. The most prominent remaining US population of this rare species is not clonal and does not seem to be threatened by a lack of genetic and microbial diversity. These results prompt further efforts to investigate factors affecting Agave's reproduction and fitness.}, }
@article {pmid33614005, year = {2021}, author = {Muletz-Wolz, CR and Wilson Rankin, E and McGrath-Blaser, S and Venkatraman, M and Maldonado, JE and Gruner, DS and Fleischer, RC}, title = {Identification of novel bacterial biomarkers to detect bird scavenging by invasive rats.}, journal = {Ecology and evolution}, volume = {11}, number = {4}, pages = {1814-1828}, doi = {10.1002/ece3.7171}, pmid = {33614005}, issn = {2045-7758}, abstract = {Rapid advances in genomic tools for use in ecological contexts and non-model systems allow unprecedented insight into interactions that occur beyond direct observation. We developed an approach that couples microbial forensics with molecular dietary analysis to identify species interactions and scavenging by invasive rats on native and introduced birds in Hawaii. First, we characterized bacterial signatures of bird carcass decay by conducting 16S rRNA high-throughput sequencing on chicken (Gallus gallus domesticus) tissues collected over an 11-day decomposition study in natural Hawaiian habitats. Second, we determined if field-collected invasive black rats (Rattus rattus; n = 51, stomach and fecal samples) had consumed birds using molecular diet analysis with two independent PCR assays (mitochondrial Cytochrome Oxidase I and Cytochrome b genes) and Sanger sequencing. Third, we characterized the gut microbiome of the same rats using 16S rRNA high-throughput sequencing and identified 15 bacterial taxa that were (a) detected only in rats that consumed birds (n = 20/51) and (b) were indicative of decaying tissue in the chicken decomposition experiment. We found that 18% of rats (n = 9/51) likely consumed birds as carrion by the presence of bacterial biomarkers of decayed tissue in their gut microbiome. One species of native bird (Myadestes obscurus) and three introduced bird species (Lophura leucomelanos, Meleagris gallopavo, Zosterops japonicus) were detected in the rats' diets, with individuals from these species (except L. nycthemera) likely consumed through scavenging. Bacterial biomarkers of bird carcass decay can persist through rat digestion and may serve as biomarkers of scavenging. Our approach can be used to reveal trophic interactions that are challenging to measure through direct observation.}, }
@article {pmid33613943, year = {2021}, author = {Mullish, BH and Quraishi, MN and Segal, JP and Ianiro, G and Iqbal, TH}, title = {The gut microbiome: what every gastroenterologist needs to know.}, journal = {Frontline gastroenterology}, volume = {12}, number = {2}, pages = {118-127}, doi = {10.1136/flgastro-2019-101376}, pmid = {33613943}, issn = {2041-4137}, abstract = {The mucosal surfaces of the body are characterised by complex, specialised microbial communities, often referred to as the microbiome. However, only much more recently-with the development of technologies allowing exploration of the composition and functionality of these communities-has meaningful research in this area become feasible. Over the past few years, there has been rapid growth in interest in the gut microbiome in particular, and its potential contribution to gastrointestinal and liver disease. This interest has already extended beyond clinicians to pharmaceutical companies, medical regulators and other stakeholders, and is high profile among patients and the lay public in general. Such expansion of knowledge holds the intriguing potential for translation into novel diagnostics and therapeutics; however, being such a nascent field, there remain many uncertainties, unanswered questions and areas of debate.}, }
@article {pmid33613868, year = {2021}, author = {Strand, MA and Jin, Y and Sandve, SR and Pope, PB and Hvidsten, TR}, title = {Transkingdom network analysis provides insight into host-microbiome interactions in Atlantic salmon.}, journal = {Computational and structural biotechnology journal}, volume = {19}, number = {}, pages = {1028-1034}, doi = {10.1016/j.csbj.2021.01.038}, pmid = {33613868}, issn = {2001-0370}, abstract = {Background: The Atlantic salmon gut constitutes an intriguing system for studying host-microbiota interactions due to the dramatic environmental change salmon experiences during its life cycle. Yet, little is known about the role of interactions in this system and there is a general deficit in computational methods for integrative analysis of omics data from host-microbiota systems.<br><br>Methods: We developed a pipeline to integrate host RNAseq data and microbial 16S rRNA amplicon sequencing data using weighted correlation network analysis. Networks are first inferred from each dataset separately, followed by module detections and finally robust identification of interactions via comparisons of representative module profiles. Through the use of module profiles, this network-based dimensionality reduction approach provides a holistic view into the discovery of potential host-microbiota symbionts.<br><br>Results: We analyzed host gene expression from the gut epithelial tissue and microbial abundances from the salmon gut in a long-term feeding trial spanning the fresh-/salt-water transition and including two feeds resembling the fatty acid compositions available in salt- and fresh-water environments, respectively. We identified several host modules with significant correlations to both microbiota modules and variables such as feed, growth and sex. Although the strongest associations largely coincided with the fresh-/salt-water transition, there was a second layer of correlations associating smaller host modules to both variables and microbiota modules. Hence, we identify extensive reprogramming of the gut epithelial transcriptome and large scale coordinated changes in gut microbiota composition associated with water type as well as evidence of host-microbiota interactions linked to feed.}, }
@article {pmid33613865, year = {2021}, author = {Amin, N and Seifert, J}, title = {Dynamic progression of the calf's microbiome and its influence on host health.}, journal = {Computational and structural biotechnology journal}, volume = {19}, number = {}, pages = {989-1001}, doi = {10.1016/j.csbj.2021.01.035}, pmid = {33613865}, issn = {2001-0370}, abstract = {The first year of a calf's life is a critical phase as its digestive system and immunity are underdeveloped. A high level of stress caused by separation from mothers, transportation, antibiotic treatments, dietary shifts, and weaning can have long-lasting health effects, which can reduce future production parameters, such as milk yield and reproduction, or even increase the mortality of calves. The early succession of microbes throughout the gastrointestinal tract of neonatal calves follows a sequential pattern of colonisation and is greatly influenced by their physiological state, age, diet, and environmental factors; this leads to the establishment of region- and site-specific microbial communities. This review summarises the current information on the various potential factors that may affect the early life microbial colonisation pattern in the gastrointestinal tract of calves. The possible role of host-microbe interactions in the development and maturation of host gut, immune system, and health are described. Additionally, the possibility of improving the health of calves through gut microbiome modulation and using antimicrobial alternatives is discussed. Finally, the trends, challenges, and limitations of the current research are summarised and prospective directions for future studies are highlighted.}, }
@article {pmid33613596, year = {2021}, author = {Lee, SM and Ryu, CM}, title = {Algae as New Kids in the Beneficial Plant Microbiome.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {599742}, doi = {10.3389/fpls.2021.599742}, pmid = {33613596}, issn = {1664-462X}, abstract = {Previously, algae were recognized as small prokaryotic and eukaryotic organisms found only in aquatic habitats. However, according to a recent paradigm shift, algae are considered ubiquitous organisms, occurring in plant tissues as well as in soil. Accumulating evidence suggests that algae represent a member of the plant microbiome. New results indicate that plants respond to algae and activate related downstream signaling pathways. Application of algae has beneficial effects on plant health, such as plant growth promotion and disease control. Although accumulating evidence suggests that secreted compounds and cell wall components of algae induce physiological and structural changes in plants that protect against biotic and abiotic stresses, knowledge of the underlying mechanisms and algal determinants is limited. In this review, we discuss recent studies on this topic, and highlight the bioprotectant and biostimulant roles of algae as a new member of the plant beneficial microbiome for crop improvement.}, }
@article {pmid33613519, year = {2020}, author = {Cortez, RV and Moreira, LN and Padilha, M and Bibas, MD and Toma, RK and Porta, G and Taddei, CR}, title = {Gut Microbiome of Children and Adolescents With Primary Sclerosing Cholangitis in Association With Ulcerative Colitis.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {598152}, doi = {10.3389/fimmu.2020.598152}, pmid = {33613519}, issn = {1664-3224}, abstract = {Few studies reported the relation of intestinal microbiome composition and diversity in pediatric patients with primary sclerosing cholangitis (PSC) and ulcerative colitis (UC). In this cross-sectional study, we selected patients younger than 19 years old from the pediatric gastroenterology and hepatology outpatient clinic of a tertiary hospital to describe the intestinal microbiome of pediatric patients with PSC associated or not to UC. Patients were divided in PSC, PSC+UC, and UC diagnosis. A stool sample was collected from each patient (n=30) and from a healthy relative/neighbor (n=23). The microbiome composition was assessed using MiSeq (Illumina) platform. Differences in microbial composition were found between PSC and PSC+UC groups. The relative abundance of Veillonella and Megasphaera genera were increased depending on patients' age at diagnosis. Veillonella was also increased in patients who were in an active status of the disease. Both genera were positively correlated to total bilirubin and gamma-glutamyl transferase. As a conclusion, the disease, the age and the disease activity status seem to influence the intestinal microbiome, highlighting the difference of intestinal microbiome profile for patients depending on age at diagnosis. We also showed an increase of Veillonella in patients with PSC and PSC+UC, and a positive correlation of dysbiosis and higher gamma-glutamyl transferase and total bilirubin in PSC+UC patients. Our findings are promising in the diagnosis, prognosis, and future therapeutic perspectives for PSC patients.}, }
@article {pmid33613505, year = {2021}, author = {Zwirzitz, B and Wetzels, SU and Dixon, ED and Fleischmann, S and Selberherr, E and Thalguter, S and Quijada, NM and Dzieciol, M and Wagner, M and Stessl, B}, title = {Co-Occurrence of Listeria spp. and Spoilage Associated Microbiota During Meat Processing Due to Cross-Contamination Events.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {632935}, doi = {10.3389/fmicb.2021.632935}, pmid = {33613505}, issn = {1664-302X}, abstract = {A large part of foodborne outbreaks related to Listeria monocytogenes are linked to meat and meat products. Especially, recontamination of meat products and deli-meat during slicing, packaging, and repackaging is in the focus of food authorities. In that regard, L. monocytogenes persistence in multi-species biofilms is one major issue, since they survive elaborate cleaning and disinfection measures. Here, we analyzed the microbial community structure throughout a meat processing facility using a combination of high-throughput full-length 16S ribosomal RNA (rRNA) gene sequencing and traditional microbiological methods. Samples were taken at different stages during meat cutting as well as from multiple sites throughout the facility environment to capture the product and the environmental associated microbiota co-occurring with Listeria spp. and L. monocytogenes. The listeria testing revealed a widely disseminated contamination (50%; 88 of 176 samples were positive for Listeria spp. and 13.6%; 24 of 176 samples were positive for L. monocytogenes). The pulsed-field gel electrophoresis (PFGE) typing evidenced 14 heterogeneous L. monocytogenes profiles with PCR-serogroup 1/2a, 3a as most dominant. PFGE type MA3-17 contributed to the resilient microbiota of the facility environment and was related to environmental persistence. The core in-house microbiota consisted mainly of the genera Acinetobacter, Pseudomonas, Psychrobacter (Proteobacteria), Anaerobacillus, Bacillus (Firmicutes), and Chryseobacterium (Bacteroidota). While the overall microbial community structure clearly differed between product and environmental samples, we were able to discern correlation patterns regarding the presence/absence of Listeria spp. in both sample groups. Specifically, our longitudinal analysis revealed association of Listeria spp. with known biofilm-producing Pseudomonas, Acinetobacter, and Janthinobacterium species on the meat samples. Similar patterns were also observed on the surface, indicating dispersal of microorganisms from this multispecies biofilm. Our data provided a better understanding of the built environment microbiome in the meat processing context and promoted more effective options for targeted disinfection in the analyzed facility.}, }
@article {pmid33613481, year = {2021}, author = {Almeida-Santos, A and Martins-Mendes, D and Gayà-Vidal, M and Pérez-Pardal, L and Beja-Pereira, A}, title = {Characterization of the Oral Microbiome of Medicated Type-2 Diabetes Patients.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {610370}, doi = {10.3389/fmicb.2021.610370}, pmid = {33613481}, issn = {1664-302X}, abstract = {Type 2 diabetes mellitus (T2DM) is a chronic metabolic disease that is becoming a significant global health care problem. Several studies have shown that people with diabetes are more susceptible to oral problems, such as periodontitis and, although the causes are still inconclusive, oral microbiota is considered to play a major role in oral health. This study aimed to characterize the oral microbiome of a sample representing T2DM patients from Portugal and exploit potential associations between some microorganisms and variables like teeth brushing, smoking habits, average blood sugar levels, medication and nutrient intake. By sequencing the hypervariable regions V3-V4 of the 16S rRNA gene in 50 individuals belonging to a group of diabetes patients and a control group, we found a total of 232 taxa, from which only 65% were shared between both groups. No differences were found in terms of alpha and beta diversity between categories. We did not find significant differences in the oral microbiome profiles of control and diabetes patients. Only the class Synergistia and the genus TG5, which are related to periodontitis, were statistically more frequent in the control group. The similar microbiome profiles of medicated diabetics and the control group indicates that the relationship between the T2DM and the oral microbiome might be more related to either the lifestyle/diet rather than diabetes per se. Moreover, this study provides, for the first time, insights into the oral microbiome of a population with a high prevalence of diabetes.}, }
@article {pmid33613418, year = {2020}, author = {Rolle, T and Ponzetto, A and Malinverni, L}, title = {The Role of Neuroinflammation in Glaucoma: An Update on Molecular Mechanisms and New Therapeutic Options.}, journal = {Frontiers in neurology}, volume = {11}, number = {}, pages = {612422}, doi = {10.3389/fneur.2020.612422}, pmid = {33613418}, issn = {1664-2295}, abstract = {Glaucoma is a multifactorial optic neuropathy characterized by the continuous loss of retinal ganglion cells, leading to progressive and irreversible visual impairment. In this minireview, we report the results of the most recent experimental studies concerning cells, molecular mechanisms, genes, and microbiome involved in neuroinflammation processes correlated to glaucoma neurodegeneration. The identification of cellular mechanisms and molecular pathways related to retinal ganglion cell death is the first step toward the discovery of new therapeutic strategies. Recent experimental studies identified the following possible targets: adenosine A2A receptor, sterile alpha and TIR motif containing 1 (neurofilament light chain), toll-like receptors (TLRs) 2 and 4, phosphodiesterase type 4 (PDE4), and FasL-Fas signaling (in particular ONL1204, a small peptide antagonist of Fas receptors), and therapies directed against them. The continuous progress in knowledge provides interesting data, although the total lack of human studies remains an important limitation. Further research is required to better define the role of neuroinflammation in the neurodegeneration processes that occur in glaucomatous disease and to discover neuroprotective treatments amenable to clinical trials. The hereinafter reviewed studies are reported and evaluated according to their translational relevance.}, }
@article {pmid33613097, year = {2020}, author = {Kaźmierczak-Siedlecka, K and Daca, A and Folwarski, M and Witkowski, JM and Bryl, E and Makarewicz, W}, title = {The role of Lactobacillus plantarum 299v in supporting treatment of selected diseases.}, journal = {Central-European journal of immunology}, volume = {45}, number = {4}, pages = {488-493}, doi = {10.5114/ceji.2020.101515}, pmid = {33613097}, issn = {1426-3912}, abstract = {Alterations in composition of human gut microbiome can lead to its dysbiosis. It is associated with gastrointestinal side effects during anti-cancer treatment, antibiotics administration, or infectious agents. There are studies confirming positive effect of consuming Lactobacillus plantarum 299v on intestinal microflora. This review summarizes the current knowledge about the role of L. plantarum 299v in supporting treatment of selected diseases, such as cancer, irritable bowel syndrome (IBS), and Clostridium difficile infection. The immunomodulating properties of L. plantarum 299v include an increase in the level of anti-inflammatory cytokines, which reduce the risk of cancer and improve the efficacy of regimens. The intake of L. plantarum 299v provides benefits for IBS patients, mainly due to normalization of stool and relief of abdominal pain, which significantly improves the quality of life of IBS patients. In addition, the intake of L. plantarum 299v prevents C. difficile-associated diarrhea among patients receiving antibiotic treatment. Due to the limited possibilities of treating these diseases and numerous complications of cancer treatment, there is a need for new therapeutic strategies. The administration of L. plantarum 299v seems to be useful in these cases.}, }
@article {pmid33613095, year = {2020}, author = {Kaźmierczak-Siedlecka, K and Daca, A and Folwarski, M and Makarewicz, W and Lebiedzińska, A}, title = {Immunonutritional support as an important part of multidisciplinary anti-cancer therapy.}, journal = {Central-European journal of immunology}, volume = {45}, number = {4}, pages = {454-460}, doi = {10.5114/ceji.2020.103339}, pmid = {33613095}, issn = {1426-3912}, abstract = {Immunonutrition is one of the most important parts of nutritional treatment in patients with cancer. There are studies which confirm positive effects of using immunonutrition (arginine, glutamine, omega-3 fatty acids, nucleotides, pre- and probiotics) among others on the reduction of the pro-inflammatory cytokines concentrations, shortening of the hospital stay and improvement of the nutritional status. Arginine takes part not only in wound healing process, but also it improves body's immunity and reduces the incidence of infections. Glutamine reduces the incidence of acute grade 2 and 3 esophagitis and improves quality of life of gastric cancer patients. Omega 3-fatty acids have the ability to inhibit the activity of NF-κB. They also reduce the symptoms of graft-versus-host disease in patients undergoing hematopoietic cell transplantation. Nucleotides support the regeneration of intestinal villi. Probiotics play many roles, mainly inhibit the process of carcinogenesis, reduce the incidence of diarrhea and modify intestinal microbiome. However, there are studies indicating the lack of advantages of using immunonutrition compared to standard nutrition. Currently, there is no clear evidence for the use of formulae enriched with immunonutrients versus standard oral nutritional supplements exclusively in the preoperative period. This review summarizes the current knowledge about the role of immunonutrition in supporting treatment of cancer diseases.}, }
@article {pmid33613025, year = {2021}, author = {Pecundo, MH and Chang, ACG and Chen, T and Dela Cruz, TEE and Ren, H and Li, N}, title = {Full-Length 16S rRNA and ITS Gene Sequencing Revealed Rich Microbial Flora in Roots of Cycas spp. in China.}, journal = {Evolutionary bioinformatics online}, volume = {17}, number = {}, pages = {1176934321989713}, doi = {10.1177/1176934321989713}, pmid = {33613025}, issn = {1176-9343}, abstract = {Cycads have developed a complex root system categorized either as normal or coralloid roots. Past literatures revealed that a great diversity of key microbes is associated with these roots. This recent study aims to comprehensively determine the diversity and community structure of bacteria and fungi associated with the roots of two Cycas spp. endemic to China, Cycas debaoensis Zhong &amp; Chen and Cycas fairylakea D.Y. Wang using high-throughput amplicon sequencing of the full-length 16S rRNA (V1-V9 hypervariable) and short fragment ITS region. The total DNA from 12 root samples were extracted, amplified, sequenced, and analyzed. Resulting sequences were clustered into 61 bacteria and 2128 fungal OTUs. Analysis of community structure revealed that the coralloid roots were dominated mostly by the nitrogen-fixer Nostocaceae but also contain other non-diazotrophic bacteria. The sequencing of entire 16S rRNA gene identified four different strains of cyanobacteria under the heterocystous genera Nostoc and Desmonostoc. Meanwhile, the top bacterial families in normal roots were Xanthobacteraceae, Burkholderiaceae, and Bacillaceae. Moreover, a diverse fungal community was also found in the roots of cycads and the predominating families were Ophiocordycipitaceae, Nectriaceae, Bionectriaceae, and Trichocomaceae. Our results demonstrated that bacterial diversity in normal roots of C. fairylakea is higher in richness and abundance than C. debaoensis. On the other hand, a slight difference, albeit insignificant, was noted for the diversity of fungi among root types and host species as the number of shared taxa is relatively high (67%). Our results suggested that diverse microbes are present in roots of cycads which potentially interact together to support cycads survival. Our study provided additional knowledge on the microbial diversity and composition in cycads and thus expanding our current knowledge on cycad-microbe association. Our study also considered the possible impact of ex situ conservation on cyanobiont community of cycads.}, }
@article {pmid33612870, year = {2021}, author = {Srivastava, S and Singh, A and Sandeep, K and Yadav, D}, title = {Epigenetic Regulation of Gut Microbial Dysbiosis.}, journal = {Indian journal of microbiology}, volume = {}, number = {}, pages = {1-5}, doi = {10.1007/s12088-021-00920-y}, pmid = {33612870}, issn = {0046-8991}, abstract = {Microbiota inside the gut plays a vital role in maintaining human health. Microbial dysbiosis is associated with various complications leading to a range of diseases. Epigenetic changes enforced by various environmental and lifestyle factors lead to heritable modifications. These epigenetic modifications include DNA methylation, histone modifications, chromatin remodelling, and ribonucleic acid-based mechanisms. This review summarizes the impacts of environmental factors on the gut microbiome, epigenetic modifications, and their role in cardiovascular diseases.}, }
@article {pmid33612480, year = {2021}, author = {Wu, CS and Muthyala, SDV and Klemashevich, C and Ufondu, AU and Menon, R and Chen, Z and Devaraj, S and Jayaraman, A and Sun, Y}, title = {Age-dependent remodeling of gut microbiome and host serum metabolome in mice.}, journal = {Aging}, volume = {13}, number = {}, pages = {}, doi = {10.18632/aging.202525}, pmid = {33612480}, issn = {1945-4589}, abstract = {The interplay between microbiota and host metabolism plays an important role in health. Here, we examined the relationship between age, gut microbiome and host serum metabolites in male C57BL/6J mice. Fecal microbiome analysis of 3, 6, 18, and 28 months (M) old mice showed that the Firmicutes/Bacteroidetes ratio was highest in the 6M group; the decrease of Firmicutes in the older age groups suggests a reduced capacity of gut microflora to harvest energy from food. We found age-dependent increase in Proteobacteria, which may lead to altered mucus structure more susceptible to bacteria penetration and ultimately increased intestinal inflammation. Metabolomic profiling of polar serum metabolites at fed state in 3, 12, 18 and 28M mice revealed age-associated changes in metabolic cascades involved in tryptophan, purine, amino acids, and nicotinamide metabolism. Correlation analyses showed that nicotinamide decreased with age, while allantoin and guanosine, metabolites in purine metabolism, increased with age. Notably, tryptophan and its microbially derived compounds indole and indole-3-lactic acid significantly decreased with age, while kynurenine increased with age. Together, these results suggest a significant interplay between bacterial and host metabolism, and gut dysbiosis and altered microbial metabolism contribute to aging.}, }
@article {pmid33612452, year = {2021}, author = {Spakowicz, D and Bibi, A and Muniak, M and Williams, NF and Hoyd, R and Presley, CJ}, title = {The aging microbiome and response to immunotherapy: Considerations for the treatment of older adults with cancer.}, journal = {Journal of geriatric oncology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jgo.2021.02.001}, pmid = {33612452}, issn = {1879-4076}, }
@article {pmid33612109, year = {2021}, author = {Reverter, A and Ballester, M and Alexandre, PA and Mármol-Sánchez, E and Dalmau, A and Quintanilla, R and Ramayo-Caldas, Y}, title = {A gene co-association network regulating gut microbial communities in a Duroc pig population.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {52}, pmid = {33612109}, issn = {2049-2618}, abstract = {BACKGROUND: Analyses of gut microbiome composition in livestock species have shown its potential to contribute to the regulation of complex phenotypes. However, little is known about the host genetic control over the gut microbial communities. In pigs, previous studies are based on classical &quot;single-gene-single-trait&quot; approaches and have evaluated the role of host genome controlling gut prokaryote and eukaryote communities separately.<br><br>RESULTS: In order to determine the ability of the host genome to control the diversity and composition of microbial communities in healthy pigs, we undertook genome-wide association studies (GWAS) for 39 microbial phenotypes that included 2 diversity indexes, and the relative abundance of 31 bacterial and six commensal protist genera in 390 pigs genotyped for 70 K SNPs. The GWAS results were processed through a 3-step analytical pipeline comprised of (1) association weight matrix; (2) regulatory impact factor; and (3) partial correlation and information theory. The inferred gene regulatory network comprised 3561 genes (within a 5 kb distance from a relevant SNP-P < 0.05) and 738,913 connections (SNP-to-SNP co-associations). Our findings highlight the complexity and polygenic nature of the pig gut microbial ecosystem. Prominent within the network were 5 regulators, PRDM15, STAT1, ssc-mir-371, SOX9 and RUNX2 which gathered 942, 607, 588, 284 and 273 connections, respectively. PRDM15 modulates the transcription of upstream regulators of WNT and MAPK-ERK signaling to safeguard naive pluripotency and regulates the production of Th1- and Th2-type immune response. The signal transducer STAT1 has long been associated with immune processes and was recently identified as a potential regulator of vaccine response to porcine reproductive and respiratory syndrome. The list of regulators was enriched for immune-related pathways, and the list of predicted targets includes candidate genes previously reported as associated with microbiota profile in pigs, mice and human, such as SLIT3, SLC39A8, NOS1, IL1R2, DAB1, TOX3, SPP1, THSD7B, ELF2, PIANP, A2ML1, and IFNAR1. Moreover, we show the existence of host-genetic variants jointly associated with the relative abundance of butyrate producer bacteria and host performance.<br><br>CONCLUSIONS: Taken together, our results identified regulators, candidate genes, and mechanisms linked with microbiome modulation by the host. They further highlight the value of the proposed analytical pipeline to exploit pleiotropy and the crosstalk between bacteria and protists as significant contributors to host-microbiome interactions and identify genetic markers and candidate genes that can be incorporated in breeding program to improve host-performance and microbial traits. Video Abstract.}, }
@article {pmid33611938, year = {2021}, author = {, }, title = {Hypertension Editors' Picks: Gut Microbiome.}, journal = {Hypertension (Dallas, Tex. : 1979)}, volume = {}, number = {}, pages = {HYPERTENSIONAHA12116874}, doi = {10.1161/HYPERTENSIONAHA.121.16874}, pmid = {33611938}, issn = {1524-4563}, }
@article {pmid33611628, year = {2021}, author = {Babalola, OO and Emmanuel, OC and Adeleke, BS and Odelade, KA and Nwachukwu, BC and Ayiti, OE and Adegboyega, TT and Igiehon, NO}, title = {Rhizosphere Microbiome Cooperations: Strategies for Sustainable Crop Production.}, journal = {Current microbiology}, volume = {}, number = {}, pages = {}, pmid = {33611628}, issn = {1432-0991}, support = {123634//National Research Foundation, South Africa/ ; }, abstract = {Interactions between microorganisms and host plants determine the growth and development as well as the health of the host plant. Various microbial groups inhabit the rhizosphere, each with its peculiar function. The survival of each microbial group depends to a large extent on its ability to colonize the plant root and outcompete the native organisms. The role of the rhizospheric microbiome in enhancing plant growth has not been fully maximized. An understanding of the complexities of microbial interactions and factors affecting their assembly in the community is necessary to benefit maximally from the cooperations of various microbial communities for sustainable crop production. In this review, we outline the various organisms associated with the plant rhizosphere with emphasis on their interactions and mechanisms used in plant growth promotion.}, }
@article {pmid33611020, year = {2021}, author = {He, Q and Dasi, EA and Cheng, Z and Talla, E and Main, K and Feng, C and Ergas, SJ}, title = {Wood and sulfur-based cyclic denitrification filters for treatment of saline wastewaters.}, journal = {Bioresource technology}, volume = {328}, number = {}, pages = {124848}, doi = {10.1016/j.biortech.2021.124848}, pmid = {33611020}, issn = {1873-2976}, abstract = {This study investigated the performance and microbiome of cyclic denitrification filters (CDFs) for wood and sulfur heterotrophic-autotrophic denitrification (WSHAD) of saline wastewater. Wood-sulfur CDFs integrated into two pilot-scale marine recirculating aquaculture systems achieved high denitrification rates (103 ± 8.5 g N/(m3·d)). The combined use of pine wood and sulfur resulted in lower SO42- accumulation compared with prior saline wastewater denitrification studies with sulfur alone. Although fish tank water quality parameters, including ammonia, nitrite, nitrate and sulfide, were below the inhibitory levels for marine fish production, lower survival rates of Poecilia sphenops were observed compared with prior studies. Heterotrophic denitrification was the dominant removal mechanism during the early operational stages, while sulfur autotrophic denitrification increased as readily biodegradable organic carbon released from wood chips decreased over time. 16S rRNA-based analysis of the CDF microbiome revealed that Sulfurimonas, Thioalbus, Defluviimonas, and Ornatilinea as notable genera that contributed to denitrification performance.}, }
@article {pmid33610988, year = {2021}, author = {Sun, Z and Li, J and Fan, Y and Meng, J and Deng, K}, title = {Efficiency and mechanism of nitrogen removal from piggery wastewater in an improved microaerobic process.}, journal = {The Science of the total environment}, volume = {774}, number = {}, pages = {144925}, doi = {10.1016/j.scitotenv.2020.144925}, pmid = {33610988}, issn = {1879-1026}, abstract = {Characterized by high ammonium (NH4+ - N) and low ratio of chemical oxygen demand (COD) to total nitrogen (COD/TN), discharge of piggery wastewater has been identified as a primary pollution source resulting in water eutrophication. An improved microaerobic reactor, internal aerating microaerobic reactor (IAMR), was constructed to treat manure-free piggery wastewater without effluent recycle at dissolved oxygen of 0.3 mg/L and 32 °C. A removal rate of COD, NH4+ - N and TN averaged 77.9%, 94.6% and 82.6% was obtained in the reactor, with the concentration of 258.5, 235.5 and 335.2 mg/L in influent, respectively. 16S rDNA amplicon sequencing, carbon and nitrogen mass balance and stoichiometry indicated that heterotrophic nitrification-anammox was the dominant approach to nitrogen removal. Microbiome phenotypes showed that aerobic bacteria were the dominant microorganisms, and the microbiome oxidative stress tolerance was intensified along with the continuous operation of the IAMR, resulting in the survival of various facultative and anaerobic bacteria for nutrients removal. With the good nutrients removal, less energy consumption, and high tolerance to influent fluctuation, the improved IAMR was confirmed as a promising process for treating wastewater with high NH4+ - N and low COD/TN.}, }
@article {pmid33610778, year = {2021}, author = {Cyprian, F and Sohail, MU and Abdelhafez, I and Salman, S and Attique, Z and Kamareddine, L and Al-Asmakh, M}, title = {SARS-CoV-2-Immune-Microbiome Interaction: Lessons from Respiratory Viral Infections.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ijid.2021.02.071}, pmid = {33610778}, issn = {1878-3511}, abstract = {By the beginning of 2020, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has rapidly evolved into an emergent worldwide pandemic, an outbreak whose unprecedented consequences highlighted the existing flaws within the global public healthcare systems. While the coronavirus disease 2019 (COVID-19) is bestowed with a broad spectrum of clinical manifestation involving vital organs, the respiratory system transpires as the main route of entry of SARS-CoV-2, with the lungs being its primary target. Of those infected, up to 20% require hospitalization on account of severity, while the majority of patients are either asymptomatic or exhibit mild symptoms. Exacerbation in disease severity and complications of COVID-19 infection have been allied with multiple comorbidities including hypertension, diabetes mellitus, cardiovascular disorders, cancer, and chronic lung disease. Interestingly, a recent body of evidence have foregrounded the pulmonary and gut microbiome as potential modulators in altering the course of COVID-19, plausibly via the microbiome-immune system axis. While relative concordance between microbes and immunity is still not fully elucidated in a COVID-19 disease context, we present here an overview of our current understanding of this COVID-19-microbiome-immune cross talk and discuss the potential contributions of microbiome-related immunity to SARS-CoV-2 pathogenesis and COVID-19 disease progression.}, }
@article {pmid33610694, year = {2021}, author = {Vinarov, Z and Abrahamsson, B and Artursson, P and Batchelor, H and Berben, P and Bernkop-Schnürch, A and Butler, J and Ceulemans, J and Davies, N and Dupont, D and Flaten, GE and Fotaki, N and Griffin, BT and Jannin, V and Keemink, J and Kesisoglou, F and Koziolek, M and Kuentz, M and Mackie, A and Meléndez Martinez, AJ and McAllister, M and Müllertz, A and O'Driscoll, CM and Parrott, N and Paszkowska, J and Pavek, P and Porter, CJH and Reppas, C and Stillhart, C and Sugano, K and Toader, E and Valentová, K and Vertzoni, M and De Wildt, S and Wilson, CG and Augustijns, P}, title = {Current challenges and future perspectives in oral absorption research: An opinion of the UNGAP network.}, journal = {Advanced drug delivery reviews}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.addr.2021.02.001}, pmid = {33610694}, issn = {1872-8294}, abstract = {Although oral drug delivery is the preferred administration route and has been used for centuries, modern drug discovery and development pipelines challenge conventional formulation approaches and highlight the insufficient mechanistic understanding of processes critical to oral drug absorption. This review presents the opinion of UNGAP scientists on four key themes across the oral absorption landscape: (1) specific patient populations, (2) regional differences in the gastrointestinal tract, (3) advanced formulations and (4) food-drug interactions. The differences of oral absorption in pediatric and geriatric populations, the specific issues in colonic absorption, the formulation approaches for poorly water-soluble (small molecules) and poorly permeable (peptides, RNA etc.) drugs, as well as the vast realm of food effects, are some of the topics discussed in detail. The identified controversies and gaps in the current understanding of gastrointestinal absorption-related processes are used to create a roadmap for the future of oral drug absorption research.}, }
@article {pmid33610260, year = {2021}, author = {Shah Utsav, S and Subramaniam, V and Tamhankar Ashwin, S}, title = {Microbiome studies in urology- where do we stand and where can we reach?.}, journal = {Indian journal of medical microbiology}, volume = {39}, number = {1}, pages = {98-103}, doi = {10.1016/j.ijmmb.2020.10.009}, pmid = {33610260}, issn = {1998-3646}, abstract = {The role of microbiome milieu in the urinary tract, their interplay in diverse urological conditions and their therapeutic implications are not completely understood. The microbiome has contributed towards urinary tract infections, urolithiasis and urological cancers. The possibility of manipulating microbiome for diagnosis and treatment is evolving. Probiotics might help in overcoming the problems of recurrent infection and antibiotic resistance. Novel applications like stents and catheters coated with non-pathogenic organisms are being developed. Research in the urinary microbiome has progressed from using mouse models to the presently available three- dimensional cultured organoids, thus making it more feasible. As our knowledge regarding the urinary microbiome increases, justice can be done to many patients in whom the advancements can be used for prophylaxis, diagnosis, treatment and even in improving their quality of life. The growing amount of antibiotic resistance is also a matter of concern and probiotics might be the answer to this upcoming calamity. In this review, we have discussed the role of the urinary microbiome in pathogenesis, diagnosis and treatment of urological conditions and pondered upon its future prospects.}, }
@article {pmid33596629, year = {2021}, author = {Lee, TY}, title = {Lactate: a multifunctional signaling molecule.}, journal = {Yeungnam University journal of medicine}, volume = {}, number = {}, pages = {}, doi = {10.12701/yujm.2020.00892}, pmid = {33596629}, issn = {2384-0293}, abstract = {Since its discovery in 1780, lactate has long been misunderstood as a waste by-product of anaerobic glycolysis with multiple deleterious effects. Owing to the lactate shuttle concept introduced in the early 1980s, a paradigm shift began to occur. Increasing evidence indicates that lactate is a coordinator of whole-body metabolism. Lactate is not only a readily accessible fuel that is shuttled throughout the body but also a metabolic buffer that bridges glycolysis and oxidative phosphorylation between cells and intracellular compartments. Lactate also acts as a multifunctional signaling molecule through receptors expressed in various cells and tissues, resulting in diverse biological consequences including decreased lipolysis, immune regulation, anti-inflammation, wound healing, and enhanced exercise performance in association with the gut microbiome. Furthermore, lactate contributes to epigenetic gene regulation by lactylating lysine residues of histones, accounting for its key role in immune modulation and maintenance of homeostasis.}, }
@article {pmid33610085, year = {2021}, author = {Chen, Q and Wu, J and Dong, X and Yin, H and Shi, X and Su, S and Che, B and Li, Y and Yang, J}, title = {Gut flora-targeted photobiomodulation therapy improves senile dementia in an Aß-induced Alzheimer's disease animal model.}, journal = {Journal of photochemistry and photobiology. B, Biology}, volume = {216}, number = {}, pages = {112152}, doi = {10.1016/j.jphotobiol.2021.112152}, pmid = {33610085}, issn = {1873-2682}, abstract = {BACKGROUND: Emerging evidence suggests that the gut microbiota plays an important role in the pathological progression of Alzheimer's disease (AD). Photobiomodulation (PBM) therapy is believed to have a positive regulatory effect on the imbalance of certain body functions, including inflammation, immunity, wound healing, nerve repair, and pain. Previous studies have found that the intestinal flora of patients with AD is in an unbalanced state. Therefore, we have proposed the use of gut flora-targeted PBM (gf-targeted PBM) as a method to improve AD in an Aß-induced AD mouse model.<br><br>METHODS: PBM was performed on the abdomen of the mice at the wavelengths of 630 nm, 730 nm, and 850 nm at 100 J/cm2 for 8 weeks. Morris water maze test, immunofluorescence and proteomic of hippocampus, and intestinal flora detection of fecal were used to evaluate the treatment effects of gf-targeted PBM on AD rats.<br><br>RESULTS: PBM at all three wavelengths (especially 630 nm and 730 nm) significantly improved learning retention as measured by the Morris water maze. In addition, we found reduced amyloidosis and tau phosphorylation in the hippocampus by immunofluorescence in AD mice. By using a quantitative proteomic analysis of the hippocampus, we found that gf-targeted PBM significantly altered the expression levels of 509 proteins (the same differentially expressed proteins in all three wavelengths of PBM), which involved the pathways of hormone synthesis, phagocytosis, and metabolism. The 16 s rRNA gene sequencing of fecal contents showed that PBM significantly altered the diversity and abundance of intestinal flora. Specifically, PBM treatment reversed the typical increase of Helicobacter and uncultured Bacteroidales and the decrease of Rikenella seen in AD mice.<br><br>CONCLUSIONS: Our data indicate that gf-targeted PBM regulates the diversity of intestinal flora, which may improve damage caused by AD. Gf-targeted PBM has the potential to be a noninvasive microflora regulation method for AD patients.}, }
@article {pmid33609647, year = {2021}, author = {Gunaratnam, S and Millette, M and McFarland, LV and DuPont, HL and Lacroix, M}, title = {Potential role of probiotics in reducing Clostridioides difficile virulence: Interference with quorum sensing systems.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {104798}, doi = {10.1016/j.micpath.2021.104798}, pmid = {33609647}, issn = {1096-1208}, abstract = {Opportunistic pathogenic bacteria may cause disease after the normally protective microbiome is disrupted (typically by antibiotic exposure). Clostridioides difficile is one such pathogen having a severe impact on healthcare facilities and increasing costs of medical care. The search for new therapeutic strategies that are not reliant on additional antibiotic exposures are currently being explored. One such strategy is to disrupt the production of C. difficile virulence factors by interfering with quorum sensing (QS) systems. QS has been well studied in other bacteria, but our understanding in C. difficile is not so well understood. Some probiotic strains or combinations of strains have been shown to be effective in the treatment or primary prevention of C. difficile infections and may possess multiple mechanisms of action. One mechanism of probiotics might be the inhibition of QS, but their role has not been clearly defined yet. A literature search was conducted using standard databases (PubMed, Google Scholar) from database inception to August 2020. The objective of this paper is to update our understanding of how QS leads to toxin production by C. difficile, which is important in pathogenesis, and how QS inhibitors or probiotics may disrupt this pathway. We found two main QS systems for C. difficile (Agr and Lux systems) that are involved in C. difficile pathogenesis by regulating toxin production, motility and adherence. Probiotics and other QS inhibitors targeting QS systems may represent important new directions of therapy and prevention of CDI.}, }
@article {pmid33609630, year = {2021}, author = {Li, Y and Hintze, KJ and Ward, RE}, title = {Effect of supplemental prebiotics, probiotics and bioactive proteins on the microbiome composition and fecal calprotectin in C57BL6/j mice.}, journal = {Biochimie}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.biochi.2021.02.010}, pmid = {33609630}, issn = {1638-6183}, abstract = {The composition and metabolic activity of the microbiome affect many aspects of health, and there is current interest in dietary constituents that may affect this system. The purpose of this study was to evaluate the effects of a mix of probiotics, a mix of prebiotics and a bioactive protein fraction on the microbiome, when fed to mice alone and in combination at physiologically relevant doses. Mice were fed the total western diet (TWD) supplemented with prebiotics, probiotics, and bioactive proteins individually and in combination for four weeks. Subsequently, effects on the composition of gut microbiome, gut short-chain fatty acid (SCFAs) concentration, gut inflammation and integrity of the mucosal barrier were measured. Ruminococcus gnavus was increased in mice gut microbiome after feeding prebiotics. Bifidobacterium longum was increased after feeding probiotics. The treatments significantly affected beta-diversity with minor treatment effects on cecal or fecal SCFAs levels, and the treatments did not affect gut inflammation as measured by fecal calprotectin.}, }
@article {pmid33609583, year = {2021}, author = {Wouk, J and Dekker, RFH and Queiroz, EAIF and Barbosa-Dekker, AM}, title = {β-Glucans as a panacea for a healthy heart? Their roles in preventing and treating cardiovascular diseases.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ijbiomac.2021.02.087}, pmid = {33609583}, issn = {1879-0003}, abstract = {Cardiovascular diseases (CVDs) are the leading cause of death worldwide. Factors increasing the risks for CVD development are related to obesity, diabetes, high blood cholesterol, high blood pressure and lifestyle. CVD risk factors may be treated with appropriate drugs, but prolonged can use cause undesirable side-effects. Among the natural products used in complementary and alternative medicines, are the β-ᴅ-glucans; biopolymers found in foods (cereals, mushrooms), and can easily be produced by microbial fermentation. Independent of source, β-glucans of the mixed-linked types [(1 → 3)(1 → 6)-β-ᴅ-glucans - fungal, and (1 → 3)(1 → 4)-β-ᴅ-glucans - cereal] have widely been studied because of their biological activities, and have demonstrated cardiovascular protective effects. In this review, we discuss the roles of β-ᴅ-glucans in various pathophysiological conditions that lead to CVDs including obesity, dyslipidemia, hyperglycemia, oxidative stress, hypertension and atherosclerosis. The β-glucans from all of the sources cited demonstrated potential hypoglycemic, hypocholesterolemic and anti-obesogenicity activities, reduced hypertension and ameliorated the atherosclerosis condition. More recently, β-glucans are recognized as possessing prebiotic properties that modulate the gut microbiome and impact on the health benefits including cardiovascular. Overall, all the studies investigated unequivocally demonstrated the dietary benefits of consuming β-glucans regardless of source, thus constituting a promising panaceutical approach to reduce CVD risk factors.}, }
@article {pmid33609209, year = {2021}, author = {Luo, W and Tian, L and Tan, B and Shen, Z and Xiao, M and Wu, S and Meng, X and Wu, X and Wang, X}, title = {Update: Innate Lymphoid Cells in Inflammatory Bowel Disease.}, journal = {Digestive diseases and sciences}, volume = {}, number = {}, pages = {}, pmid = {33609209}, issn = {1573-2568}, support = {no. 81970494 and 81670504//National Natural Science Foundation of China/ ; no. 2019SK2041//Key Research and Development Program of Hunan Province/ ; }, abstract = {Inflammatory bowel disease (IBD) is a chronic and nonspecific intestinal inflammatory condition with high relapse rate. Its pathogenesis has been linked to dysbacteriosis, genetic and environmental factors. In recent years, a new type of lymphocytes, termed innate lymphoid cells, has been described and classified into three subtypes of innate lymphoid cells-group 1, group 2 and group 3. An imbalance among these subsets' interaction with gut microbiome, and other immune cells affects intestinal mucosal homeostasis. Understanding the role of innate lymphoid cells may provide ideas for developing novel and targeted approaches for treatment of IBD.}, }
@article {pmid33609143, year = {2021}, author = {Green, EA and Smedley, SR and Klassen, JL}, title = {North American Fireflies Host Low Bacterial Diversity.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33609143}, issn = {1432-184X}, abstract = {Although there are numerous studies of firefly mating flashes, lantern bioluminescence, and anti-predation lucibufagin metabolites, almost nothing is known about their microbiome. We therefore used 16S rRNA community amplicon sequencing to characterize the gut and body microbiomes of four North American firefly taxa: Ellychnia corrusca, the Photuris versicolor species complex, Pyractomena borealis, and Pyropyga decipiens. These firefly microbiomes all have very low species diversity, often dominated by a single species, and each firefly type has a characteristic microbiome. Although the microbiomes of male and female fireflies did not differ from each other, Ph. versicolor gut and body microbiomes did, with their gut microbiomes being enriched in Pseudomonas and Acinetobacter. Ellychnia corrusca egg and adult microbiomes were unique except for a single egg microbiome that shared a community type with E. corrusca adults, which could suggest microbial transmission from mother to offspring. Mollicutes that had been previously isolated from fireflies were common in our firefly microbiomes. These results set the stage for further research concerning the function and transmission of these bacterial symbionts.}, }
@article {pmid33609137, year = {2021}, author = {Neal, AL and McLaren, T and Campolino, ML and Hughes, D and Coelho, AM and Lana, UGP and Gomes, EA and de Sousa, SM}, title = {Crop type exerts greater influence upon rhizosphere phosphohydrolase gene abundance and phylogenetic diversity than phosphorus fertilization.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiab033}, pmid = {33609137}, issn = {1574-6941}, abstract = {Rock phosphate is an alternative form of phosphorus (P) fertilizer, however there is no information regarding the influence of P fertilizer sources in Brazilian Cerrado soils upon microbial genes coding for phosphohydrolase enzymes in crop rhizospheres. Here, we analyse a field experiment comparing maize and sorghum grown under different P fertilization (rock phosphate and triple superphosphate) upon crop performance, phosphatase activity and rhizosphere microbiomes at three levels of diversity: small subunit rRNA marker genes of bacteria, archaea and fungi; a suite of alkaline and acid phosphatase and phytase genes; and ecotypes of individual genes. We showed no significant difference in crop performance between the fertilizer sources, but the accumulation of fertilizer P into pools of organic soil P differed. Phosphatase activity was the only biological parameter influenced by P fertilization. Differences in rhizosphere microbiomes were observed at all levels of biodiversity due to crop type, but not fertilization. Inspection of phosphohydrolase gene ecotypes responsible for differences between the crops suggests a role for lateral genetic transfer in establishing ecotype distributions. Moreover, they were not reflected in microbial community composition, suggesting that they confer competitive advantage to individual cells rather than species in the sorghum rhizosphere.}, }
@article {pmid33608675, year = {2021}, author = {Guilleman, MM and Stevens, BAY and Van Lieshout, LP and Rghei, AD and Pei, Y and Santry, LA and Thompson, B and Wootton, SK}, title = {AAV-mediated delivery of actoxumab and bezlotoxumab results in serum and mucosal antibody concentrations that provide protection from C. difficile toxin challenge.}, journal = {Gene therapy}, volume = {}, number = {}, pages = {}, pmid = {33608675}, issn = {1476-5462}, support = {RGPIN-2018-04737//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada)/ ; }, abstract = {Clostridium difficile is the leading cause of antibiotic-associated nosocomial diarrhea in the developed world. When the host-associated colon microbiome is disrupted by the ingestion of antibiotics, C. difficile spores can germinate, resulting in infection. C. difficile secretes enterotoxin A (TcdA) and cytotoxin B (TcdB) that are responsible for disease pathology. Treatment options are limited as the bacterium demonstrates resistance to many antibiotics, and even with antibacterial therapies, recurrences of C. difficile are common. Actotoxumab and bezlotoxumab are human monoclonal antibodies that bind and neutralize TcdA and TcdB, respectively. In 2016, the US food and drug administration (FDA) approved bezlotoxumab for use in the prevention of C. difficile infection recurrence. To ensure the long-term expression of antibodies, gene therapy can be used. Here, adeno-associated virus (AAV)6.2FF, a novel triple mutant of AAV6, was engineered to express either actotoxumab or bezlotoxumab in mice and hamsters. Both antibodies expressed at greater than 90 μg/mL in the serum and were detected at mucosal surfaces in both models. Hundred percent of mice given AAV6.2FF-actoxumab survived a lethal dose of TcdA. This proof of concept study demonstrates that AAV-mediated expression of C. difficile toxin antibodies is a viable approach for the prevention of recurrent C. difficile infections.}, }
@article {pmid33608630, year = {2021}, author = {Kim, G and Kim, M and Kim, M and Park, C and Yoon, Y and Lim, DH and Yeo, H and Kang, S and Lee, YG and Beak, NI and Lee, J and Kim, S and Kwon, JY and Choi, WW and Lee, C and Yoon, KW and Park, H and Lee, DG}, title = {Spermidine-induced recovery of human dermal structure and barrier function by skin microbiome.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {231}, pmid = {33608630}, issn = {2399-3642}, abstract = {An unbalanced microbial ecosystem on the human skin is closely related to skin diseases and has been associated with inflammation and immune responses. However, little is known about the role of the skin microbiome on skin aging. Here, we report that the Streptococcus species improved the skin structure and barrier function, thereby contributing to anti-aging. Metagenomic analyses showed the abundance of Streptococcus in younger individuals or those having more elastic skin. Particularly, we isolated Streptococcus pneumoniae, Streptococcus infantis, and Streptococcus thermophilus from face of young individuals. Treatment with secretions of S. pneumoniae and S. infantis induced the expression of genes associated with the formation of skin structure and the skin barrier function in human skin cells. The application of culture supernatant including Streptococcal secretions on human skin showed marked improvements on skin phenotypes such as elasticity, hydration, and desquamation. Gene Ontology analysis revealed overlaps in spermidine biosynthetic and glycogen biosynthetic processes. Streptococcus-secreted spermidine contributed to the recovery of skin structure and barrier function through the upregulation of collagen and lipid synthesis in aged cells. Overall, our data suggest the role of skin microbiome into anti-aging and clinical applications.}, }
@article {pmid33608575, year = {2021}, author = {Kazemian, N and Ramezankhani, M and Sehgal, A and Khalid, FM and Kalkhoran, AHZ and Narayan, A and Wong, GK and Kao, D and Pakpour, S}, title = {Author Correction: The trans-kingdom battle between donor and recipient gut microbiome influences fecal microbiota transplantation outcome.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {4546}, doi = {10.1038/s41598-021-82644-z}, pmid = {33608575}, issn = {2045-2322}, }
@article {pmid33608551, year = {2021}, author = {Ho, SX and Min, N and Wong, EPY and Chong, CY and Chu, JJH}, title = {Characterization of oral virome and microbiome revealed distinctive microbiome disruptions in paediatric patients with hand, foot and mouth disease.}, journal = {NPJ biofilms and microbiomes}, volume = {7}, number = {1}, pages = {19}, pmid = {33608551}, issn = {2055-5008}, support = {2017-T2-2-014//Ministry of Education - Singapore (MOE)/ ; }, abstract = {While the underlying determinants are unclear, hand, foot and mouth disease (HFMD) presents a wide spectrum of clinical manifestations with varying severity in different individuals. Recently, many studies identified the human microbiome as a critical factor in the pathogenesis of various diseases. Therefore, we here investigated the ecological dynamics of the oral microbiome changes during the HFMD infection. After targeted enrichment of all known vertebrate viruses, the virome profiles of symptomatic and asymptomatic HFMD patients were examined and revealed to be significantly altered from those of healthy individuals, with nine discriminative viruses detected. Further characterization of the prokaryotic microbiome revealed an elevated level of Streptococcus sp. as the most important signature of the symptomatic HFMD cohort, positively correlating to the level of enterovirus A RNA. In addition, we found that while coxsackievirus A5 is detected in saliva RNA of all asymptomatic cases, coxsackievirus A6 dominates the majority of the symptomatic cohort.}, }
@article {pmid33608307, year = {2021}, author = {Ueda, S and Goto, M and Hashimoto, K and Hasegawa, S and Imazawa, M and Takahashi, M and Oh-Iwa, I and Shimozato, K and Nagao, T and Nomoto, S}, title = {Salivary CCL20 Level as a Biomarker for Oral Squamous Cell Carcinoma.}, journal = {Cancer genomics &amp; proteomics}, volume = {18}, number = {2}, pages = {103-112}, doi = {10.21873/cgp.20245}, pmid = {33608307}, issn = {1790-6245}, abstract = {BACKGROUND/AIM: This study investigated the utility of C-C motif chemokine ligand 20 (CCL20) expression in saliva as a biomarker for oral squamous cell carcinoma (OSCC) and also examined the associated microbiome.<br><br>MATERIALS AND METHODS: The study group included patients with OSCC or oral potentially malignant disorder (OPMD), and healthy volunteers (HVs). microarray and qRT-PCR were used to compare salivary CCL20 expression levels among groups. Data on CCL20 levels in oral cancer tissues and normal tissues were retrieved from a public database and examined. Furthermore, next-generation sequencing was used to investigate the salivary microbiome.<br><br>RESULTS: A significant increase in the expression level of CCL20 was observed in both OSCC tissues and saliva from patients with oral cancer. Fusobacterium was identified as the predominant bacteria in OSCC and correlated with CCL20 expression level. OSCC screening based on salivary CCL20 expression enabled successful differentiation between patients with OSCC and HVs.<br><br>CONCLUSION: CCL20 expression may be a useful biomarker for OSCC.}, }
@article {pmid33608301, year = {2021}, author = {Zhang, H and Du, H and Xu, Y}, title = {Volatile organic compounds mediated antifungal activity of Pichia and its effect on the metabolic profiles of fermentation communities.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02992-20}, pmid = {33608301}, issn = {1098-5336}, abstract = {Volatile Organic Compounds (VOCs) are chemicals responsible for antagonistic activity between microorganisms. The impact of VOCs on microbial community succession of fermentation is not well understood. In this study, Pichia were evaluated for VOCs production as a part of antifungal activity during Baijiu fermentation. Results showed that the abundance of Pichia in the defect group (agglomerated fermented grains) was lower than that in control group, and a negative interaction between Pichia and Monascus was determined (P < 0.05). In addition, the disruption of fungi was significantly related to the differences of metabolic profiles in fermented grains. To determine VOCs from Pichia and its effect on Monascus purpureus, a double-dishes system was assessed, and where the incidence of M. purpureus reduction was 39.22% after 7 days. As to antifungal volatile compounds, 2-phenylethanol was identified had effective antifungal effect on M. purpureus through contact and non-contact. To further confirm the antifungal activity of 2-phenylethanol, scanning electron microscopy showed that 2-phenylethanol widely and significantly inhibited conidia germination and mycelial growth of filamentous fungi. Metatranscriptomic analysis revealed that the Ehrlich pathway is the metabolic path of 2-phenylethanol in Pichia, and identified potential antifungal mechanisms that including protein synthesis and DNA damage. This study demonstrated the role of volatile-mediated microbial interaction in microbiome assembly and discovered a plausible scenario in which Pichia antagonized fungal blooms. The results may improve the niche establishment and growth of the functional yeast that enhances the flavor of BaijiuIMPORTANCE Fermentation of food occurs within communities of interacting species. The importance of microbial interactions in shaping microbial structure and metabolic performance to optimize the traditional fermentation process has long been emphasized, but the interaction mechanisms remain unclear. This study applied metabolome analysis and amplicon sequencing along with metatranscriptomic analysis to study the volatile-mediated antifungal activity of Pichia and its effect on the metabolism of ethanol during Baijiu fermentation, potentially enhancing the establishment of the fermentation niche and improving ethanol metabolism.}, }
@article {pmid33608155, year = {2021}, author = {Bajic, P and Wolfe, AJ}, title = {The Microbiome of Male Infertility: Paving the Road Ahead.}, journal = {European urology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.eururo.2021.02.009}, pmid = {33608155}, issn = {1873-7560}, }
@article {pmid33608141, year = {2021}, author = {Guo, R and Zheng, Y and Zhang, L and Shi, J and Li, W}, title = {Salivary microbiome and periodontal status of patients with periodontitis during the initial stage of orthodontic treatment.}, journal = {American journal of orthodontics and dentofacial orthopedics : official publication of the American Association of Orthodontists, its constituent societies, and the American Board of Orthodontics}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ajodo.2019.11.026}, pmid = {33608141}, issn = {1097-6752}, abstract = {INTRODUCTION: Patients with severe periodontitis typically present with pathologic tooth migration. To improve esthetics and masticatory function, orthodontic treatment is required. Research on periodontal orthodontic treatment has been sparse, particularly from the microbial perspective. Hence, we analyzed the microbial and clinical changes in patients with well-controlled periodontitis in the early stage of orthodontic treatment.<br><br>METHODS: Ten patients with well-controlled periodontitis were asked to collect saliva before and 1 and 3 months after appliance placement (T0, T1, and T2, respectively) and underwent clinical examinations before and 1, 3, and 6 months after appliance placement (T0, T1, T2, and T3, respectively). The microbial community of saliva was analyzed by 16S rRNA gene sequencing. Gingival index, the plaque index, and the probing pocket depth were clinically assessed.<br><br>RESULTS: The plaque index significantly increased from T0 to T1 and decreased at T2 and T3. The probing pocket depth and gingival index increased slightly at T2, but not significantly, in both the high-risk site and low-risk site. The alpha and beta diversity increased at T1. The microbial community structure was similar at T0 and T2. The relative abundance of core genera and periodontal pathogens was stable during the initial 3 months of orthodontic treatment.<br><br>CONCLUSIONS: The orthodontic appliance promoted plaque accumulation and altered the microbial community of patients with well-controlled periodontitis during the first month of orthodontic treatment. The microbial community returned to the basal composition at 3 months after appliance placement, and the periodontal inflammation during the 6-months orthodontic treatment was under control.}, }
@article {pmid33608131, year = {2021}, author = {Wei, W and Jiang, W and Tian, Z and Wu, H and Ning, H and Yan, G and Zhang, Z and Li, Z and Dong, F and Sun, Y and Li, Y and Han, T and Wang, M and Sun, C}, title = {Fecal g. Streptococcus and g. Eubacterium_coprostanoligenes_group combined with sphingosine to modulate the serum dyslipidemia in high-fat diet mice.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.clnu.2021.01.031}, pmid = {33608131}, issn = {1532-1983}, abstract = {BACKGROUND &amp; AIMS: Although high-fat diet (HFD) could impact the composition of fecal microbiome and their metabolites, it is still largely unknown which fecal bacteria and metabolites are relatively important in responding to the HFD. This study aimed to identify the crucial fecal bacteria and metabolites in the HFD mice using a microbial-metabolite network, and to investigate the synergistic mediation effect of the crucial fecal bacteria and metabolites on serum dyslipidemia induced by the HFD.<br><br>METHODS: The 16srDNA sequencing and the ultra-performance liquid chromatography (UPLC/TOF MSMS) platform were performed to characterize the composition and function of fecal microbiome, and metabolites in the HFD. The microbial-metabolite network, correlation and mediation analyses were performed to examine the relationships among fecal microbiome, metabolites, and serum dyslipidemia indicators. Mice models were conducted to evaluate the effect of fecal metabolite on dyslipidemia.<br><br>RESULTS: Compared to the control, 32 genera were altered in the HFD, including 26 up-regulated and 6 down-regulated. A total of 42 altered pathways were observed between the control and HFD, and the &quot;Glycosphingolipid biosynthesis&quot; was identified as the most significant pathway (fold change = 0.64; p < 0.001). Meanwhile, 49 fecal metabolites were altered in the HFD, and the fecal microbiome was associated with the fecal metabolism (M2 = 0.776, p = 0.008). Based on the microbial-metabolite network, two major hub genera were screened (HUB1: g. Streptococcus, HUB2: g. Eubacterium_coprostanoligenes_group), and one bacterial metabolite, sphingosine, was found in this study. Further, the HUB2 was positively associated with fecal sphingosine (r = 0.646, p = 0.001), and its downstream metabolic pathway, &quot;Glycosphingolipid biosynthesis&quot; pathway (r = 0.544, p = 0.009). The regulatory relationship between the HUB2 and sphingosine synergistically mediated the effect of HFD on TCHO (33.7%), HDL-C (37.3%), and bodyweight (36.7%). Besides, compared to the HFD, the HFD with sphingosine supplementation had lower bodyweight (35.12 ± 1.23 vs. 39.42 ± 1.25, p < 0.001), TG (0.44 ± 0.08 vs. 0.52 ± 0.05, p = 0.002), TCHO (3.81 ± 0.34 vs. 4.51 ± 0.38, p = 0.002), and LDL-c (0.82 ± 0.09 vs. 0.97 ± 0.15, p = 0.016).<br><br>CONCLUSIONS: The g. Streptococcus and g. Eubacterium_coprostanoligenes are two hub genera in the fecal micro-ecosystem of the HFD, and the g. Eubacterium_coprostanoligenes mediates the effect of HFD on dyslipidemia through sphingosine. Sphingosine supplementation can improve dyslipidemia induced by HFD.}, }
@article {pmid33607938, year = {2021}, author = {Siebert, JC and Saint-Cyr, M and Borengasser, SJ and Wagner, BD and Lozupone, CA and Görg, C}, title = {CANTARE: finding and visualizing network-based multi-omic predictive models.}, journal = {BMC bioinformatics}, volume = {22}, number = {1}, pages = {80}, pmid = {33607938}, issn = {1471-2105}, abstract = {BACKGROUND: One goal of multi-omic studies is to identify interpretable predictive models for outcomes of interest, with analytes drawn from multiple omes. Such findings could support refined biological insight and hypothesis generation. However, standard analytical approaches are not designed to be &quot;ome aware.&quot; Thus, some researchers analyze data from one ome at a time, and then combine predictions across omes. Others resort to correlation studies, cataloging pairwise relationships, but lacking an obvious approach for cohesive and interpretable summaries of these catalogs.<br><br>METHODS: We present a novel workflow for building predictive regression models from network neighborhoods in multi-omic networks. First, we generate pairwise regression models across all pairs of analytes from all omes, encoding the resulting &quot;top table&quot; of relationships in a network. Then, we build predictive logistic regression models using the analytes in network neighborhoods of interest. We call this method CANTARE (Consolidated Analysis of Network Topology And Regression Elements).<br><br>RESULTS: We applied CANTARE to previously published data from healthy controls and patients with inflammatory bowel disease (IBD) consisting of three omes: gut microbiome, metabolomics, and microbial-derived enzymes. We identified 8 unique predictive models with AUC > 0.90. The number of predictors in these models ranged from 3 to 13. We compare the results of CANTARE to random forests and elastic-net penalized regressions, analyzing AUC, predictions, and predictors. CANTARE AUC values were competitive with those generated by random forests and penalized regressions. The top 3 CANTARE models had a greater dynamic range of predicted probabilities than did random forests and penalized regressions (p-value = 1.35 × 10-5). CANTARE models were significantly more likely to prioritize predictors from multiple omes than were the alternatives (p-value = 0.005). We also showed that predictive models from a network based on pairwise models with an interaction term for IBD have higher AUC than predictive models built from a correlation network (p-value = 0.016). R scripts and a CANTARE User's Guide are available at https://sourceforge.net/projects/cytomelodics/files/CANTARE/ .<br><br>CONCLUSION: CANTARE offers a flexible approach for building parsimonious, interpretable multi-omic models. These models yield quantitative and directional effect sizes for predictors and support the generation of hypotheses for follow-up investigation.}, }
@article {pmid33607506, year = {2021}, author = {Rahman, Z and Dandekar, MP}, title = {Crosstalk between gut microbiome and immunology in the management of ischemic brain injury.}, journal = {Journal of neuroimmunology}, volume = {353}, number = {}, pages = {577498}, doi = {10.1016/j.jneuroim.2021.577498}, pmid = {33607506}, issn = {1872-8421}, abstract = {Ischemic brain injury is a serious neurological complication, which accrues an immense activation of neuroinflammatory responses. Several lines of research suggested the interconnection of gut microbiota perturbation with the activation of proinflammatory mediators. Intestinal microbial communities also interchange information with the brain through various afferent and efferent channels and microbial by-products. Herein, we discuss the different microelements of gut microbiota and its connection with the host immune system and how change in immune-microbial signatures correlates with the stroke incidence and post-injury neurological sequelae. The activated inflammatory cells increase the production of proinflammatory cytokines, chemokines, proteases and adhesive proteins that are involved in the systemic inflammation, blood brain barrier disruption, gut dysbiosis and aggravation of ischemic brain injury. We suggest that fine-tuning of commensal gut microbiota (eubiosis) may regulate the activation of CNS resident cells like microglial, astrocytes, mast cells and natural killer cells.}, }
@article {pmid33607375, year = {2021}, author = {Tijeras-Raballand, A and Hilmi, M and Astorgues-Xerri, L and Nicolle, R and Bièche, I and Neuzillet, C}, title = {Microbiome and pancreatic ductal adenocarcinoma.}, journal = {Clinics and research in hepatology and gastroenterology}, volume = {45}, number = {2}, pages = {101589}, doi = {10.1016/j.clinre.2020.101589}, pmid = {33607375}, issn = {2210-741X}, abstract = {Pancreatic ductal adenocarcinoma (PDAC) incidence and related-deaths are increasing worldwide. PDAC is characterized by poor prognosis due to late diagnosis, high metastatic capacity and resistance to therapy. This is partially due to its specific microenvironment, where the stroma is prominent over tumor cells. Besides the oral and gut microbiota, the intratumor microbiome, i.e. the bacterial and fungal microorganisms present within the tumor, was recently introduced as a new partner of the tumor microenvironment of PDAC modulating pancreatic carcinogenesis, intratumor immune infiltrates, and response to chemotherapy. In this review, we propose an overview of current knowledge about the roles of bacteria and fungi in PDAC development and biology, and discuss potential therapeutic implications.}, }
@article {pmid33607218, year = {2021}, author = {Li, T and Liu, Z and Zhang, Z and Bai, H and Zong, X and Wang, F and Fan, L}, title = {Comparative analysis of the vaginal microbiome of Chinese women with Trichomonas vaginalis and mixed infection.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {104790}, doi = {10.1016/j.micpath.2021.104790}, pmid = {33607218}, issn = {1096-1208}, abstract = {The high prevalence and serious long-term sequelae of Trichomonas vaginalis (TV) infection worldwide is of a particular concern; however, data regarding the differences in the composition of the vaginal microbiome in cases of single TV infection or mixed infections (i.e., presence of TV and bacterial vaginosis) are scarce. We employed metagenomic sequencing analyses to study gene expression in the vaginal microbiota of women with single TV infection and mixed infection. Women infected with only TV had significantly higher abundance of Mycoplasma, Prevotella, and Streptococcus compared to women without vaginal infection (control). Women infected with mixed infections had a significantly higher abundance of Mycoplasma, Prevotella, Streptococcus, Anaerococcus, Dialister, Peptostreptococcus, Peptoniphilus and a significantly lower abundance of Lactobacillus than TV alone. Mixed infections had a significantly higher abundance of Prevotella, Anaerococcus and Dialister. Our findings suggest that the bacterial community composition varies among healthy women, women with TV alone, and those with mixed infection, and we hypothesize that these bacterial vaginosis (BV)-associated bacterium may play a role in the pathogenesis and recurrence of TV. Probiotic pessaries may necessarily be the answer because shifting the vaginal microbiome and host responses is probably a complex undertaking.}, }
@article {pmid33606979, year = {2021}, author = {Camarillo-Guerrero, LF and Almeida, A and Rangel-Pineros, G and Finn, RD and Lawley, TD}, title = {Massive expansion of human gut bacteriophage diversity.}, journal = {Cell}, volume = {184}, number = {4}, pages = {1098-1109.e9}, doi = {10.1016/j.cell.2021.01.029}, pmid = {33606979}, issn = {1097-4172}, abstract = {Bacteriophages drive evolutionary change in bacterial communities by creating gene flow networks that fuel ecological adaptions. However, the extent of viral diversity and its prevalence in the human gut remains largely unknown. Here, we introduce the Gut Phage Database, a collection of ∼142,000 non-redundant viral genomes (>10 kb) obtained by mining a dataset of 28,060 globally distributed human gut metagenomes and 2,898 reference genomes of cultured gut bacteria. Host assignment revealed that viral diversity is highest in the Firmicutes phyla and that ∼36% of viral clusters (VCs) are not restricted to a single species, creating gene flow networks across phylogenetically distinct bacterial species. Epidemiological analysis uncovered 280 globally distributed VCs found in at least 5 continents and a highly prevalent phage clade with features reminiscent of p-crAssphage. This high-quality, large-scale catalog of phage genomes will improve future virome studies and enable ecological and evolutionary analysis of human gut bacteriophages.}, }
@article {pmid33606846, year = {2021}, author = {Akhtar, I and Stewart, FA and Härle, A and Droste, A and Beller, M}, title = {Visualization of endogenous gut bacteria in Drosophila melanogaster using fluorescence in situ hybridization.}, journal = {PloS one}, volume = {16}, number = {2}, pages = {e0247376}, doi = {10.1371/journal.pone.0247376}, pmid = {33606846}, issn = {1932-6203}, abstract = {All metazoans are colonized by a complex and diverse set of microorganisms. The microbes colonize all parts of the body and are especially abundant in the gastrointestinal tract, where they constitute the gut microbiome. The fruit fly Drosophila melanogaster turned out to be an exquisite model organism to functionally test the importance of an intact gut microbiome. Still, however, fundamental questions remain unanswered. For example, it is unknown whether a fine-tuned regionalization of the gut microbiome exists and how such a spatial organization could be established. In order to pave the way for answering this question, we generated an optimized and adapted fluorescence in situ hybridization (FISH) protocol. We focused on the detection of the two major Drosophila gut microbiome constituting bacteria genera: Acetobacter and Lactobacillus. FISH allows to detect the bacteria in situ and thus to investigate their spatial localization in respect to the host as well as to other microbiome members. We demonstrate the applicability of the protocol using a diverse set of sample types.}, }
@article {pmid33606829, year = {2021}, author = {Leis, ML and Madruga, GM and Costa, MO}, title = {The porcine corneal surface bacterial microbiome: A distinctive niche within the ocular surface.}, journal = {PloS one}, volume = {16}, number = {2}, pages = {e0247392}, doi = {10.1371/journal.pone.0247392}, pmid = {33606829}, issn = {1932-6203}, abstract = {PURPOSE: The ocular surface microbiome has been described as paucibacterial. Until now, studies investigating the bacterial community associated with the ocular surface through high-throughput sequencing have focused on the conjunctiva. Conjunctival samples are thought to reflect and be representative of the microbiome residing on the ocular surface, including the cornea. Here, we hypothesized that the bacterial community associated with the corneal surface was different from those of the inferonasal and superotemporal conjunctival fornices, and from the tear film.<br><br>METHODS: Both eyes from 15 healthy piglets were sampled using swabs (inferonasal fornix, superotemporal fornix, and corneal surface, n = 30 each) and Schirmer tear test strips (STT, n = 30). Negative sampling controls (swabs and STT, n = 2 each) and extraction controls (n = 4) were included. Total DNA was extracted and high-throughput sequencing targeting the 16S rRNA gene was performed. Bioinformatic analyses included multiple contamination-controlling steps.<br><br>RESULTS: Corneal surface samples had a significantly lower number of taxa detected (P<0.01) and were compositionally different from all other sample types (Bray-Curtis dissimilarity, P<0.04). It also harbored higher levels of Proteobacteria (P<0.05), specifically Brevundimonas spp. (4.1-fold) and Paracoccus spp. (3.4-fold) than other sample types. Negative control STT strip samples yielded the highest amount of 16S rRNA gene copies across all sample types (P<0.05).<br><br>CONCLUSIONS: Our data suggests that the corneal surface provides a distinct environmental niche within the ocular surface, leading to a bacterial community compositionally different from all other sample types.}, }
@article {pmid33606747, year = {2021}, author = {Brown, R and Moore, L and Mani, A and Patel, S and Salinas, I}, title = {Effects of ploidy and salmonid alphavirus infection on the skin and gill microbiome of Atlantic salmon (Salmo salar).}, journal = {PloS one}, volume = {16}, number = {2}, pages = {e0243684}, doi = {10.1371/journal.pone.0243684}, pmid = {33606747}, issn = {1932-6203}, abstract = {The microbial communities that live in symbiosis with the mucosal surfaces of animals provide the host with defense strategies against pathogens. These microbial communities are largely shaped by the environment and the host genetics. Triploid Atlantic salmon (Salmo salar) are being considered for aquaculture as they are reproductively sterile and thus cannot contaminate the natural gene pool. It has not been previously investigated how the microbiome of triploid salmon compares to that of their diploid counterparts. In this study, we compare the steady-state skin and gill microbiome of both diploid and triploid salmon, and determine the effects of salmonid alphavirus 3 experimental infection on their microbial composition. Our results show limited differences in the skin-associated microbiome between triploid and diploid salmon, irrespective of infection. In the gills, we observed a high incidence of the bacterial pathogen Candidatus Branchiomonas, with higher abundance in diploid compared to triploid control fish. Diploid salmon infected with SAV3 showed greater histopathological signs of epitheliocystis compared to controls, a phenomenon not observed in triploid fish. Our results indicate that ploidy can affect the alpha diversity of the gills but not the skin-associated microbial community. Importantly, during a natural outbreak of Branchiomonas sp. the gill microbiome of diploid Atlantic salmon became significantly more dominated by this pathogen than in triploid animals. Thus, our results suggest that ploidy may play a role on Atlantic salmon gill health and provide insights into co-infection with SAV3 and C. Branchiomonas in Atlantic salmon.}, }
@article {pmid33606675, year = {2021}, author = {Coyte, KZ and Rao, C and Rakoff-Nahoum, S and Foster, KR}, title = {Ecological rules for the assembly of microbiome communities.}, journal = {PLoS biology}, volume = {19}, number = {2}, pages = {e3001116}, doi = {10.1371/journal.pbio.3001116}, pmid = {33606675}, issn = {1545-7885}, abstract = {Humans and many other hosts establish a diverse community of beneficial microbes anew each generation. The order and identity of incoming symbionts is critical for health, but what determines the success of the assembly process remains poorly understood. Here we develop ecological theory to identify factors important for microbial community assembly. Our method maps out all feasible pathways for the assembly of a given microbiome-with analogies to the mutational maps underlying fitness landscapes in evolutionary biology. Building these &quot;assembly maps&quot; reveals a tradeoff at the heart of the assembly process. Ecological dependencies between members of the microbiota make assembly predictable-and can provide metabolic benefits to the host-but these dependencies may also create barriers to assembly. This effect occurs because interdependent species can fail to establish when each relies on the other to colonize first. We support our predictions with published data from the assembly of the preterm infant microbiota, where we find that ecological dependence is associated with a predictable order of arrival. Our models also suggest that hosts can overcome barriers to assembly via mechanisms that either promote the uptake of multiple symbiont species in one step or feed early colonizers. This predicted importance of host feeding is supported by published data on the impacts of breast milk in the assembly of the human microbiome. We conclude that both microbe-microbe and host-microbe interactions are important for the trajectory of microbiome assembly.}, }
@article {pmid33606258, year = {2021}, author = {Danilevsky, A and Shomron, N}, title = {Deep Learning Applied on Next Generation Sequencing Data Analysis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2243}, number = {}, pages = {169-182}, pmid = {33606258}, issn = {1940-6029}, abstract = {Deep learning is defined as the group of computational techniques allowing for the discovery of latent information within large amounts of data. Recently, many fields have seen the immense potential of deep learning to solve various tasks in ways which outperformed many other traditional methods. Genomic research could be the next frontier to take advantage of deep learning, as it has the perfect combination of vast amounts of data and diverse tasks. Here we present the platform we generated to combine deep learning and genomic sequencing data. We tested the platform on publicly available sequencing data from the gut microbiome of cancer patients. We showed that our platform is capable of classifying patients with higher accuracy than other methods, with some caveats. Overall, we believe genomic research is the next frontline for deep learning as there are exciting avenues waiting to be explored. We think that our platform, presented here, could serve as the basis for such future research.}, }
@article {pmid33606256, year = {2021}, author = {Amir, A}, title = {Microbiome Analysis Using 16S Amplicon Sequencing: From Samples to ASVs.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2243}, number = {}, pages = {123-141}, pmid = {33606256}, issn = {1940-6029}, abstract = {In this chapter, we will present an outline of a typical experimental and bioinformatic workflow for identification of bacterial amplicon sequence variants (ASVs) present in a set of samples. This chapter is written from a bioinformatic point of view; therefore, the specific experimental protocols are not detailed, but rather the impact of various experimental decisions on the downstream analysis is described. Emphasis is made on the transition from reads to ASVs, describing the Deblur algorithm.}, }
@article {pmid33606255, year = {2021}, author = {Joseph, TA and Pe'er, I}, title = {An Introduction to Whole-Metagenome Shotgun Sequencing Studies.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2243}, number = {}, pages = {107-122}, pmid = {33606255}, issn = {1940-6029}, abstract = {Microbial communities are found across diverse environments, including within and across the human body. As many microbes are unculturable in the lab, much of what is known about a microbiome-a collection of bacteria, fungi, archaea, and viruses inhabiting an environment--is from the sequencing of DNA from within the constituent community. Here, we provide an introduction to whole-metagenome shotgun sequencing studies, a ubiquitous approach for characterizing microbial communities, by reviewing three major research areas in metagenomics: assembly, community profiling, and functional profiling. Though not exhaustive, these areas encompass a large component of the metagenomics literature. We discuss each area in depth, the challenges posed by whole-metagenome shotgun sequencing, and approaches fundamental to the solutions of each. We conclude by discussing promising areas for future research. Though our emphasis is on the human microbiome, the methods discussed are broadly applicable across study systems.}, }
@article {pmid33606040, year = {2021}, author = {Goossens, E and Boonyarittichaikij, R and Dekeukeleire, D and Van Praet, S and Bonte, D and Verheyen, K and Lens, L and Martel, A and Verbrugghe, E}, title = {Exploring the faecal microbiome of the Eurasian nuthatch (Sitta europaea).}, journal = {Archives of microbiology}, volume = {}, number = {}, pages = {}, pmid = {33606040}, issn = {1432-072X}, support = {12E6616N//Fonds Wetenschappelijk Onderzoek/ ; 1507119N//Fonds Wetenschappelijk Onderzoek/ ; 12W8919N//Fonds Wetenschappelijk Onderzoek/ ; }, abstract = {Gastrointestinal microbiota fulfill pivotal roles in providing a host with nutrition and protection from pathogenic microorganisms. Up to date, most microbiota research has focused on humans and other mammals, whereas birds and especially wild birds lag behind. Within the field of the avian gut microbiome, research is heavily biased towards poultry. In this study, we analyzed the gut microbiome of the Eurasian nuthatch (Sitta europaea), using faecal samples of eight nestlings originating from three nuthatch nests in the south of Ghent (Belgium), using Illumina sequencing of the 16S rRNA gene. Relative frequency analysis showed a dominance of Firmicutes and Actinobacteria and to a lesser extent Proteobacteria. Bacteroidetes and other phyla were relatively rare. At higher taxonomic levels, a high degree of inter-individual variation in terms of overall microbiota community structure as well as dominance of certain bacteria was observed, but with a higher similarity for the nestlings sharing the same nest. When comparing the nuthatch faecal microbiome to that of great tit nestlings that were sampled during the same breeding season and in the same forest fragment, differences in the microbial community structure were observed, revealing distinct dissimilarities in the relative abundancy of taxa between the two bird species. This study is the first report on the nuthatch microbiome and serves as a reference study for nuthatch bacterial diversity and can be used for targeted screening of the composition and general functions of the avian gut microbiome.}, }
@article {pmid33605849, year = {2021}, author = {de Waal, GM and de Villiers, WJ and Pretorius, E}, title = {The link between bacterial inflammagens, leaky gut syndrome and colorectal cancer.}, journal = {Current medicinal chemistry}, volume = {}, number = {}, pages = {}, doi = {10.2174/0929867328666210219142737}, pmid = {33605849}, issn = {1875-533X}, abstract = {There is a causal relationship between cancer (including colorectal cancer), chronic systemic inflammation and persistent infections, and the presence of dysregulated circulating inflammatory markers. It is known that aberrant clot formation and coagulopathies occur in systemic inflammation. In colorectal cancer, there is close link between gut dysbiosis and an inflammatory profile. In this review we present evidence of the connection between gut dysbiosis, the entry of bacteria into the internal environment and the presence of their highly potent inflammagenic molecules, such as lipopolysaccharide and lipoteichoic acid, in circulation. These bacterial components may act as one of the main drivers of the inflammatory process (including hypercoagulation) in colorectal cancer. We review literature that points to the role of these bacterial inflammagens and how they contribute to colorectal carcinogenesis. Insight into the factors that promote carcinogenesis is crucial to effectively prevent and screen for colorectal cancer. Early diagnosis of an activated coagulation system and the detection of bacterial components in circulation and also in the tumour microenvironment, could therefore be important, and may also, together with modulation of the gut microbiota, serve as potential therapeutic targets.}, }
@article {pmid33605840, year = {2021}, author = {Porto, BN and Moraes, TJ}, title = {The triad: respiratory microbiome - virus - immune response in the pathophysiology of pulmonary viral infections.}, journal = {Expert review of respiratory medicine}, volume = {}, number = {}, pages = {}, doi = {10.1080/17476348.2021.1893168}, pmid = {33605840}, issn = {1747-6356}, abstract = {INTRODUCTION: The longstanding dogma that the healthy lung is sterile has been refuted by recent advances in culture-independent analyses of airway samples. The respiratory microbiome comprises all airway and lung tissue-associated microbes. These micro-organisms occur throughout the upper and lower respiratory tracts, with different populations and distinct burdens at specific sites and can be classified as pathogenic or commensals.<br><br>AREAS COVERED: The majority of studies investigating the respiratory microbiome has focused on bacteria; however, emerging evidence has revealed the composition of the lung virome, the global viral communities present in the lung tissue. In this review, we searched Pubmed and used keywords such as airway microbiome. We restricted outputs to English language and did not limit by any dates. We summarize the up-to-date knowledge on how the microbiome interacts with the host immune system and influences the pathogenesis of pulmonary viral infections.<br><br>EXPERT OPINION: The relationship between colonizing microbes and the host is complex and various factors need to be considered in order to appreciate its pathophysiological consequences. Understanding these intricate mechanisms of interaction among the respiratory microbiome, viruses and the immune response may lead to the development of better therapies to treat or prevent respiratory viral infections.}, }
@article {pmid33605632, year = {2021}, author = {Pulik, L and Grabowska, N and Olbrys, M and Gorecka, K and Legosz, P}, title = {Letter to the Editor: Disruption of the Gut Microbiome Increases the Risk of Periprosthetic Joint Infection in Mice.}, journal = {Clinical orthopaedics and related research}, volume = {}, number = {}, pages = {}, doi = {10.1097/CORR.0000000000001680}, pmid = {33605632}, issn = {1528-1132}, }
@article {pmid33604753, year = {2021}, author = {Shen, Z and Gu, X and Cao, H and Mao, W and Yang, L and He, M and Zhang, R and Zhou, Y and Liu, K and Wang, L and Liu, L and Yu, J and Yin, L}, title = {Characterization of microbiota in acute leukemia patients following successful remission induction chemotherapy without antimicrobial prophylaxis.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {33604753}, issn = {1618-1905}, support = {81360089//National Natural Science Foundation of China/ ; 2015FB072//Scientific and Technological Commission of Yunnan Province/ ; 2017FE468 (-204)//Scientific and Technological Commission of Yunnan Province/ ; 2018FE001 (-113)//Scientific and Technological Commission of Yunnan Province/ ; 202001AY070001-070//Science and Technology Program of Department of Science and Technology of Yunnan Province/ ; }, abstract = {PURPOSE: In the present study, we characterized the microbiomes of acute leukemia (AL) patients who achieved complete remission following remission induction chemotherapy (RIC) as outpatients, but who did not receive antimicrobials to treat or prevent febrile neutropenia.<br><br>METHODS: Saliva and stool samples from 9 patients with acute myeloid leukemia, 11 patients with acute lymphoblastic leukemia, and 5 healthy controls were subjected to 16S ribosomal RNA sequencing at baseline and at 3 months following RIC. Only patients who achieved remission at 3 months post-treatment were included. We excluded anyone who used antimicrobials within 2 months of enrollment or at any time during the study period.<br><br>RESULTS: At baseline, the relative abundances of species of Prevotella maculosa (P=0.001), Megasphaera micronuciformis (P=0.014), Roseburia inulinivorans (P=0.021), and Bacteroides uniformis (P=0.004) in saliva and Prevotella copri (P=0.002) in the stools of controls were significantly higher than in AL patients. Following RIC, the relative abundances of Eubacterium sp. oral clone DO008 (P=0.012), Leptotrichia sp. oral clone IK040 (P=0.002), Oribacterium sp. oral taxon 108 (P=0.029), Megasphaera micronuciformis (P=0.016), TM7 phylum sp. oral clone DR034 (P<0.001), Roseburia inulinivorans (P=0.034), Actinomyces odontolyticus (P=0.014), Leptotrichia buccalis (P=0.005), and Prevotella melaninogenica (P=0.046) in saliva and Lactobacillus fermentum (P=0.046), Coprococcus catus (P=0.050), butyrate-producing bacterium SS3/4 (P=0.013), and Bacteroides coprocola (P=0.027) in the stools of AL patients were significantly greater than in controls.<br><br>CONCLUSION: Following RIC, several taxa are changed in stool and salvia samples of AL patients. Our results warrant future large-scale multicenter studies to examine whether the microbiota might have an effect on clinical outcomes of AL patients.}, }
@article {pmid33604488, year = {2021}, author = {Møller, G and Lind, MV and Hauptmann, AL and Senftleber, N and Hansen, CB and Hansen, T and Jørgensen, ME and Lauritzen, L}, title = {The role of a traditional and western diet on glucose homeostasis in Greenlandic Inuit carriers and non-carriers of type 2 diabetes variant in the TBC1D4 gene: A protocol for a randomized clinical trial.}, journal = {Contemporary clinical trials communications}, volume = {21}, number = {}, pages = {100734}, doi = {10.1016/j.conctc.2021.100734}, pmid = {33604488}, issn = {2451-8654}, abstract = {Introduction: The lifestyle of Inuit in Greenland and worldwide is undergoing a transition from a fisher-hunter to a westernized society and meanwhile the prevalence of type-2 diabetes (T2D) has increased dramatically. Studies have shown that a common nonsense p.Arg684Ter variant in TBC1D4, which is frequent in Greenland, confers genetic susceptibility towards high risk of T2D. The aim of the study is to investigate whether a traditional marine diet, with high fat and low carbohydrate, will improve glycemic control in Greenland Inuit compared to a western diet. Moreover, we want to examine if the response is more pronounced in carriers of the p.Arg684Ter variant.<br><br>Materials and methods: We will conduct a randomized, clinical cross-over trial with two dietary intervention periods of four weeks duration. The diet intervention comprise provision of >20E% and instruction for the remaining part of the diet. We expect to include 30 homozygous carriers and 30 homozygous non-carriers of the p.Arg684Ter variant, aged 18-80 years, across three Greenlandic towns. The primary outcome is plasma (p)-glucose 2 h post an oral glucose tolerance test and we aim to have 80% power, at α = 0.05, to detect a difference of 1.1 mmol/L. We will also include supporting measures of glucose homeostasis, assess other markers of the metabolic syndrome and perform metabolome and microbiome profiling. The statistical analysis will be performed as complete case analyses using linear mixed models.<br><br>Ethics and dissemination: The study received approval by the Ethics Committee of Greenland (KVUG 2018-26) and will be disseminated via international peer-reviewed journal articles and conferences.<br><br>Trial registration number: Clinicaltrials.gov identifier no. NCT04011904.}, }
@article {pmid33604351, year = {2020}, author = {Dawczynski, C}, title = {A Study Protocol for a Parallel-Designed Trial Evaluating the Impact of Plant-Based Diets in Comparison to Animal-Based Diets on Health Status and Prevention of Non-communicable Diseases-The Nutritional Evaluation (NuEva) Study.}, journal = {Frontiers in nutrition}, volume = {7}, number = {}, pages = {608854}, doi = {10.3389/fnut.2020.608854}, pmid = {33604351}, issn = {2296-861X}, abstract = {Background and Aims: Currently, there is a continuing upward trend for plant-based lifestyles in Germany and Europe. The implementation of vegetarian and vegan lifestyles is characterized by omitting defined food groups such as fish, meat, sausage (vegetarians), or dairy products and honey (vegans). This carries the risk of an undersupply of valuable nutrients. The NuEva study is designed to examine this hypothesis and to evaluate the impact of plant-based diets on health status and disease risk. Methods: The NuEva study is a parallel-designed trial with at least 55 participants for each diet (vegetarian, vegan, flexitarian [rare meat/sausage consumption, once or twice per week]), and participants who consume a traditional Western diet as the control group. In the screening period critical nutrients are identified for the studied diets by analysis of a broad spectrum of nutrients in the human samples (fatty acids, vitamins, minerals, trace elements, nutrient metabolites). Results: Based on the data from the screening period, defined menu plans, ensuring an adequate nutrient intake in accordance with the nutritional guidelines are prepared for each group. The plans are adapted and personalized to individual energy requirements based on the basal metabolic rate and physical activity level. The compliance with the NuEva concept and their impact on nutrient status and cardiovascular risk factors are validated during the intervention period of the NuEva study over 1 year. To investigate the impact of the studied diets on the microbiome, feces samples are collected at the beginning and after the 12 months intervention period (follow up: 12 months). Conclusion: The NuEva study is designed to investigate the impact of common diets on health and disease status, with focus on prevention of cardiovascular diseases. In addition, the effectiveness of the prepared nutritional coaching strategy, ensuring optimal nutrient intake in accordance with the guidelines, is validated during the intervention period of the NuEva study. Clinical Trial Registration: Registered under ClinicalTrials.gov Identifier no. NCT03582020.}, }
@article {pmid33604346, year = {2021}, author = {Chioma, OS and Hesse, LE and Chapman, A and Drake, WP}, title = {Role of the Microbiome in Interstitial Lung Diseases.}, journal = {Frontiers in medicine}, volume = {8}, number = {}, pages = {595522}, doi = {10.3389/fmed.2021.595522}, pmid = {33604346}, issn = {2296-858X}, abstract = {There are trillions of microorganisms in the human body, consisting of bacteria, viruses, fungi, and archaea; these collectively make up the microbiome. Recent studies suggest that the microbiome may serve as a biomarker for disease, a therapeutic target, or provide an explanation for pathophysiology in lung diseases. Studies describing the impact of the microorganisms found in the respiratory tract on lung health have been published and are discussed here in the context of interstitial lung diseases. Additionally, epidemiological and experimental evidence highlights the importance of cross-talk between the gut microbiota and the lungs, called the gut-lung axis. The gut-lung axis postulates that alterations in gut microbial communities may have a profound effect on lung disease. Dysbiosis in the microbial community of the gut is linked with changes in immune responses, homeostasis in the airways, and inflammatory conditions in the gastrointestinal tract itself. In this review, we summarize studies describing the role of the microbiome in interstitial lung disease and discuss the implications of these findings on the diagnosis and treatment of these diseases. This paper describes the impact of the microbial communities on the pathogenesis of lung diseases by assessing recent original research and identifying remaining gaps in knowledge.}, }
@article {pmid33604195, year = {2021}, author = {Li, J and Luo, W and Zhu, Y and Dai, Q and Liu, G and Zheng, C and Zhou, L and Li, S and Chen, Z and Wang, J and Feng, D and Yang, K and Yang, Z and Zhu, L}, title = {Social behavior of musk deer during the mating season potentially influences the diversity of their gut microbiome.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e10860}, doi = {10.7717/peerj.10860}, pmid = {33604195}, issn = {2167-8359}, abstract = {An increasing body of research has revealed that social behavior shapes the animal gut microbiome community and leads to the similarity among the same social group. However, some additional factors (e.g., diet and habitat within each social group) may also contribute to this similarity within the social group and dissimilarity between social groups. Here, we investigated the potential correlation between social behavior and the gut microbiome community in 179 musk deer from four breeding regions in the Maerkang Captive Center, Sichuan. The dominant gut microbiome phyla in the musk deer in this study were Firmicutes, Bacteroidetes, and Proteobacteria. We found significant effects on the alpha and beta diversity of the gut microbiome due to the breeding regions. The similarity within breeding regions was higher than that between the breeding regions. Due to their solitary lifestyle, captive musk deer are raised in single cages with no direct social contact most of the time. Deer in all of the breeding regions have the same diet and similar living conditions. However, during each mating season from November to January, in each region, one adult male and about six adult females will be put together into a large cage. Social behavior happens during cohabitation, including mating behavior, grooming within the same sex or between different sexes, and other social contact. Therefore, we speculated that high similarity within the breeding region might be associated with the social behavior during the mating season. This was a simple and straightforward example of the relationship between animal social behavior and the gut microbiome.}, }
@article {pmid33604194, year = {2021}, author = {Steenwerth, KL and Morelan, I and Stahel, R and Figueroa-Balderas, R and Cantu, D and Lee, J and Runnebaum, RC and Poret-Peterson, AT}, title = {Fungal and bacterial communities of 'Pinot noir' must: effects of vintage, growing region, climate, and basic must chemistry.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e10836}, doi = {10.7717/peerj.10836}, pmid = {33604194}, issn = {2167-8359}, abstract = {Background: The geographic and temporal distributions of bacterial and fungal populations are poorly understood within the same wine grape cultivar. In this work, we describe the microbial composition from 'Pinot noir' must with respect to vintage, growing region, climate, and must chemistry across the states of California and Oregon, USA.<br><br>Materials and Methods: We sampled 'Pinot noir' clone 667 clusters from 15 vineyards existing in a latitudinal gradient spanning nearly 1,200 km in California and Oregon for two vintages (2016 and 2017). Regions included five American Viticultural Areas (AVA). In order from southern California to Oregon, these AVAs were Santa Barbara, Monterey, Sonoma, Mendocino, and Willamette Valley. Uninoculated grape musts were subjected to 16S rRNA gene and ITS-1 amplicon sequencing to assess composition of microbial communities. We also measured grape maturity metrics. Finally, to describe regions by precipitation and growing degree days, we queried the Parameter-elevation Regressions on Independent Slopes Model (PRISM) spatial climate dataset.<br><br>Results: Most of the dominant bacterial taxa in must samples were in the family Enterobacteriaceae, notably the lactic acid bacteria or the acetic acid bacteria groups, but some, like the betaproteobacterial genus Massilia, belonged to groups not commonly found in grape musts. Fungal communities were dominated by Hanseniaspora uvarum (Saccharomycetaceae). We detected relationships between covariates (e.g., vintage, precipitation during the growing season, pH, titratable acidity, and total soluble solids) and bacterial genera Gluconobacter and Tatumella in the family Enterobacteraceae, Sphingomonas (Sphingomonodaceae), Lactobacillus (Lactobacillaceae), and Massilia (Oxalobacteraceae), as well as fungal genera in Hanseniaspora, Kazachstania, Lachancea, Torulaspora in the family Saccharomycetaceae, as well as Alternaria (Pleosporaceae), Erysiphe (Erysiphaceae), and Udeniomyces (Cystofilobasidiaceae). Fungal community distances were significantly correlated with geographic distances, but this was not observed for bacterial communities. Climate varied across regions and vintages, with growing season precipitation ranging from 11 mm to 285 mm and growing degree days ranging from 1,245 to 1,846.<br><br>Discussion: We determined that (1) bacterial beta diversity is structured by growing season precipitation, (2) fungal beta diversity reflects growing season precipitation and growing degree days, and (3) microbial differential abundances of specific genera vary with vintage, growing season precipitation, and fruit maturity metrics. Further, the correlation between fungal community dissimilarities and geographic distance suggests dispersal limitation and the vineyard as a source for abundant fungal taxa. Contrasting this observation, the lack of correlation between bacterial community dissimilarity and geographic distance suggests that environmental filtering is shaping these communities.}, }
@article {pmid33604172, year = {2021}, author = {Thome, PE and Rivera-Ortega, J and Rodríguez-Villalobos, JC and Cerqueda-García, D and Guzmán-Urieta, EO and García-Maldonado, JQ and Carabantes, N and Jordán-Dahlgren, E}, title = {Local dynamics of a white syndrome outbreak and changes in the microbial community associated with colonies of the scleractinian brain coral Pseudodiploria strigosa.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e10695}, doi = {10.7717/peerj.10695}, pmid = {33604172}, issn = {2167-8359}, abstract = {Reef corals in the Mexican Reef System have been severely affected by the emergence of a white syndrome that resembles both White Plague II and SCTLD descriptions. Meandroid scleractinian coral species are among the most severely affected. To gain insight into this affliction we conducted a broad study in the brain coral Pseudodiploria strigosa at a rear reef site in the NE Mexican Caribbean. We describe macro and microscopical signals of the disease, characterize the outbreak dynamics, the tissue histopathology, explore immunological responses in the individuals, and compare microbial assemblages associated with the surface mucus layer of healthy and unhealthy colonies. At the study site, the white syndrome outbreak on P. strigosa showed a high incidence rate in summer-fall and a low one in winter, as well as low survival expectation of diseased colonies at the end of the study. After 306 days of observation, out of 96 tracked colonies, eight remained apparently healthy and seven were diseased. No effective resistance to colony disease progression was observed once white syndrome signs developed. Tissue loss rate during the study varied among colonies (mean = 10.8 cm2, s.d. = 7.8 cm2) suggesting a complex relation between causal agents and colony resistance. The deterioration of tissues was evidenced from the basal to the surface body wall of polyps (up to 66% hypertrophy and liquefactive necrosis in unhealthy colonies), implying that microscopic alterations begin before macroscopic signals develop, suggesting this may be a systemic disease. We measured high levels of phenoloxidase (two orders of magnitude higher PO activity than P. strigosa affected by BBD) and antibacterial activity without significant reduction in unhealthy samples from the mucus layer, indicative of an enhanced immunological response. Results showed that opportunistic bacteria dominated damaged colonies, where six genera of the Bacteroidia class were found with significant changes in unhealthy colonies after DeSeq2 analysis. Nevertheless, histological observations did not support infection of the tissues. The opportunistic overload seems to be contained within the mucus layer but may be associated with the mortality of tissues in a yet unclear way. Future research should focus on experimental infections, the tracking of natural infections, and the immunocompetence of corals in the face of environmental pressures due to local, regional, and global impacts. If environmental deterioration is the primary cause of the continuing emergence and re-emergence of lethal coral diseases, as has been proposed by many authors, the only true option to effectively help preserve the coral reef biodiversity and services, is to restore the environmental quality of reef waters at the local scale and reduce greenhouse gases at the global scale.}, }
@article {pmid33604161, year = {2021}, author = {Abdelrahman, SM and Patin, NV and Hanora, A and Aboseidah, A and Desoky, S and Desoky, SG and Stewart, FJ and Lopanik, NB}, title = {The natural product biosynthetic potential of Red Sea nudibranch microbiomes.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e10525}, doi = {10.7717/peerj.10525}, pmid = {33604161}, issn = {2167-8359}, abstract = {Background: Antibiotic resistance is a growing problem that can be ameliorated by the discovery of novel drug candidates. Bacterial associates are often the source of pharmaceutically active natural products isolated from marine invertebrates, and thus, important targets for drug discovery. While the microbiomes of many marine organisms have been extensively studied, microbial communities from chemically-rich nudibranchs, marine invertebrates that often possess chemical defences, are relatively unknown.<br><br>Methods: We applied both culture-dependent and independent approaches to better understand the biochemical potential of microbial communities associated with nudibranchs. Gram-positive microorganisms isolated from nudibranchs collected in the Red Sea were screened for antibacterial and antitumor activity. To assess their biochemical potential, the isolates were screened for the presence of natural product biosynthetic gene clusters, including polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) genes, using PCR. The microbiomes of the nudibranchs were investigated by high-throughput sequencing of 16S rRNA amplicons.<br><br>Results: In screens against five model microorganisms, 51% of extracts displayed antimicrobial activity against more than one organism, and 19% exhibited antitumor activity against Ehrlich's ascites carcinoma. Sixty-four percent of isolates contained PKS and NRPS genes, suggesting their genomes contain gene clusters for natural product biosynthesis. Thirty-five percent were positive for more than one class of biosynthetic gene. These strains were identified as belonging to the Firmicutes and Actinobacteria phyla via 16S rRNA gene sequencing. In addition, 16S rRNA community amplicon sequencing revealed all bacterial isolates were present in the uncultured host-associated microbiome, although they were a very small percentage of the total community. Taken together, these results indicate that bacteria associated with marine nudibranchs are potentially a rich source of bioactive compounds and natural product biosynthetic genes.}, }
@article {pmid33603805, year = {2020}, author = {Brandão, P and Gonçalves-Henriques, M}, title = {The Impact of Female Genital Microbiota on Fertility and Assisted Reproductive Treatments.}, journal = {Journal of family &amp; reproductive health}, volume = {14}, number = {3}, pages = {131-149}, doi = {10.18502/jfrh.v14i3.4666}, pmid = {33603805}, issn = {1735-8949}, abstract = {Objective: To review publish data about human microbiome. It is known to modulate many body functions. In the field of Reproductive Medicine, the main question is in what extent may female genital tract microbiome influence fertility, both by spontaneous conception or after Assisted Reproductive Treatments (ART). The aim of this work is to review publish data about this matter. Materials and methods: This is a systematic review on the effect of the microbiota of the female genital tract on human fertility and on the outcomes of ART. Results: Fourteen articles were retrieved, concerning female lower genital tract and endometrium microbiota, including 5 case-controls studies about its impact on fertility, 8 cohort studies regarding ART outcomes and 1 mixed study. The main variables considered were richness and diversity of species, Lactobacillus dominance and the role of other bacteria. Results and conclusions of the various studies were quite diverse and incoherent. Despite the inconsistency of the studies, it seems that vaginal, cervical and endometrial microbiome may eventually play a role. Whether high richness and diversity of species, low amounts of Lactobacillus spp. or the presence of other bacteria, such as Gardnerella spp., may adversely affect reproductive outcomes is not clear. Conclusion: The influence of female genital microbiota on the ability to conceive is still unclear, due to the paucity and inconsistency of published data.}, }
@article {pmid33603766, year = {2021}, author = {Fresno, DH and Munné-Bosch, S}, title = {Differential Tissue-Specific Jasmonic Acid, Salicylic Acid, and Abscisic Acid Dynamics in Sweet Cherry Development and Their Implications in Fruit-Microbe Interactions.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {640601}, doi = {10.3389/fpls.2021.640601}, pmid = {33603766}, issn = {1664-462X}, abstract = {Sweet cherry is an important non-climacteric fruit with a high commercial interest, but exploitation of sweet cherry trees (Prunus avium L.) in orchards is usually subject to important economic losses due to fruit decay by pathogenic fungi and other microorganisms. Sweet cherries development and ripening are characterized by profound physiological changes in the fruit, among which the phytohormone abscisic acid (ABA) plays a pivotal role. In addition, sweet cherries are usually affected by fruit decay pathogens, and the role of other stress-related hormones such as jasmonic acid (JA) and salicylic acid (SA) may also be of paramount importance, not only from a developmental point of view, but also from a fruit-microbe interaction perspective. Here, a tissue-specific hormone quantification by LC-MS/MS, including the contents of JA, SA, and ABA, in the fruit exocarp and mesocarp of sweet cherries during fruit development from trees growing in a commercial orchard was carried out. Additionally, this study was complemented with the characterization of the culturable epiphytic and endophytic microbial communities of sweet cherries at various stages of fruit development and during cracking lesion formation. Our results revealed a completely differential behavior of phytohormones between both tissues (the exocarp and mesocarp), with a more dynamic exocarp in front of a more stable mesocarp, and with marked variations during fruit development. Microbial epiphytic community was mainly composed by yeasts, although rot-causing fungi like Alternaria spp. were always also present throughout fruit development. Endophytic colonization was poor, but it increased throughout fruit development. Furthermore, when the exocarp was naturally disrupted in sweet cherries suffering from cracking, the colonization by Alternaria spp. markedly increased. Altogether, results suggest that the fruit exocarp and mesocarp are very dynamic tissues in which endogenous phytohormones not only modulate fruit development and ripening but also fruit-microbe interactions.}, }
@article {pmid33603734, year = {2020}, author = {Liu, W and Wang, Y and Luo, J and Liu, M and Luo, Z}, title = {Pleiotropic Effects of Metformin on the Antitumor Efficiency of Immune Checkpoint Inhibitors.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {586760}, doi = {10.3389/fimmu.2020.586760}, pmid = {33603734}, issn = {1664-3224}, abstract = {Cancer is an important threat to public health because of its high morbidity and mortality. In recent decades, immune checkpoint inhibitors (ICIs) have ushered a new therapeutic era in clinical oncology. The rapid development of immune checkpoint therapy is due to its inspiring clinical efficacy in a group of cancer types. Metformin, an effective agent for the management of type 2 diabetes mellitus (T2DM), has shown beneficial effects on cancer prevention and cancer treatment. Emerging studies have suggested that metformin in combination with ICI treatment could improve the anticancer effects of ICIs. Hence, we conducted a review to summarize the effects of metformin on ICI therapy. We also review the pleiotropic mechanisms of metformin combined with ICIs in cancer therapy, including its direct and indirect effects on the host immune system.}, }
@article {pmid33603718, year = {2020}, author = {Zhao, Y and Zeng, Y and Zeng, D and Wang, H and Zhou, M and Sun, N and Xin, J and Khalique, A and Rajput, DS and Pan, K and Shu, G and Jing, B and Ni, X}, title = {Probiotics and MicroRNA: Their Roles in the Host-Microbe Interactions.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {604462}, doi = {10.3389/fmicb.2020.604462}, pmid = {33603718}, issn = {1664-302X}, abstract = {Probiotics are widely accepted to be beneficial for the maintenance of the gut homeostasis - the dynamic and healthy interactions between host and gut microorganisms. In addition, emerging as a key molecule of inter-domain communication, microRNAs (miRNAs) can also mediate the host-microbe interactions. However, a comprehensive description and summary of the association between miRNAs and probiotics have not been reported yet. In this review, we have discussed the roles of probiotics and miRNAs in host-microbe interactions and proposed the association of probiotics with altered miRNAs in various intestinal diseases and potential molecular mechanisms underlying the action of probiotics. Furthermore, we provided a perspective of probiotics-miRNA-host/gut microbiota axis applied in search of disease management highly associated with the gut microbiome, which will potentially prove to be beneficial for future studies.}, }
@article {pmid33603667, year = {2020}, author = {Wen, X and Lou, Y and Song, S and He, Z and Chen, J and Xie, Z and Shi, X and Wen, C and Shao, T}, title = {Qu-Zhuo-Tong-Bi Decoction Alleviates Gouty Arthritis by Regulating Butyrate-Producing Bacteria in Mice.}, journal = {Frontiers in pharmacology}, volume = {11}, number = {}, pages = {610556}, doi = {10.3389/fphar.2020.610556}, pmid = {33603667}, issn = {1663-9812}, abstract = {Qu-zhuo-tong-bi decoction (QZTBD) is a traditional Chinese medicine prescription used to treat hyperuricemia and gout with no obvious adverse effects. However, the mechanism by which QZTBD treats gout has not been fully explored. Here, we investigated the effects of QZTBD on gouty arthritis and its therapeutic mechanism from the perspective of the gut microbiome. Our results demonstrated that QZTBD was effective for reducing serum uric acid level and attenuating paw edema and mechanical allodynia. QZTBD promoted the abundance of butyrate-producing bacteria and the production of SCFAs. Further study revealed that QZTBD restored the intestinal barrier function, modulated the expression of GPR43 and ABCG2, suppressed the activity of key glycolysis-related enzymes, and inhibited the generation of intestinal inflammatory factors. These findings suggested that QZTBD is an effective therapeutic drug for gouty arthritis. Butyrate-producing bacteria and its metabolites SCFAs might act as a potential target of QZTBD.}, }
@article {pmid33603502, year = {2021}, author = {Bozca, BC and Alpsoy, E}, title = {Experimental Therapeutic Solutions for Behcet's Disease.}, journal = {Journal of experimental pharmacology}, volume = {13}, number = {}, pages = {127-145}, doi = {10.2147/JEP.S265645}, pmid = {33603502}, issn = {1179-1454}, abstract = {Behcet's disease (BD) is a chronic systemic vasculitis with inflammation attacks that involve multiple organs. In addition to numerous mucocutaneous symptoms, notably recurrent oral and genital ulcers, ocular, articular, vascular, gastrointestinal, cardiac, and neurological system involvement can be observed. Mucocutaneous lesions are the primary symptom of the disease in most patients, and they usually occur before major organ involvement and other symptoms of the disease. Recognizing the disease's mucocutaneous lesions is very important to diagnose at an early stage, control with appropriate treatment and close follow-up, and prevent major organ involvement. Genome-wide association studies (GWAS) in recent years have confirmed that HLA-B*51 is the most significant genetic predisposing factor. The majority of gene polymorphisms have been detected in molecules that respond to microorganisms and genes encoding cytokines and adhesion molecules. The infectious agent S. sanguinis -commonly found in the oral mucosa of patients with BD- or the differences in the salivary or intestinal microbiome composition can trigger innate immune-mediated inflammation sustained by acquired or adaptive immune responses. In antigen-presenting cells (APCs), epistatic interactions between HLA-B*51 and endoplasmic reticulum aminopeptidase 1 (ERAP1) variants lead to the disruption of T-cell homeostasis, especially the activation of Type1 T-helper and Th17 pathway and suppression of regulatory T-cells. Recent developments to clarify the disease's etiopathogenesis provided us with a better understanding of the mechanism of action of the relatively old drugs while opening a way for many new treatment methods. Apremilast has become an important option in the treatment of mucocutaneous symptoms with its high efficacy and safety. The disease increases the mortality rate, especially in young male patients. New treatments, especially anti-TNF-α agents, have provided significant progress and decreased the mortality rates with their rapid effect and high efficacy in patients with severe organ involvement and resistance to traditional immunosuppressive and immunomodulatory therapies. The use of IL-1, IL-6, IL-17, IL-12/IL-23 antagonists in different organ involvement has gradually increased, and the quality of life has significantly improved in many patients.}, }
@article {pmid33603248, year = {2015}, author = {Homburger, SA and Drits-Esser, D and Malone, M and Stark, LA}, title = {Microbes As Friends, Not Foes: Shifting the Focus from Pathogenesis to Symbiosis.}, journal = {The American biology teacher}, volume = {77}, number = {9}, pages = {659-668}, doi = {10.1525/abt.2015.77.9.3}, pmid = {33603248}, issn = {0002-7685}, abstract = {Until about two decades ago, the standard method of studying a microbe was to isolate it, grow it in culture, stain it, and examine it under a microscope. Today, new genomic tools are helping expand our view of the microbial world. Instead of viewing them as &quot;germs&quot; to be eliminated, we are beginning to perceive our microbes as an extension of ourselves - an important organ with unique functions essential to our well-being. Scientists even came up with a new term, &quot;microbiome,&quot; to define our microbes' genes as an important counterpart to our human genome. With new information about the human microbiome comes the challenge of shifting biology students' focus from casting microbes as pathogens toward appreciating microbes as symbionts. &quot;The Human Microbiome,&quot; a curriculum supplement produced by the Genetic Science Learning Center, emphasizes that microbes living in and on our bodies perform neutral and beneficial functions, that human microbiota form thriving ecosystems, and that disruptions to our microbial ecosystems may have consequences. In this article, we describe the curriculum materials, provide strategies for incorporating this cutting-edge topic into biology classrooms, list connections to the Next Generation Science Standards, and report on recent research testing the curriculum supplement's effectiveness for student learning.}, }
@article {pmid33603147, year = {2021}, author = {Jahn, MT and Lachnit, T and Markert, SM and Stigloher, C and Pita, L and Ribes, M and Dutilh, BE and Hentschel, U}, title = {Lifestyle of sponge symbiont phages by host prediction and correlative microscopy.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {33603147}, issn = {1751-7370}, abstract = {Bacteriophages (phages) are ubiquitous elements in nature, but their ecology and role in animals remains little understood. Sponges represent the oldest known extant animal-microbe symbiosis and are associated with dense and diverse microbial consortia. Here we investigate the tripartite interaction between phages, bacterial symbionts, and the sponge host. We combined imaging and bioinformatics to tackle important questions on who the phage hosts are and what the replication mode and spatial distribution within the animal is. This approach led to the discovery of distinct phage-microbe infection networks in sponge versus seawater microbiomes. A new correlative in situ imaging approach ('PhageFISH-CLEM') localised phages within bacterial symbiont cells, but also within phagocytotically active sponge cells. We postulate that the phagocytosis of free virions by sponge cells modulates phage-bacteria ratios and ultimately controls infection dynamics. Prediction of phage replication strategies indicated a distinct pattern, where lysogeny dominates the sponge microbiome, likely fostered by sponge host-mediated virion clearance, while lysis dominates in seawater. Collectively, this work provides new insights into phage ecology within sponges, highlighting the importance of tripartite animal-phage-bacterium interplay in holobiont functioning. We anticipate that our imaging approach will be instrumental to further understanding of viral distribution and cellular association in animal hosts.}, }
@article {pmid33603089, year = {2021}, author = {Yu, L and Wang, L and Wu, X and Yi, H}, title = {RSPO4-CRISPR alleviates liver injury and restores gut microbiota in a rat model of liver fibrosis.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {230}, pmid = {33603089}, issn = {2399-3642}, support = {LY16H030016, LY17H030012//Natural Science Foundation of Zhejiang Province (Zhejiang Provincial Natural Science Foundation)/ ; }, abstract = {Wnt signaling dysfunction and gut dysbiosis may lead to liver fibrosis, yet the underlying mechanisms are not well elucidated. This study demonstrated the role of RSPO4, a Wnt signaling agonist, in liver fibrogenesis and its impact on the gut microbiome. RSPO4 gene in CCl4-induced fibrotic-liver rats was knockout by Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) system, with healthy rats served as the control. Tissue samples and hepatic stellate cells (HSCs) isolated from rats were examined for curative effect of RSPO4-CRISPR treatment. Fecal sample were collected and analyzed with 16 S rRNA sequencing. We found RSPO4-CRISPR relieved liver fibrosis in rats and reversed HSC activation. Further, results showed RSPO4-CRISPR tended to restore the microflora composition. Significance species between groups were identified. Bacteroides and Escherichia-Shigella were the key microbes in the model and negative group, whereas Lactobacillus, Romboutsia, and Lachnospiraceae NK4A136 group were abundant in the control. Notably, Bacteroidales S24-7 group and Ruminococcaceae UCG-005 were the significantly enriched in CRISPR group. We show that the microbiome of rats treated with RSPO4-CRISPR presents a trend towards the restoration of the original condition. Our findings pave a new way to evaluate the curative effect of liver fibrosis treatment.}, }
@article {pmid33603076, year = {2021}, author = {Xu, R and Lu, R and Zhang, T and Wu, Q and Cai, W and Han, X and Wan, Z and Jin, X and Zhang, Z and Zhang, C}, title = {Temporal association between human upper respiratory and gut bacterial microbiomes during the course of COVID-19 in adults.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {240}, pmid = {33603076}, issn = {2399-3642}, support = {2017ZX10103009-002//Chinese Academy of Sciences Key Project (CAS Key Project)/ ; 2018YFC2000500//Chinese Academy of Sciences Key Project (CAS Key Project)/ ; }, abstract = {SARS-CoV-2 is the cause of COVID-19. It infects multiple organs including the respiratory tract and gut. Dynamic changes of regional microbiomes in infected adults are largely unknown. Here, we performed longitudinal analyses of throat and anal swabs from 35 COVID-19 and 19 healthy adult controls, as well as 10 non-COVID-19 patients with other diseases, by 16 S rRNA gene sequencing. The results showed a partitioning of the patients into 3-4 categories based on microbial community types (I-IV) in both sites. The bacterial diversity was lower in COVID-19 patients than healthy controls and decreased gradually from community type I to III/IV. Although the dynamic change of microbiome was complex during COVID-19, a synchronous restoration of both the upper respiratory and gut microbiomes from early dysbiosis towards late more diverse status was observed in 6/8 mild COVID-19 adult patients. These findings reveal previously unknown interactions between upper respiratory and gut microbiomes during COVID-19.}, }
@article {pmid33602926, year = {2021}, author = {Wipperman, MF and Bhattarai, SK and Vorkas, CK and Maringati, VS and Taur, Y and Mathurin, L and McAulay, K and Vilbrun, SC and Francois, D and Bean, J and Walsh, KF and Nathan, C and Fitzgerald, DW and Glickman, MS and Bucci, V}, title = {Gastrointestinal microbiota composition predicts peripheral inflammatory state during treatment of human tuberculosis.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {1141}, pmid = {33602926}, issn = {2041-1723}, support = {TL1 TR002386/TR/NCATS NIH HHS/United States ; U19 AI111143/AI/NIAID NIH HHS/United States ; K08 AI132739/AI/NIAID NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; }, abstract = {The composition of the gastrointestinal microbiota influences systemic immune responses, but how this affects infectious disease pathogenesis and antibiotic therapy outcome is poorly understood. This question is rarely examined in humans due to the difficulty in dissociating the immunologic effects of antibiotic-induced pathogen clearance and microbiome alteration. Here, we analyze data from two longitudinal studies of tuberculosis (TB) therapy (35 and 20 individuals) and a cross sectional study from 55 healthy controls, in which we collected fecal samples (for microbiome analysis), sputum (for determination of Mycobacterium tuberculosis (Mtb) bacterial load), and peripheral blood (for transcriptomic analysis). We decouple microbiome effects from pathogen sterilization by comparing standard TB therapy with an experimental TB treatment that did not reduce Mtb bacterial load. Random forest regression to the microbiome-transcriptome-sputum data from the two longitudinal datasets reveals that renormalization of the TB inflammatory state is associated with Mtb pathogen clearance, increased abundance of Clusters IV and XIVa Clostridia, and decreased abundance of Bacilli and Proteobacteria. We find similar associations when applying machine learning to peripheral gene expression and microbiota profiling in the independent cohort of healthy individuals. Our findings indicate that antibiotic-induced reduction in pathogen burden and changes in the microbiome are independently associated with treatment-induced changes of the inflammatory response of active TB, and the response to antibiotic therapy may be a combined effect of pathogen killing and microbiome driven immunomodulation.}, }
@article {pmid33602895, year = {2021}, author = {Zhang, W and Qu, W and Wang, H and Yan, H}, title = {Antidepressants fluoxetine and amitriptyline induce alterations in intestinal microbiota and gut microbiome function in rats exposed to chronic unpredictable mild stress.}, journal = {Translational psychiatry}, volume = {11}, number = {1}, pages = {131}, pmid = {33602895}, issn = {2158-3188}, abstract = {Antidepressant medications are known to modulate the central nervous system, and gut microbiota can play a role in depression via microbiota-gut-brain axis. But the impact of antidepressants on gut microbiota function and composition remains poorly understood. Thus this study assessed the effect of serotonin reuptake inhibitor antidepressant fluoxetine (Flu) and tricyclic antidepressant amitriptyline (Ami) administration on gut microbiota composition, diversity, and species abundance, along with microbial function in a chronic unpredictable mild stress (CUMS)-induced depression rat model. Oral administration of Ami and Flu significantly altered the overall gut microbiota profile of CUMS-induced rats, as assessed using the permutational multivariate analysis of variance test. At the phylum level, 6-week of antidepressant treatment led to a decreased Firmicutes/Bacteroidetes ratio due to an enhanced Bacteroidetes and reduced Firmicutes relative abundance. Flu was more potent than Ami at altering the Firmicutes and Bacteroidetes levels in the CUMS rats. At the family level, both antidepressants significantly increased the abundance of Porphyromonadaceae. However, an increased Bacteroidaceae level was significantly associated with Ami, not Flu treatment. Furthermore, at the genus level, an increase in the relative abundance of Parabacteroides, Butyricimonas, and Alistipes was observed following Ami and Flu treatment. Subsequent metagenomics and bioinformatics analysis further indicated that Ami and Flu likely also modulated metabolic pathways, such as those involved in carbohydrate metabolism, membrane transport, and signal transduction. Additionally, both antidepressants affected antibiotic resistome, such as for aminoglycoside (aph3iiiA), multidrug (mdtK, mdtP, mdtH, mdtG, acrA), and tetracycline (tetM) resistance in CUMS rats. These data clearly illustrated the direct impact of oral administration of Flu and Ami on the gut microbiome, thus set up the foundation to reveal more insights on the therapeutic function of the antidepressants and their overall contribution to host health.}, }
@article {pmid33602737, year = {2021}, author = {Ilieva, V and Steel, B and Pratscher, J and Olsson-Francis, K and Macey, MC}, title = {Assembly of Bacterial Genome Sequences from Metagenomes of Spacecraft Assembly Cleanrooms.}, journal = {Microbiology resource announcements}, volume = {10}, number = {7}, pages = {}, pmid = {33602737}, issn = {2576-098X}, abstract = {Characterizing the microbiome of spacecraft assembly cleanrooms is important for planetary protection. We report two bacterial metagenome-assembled genomes (MAGs) reconstructed from metagenomes produced from cleanroom samples from the Kennedy Space Center's Payload Hazardous Servicing Facility (KSC-PHSF) during the handling of the Phoenix spacecraft. Characterization of these MAGs will enable identification of the strategies underpinning their survival.}, }
@article {pmid33602613, year = {2021}, author = {Ding, M and Yang, B and Ross, RP and Stanton, C and Zhao, J and Zhang, H and Chen, W}, title = {Crosstalk between sIgA-Coated Bacteria in Infant Gut and Early-Life Health.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2021.01.012}, pmid = {33602613}, issn = {1878-4380}, abstract = {Gut microbiota transmission from mother to offspring has attracted much interest in recent years. The gut microbiota in the infant plays a potentially significant role in modulating and maintaining the development of infant immunity. Secretory immunoglobulin A (sIgA), the major immunoglobulin in the intestine, can target polysaccharides and flagellin on the bacterial surface, resulting in sIgA-coated bacteria. The presentation of specific bacteria coated with sIgA may be a signal of disease and provide novel insights into the relationship between infant microbiota and disease. Here, we review the composition of sIgA-coated bacteria in the adult intestine, human milk, and the infant intestine, as well as the factors that influence the development of gut microbiota in early life. Then, we highlight the diseases that are related to variations in sIgA-coated bacteria in the infant and adult intestine. Furthermore, we discuss the possibility that sIgA-coated bacteria could play a role in mediating both innate and adaptive immune responses. Finally, we propose directions for future research to promote our understanding within this field.}, }
@article {pmid33602336, year = {2021}, author = {Bashir, AK and Wink, L and Duller, S and Schwendner, P and Cockell, C and Rettberg, P and Mahnert, A and Beblo-Vranesevic, K and Bohmeier, M and Rabbow, E and Gaboyer, F and Westall, F and Walter, N and Cabezas, P and Garcia-Descalzo, L and Gomez, F and Malki, M and Amils, R and Ehrenfreund, P and Monaghan, E and Vannier, P and Marteinsson, V and Erlacher, A and Tanski, G and Strauss, J and Bashir, M and Riedo, A and Moissl-Eichinger, C}, title = {Taxonomic and functional analyses of intact microbial communities thriving in extreme, astrobiology-relevant, anoxic sites.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {50}, pmid = {33602336}, issn = {2049-2618}, support = {607297//Seventh Framework Programme/ ; }, abstract = {BACKGROUND: Extreme terrestrial, analogue environments are widely used models to study the limits of life and to infer habitability of extraterrestrial settings. In contrast to Earth's ecosystems, potential extraterrestrial biotopes are usually characterized by a lack of oxygen.<br><br>METHODS: In the MASE project (Mars Analogues for Space Exploration), we selected representative anoxic analogue environments (permafrost, salt-mine, acidic lake and river, sulfur springs) for the comprehensive analysis of their microbial communities. We assessed the microbiome profile of intact cells by propidium monoazide-based amplicon and shotgun metagenome sequencing, supplemented with an extensive cultivation effort.<br><br>RESULTS: The information retrieved from microbiome analyses on the intact microbial community thriving in the MASE sites, together with the isolation of 31 model microorganisms and successful binning of 15 high-quality genomes allowed us to observe principle pathways, which pinpoint specific microbial functions in the MASE sites compared to moderate environments. The microorganisms were characterized by an impressive machinery to withstand physical and chemical pressures. All levels of our analyses revealed the strong and omnipresent dependency of the microbial communities on complex organic matter. Moreover, we identified an extremotolerant cosmopolitan group of 34 poly-extremophiles thriving in all sites.<br><br>CONCLUSIONS: Our results reveal the presence of a core microbiome and microbial taxonomic similarities between saline and acidic anoxic environments. Our work further emphasizes the importance of the environmental, terrestrial parameters for the functionality of a microbial community, but also reveals a high proportion of living microorganisms in extreme environments with a high adaptation potential within habitability borders. Video abstract.}, }
@article {pmid33602335, year = {2021}, author = {Bodawatta, KH and Freiberga, I and Puzejova, K and Sam, K and Poulsen, M and Jønsson, KA}, title = {Flexibility and resilience of great tit (Parus major) gut microbiomes to changing diets.}, journal = {Animal microbiome}, volume = {3}, number = {1}, pages = {20}, pmid = {33602335}, issn = {2524-4671}, support = {CF17-0248//Carlsbergfondet/ ; 18-23794Y//Grantová Agentura České Republiky/ ; GAJU n.048/2019/P//Jihočeská Univerzita v Českých Budějovicích/ ; }, abstract = {BACKGROUND: Gut microbial communities play important roles in nutrient management and can change in response to host diets. The extent of this flexibility and the concomitant resilience is largely unknown in wild animals. To untangle the dynamics of avian-gut microbiome symbiosis associated with diet changes, we exposed Parus major (Great tits) fed with a standard diet (seeds and mealworms) to either a mixed (seeds, mealworms and fruits), a seed, or a mealworm diet for 4 weeks, and examined the flexibility of gut microbiomes to these compositionally different diets. To assess microbiome resilience (recovery potential), all individuals were subsequently reversed to a standard diet for another 4 weeks. Cloacal microbiomes were collected weekly and characterised through sequencing the v4 region of the 16S rRNA gene using Illumina MiSeq.<br><br>RESULTS: Initial microbiomes changed significantly with the diet manipulation, but the communities did not differ significantly between the three diet groups (mixed, seed and mealworm), despite multiple diet-specific changes in certain bacterial genera. Reverting birds to the standard diet led only to a partial recovery in gut community compositions. The majority of the bacterial taxa that increased significantly during diet manipulation decreased in relative abundance after reversion to the standard diet; however, bacterial taxa that decreased during the manipulation rarely increased after diet reversal CONCLUSIONS: The gut microbial response and partial resilience to dietary changes support that gut bacterial communities of P. major play a role in accommodating dietary changes experienced by wild avian hosts. This may be a contributing factor to the relaxed association between microbiome composition and the bird phylogeny. Our findings further imply that interpretations of wild bird gut microbiome analyses from single-time point sampling, especially for omnivorous species or species with seasonally changing diets, should be done with caution. The partial community recovery implies that ecologically relevant diet changes (e.g., seasonality and migration) open up gut niches that may be filled by previously abundant microbes or replaced by different symbiont lineages, which has important implications for the integrity and specificity of long-term avian-symbiont associations.}, }
@article {pmid33602197, year = {2021}, author = {Wang, Y and Zeng, J and Yuan, Q and Luan, Q}, title = {Efficacy of (-)-epigallocatechin gallate delivered by a new-type scaler tip during scaling and root planing on chronic periodontitis: a split-mouth, randomized clinical trial.}, journal = {BMC oral health}, volume = {21}, number = {1}, pages = {79}, pmid = {33602197}, issn = {1472-6831}, support = {2020-2-4103//Capital's Funds for Health Improvement and Research/ ; }, abstract = {BACKGROUND: (-)-Epigallocatechin Gallate (EGCG) as green tea catechins possessed antibacterial and anti-inflammatory effects on periodontal disease. This study was designed to evaluate the clinical and microbiological efficacy of scaling and root planing (SRP) using EGCG aqueous solution as coolants through a new-type ultrasonic scaler tip on chronic periodontitis.<br><br>METHODS: This split-mouth, randomized clinical trial included 20 patients (2 drop-outs) with chronic periodontitis and the maxillary contra-lateral sides were allocated into test and control groups randomly. Through the new-type scaler tip, 762 sites with probing depth (PD) ≥ 4 mm were treated by SRP using EGCG solution or distilled water as coolants respectively. Clinical parameters and red complex pathogens in subgingival microbiome were evaluated at baseline, 3 and 6 months after treatments.<br><br>RESULTS: During 6 months, the SRP plus EGCG medication contributed to additional PD reduction as 0.33 mm and gain of clinical attachment level as 0.3 mm compared with SRP alone, and approximate 8% more sites obtained PD reduction ≥ 2 mm (p < 0.05). Meanwhile, the mean relative abundance of Tannerella forsythia was significantly lower in the combined treatment group (p < 0.05).<br><br>CONCLUSION: The purified EGCG showed the potential to improve the outcome of periodontal non-surgical treatment and the new-type scaler tip provided an alternative vehicle for subgingival medication. Trial registration The trial was registered in Chinese Clinical Trial Registry on 15 February 2020 (No.: ChiCTR2000029831, retrospectively registered). http://www.chictr.org.cn/showprojen.aspx?proj=49441 .}, }
@article {pmid33602131, year = {2021}, author = {Ogai, K and Shibata, K and Takahashi, N and Ogura, K and Okamoto, S and Sugama, J}, title = {Amplicon-based skin microbiome profiles collected by tape stripping with different adhesive film dressings: a comparative study.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {54}, pmid = {33602131}, issn = {1471-2180}, support = {17H04428//Ministry of Education, Culture, Sports, Science and Technology/ ; }, abstract = {BACKGROUND: Medical film dressings have been used to obtain skin microbiota for skin microbiome studies, although their adhesive force may be so strong that the skin could be injured when applied to those who have fragile skin, such as older people. Several products with less adhesive force are available, although their applicability for skin microbiome studies remains unknown. This study aimed to test whether the dressings with less adhesive force could be used for amplicon-based skin microbiome studies. A set of three different film dressings, with acrylic, urethane, or silicone adhesive, was applied to the back skin of nine healthy young participants. The copy number of the 16S ribosomal RNA (rRNA) gene, microbial compositions, and alpha and beta diversity indices were analyzed by amplicon analysis of the 16S rRNA gene using next-generation sequencing and were compared among the three film dressings.<br><br>RESULTS: The dressing with acrylic adhesive yielded the highest copy number of 16S rRNA genes, followed by that with urethane adhesive. The silicone-adhesive dressing yielded a significantly lower copy number of the 16S rRNA gene. The microbial composition of skin microbiota was similar among the three film dressings, although significant differences in the relative abundance of Pseudomonas species and alpha diversity indices were found in the silicone-adhesive dressing. The Bray-Curtis dissimilarity was significantly higher between the acrylic- and silicone-adhesive dressings than between the acrylic- and urethane-adhesive dressings. No adverse effects related to tape stripping were observed for any of the film dressings.<br><br>CONCLUSION: We recommend dressings with acrylic or urethane adhesive for amplicon-based skin microbiome studies. An acrylic adhesive has an advantage in the yield of skin microbiota, and a urethane adhesive should be chosen when applied to fragile skin. The adhesive force of the dressing with silicone adhesive was too weak to be used for collecting skin microbiota.}, }
@article {pmid33602058, year = {2021}, author = {Coughlan, S and Das, A and O'Herlihy, E and Shanahan, F and O'Toole, PW and Jeffery, IB}, title = {The gut virome in Irritable Bowel Syndrome differs from that of controls.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1-15}, doi = {10.1080/19490976.2021.1887719}, pmid = {33602058}, issn = {1949-0984}, abstract = {Irritable Bowel Syndrome (IBS), the most common gastrointestinal disorder, is diagnosed solely on symptoms. Potentially diagnostic alterations in the bacterial component of the gut microbiome (the bacteriome) are associated with IBS, but despite the known role of the virome (particularly bacteriophages), in shaping the gut bacteriome, few studies have investigated the virome in IBS. We performed metagenomic sequencing of fecal Virus-Like Particles (VLPs) from 55 patients with IBS and 51 control individuals. We detected significantly lower alpha diversity of viral clusters comprising both known and novel viruses (viral 'dark matter') in IBS and a significant difference in beta diversity compared to controls, but not between IBS symptom subtypes. The three most abundant bacteriophage clusters belonged to the Siphoviridae, Myoviridae, and Podoviridae families (Order Caudovirales). A core virome (defined as a cluster present in at least 50% of samples) of 5 and 12 viral clusters was identified in IBS and control subjects, respectively. We also identified a subset of viral clusters that showed differential abundance between IBS and controls. The virome did not co-vary significantly with the bacteriome, with IBS clinical subtype, or with Bile Acid Malabsorption status. However, differences in the virome could be related back to the bacteriome as analysis of CRISPR spacers indicated that the virome alterations were at least partially related to the alterations in the bacteriome. We found no evidence for a shift from lytic to lysogenic replication of core viral clusters, a phenomenon reported for the gut virome of patients with Inflammatory Bowel Disease. Collectively, our data show alterations in the virome of patients with IBS, regardless of clinical subtype, which may facilitate development of new microbiome-based therapeutics.}, }
@article {pmid33600745, year = {2021}, author = {Graeber, SY and Boutin, S and Wielpütz, MO and Joachim, C and Frey, DL and Wege, S and Sommerburg, O and Kauczor, HU and Stahl, M and Dalpke, AH and Mall, MA}, title = {Effects of Lumacaftor-Ivacaftor on Lung Clearance Index, Magnetic Resonance Imaging and Airway Microbiome in Phe508del Homozygous Patients with Cystic Fibrosis.}, journal = {Annals of the American Thoracic Society}, volume = {}, number = {}, pages = {}, doi = {10.1513/AnnalsATS.202008-1054OC}, pmid = {33600745}, issn = {2325-6621}, abstract = {RATIONALE: Previous studies showed that lumacaftor-ivacaftor therapy results in partial rescue of cystic fibrosis transmembrane conductance regulator (CFTR) activity and moderate improvement of spirometry in Phe508del homozygous patients with cystic fibrosis (CF). However, the effects of lumacaftor-ivacaftor on lung clearance index (LCI), lung morphology and perfusion detected by chest magnetic resonance imaging (MRI), and effects on the airway microbiome and inflammation remain unknown.<br><br>OBJECTIVES: To investigate the effects of lumacaftor-ivacaftor on LCI, lung MRI scores, and airway microbiome and inflammation.<br><br>METHODS: In this prospective observational study we assessed clinical outcomes including spirometry and body mass index, LCI, lung MRI scores, sputum microbiome and pro-inflammatory cytokines in 30 Phe508del homozygous patients with CF 12 years and older before and 8-16 weeks after initiation of lumacaftor-ivacaftor therapy.<br><br>MEASUREMENTS AND MAIN RESULTS: Lumacaftor-ivacaftor had no effects on FEV1 % predicted (1.7%, 95% confidence interval (CI) -1.0 to 4.3%; P = 0.211), but improved LCI (-1.6, 95% CI -2.6 to -0.5; P < 0.01) and MRI morphology (-1.3, 95% CI -2.3 to -0.3; P < 0.05) and perfusion score (-1.2, 95% CI -2.3 to -0.2; P < 0.05) in our study cohort. Further, lumacaftor-ivacaftor decreased the total bacterial load (-1.8, 95% CI -3.3 to -0.34; P < 0.05) and increased the Shannon diversity of the airway microbiome (0.4, 95% CI 0.1 to 0.8; P < 0.05), and reduced IL-1β levels (median change -324.2 pg/ml, 95% CI -938.7 to 290.4 pg/ml; P < 0.05) in sputum of Phe508del homozygous patients.<br><br>CONCLUSIONS: This study shows that lumacaftor-ivacaftor has beneficial effects on lung ventilation, morphology and perfusion, as well as on the airway microbiome and inflammation in Phe508del homozygous patients. Our results suggest that LCI and MRI may be more sensitive than FEV1 % predicted to detect response to CFTR modulator therapy in patients with chronic CF lung disease. Clinical trial registered with ClinicalTrials.gov (NCT02807415).}, }
@article {pmid33600606, year = {2021}, author = {Jansa, J and Hodge, A}, title = {Swimming, gliding, or hyphal riding? On microbial migration along the arbuscular mycorrhizal hyphal highway and functional consequences thereof.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.17244}, pmid = {33600606}, issn = {1469-8137}, support = {18-04892S//Czech Science Foundation/ ; }, }
@article {pmid33600603, year = {2021}, author = {Ma, J and Zhu, W and Liu, B}, title = {Role of Gut Microbiome in the Outcome of Cancer Immunotherapy.}, journal = {International journal of cancer}, volume = {}, number = {}, pages = {}, doi = {10.1002/ijc.33524}, pmid = {33600603}, issn = {1097-0215}, abstract = {Nearly 3 × 1013 types of bacteria colonize the human intestine. These colonized bacteria help in maintaining intestinal homeostasis by establishing a complex relationship with the intestinal epithelium and lymphoid tissue. Alteration in the composition of the intestinal microbiota is associated with susceptibility to various pathological conditions, such as autoimmune disorders, diabetes, inflammation, and cancer. Of late, several researchers have focused on examining the effects of gut microbiota on the outcome of various cancer treatment protocols. Side effects and complications of traditional chemotherapy and allogeneic hematopoietic cell transplantation are associated with intestinal dysbiosis. Gut microbiota affects the efficacy of immune checkpoint inhibitor-based immunotherapy. The gut is inhabited by diverse resident bacteria, of which, few enhance, while others inhibit the host response to immunotherapy. This review focuses on the correlation between intestinal microbiota and the outcome of tumor immunotherapy. Additionally, the molecular mechanisms underlying the effects of gut microbiota on the efficacy of cancer immunotherapy have been reviewed. Further studies are needed for the identification of distinct gut microbiota and their efficacy in tumor immunotherapy as certain types of intestinal bacteria could function as novel adjuvant drugs to enhance the effectiveness of anti-tumor therapy in humans.}, }
@article {pmid33600597, year = {2020}, author = {Das, S and Smith, K and Sarker, S and Peters, A and Adriaanse, K and Eden, P and Ghorashi, SA and Forwood, JK and Raidal, SR}, title = {REPEAT SPILLOVER OF BEAK AND FEATHER DISEASE VIRUS INTO AN ENDANGERED PARROT HIGHLIGHTS THE RISK ASSOCIATED WITH ENDEMIC PATHOGEN LOSS IN ENDANGERED SPECIES.}, journal = {Journal of wildlife diseases}, volume = {56}, number = {4}, pages = {896-906}, doi = {10.7589/2018-06-154}, pmid = {33600597}, issn = {1943-3700}, abstract = {Conservation efforts for the orange-bellied parrot (Neophema chrysogaster), one of the world's most critically endangered bird species, have been hampered by beak and feather disease virus (BFDV) spillover infection. To understand the vulnerability of orange-bellied parrots to potential reservoirs of infection we investigated geographic versus taxonomic structure in 160 full-genome and 319 partial Rep gene BFDV sequences from captive and wild orange-bellied parrots and other wild parrot species in Australia. We found that Australian BFDV populations are structured by host taxonomy. By identifying genetic stratification of BFDV in reservoir hosts we characterized three separate recent incursions of BFDV into orange-bellied parrots from other wild parrots, which demonstrates the susceptibility of critically endangered species to multiple threats of pathogen re-emergence. Our study highlighted how loss of endemic circulating BFDV in orange-bellied parrots precipitated repeated spillover into an immunologically naïve population, causing significant disease.}, }
@article {pmid33600433, year = {2021}, author = {Carter, ED and Bletz, MC and Le Sage, M and LaBumbard, B and Rollins-Smith, LA and Woodhams, DC and Miller, DL and Gray, MJ}, title = {Winter is coming-Temperature affects immune defenses and susceptibility to Batrachochytrium salamandrivorans.}, journal = {PLoS pathogens}, volume = {17}, number = {2}, pages = {e1009234}, doi = {10.1371/journal.ppat.1009234}, pmid = {33600433}, issn = {1553-7374}, abstract = {Environmental temperature is a key factor driving various biological processes, including immune defenses and host-pathogen interactions. Here, we evaluated the effects of environmental temperature on the pathogenicity of the emerging fungal pathogen, Batrachochytrium salamandrivorans (Bsal), using controlled laboratory experiments, and measured components of host immune defense to identify regulating mechanisms. We found that adult and juvenile Notophthalmus viridescens died faster due to Bsal chytridiomycosis at 14°C than at 6 and 22°C. Pathogen replication rates, total available proteins on the skin, and microbiome composition likely drove these relationships. Temperature-dependent skin microbiome composition in our laboratory experiments matched seasonal trends in wild N. viridescens, adding validity to these results. We also found that hydrophobic peptide production after two months post-exposure to Bsal was reduced in infected animals compared to controls, perhaps due to peptide release earlier in infection or impaired granular gland function in diseased animals. Using our temperature-dependent susceptibility results, we performed a geographic analysis that revealed N. viridescens populations in the northeastern United States and southeastern Canada are at greatest risk for Bsal invasion, which shifted risk north compared to previous assessments. Our results indicate that environmental temperature will play a key role in the epidemiology of Bsal and provide evidence that temperature manipulations may be a viable disease management strategy.}, }
@article {pmid33600415, year = {2021}, author = {Chen, B and He, X and Pan, B and Zou, X and You, N}, title = {Comparison of beta diversity measures in clustering the high-dimensional microbial data.}, journal = {PloS one}, volume = {16}, number = {2}, pages = {e0246893}, doi = {10.1371/journal.pone.0246893}, pmid = {33600415}, issn = {1932-6203}, abstract = {The heterogeneity of disease is a major concern in medical research and is commonly characterized as subtypes with different pathogeneses exhibiting distinct prognoses and treatment effects. The classification of a population into homogeneous subgroups is challenging, especially for complex diseases. Recent studies show that gut microbiome compositions play a vital role in disease development, and it is of great interest to cluster patients according to their microbial profiles. There are a variety of beta diversity measures to quantify the dissimilarity between the compositions of different samples for clustering. However, using different beta diversity measures results in different clusters, and it is difficult to make a choice among them. Considering microbial compositions from 16S rRNA sequencing, which are presented as a high-dimensional vector with a large proportion of extremely small or even zero-valued elements, we set up three simulation experiments to mimic the microbial compositional data and evaluate the performance of different beta diversity measures in clustering. It is shown that the Kullback-Leibler divergence-based beta diversity, including the Jensen-Shannon divergence and its square root, and the hypersphere-based beta diversity, including the Bhattacharyya and Hellinger, can capture compositional changes in low-abundance elements more efficiently and can work stably. Their performance on two real datasets demonstrates the validity of the simulation experiments.}, }
@article {pmid33600401, year = {2021}, author = {Goldberg, Y and Friedman, J}, title = {Positive interactions within and between populations decrease the likelihood of evolutionary rescue.}, journal = {PLoS computational biology}, volume = {17}, number = {2}, pages = {e1008732}, doi = {10.1371/journal.pcbi.1008732}, pmid = {33600401}, issn = {1553-7358}, abstract = {Positive interactions, including intraspecies cooperation and interspecies mutualisms, play crucial roles in shaping the structure and function of many ecosystems, ranging from plant communities to the human microbiome. While the evolutionary forces that form and maintain positive interactions have been investigated extensively, the influence of positive interactions on the ability of species to adapt to new environments is still poorly understood. Here, we use numerical simulations and theoretical analyses to study how positive interactions impact the likelihood that populations survive after an environment deteriorates, such that survival in the new environment requires quick adaptation via the rise of new mutants-a scenario known as evolutionary rescue. We find that the probability of evolutionary rescue in populations engaged in positive interactions is reduced significantly. In cooperating populations, this reduction is largely due to the fact that survival may require at least a minimal number of individuals, meaning that adapted mutants must arise and spread before the population declines below this threshold. In mutualistic populations, the rescue probability is decreased further due to two additional effects-the need for both mutualistic partners to adapt to the new environment, and competition between the two species. Finally, we show that the presence of cheaters reduces the likelihood of evolutionary rescue even further, making it extremely unlikely. These results indicate that while positive interactions may be beneficial in stable environments, they can hinder adaptation to changing environments and thereby elevate the risk of population collapse. Furthermore, these results may hint at the selective pressures that drove co-dependent unicellular species to form more adaptable organisms able to differentiate into multiple phenotypes, including multicellular life.}, }
@article {pmid33600151, year = {2021}, author = {Brimberry, M and Toma, MA and Hines, KM and Lanzilotta, WN}, title = {HutW from Vibrio cholerae Is an Anaerobic Heme-Degrading Enzyme with Unique Functional Properties.}, journal = {Biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.biochem.0c00950}, pmid = {33600151}, issn = {1520-4995}, abstract = {Increasing antibiotic resistance, and a growing recognition of the importance of the human microbiome, demand that new therapeutic targets be identified. Characterization of metabolic pathways that are unique to enteric pathogens represents a promising approach. Iron is often the rate-limiting factor for growth, and Vibrio cholerae, the causative agent of cholera, has been shown to contain numerous genes that function in the acquisition of iron from the environment. Included in this arsenal of genes are operons dedicated to obtaining iron from heme and heme-containing proteins. Given the persistence of cholera, an important outstanding question is whether V. cholerae is capable of anaerobic heme degradation as was recently reported for enterohemorrhagic Escherichia coli O157:H7. In this work, we demonstrate that HutW from V. cholerae is a radical S-adenosylmethionine methyl transferase involved in the anaerobic opening of the porphyrin ring of heme. However, in contrast to the enzyme ChuW, found in enterohemorrhagic E. coli O157:H7, there are notable differences in the mechanism and products of the HutW reaction. Of particular interest are data that demonstrate HutW will catalyze ring opening as well as tetrapyrrole reduction and can utilize reduced nicotinamide adenine dinucleotide phosphate as an electron source. The biochemical and biophysical properties of HutW are presented, and the evolutionary implications are discussed.}, }
@article {pmid33599739, year = {2021}, author = {Breakfield, NW and Collett, D and Frodyma, ME}, title = {Plant growth-promoting microbes - an industry view.}, journal = {Emerging topics in life sciences}, volume = {}, number = {}, pages = {}, doi = {10.1042/ETLS20200313}, pmid = {33599739}, issn = {2397-8554}, abstract = {Plant growth-promoting microbes can affect the plant microbiome, improving different properties of the plant such as yield and health. Many companies are commercializing these microbes as products called biologicals. Defining the product concept is one of the first and most important steps in making a biological product. Companies can use phenotyping and genotyping approaches to identify the microbe to make into a live bacterial product. Screening usually begins in the laboratory and often moves from high-throughput methods to more time and resource-intensive methods culminating in large scale field testing. Once the microbe is chosen, the fermentation process grows the bacteria to the necessary amounts, while the formulation process ensures a stable product in the desired form such as a liquid or powder. The products must show yield increases in the field over several seasons and conditions, but also must be easy to use and cost-effective to be adopted by farmers and other customers. Tying all these data together from the selection process to test results gives a customer a 'reason to believe' for the marketing and launch of a successful product.}, }
@article {pmid33599094, year = {2021}, author = {Mayneris-Perxachs, J and Amaral, W and Lubach, GR and Posma, JM and Coe, CL and Swann, JR}, title = {Gut Microbial and Metabolic Profiling Reveal the Lingering Effects of Infantile Iron Deficiency Unless Treated with Iron.}, journal = {Molecular nutrition &amp; food research}, volume = {}, number = {}, pages = {e2001018}, doi = {10.1002/mnfr.202001018}, pmid = {33599094}, issn = {1613-4133}, abstract = {SCOPE: Iron deficiency (ID) compromises the health of infants worldwide. Although readily treated with iron, concerns remain about the persistence of some effects. Metabolic and gut microbial consequences of infantile ID were investigated in juvenile monkeys after natural recovery (pID) from iron deficiency or post-treatment with iron dextran and B vitamins (pID+Fe).<br><br>METHODS AND RESULTS: Metabolomic profiling of urine and plasma was conducted with 1 H nuclear magnetic resonance (NMR) spectroscopy. Gut microbiota were characterized from rectal swabs by amplicon sequencing of the 16S rRNA gene. Urinary metabolic profiles of pID monkeys significantly differed from pID+Fe and continuously iron-sufficient controls (IS) with higher maltose and lower amounts of microbial-derived metabolites. Persistent differences in energy metabolism were apparent from the plasma metabolic phenotypes with greater reliance on anaerobic glycolysis in pID monkeys. Microbial profiling indicated higher abundances of Methanobrevibacter, Lachnobacterium and Ruminococcus in pID monkeys and any history of ID resulted in a lower Prevotella abundance compared to the IS controls.<br><br>CONCLUSIONS: Lingering metabolic and microbial effects were found after natural recovery from ID. These long-term biochemical derangements were not present in the pID+Fe animals emphasizing the importance of the early detection and treatment of early-life ID to ameliorate its chronic metabolic effects. This article is protected by copyright. All rights reserved.}, }
@article {pmid33598856, year = {2021}, author = {Mombach, MA and da Silva Cabral, L and Lima, LR and Ferreira, DC and Pedreira, BCOE and Pereira, DH}, title = {Association of ionophores, yeast, and bacterial probiotics alters the abundance of ruminal microbial species of pasture intensively finished beef cattle.}, journal = {Tropical animal health and production}, volume = {53}, number = {1}, pages = {172}, pmid = {33598856}, issn = {1573-7438}, support = {02.13.11.001.00.00//Embrapa Agrossilvipastoril/ ; }, abstract = {The effect of the association of non-protein nitrogen, yeast, and bacterial probiotics on the ruminal microbiome of beef cattle intensively finished on pasture was evaluated. The experiment was carried out in a completely randomized design with five treatments and four replications. The treatments consisted of a group of animals kept on pasture that received low consumption supplementation (LS) and four groups that received for 98 days, 17.5 g concentrate kg-1 body weight. The supplements were composed of the association of additives: urea (U), slow-release non-protein nitrogen (U+SRN), yeast (Saccharomyces cerevisiae; U+SRN+Y), and bacterial probiotics (live strains of bacteria; U+SRN+Y+BP). All supplements also contained salinomycin and virginiamycin. After slaughtering the animals, samples of ruminal content were collected to quantify groups of fibrolytic bacteria (Ruminococcus albus and Fibrobacter succinogenes), non-fibrolytic (Prevotella ruminicola, Selenomonas ruminantium, and Streptococcus bovis), Archaea, and ciliate protozoa, using the qPCR technique. The abundance of F. succinogenes was the same for the LS animals and those that received the supplement U+SRN+Y (1.42×108 copies mL-1) but higher than the other treatments. Supplementation reduced by 90% the abundance of S. bovis compared to the LS. The inclusion of yeast increased the abundance of fibrolytic bacteria by 2.2-fold. For animals that received the supplement U+SRN+Y+BP and the LS, there was no difference for non-fibrolytic bacteria (3.07×109 copies mL-1). The use of yeasts and sources of non-protein nitrogen in high-concentrate diets for beef cattle stimulates the growth of fibrolytic bacteria, which can contribute to the reduction of digestive disorders and metabolic diseases in animals that receive diets with high concentrate in pasture intensive termination systems.}, }
@article {pmid33598748, year = {2021}, author = {Nava-González, B and Suazo-Ortuño, I and López, PB and Maldonado-López, Y and Lopez-Toledo, L and Raggi, L and Parra-Olea, G and Alvarado-Díaz, J and Gómez-Gil, B}, title = {Inhibition of Batrachochytrium dendrobatidis Infection by Skin Bacterial Communities in Wild Amphibian Populations.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33598748}, issn = {1432-184X}, support = {2015-259173//Consejo Nacional de Ciencia y Tecnología/ ; 444637//Consejo Nacional de Ciencia y Tecnología/ ; Programa 2019//Coordinación de la Investigación Científica/ ; }, abstract = {Skin-associated bacteria are known to inhibit infection by the fungal pathogen Batrachochytrium dendrobatidis (Bd) in amphibians. It has also been postulated that skin-associated bacterial community is related to Bd infection intensity. However, our understanding of host microbial dynamics and their importance in regulating Bd intensity is limited. We analyzed Bd infection and skin-associated bacteria from two amphibian species, the salamander Ambystoma rivulare and the frog Lithobates spectabilis that co-occurred in a tropical high-altitude site in central Mexico. Sixty-three percent of sampled salamander individuals and 80% of frog individuals tested positive for Bd. Overall, we registered 622 skin-associated bacterial genera, from which 73 are known to have Bd inhibitory effects. These inhibitory taxa represented a relative abundance of 50% in relation to total relative bacterial abundance. Our results indicated that, although sharing some bacterial taxa, bacterial community from the skin of both species was different in taxonomic composition and in relative abundance. Pseudomonas spp. and Stenotrophomonas spp. were among the five most abundant bacterial taxa of both species. Both bacterial taxa inhibit Bd infection. We detected that bacterial richness and relative abundance of inhibitory Bd bacteria were negatively related to intensity of Bd infection independent of species and seasons. Despite the high Bd prevalence in both host species, no dead or sick individuals were registered during field surveys. The relatively low levels of Bd load apparently do not compromise survival of host species. Therefore, our results suggested that individuals analyzed were able to survive and thrive under a dynamic relation with enzootic infections of Bd and their microbiota.}, }
@article {pmid33598714, year = {2021}, author = {Sola-Leyva, A and Andrés-León, E and Molina, NM and Terron-Camero, LC and Plaza-Díaz, J and Sáez-Lara, MJ and Gonzalvo, MC and Sánchez, R and Ruíz, S and Martínez, L and Altmäe, S}, title = {Mapping the entire functionally active endometrial microbiota.}, journal = {Human reproduction (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/humrep/deaa372}, pmid = {33598714}, issn = {1460-2350}, abstract = {STUDY QUESTION: Does endometrium harbour functionally active microorganisms and whether the microbial composition differs between proliferative and mid-secretory phases?<br><br>SUMMARY ANSWER: Endometrium harbours functionally alive microorganisms including bacteria, viruses, archaea and fungi whose composition and metabolic functions change along the menstrual cycle.<br><br>WHAT IS KNOWN ALREADY: Resident microbes in the endometrium have been detected, where microbial dysfunction has been associated with reproductive health and disease. Nevertheless, the core microorganismal composition in healthy endometrium is not determined and whether the identified bacterial DNA sequences refer to alive/functionally active microbes is not clear. Furthermore, whether there are cyclical changes in the microbial composition remains an open issue.<br><br>STUDY DESIGN, SIZE, DURATION: RNA sequencing (RNAseq) data from 14 endometrial paired samples from healthy women, 7 samples from the mid-secretory phase and 7 samples from the consecutive proliferative phase were analysed for the microbial RNA sequences.<br><br>The raw RNAseq data were converted into FASTQ format using SRA Toolkit. The unmapped reads to human sequences were aligned to the reference database Kraken2 and visualised with Krona software. Menstrual phase taxonomic differences were performed by R package metagenomeSeq. The functional analysis of endometrial microbiota was obtained with HUMANn2 and the comparison between menstrual phases was conducted by one-way ANOVA. Human RNAseq analysis was performed using miARma-Seq and the functional enrichment analysis was carried out using gene set enrichment analysis (GSEA; HumanCyc). The integration of metabolic pathways between host and microbes was investigated. The developed method of active microbiota mapping was validated in independent sample set.<br><br>With the novel metatranscriptomic approach, we mapped the entire alive microbiota composing of >5300 microorganisms within the endometrium of healthy women. Microbes such as bacteria, fungi, viruses and archaea were identified. The validation of three independent endometrial samples from different ethnicity confirmed the findings. Significant differences in the microbial abundances in the mid-secretory vs. proliferative phases were detected with possible metabolic activity in the host-microbiota crosstalk in receptive phase endometrium, specifically in the prostanoid biosynthesis pathway and L-tryptophan metabolism.<br><br>LARGE SCALE DATA: The raw RNAseq data used in the current study are available at GEO GSE86491 and at BioProject PRJNA379542.<br><br>These pioneering results should be confirmed in a bigger sample size.<br><br>Our study confirms the presence of active microbes, bacteria, fungi, viruses and archaea in the healthy human endometrium with implications in receptive phase endometrial functions, meaning that microbial dysfunction could impair the metabolic pathways important for endometrial receptivity. The results of this study contribute to the better understanding of endometrial microbiota composition in healthy women and its possible role in endometrial functions. In addition, our novel methodological pipeline for analysing alive microbes with transcriptional and metabolic activities could serve to inspire new analysis approaches in reproductive medicine.<br><br>This work is supported by the Spanish Ministry of Economy, Industry and Competitiveness (MINECO) and European Regional Development Fund (FEDER): grants RYC-2016-21199 and ENDORE SAF2017-87526-R; FEDER/Junta de Andalucía-Consejería de Economía y Conocimiento: MENDO (B-CTS-500-UGR18) and by the University of Granada Plan Propio de Investigación 2016 - Excellence actions: Unit of Excellence on Exercise and Health (UCEES) (SOMM17/6107/UGR). A.S.-L. and N.M.M. are funded by the Spanish Ministry of Science, Innovation and Universities (PRE2018-0854409 and FPU19/01638). S.A. has received honoraria for lectures from Merck. The funder had no role in this study.}, }
@article {pmid33598648, year = {2021}, author = {Fairfield, B and Schnabl, B}, title = {Gut dysbiosis as a driver in alcohol-induced liver injury.}, journal = {JHEP reports : innovation in hepatology}, volume = {3}, number = {2}, pages = {100220}, pmid = {33598648}, issn = {2589-5559}, abstract = {Alcohol-related liver disease characterises a broad spectrum of hepatic diseases that result from heavy alcohol use, and include alcohol-related steatosis, steatohepatitis, fibrosis, cirrhosis, and alcoholic hepatitis. Amongst heavy drinkers, progression to more severe forms of alcohol-related liver disease is not universal, with only 20% developing cirrhosis and up to one-third developing alcoholic hepatitis. Non-alcohol-related triggers for severe disease are not well understood, but the intestinal microbiome is thought to be a contributing factor. This review examines the role of the microbiome in mild alcohol-related liver disease, cirrhosis, and alcoholic hepatitis. While most of the literature discusses bacterial dysbiosis, we also discuss the available evidence on fungal (mycobiome) and virome alterations in patients with alcohol-related liver disease. Additionally, we explore the mechanisms by which the microbiome contributes to the pathogenesis of alcohol-related liver disease, including effects on intestinal permeability, bile acid dysregulation, and production of hepatotoxic virulence factors.}, }
@article {pmid33598642, year = {2021}, author = {Hua, H and Zhang, Y and Zhao, F and Chen, K and Wu, T and Liu, Q and Huang, S and Zhang, A and Jia, Z}, title = {Celastrol inhibits intestinal lipid absorption by reprofiling the gut microbiota to attenuate high-fat diet-induced obesity.}, journal = {iScience}, volume = {24}, number = {2}, pages = {102077}, pmid = {33598642}, issn = {2589-0042}, abstract = {Celastrol, a compound extracted from traditional Chinese medicine, has been reported as a potent anti-obesity agent with controversial mechanisms. Here both C57BL/6J and leptin-deficient (ob/ob) mice fed a high-fat diet (HFD) displayed body weight loss after celastrol therapy, opposing the previous viewpoint that celastrol improves obesity by sensitizing leptin signaling. More importantly, celastrol downregulated lipid transporters in the intestine, increased lipid excretion in feces, and reduced body weight gain in HFD mice. Meanwhile, analysis of gut microbiota revealed that celastrol altered the gut microbiota composition in HFD-fed mice, and modulating gut microbiota by antibiotics or fecal microbiota transplantation blocked the celastrol effect on intestinal lipid transport and body weight gain, suggesting a critical role of the gut microbiota composition in mediating the anti-obesity role of celastrol under HFD. Together, the findings revealed that celastrol reduces intestinal lipid absorption to antagonize obesity by resetting the gut microbiota profile under HFD feeding.}, }
@article {pmid33598486, year = {2021}, author = {Hemida, M and Vuori, KA and Moore, R and Anturaniemi, J and Hielm-Björkman, A}, title = {Early Life Modifiable Exposures and Their Association With Owner Reported Inflammatory Bowel Disease Symptoms in Adult Dogs.}, journal = {Frontiers in veterinary science}, volume = {8}, number = {}, pages = {552350}, pmid = {33598486}, issn = {2297-1769}, abstract = {Background: Inflammatory bowel disease (IBD) is an idiopathic multifactorial disease in humans and dogs, usually assigned to the interactions between genes, gut microbiota, diet, environment, and the immune system. We aimed to investigate the modifiable early life exposures associated with IBD in dogs. Materials and Methods: The study data was extracted from the validated owner-reported DogRisk food frequency questionnaire. This was a cross-sectional questionnaire-based study that tested 21 different early life dietary and environmental, demographic and genetic variables for their association with IBD or not, in adult dogs. A total of 7,015 dogs participated in this study. The study covered early life periods; prenatal, neonatal, early, and late postnatal periods. Two feeding patterns, a non-processed meat-based diet (NPMD) and an ultra-processed carbohydrate-based diet (UPCD) were studied. Data was analyzed using logistic regression analysis with a backward stepwise deletion. Results: From the final models we found that the NPMD during early and late postnatal periods were significantly associated with lower IBD risk later in life. The UPCD during the same periods was associated with a higher risk of IBD incidence. Also, the maternal diet during the neonatal period showed a non-significant trend of lower IBD risk in the offspring with the NPMD and a higher IBD risk with the UPCD. Additionally, the normal body weight of puppies during the first 6 months of age was associated with a lower risk of IBD in adulthood while, slim puppies associated significantly with IBD in adulthood. From the non-modifiable background variables, we identified the maternal history of IBD as the strongest risk factor for later incidence of IBD. Furthermore, male dogs were twice as likely to develop IBD as female dogs were. Conclusions: It is reassuring for owners to know that they themselves can have an impact on their dog's health. A high-fat, low-carbohydrate NPMD exposure during early life, and a normal body condition in puppyhood were significantly associated with less IBD in adult dogs. The opposite was true for UPCD exposure and abnormal body condition score in 6 month old puppies.}, }
@article {pmid33598417, year = {2020}, author = {Bendriss, G and Al-Ali, D and Shafiq, A and Laswi, I and Mhaimeed, N and Salameh, M and Burney, Z and Pillai, K and Chaari, A and Zakaria, D and Yousri, NA}, title = {Targeting the gut microbiome: A brief report on the awareness, practice, and readiness to engage in clinical interventions in Qatar.}, journal = {Qatar medical journal}, volume = {2020}, number = {3}, pages = {47}, pmid = {33598417}, issn = {0253-8253}, abstract = {BACKGROUND: There has been a growing global interest in the role of gut microbiota in the pathogenesis of diseases and the potentials of targeting the microbiome in clinical interventions. Very few clinical studies in Qatar focused on gut microbiome. This study aimed to assess the awareness of healthcare professionals, scientists, and the general public on the role of gut microbiota in health and diseases and, more specifically, in disorders of the gut-brain axis such as neurodevelopmental disorders (NDDs) or gastrointestinal (GI) disorders. It also aimed to evaluate the readiness of the population to engage in clinical trials involving dietary interventions or fecal transplants.<br><br>METHODS: A total of 156 participants were recruited to answer questionnaires-from healthcare professionals and scientists (HSs; n = 44) and the general public (n = 112). Participants from the general public self-reported their diagnosis of NDDs-autism or attention deficit hyperactivity disorder (n = 36)-or GI diseases or disorders (n = 18) or as having none of them (n = 58). Two questionnaires for HSs and for the general public were distributed, and basic descriptive and statistical analyses were conducted using the Fisher's exact test.<br><br>RESULTS: Among the participating HSs, 95% admitted that they had minimum to no knowledge on the role of gut microbes in health and diseases, and only 15.9% felt that their peers were knowledgeable about it. Nevertheless, 97.7% of HSs thought that gut microbiota should be considered when devising treatment plans as 79.1% believed that gut dysbiosis is involved in the pathogenesis of diseases. For the general public, 54% stated that they have read about studies on the potential benefits of microbes in the prevention, treatment, and management of diseases, with a higher proportion of them belonging to the GI group (p = 0.0523). The GI group was also more aware of the existence of the use of fecal transplants for treating their condition (p = 0.01935). Awareness was also reflected in participants' attempts to engage in dietary changes, as 40% tried a dietary intervention, which has noticeably changed their or their child's symptoms. This study reported a highly significant association between being exposed to multiple antibiotic courses before three years of age and being part of the NDD group (p = 0.0003). Public readiness to engage in interventions that target the gut microbiome, such as intensive dietary interventions or even fecal transplants, was perceived by HSs to be lower than what was stated by the public, with 87.96% of public being ready to engage in intensive dietary interventions and 66.98% in fecal transplants.<br><br>CONCLUSION: The study revealed that the role of gut microbes in health and diseases, and especially through the gut-brain axis, is still unclear in both the scientific community and general public. While acknowledging the importance of gut microbes, the lack of information regarding the link between lifestyle and gut microbes is considered to hold the public in the precontemplation/contemplation stages of the transtheoretical model of behavioral change. An interdisciplinary approach to new knowledge produced by microbiome studies is needed to run awareness campaigns and continue professional development activities on the benefits of lifestyle-based modulation of gut microbiome, thus engaging the general public in lifestyle changes and facilitating clinical research in human microbiome investigations in Qatar.}, }
@article {pmid33598183, year = {2021}, author = {Wang, Y and Cai, W and Wang, W and Shu, N and Zhang, Z and Hou, Q and Shan, C and Guo, Z}, title = {Analysis of microbial diversity and functional differences in different types of high-temperature Daqu.}, journal = {Food science &amp; nutrition}, volume = {9}, number = {2}, pages = {1003-1016}, pmid = {33598183}, issn = {2048-7177}, abstract = {Bacterial communities that enrich in high-temperature Daqu are important for the Chinese maotai-flavor liquor brewing process. However, the bacterial communities in three different types of high-temperature Daqu (white Daqu, black Daqu, and yellow Daqu) are still undercharacterized. In this study, the bacterial diversity of three different types of high-temperature Daqu was investigated using Illumina MiSeq high-throughput sequencing. The bacterial community of high-temperature Daqu is mainly composed of thermophilic bacteria, and seven bacterial phyla along with 262 bacterial genera were identified in all 30 high-temperature Daqu samples. Firmicutes, Actinobacteria, Proteobacteria, and Acidobacteria were the dominant bacterial phyla in high-temperature Daqu samples, while Thermoactinomyces, Staphylococcus, Lentibacillus, Bacillus, Kroppenstedtia, Saccharopolyspora, Streptomyces, and Brevibacterium were the dominant bacterial genera. The bacterial community structure of three different types of high-temperature Daqu was significantly different (p < .05). In addition, the results of microbiome phenotype prediction by BugBase and bacterial functional potential prediction using PICRUSt show that bacteria from different types of high-temperature Daqu have similar functions as well as phenotypes, and bacteria in high-temperature Daqu have vigorous metabolism in the transport and decomposition of amino acids and carbohydrates. These results offer a reference for the comprehensive understanding of bacterial diversity of high-temperature Daqu.}, }
@article {pmid33597941, year = {2021}, author = {Wahdan, SFM and Heintz-Buschart, A and Sansupa, C and Tanunchai, B and Wu, YT and Schädler, M and Noll, M and Purahong, W and Buscot, F}, title = {Targeting the Active Rhizosphere Microbiome of Trifolium pratense in Grassland Evidences a Stronger-Than-Expected Belowground Biodiversity-Ecosystem Functioning Link.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {629169}, pmid = {33597941}, issn = {1664-302X}, abstract = {The relationship between biodiversity and ecosystem functioning (BEF) is a central issue in soil and microbial ecology. To date, most belowground BEF studies focus on the diversity of microbes analyzed by barcoding on total DNA, which targets both active and inactive microbes. This approach creates a bias as it mixes the part of the microbiome currently steering processes that provide actual ecosystem functions with the part not directly involved. Using experimental extensive grasslands under current and future climate, we used the bromodeoxyuridine (BrdU) immunocapture technique combined with pair-end Illumina sequencing to characterize both total and active microbiomes (including both bacteria and fungi) in the rhizosphere of Trifolium pratense. Rhizosphere function was assessed by measuring the activity of three microbial extracellular enzymes (β-glucosidase, N-acetyl-glucosaminidase, and acid phosphatase), which play central roles in the C, N, and P acquisition. We showed that the richness of overall and specific functional groups of active microbes in rhizosphere soil significantly correlated with the measured enzyme activities, while total microbial richness did not. Active microbes of the rhizosphere represented 42.8 and 32.1% of the total bacterial and fungal taxa, respectively, and were taxonomically and functionally diverse. Nitrogen fixing bacteria were highly active in this system with 71% of the total operational taxonomic units (OTUs) assigned to this group detected as active. We found the total and active microbiomes to display different responses to variations in soil physicochemical factors in the grassland, but with some degree of resistance to a manipulation mimicking future climate. Our findings provide critical insights into the role of active microbes in defining soil ecosystem functions in a grassland ecosystem. We demonstrate that the relationship between biodiversity-ecosystem functioning in soil may be stronger than previously thought.}, }
@article {pmid33597669, year = {2021}, author = {Gupta, S and Shariff, M and Chaturvedi, G and Sharma, A and Goel, N and Yadav, M and Mortensen, MS and Sørensen, SJ and Mukerji, M and Chauhan, NS}, title = {Comparative analysis of the alveolar microbiome in COPD, ECOPD, Sarcoidosis, and ILD patients to identify respiratory illnesses specific microbial signatures.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {3963}, pmid = {33597669}, issn = {2045-2322}, support = {BT/PR10801/MED/29/826/2014//Department of Biotechnology, Ministry of Science and Technology, India/ ; BT/PR10801/MED/29/826/2014//Department of Biotechnology, Ministry of Science and Technology, India/ ; }, abstract = {Studying respiratory illness-specific microbial signatures and their interaction with other micro-residents could provide a better understanding of lung microbial ecology. Each respiratory illness has a specific disease etiology, however, so far no study has revealed disease-specific microbial markers. The present study was designed to determine disease-specific microbial features and their interactions with other residents in chronic obstructive pulmonary diseases (stable and exacerbated), sarcoidosis, and interstitial lung diseases. Broncho-alveolar lavage samples (n = 43) were analyzed by SSU rRNA gene sequencing to study the alveolar microbiome in these diseases. A predominance of Proteobacteria followed by Firmicutes, Bacteroidetes, Actinobacteria, and Fusobacteria was observed in all the disease subsets. Shannon diversity was significantly higher in stable COPD when compared to exacerbated chronic obstructive pulmonary disease (ECOPD) (p = 0.0061), and ILD patient samples (p = 0.037). The lung microbiome of the patients with stable COPD was more diverse in comparison to ECOPD and ILD patients (p < 0.001). Lefse analysis identified 40 disease-differentiating microbial features (LDA score (log10) > 4). Species network analysis indicated a significant correlation (p < 0.05) of diseases specific microbial signature with other lung microbiome members. The current study strengthens the proposed hypothesis that each respiratory illness has unique microbial signatures. These microbial signatures could be used as diagnostic markers to differentiate among various respiratory illnesses.}, }
@article {pmid33597514, year = {2021}, author = {Chen, C and Zhou, Y and Fu, H and Xiong, X and Fang, S and Jiang, H and Wu, J and Yang, H and Gao, J and Huang, L}, title = {Expanded catalog of microbial genes and metagenome-assembled genomes from the pig gut microbiome.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {1106}, pmid = {33597514}, issn = {2041-1723}, abstract = {Gut microbiota plays an important role in pig health and production. Still, availability of sequenced genomes and functional information for most pig gut microbes remains limited. Here we perform a landscape survey of the swine gut microbiome, spanning extensive sample sources by deep metagenomic sequencing resulting in an expanded gene catalog named pig integrated gene catalog (PIGC), containing 17,237,052 complete genes clustered at 90% protein identity from 787 gut metagenomes, of which 28% are unknown proteins. Using binning analysis, 6339 metagenome-assembled genomes (MAGs) were obtained, which were clustered to 2673 species-level genome bins (SGBs), among which 86% (2309) SGBs are unknown based on current databases. Using the present gene catalog and MAGs, we identified several strain-level differences between the gut microbiome of wild boars and commercial Duroc pigs. PIGC and MAGs provide expanded resources for swine gut microbiome-related research.}, }
@article {pmid33597342, year = {2021}, author = {Shimojo, N}, title = {[ALLERGIC DISEASES AND MICROBIOME].}, journal = {Arerugi = [Allergy]}, volume = {70}, number = {1}, pages = {19-25}, doi = {10.15036/arerugi.70.19}, pmid = {33597342}, issn = {0021-4884}, }
@article {pmid33597276, year = {2021}, author = {Angoa-Pérez, M and Kuhn, DM}, title = {Evidence for Modulation of Substance Use Disorders by the Gut Microbiome: Hidden in Plain Sight.}, journal = {Pharmacological reviews}, volume = {73}, number = {2}, pages = {571-596}, doi = {10.1124/pharmrev.120.000144}, pmid = {33597276}, issn = {1521-0081}, abstract = {The gut microbiome modulates neurochemical function and behavior and has been implicated in numerous central nervous system (CNS) diseases, including developmental, neurodegenerative, and psychiatric disorders. Substance use disorders (SUDs) remain a serious threat to the public well-being, yet gut microbiome involvement in drug abuse has received very little attention. Studies of the mechanisms underlying SUDs have naturally focused on CNS reward circuits. However, a significant body of research has accumulated over the past decade that has unwittingly provided strong support for gut microbiome participation in drug reward. β-Lactam antibiotics have been employed to increase glutamate transporter expression to reverse relapse-induced release of glutamate. Sodium butyrate has been used as a histone deacetylase inhibitor to prevent drug-induced epigenetic alterations. High-fat diets have been used to alter drug reward because of the extensive overlap of the circuitry mediating them. This review article casts these approaches in a different light and makes a compelling case for gut microbiome modulation of SUDs. Few factors alter the structure and composition of the gut microbiome more than antibiotics and a high-fat diet, and butyrate is an endogenous product of bacterial fermentation. Drugs such as cocaine, alcohol, opiates, and psychostimulants also modify the gut microbiome. Therefore, their effects must be viewed on a complex background of cotreatment-induced dysbiosis. Consideration of the gut microbiome in SUDs should have the beneficial effects of expanding the understanding of SUDs and aiding in the design of new therapies based on opposing the effects of abused drugs on the host's commensal bacterial community. SIGNIFICANCE STATEMENT: Proposed mechanisms underlying substance use disorders fail to acknowledge the impact of drugs of abuse on the gut microbiome. β-Lactam antibiotics, sodium butyrate, and high-fat diets are used to modify drug seeking and reward, overlooking the notable capacity of these treatments to alter the gut microbiome. This review aims to stimulate research on substance abuse-gut microbiome interactions by illustrating how drugs of abuse share with antibiotics, sodium butyrate, and fat-laden diets the ability to modify the host microbial community.}, }
@article {pmid33597039, year = {2021}, author = {Li, Z and Xia, J and Jiang, L and Tan, Y and An, Y and Zhu, X and Ruan, J and Chen, Z and Zhen, H and Ma, Y and Jie, Z and Xiao, L and Yang, H and Wang, J and Kristiansen, K and Xu, X and Jin, L and Nie, C and Krutmann, J and Liu, X and Wang, J}, title = {Characterization of the human skin resistome and identification of two microbiota cutotypes.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {47}, pmid = {33597039}, issn = {2049-2618}, support = {2017SHZDZX01//Shanghai Municipal Science and Technology Major Project/ ; 31521003//National Natural Science Foundation of China/ ; 81703097//National Natural Science Foundation of China/ ; 81770066//National Natural Science Foundation of China/ ; No. 2020YFC2002902//National Key Research and Development Program of China/ ; (No. JCYJ20170412153100794, No. JCYJ20180507183615145//Development and Reform Commission of Shenzhen Municipality (CN)/ ; 2019-I2M-5-066//CAMS Innovation Fund for Medical Science/ ; B13016//111 Project/ ; }, abstract = {BACKGROUND: The human skin microbiota is considered to be essential for skin homeostasis and barrier function. Comprehensive analyses of its function would substantially benefit from a catalog of reference genes derived from metagenomic sequencing. The existing catalog for the human skin microbiome is based on samples from limited individuals from a single cohort on reference genomes, which limits the coverage of global skin microbiome diversity.<br><br>RESULTS: In the present study, we have used shotgun metagenomics to newly sequence 822 skin samples from Han Chinese, which were subsequently combined with 538 previously sequenced North American samples to construct an integrated Human Skin Microbial Gene Catalog (iHSMGC). The iHSMGC comprised 10,930,638 genes with the detection of 4,879,024 new genes. Characterization of the human skin resistome based on iHSMGC confirmed that skin commensals, such as Staphylococcus spp, are an important reservoir of antibiotic resistance genes (ARGs). Further analyses of skin microbial ARGs detected microbe-specific and skin site-specific ARG signatures. Of note, the abundance of ARGs was significantly higher in Chinese than Americans, while multidrug-resistant bacteria (&quot;superbugs&quot;) existed on the skin of both Americans and Chinese. A detailed analysis of microbial signatures identified Moraxella osloensis as a species specific for Chinese skin. Importantly, Moraxella osloensis proved to be a signature species for one of two robust patterns of microbial networks present on Chinese skin, with Cutibacterium acnes indicating the second one. Each of such &quot;cutotypes&quot; was associated with distinct patterns of data-driven marker genes, functional modules, and host skin properties. The two cutotypes markedly differed in functional modules related to their metabolic characteristics, indicating that host-dependent trophic chains might underlie their development.<br><br>CONCLUSIONS: The development of the iHSMGC will facilitate further studies on the human skin microbiome. In the present study, it was used to further characterize the human skin resistome. It also allowed to discover the existence of two cutotypes on the human skin. The latter finding will contribute to a better understanding of the interpersonal complexity of the skin microbiome. Video abstract.}, }
@article {pmid33597028, year = {2021}, author = {Duncan, JS and Angell, JW and Richards, P and Lenzi, L and Staton, GJ and Grove-White, D and Clegg, S and Oikonomou, G and Carter, SD and Evans, NJ}, title = {The dysbiosis of ovine foot microbiome during the development and treatment of contagious ovine digital dermatitis.}, journal = {Animal microbiome}, volume = {3}, number = {1}, pages = {19}, pmid = {33597028}, issn = {2524-4671}, support = {BB/N002121/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {BACKGROUND: Contagious Ovine Digital Dermatitis (CODD) is an emerging and common infectious foot disease of sheep which causes severe welfare and economic problems for the sheep industry. The aetiology of the disease is not fully understood and control of the disease is problematic. The aim of this study was to investigate the polybacterial aetiopathogenesis of CODD and the effects of antibiotic treatment, in a longitudinal study of an experimentally induced disease outbreak using a 16S rRNA gene amplicon sequencing approach.<br><br>RESULTS: CODD was induced in 15/30 experimental sheep. During the development of CODD three distinct phenotypic lesion stages were observed. These were an initial interdigital dermatitis (ID) lesion, followed by a footrot (FR) lesion, then finally a CODD lesion. Distinct microbiota were observed for each lesion in terms of microbial diversity, clustering and composition. Porphyromonadaceae, Family XI, Veillonellaceae and Fusobacteriaceae were significantly associated with the diseased feet. Veillonellaceae and Fusobacteriaceae were most associated with the earlier stages of ID and footrot rather than CODD. Following antibiotic treatment of the sheep, the foot microbiota showed a strong tendency to return to the composition of the healthy state. The microbiota composition of CODD lesions collected by swab and biopsy methods were different. In particular, the Spirochaetaceae family were more abundant in samples collected by the biopsy method, suggesting that these bacteria are present in deeper tissues of the diseased foot.<br><br>CONCLUSION: In this study, CODD presented as part of a spectrum of poly-bacterial foot disease strongly associated with bacterial families Porphyromonadaceae, Family XI (a family in Clostridiales also known as Clostridium cluster XI), Veillonellaceae and Fusobacteriaceae which are predominately Gram-negative anaerobes. Following antibiotic treatment, the microbiome showed a strong tendency to return to the composition of the healthy state. The composition of the healthy foot microbiome does not influence susceptibility to CODD. Based on the data presented here and that CODD appears to be the severest end stage of sheep infectious foot disease lesions, better control of the initial ID and FR lesions would enable better control of CODD and enable better animal welfare.}, }
@article {pmid33597026, year = {2021}, author = {de Nies, L and Lopes, S and Busi, SB and Galata, V and Heintz-Buschart, A and Laczny, CC and May, P and Wilmes, P}, title = {PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {49}, pmid = {33597026}, issn = {2049-2618}, support = {CORE/BM/11333923//Fonds National de la Recherche Luxembourg/ ; PRIDE/11823097//Fonds National de la Recherche Luxembourg/ ; PRIDE/11823097//Fonds National de la Recherche Luxembourg/ ; PRIDE/11823097//Fonds National de la Recherche Luxembourg/ ; PRIDE/11823097//Fonds National de la Recherche Luxembourg/ ; 14701//Michael J. Fox Foundation/ ; ERC-CoG 863664//H2020 European Research Council/ ; }, abstract = {BACKGROUND: Pathogenic microorganisms cause disease by invading, colonizing, and damaging their host. Virulence factors including bacterial toxins contribute to pathogenicity. Additionally, antimicrobial resistance genes allow pathogens to evade otherwise curative treatments. To understand causal relationships between microbiome compositions, functioning, and disease, it is essential to identify virulence factors and antimicrobial resistance genes in situ. At present, there is a clear lack of computational approaches to simultaneously identify these factors in metagenomic datasets.<br><br>RESULTS: Here, we present PathoFact, a tool for the contextualized prediction of virulence factors, bacterial toxins, and antimicrobial resistance genes with high accuracy (0.921, 0.832 and 0.979, respectively) and specificity (0.957, 0.989 and 0.994). We evaluate the performance of PathoFact on simulated metagenomic datasets and perform a comparison to two other general workflows for the analysis of metagenomic data. PathoFact outperforms all existing workflows in predicting virulence factors and toxin genes. It performs comparably to one pipeline regarding the prediction of antimicrobial resistance while outperforming the others. We further demonstrate the performance of PathoFact on three publicly available case-control metagenomic datasets representing an actual infection as well as chronic diseases in which either pathogenic potential or bacterial toxins are hypothesized to play a role. In each case, we identify virulence factors and AMR genes which differentiated between the case and control groups, thereby revealing novel gene associations with the studied diseases.<br><br>CONCLUSION: PathoFact is an easy-to-use, modular, and reproducible pipeline for the identification of virulence factors, bacterial toxins, and antimicrobial resistance genes in metagenomic data. Additionally, our tool combines the prediction of these pathogenicity factors with the identification of mobile genetic elements. This provides further depth to the analysis by considering the genomic context of the pertinent genes. Furthermore, PathoFact's modules for virulence factors, toxins, and antimicrobial resistance genes can be applied independently, thereby making it a flexible and versatile tool. PathoFact, its models, and databases are freely available at https://pathofact.lcsb.uni.lu . Video abstract.}, }
@article {pmid33596993, year = {2021}, author = {Deehan, EC and Colin-Ramirez, E and Triador, L and Madsen, KL and Prado, CM and Field, CJ and Ball, GDC and Tan, Q and Orsso, C and Dinu, I and Pakseresht, M and Rubin, D and Sharma, AM and Tun, H and Walter, J and Newgard, CB and Freemark, M and Wine, E and Haqq, AM}, title = {Efficacy of metformin and fermentable fiber combination therapy in adolescents with severe obesity and insulin resistance: study protocol for a double-blind randomized controlled trial.}, journal = {Trials}, volume = {22}, number = {1}, pages = {148}, pmid = {33596993}, issn = {1745-6215}, abstract = {BACKGROUND: Accumulating evidence suggests that the metabolic effects of metformin and fermentable fibers are mediated, in part, through diverging or overlapping effects on the composition and metabolic functions of the gut microbiome. Pre-clinical animal models have established that the addition of fiber to metformin monotherapy improves glucose tolerance. However, possible synergistic effects of combination therapy (metformin plus fiber) have not been investigated in humans. Moreover, the underlying mechanisms of synergy have yet to be elucidated. The aim of this study is to compare in adolescents with obesity the metabolic effects of metformin and fermentable fibers in combination with those of metformin or fiber alone. We will also determine if therapeutic responses correlate with compositional and functional features of the gut microbiome.<br><br>METHODS: This is a parallel three-armed, double-blinded, randomized controlled trial. Adolescents (aged 12-18 years) with obesity, insulin resistance (IR), and a family history of type 2 diabetes mellitus (T2DM) will receive either metformin (850 mg p.o. twice/day), fermentable fibers (35 g/day), or a combination of metformin plus fiber for 12 months. Participants will be seen at baseline, 3, 6, and 12 months, with a phone follow-up at 1 and 9 months. Primary and secondary outcomes will be assessed at baseline, 6, and 12 months. The primary outcome is change in IR estimated by homeostatic model assessment of IR; key secondary outcomes include changes in the Matsuda index, oral disposition index, body mass index z-score, and fat mass to fat-free mass ratio. To gain mechanistic insight, endpoints that reflect host-microbiota interactions will also be assessed: obesity-related immune, metabolic, and satiety markers; humoral metabolites; and fecal microbiota composition, short-chain fatty acids, and bile acids.<br><br>DISCUSSION: This study will compare the potential metabolic benefits of fiber with those of metformin in adolescents with obesity, determine if metformin and fiber act synergistically to improve IR, and elucidate whether the metabolic benefits of metformin and fiber associate with changes in fecal microbiota composition and the output of health-related metabolites. This study will provide insight into the potential role of the gut microbiome as a target for enhancing the therapeutic efficacy of emerging treatments for T2DM prevention.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov NCT04578652 . Registered on 8 October 2020.}, }
@article {pmid33596852, year = {2021}, author = {Straub, TJ and Chou, WC and Manson, AL and Schreiber, HL and Walker, BJ and Desjardins, CA and Chapman, SB and Kaspar, KL and Kahsai, OJ and Traylor, E and Dodson, KW and Hullar, MAJ and Hultgren, SJ and Khoo, C and Earl, AM}, title = {Limited effects of long-term daily cranberry consumption on the gut microbiome in a placebo-controlled study of women with recurrent urinary tract infections.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {53}, pmid = {33596852}, issn = {1471-2180}, abstract = {BACKGROUND: Urinary tract infections (UTIs) affect 15 million women each year in the United States, with > 20% experiencing frequent recurrent UTIs. A recent placebo-controlled clinical trial found a 39% reduction in UTI symptoms among recurrent UTI sufferers who consumed a daily cranberry beverage for 24 weeks. Using metagenomic sequencing of stool from a subset of these trial participants, we assessed the impact of cranberry consumption on the gut microbiota, a reservoir for UTI-causing pathogens such as Escherichia coli, which causes > 80% of UTIs.<br><br>RESULTS: The overall taxonomic composition, community diversity, carriage of functional pathways and gene families, and relative abundances of the vast majority of observed bacterial taxa, including E. coli, were not changed significantly by cranberry consumption. However, one unnamed Flavonifractor species (OTU41), which represented ≤1% of the overall metagenome, was significantly less abundant in cranberry consumers compared to placebo at trial completion. Given Flavonifractor's association with negative human health effects, we sought to determine OTU41 characteristic genes that may explain its differential abundance and/or relationship to key host functions. Using comparative genomic and metagenomic techniques, we identified genes in OTU41 related to transport and metabolism of various compounds, including tryptophan and cobalamin, which have been shown to play roles in host-microbe interactions.<br><br>CONCLUSION: While our results indicated that cranberry juice consumption had little impact on global measures of the microbiome, we found one unnamed Flavonifractor species differed significantly between study arms. This suggests further studies are needed to assess the role of cranberry consumption and Flavonifractor in health and wellbeing in the context of recurrent UTI.<br><br>TRIAL REGISTRATION: Clinical trial registration number: ClinicalTrials.gov NCT01776021 .}, }
@article {pmid33596768, year = {2021}, author = {Balakrishnan, B and Selvaraju, V and Chen, J and Ayine, P and Yang, L and Ramesh Babu, J and Geetha, T and Taneja, V}, title = {Ethnic variability associating gut and oral microbiome with obesity in children.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1-15}, doi = {10.1080/19490976.2021.1882926}, pmid = {33596768}, issn = {1949-0984}, abstract = {Obesity is a growing worldwide problem that generally starts in the early years of life and affects minorities more often than Whites. Thus, there is an urgency to determine factors that can be used as targets as indicators of obesity. In this study, we attempt to generate a profile of gut and oral microbial clades predictive of disease status in African American (AA) and European American (EA) children. 16S rDNA sequencing of the gut and saliva microbial profiles were correlated with salivary amylase, socioeconomic factors (e.g., education and family income), and obesity in both ethnic populations. Gut and oral microbial diversity between AA and EA children showed significant differences in alpha-, beta-, and taxa-level diversity. While gut microbial diversity between obese and non-obese was not evident in EA children, the abundance of gut Klebsiella and Magasphaera was associated with obesity in AA children. In contrast, an abundance of oral Aggregatibacter and Eikenella in obese EA children was observed. These observations suggest an ethnicity-specific association with gut and oral microbial profiles. Socioeconomic factors influenced microbiota in obesity, which were ethnicity dependent, suggesting that specific approaches to confront obesity are required for both populations.}, }
@article {pmid33596387, year = {2021}, author = {Mac Aogáin, M and Baker, JM and Dickson, RP}, title = {On Bugs and Blowholes: Why is Aspiration the Rule, Not the Exception?.}, journal = {American journal of respiratory and critical care medicine}, volume = {}, number = {}, pages = {}, doi = {10.1164/rccm.202011-4257ED}, pmid = {33596387}, issn = {1535-4970}, }
@article {pmid33596345, year = {2021}, author = {Gantuya, B and El Serag, HB and Saruuljavkhlan, B and Azzaya, D and Matsumoto, T and Uchida, T and Oyuntsetseg, K and Oyunbileg, N and Davaadorj, D and Yamaoka, Y}, title = {Advantage of 16S rRNA amplicon sequencing in Helicobacter pylori diagnosis.}, journal = {Helicobacter}, volume = {}, number = {}, pages = {e12790}, doi = {10.1111/hel.12790}, pmid = {33596345}, issn = {1523-5378}, support = {RP150587//Cancer Prevention and Research Institute of Texas/ ; 16H06279//Ministry of Education, Culture, Sports, Science and Technology/ ; 18K16182//Ministry of Education, Culture, Sports, Science and Technology/ ; 18KK0266//Ministry of Education, Culture, Sports, Science and Technology/ ; 19H03473//Ministry of Education, Culture, Sports, Science and Technology/ ; 221S0002//Ministry of Education, Culture, Sports, Science and Technology/ ; NIDDK P30 DK 56338//Center for Gastrointestinal Development, Infection, and Injury/ ; }, abstract = {BACKGROUND: 16S rRNA amplicon sequencing is an accurate method of detecting microbial infection without culture. It is unclear if sequencing has additional benefits over routine diagnostic methods for Helicobacter pylori testing.<br><br>METHODS: We enrolled Mongolian volunteers with dyspepsia. Using routine diagnostic methods, positive H. pylori was defined as positive results on histology/immunohistochemistry, culture, rapid urease test, or serology; negative H. pylori was defined by negative results from all these tests. We performed 16S rRNA sequencing on gastric biopsy specimens and calculated cutoffs for operational taxonomic units (OTUs) and relative abundance (RA) to define positive results using ROC curves.<br><br>RESULTS: We examined 161 individuals with a mean age of 43.6 years, and 64.6% were women. Using routine diagnostic methods, 122 (75.8%) participants were H. pylori positive, the sensitivity and specificity for 16S rRNA sequencing were 94.3% and 82.1% or 93.4% and 82.1% when cutoff values were set to 1113 (OTU number) or 4.4% RA, respectively (both p < .001). When combining the validated values, the concordance rate was high (91.1%); however, 16S rRNA sequencing had additional positive yield in 9 cases (5.6%) compared with routine diagnostic methods, and much greater additional positive yield compared to histopathology/IHC, culture, RUT, serology separately with 12 (7.4%), 37 (23.0%) and 43 (26.7%).<br><br>CONCLUSION: 16S rRNA amplicon sequencing detects potentially important proportion of H. pylori-positive cases that test negative with routine diagnostic methods. The quantitative number of H. pylori can help to understand how it can be changing by diseases and RA give opportunity to understand how H. pylori communicate with other microbiota.}, }
@article {pmid33596339, year = {2021}, author = {Wu, ZF and Zou, K and Xiang, CJ and Jin, ZJ and Ding, HH and Xu, S and Wu, GN and Wang, YH and Wu, XY and Chen, C and Yao, XQ and Zhang, JF and Liu, FK}, title = {Helicobacter pylori infection is associated with the co-occurrence of bacteria in the oral cavity and the gastric mucosa.}, journal = {Helicobacter}, volume = {}, number = {}, pages = {e12786}, doi = {10.1111/hel.12786}, pmid = {33596339}, issn = {1523-5378}, support = {K2019029//Natural Science Foundation of Jiangsu Commission of Health/ ; Y2018CX83//Youth Projects of Jiangsu traditional Chinese Medicine Hospital/ ; 81473458//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Pathogens capable of impacting gastrointestinal tract tumor development are located in the oral cavity, but whether these oral bacteria are able to colonize the gastric mucosa in gastric cancer (GC) patients and whether Helicobacter pylori infection can influence this process remains to be established.<br><br>METHODS: Microbial 16S rDNA deep sequencing was conducted to characterize bacteria present in paired gastric mucosa and tongue coating samples in 27 patients with superficial gastritis (SG) and 11 GC patients.<br><br>RESULTS: While the overall composition of the gastric mucosa and tongue coating microbiomes differed substantially, certain bacteria were present in both of these communities. The co-occurrence of bacteria between the tongue coating and gastric mucosa differed significantly between SG and GC patients. Of the 15 most abundant shared oral bacteria genera (the core shared oral bacteria), which were associated with differences in microbiota composition between these tongue coating and gastric mucosa, three were enriched in the gastric mucosa of GC patients relative to SG patients, whereas, 12 were depleted in GC patient samples. Furthermore, the prevalence and relative abundance of these core shared oral bacteria in the gastric mucosa were also linked to H. pylori infection status, and the core shared oral bacteria were also associated with the overall composition of the gastric mucosal microbiome.<br><br>CONCLUSIONS: Helicobacter pylori infections are linked to the co-occurrence of bacteria in the oral microbiome and the gastric mucosal microbiome. Ectopic colonization of oral microbes may be a primary driver of H. pylori-induced gastric microbial dysbiosis in patients with GC.}, }
@article {pmid33596076, year = {2021}, author = {Palmer, KS and Makarewicz, CA and Tishkin, AA and Tur, SS and Chunag, A and Diimajav, E and Jamsranjav, B and Buckley, M}, title = {Comparing the Use of Magnetic Beads with Ultrafiltration for Ancient Dental Calculus Proteomics.}, journal = {Journal of proteome research}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jproteome.0c00862}, pmid = {33596076}, issn = {1535-3907}, abstract = {Over the past two decades, proteomic analysis has greatly developed in application to the field of biomolecular archaeology, coinciding with advancements in LC-MS/MS instrumentation sensitivity and improvements in sample preparation methods. Recently, human dental calculus has received much attention for its well-preserved proteomes locked in mineralized dental plaque which stores information on human diets and the oral microbiome otherwise invisible to other biomolecular approaches. Maximizing proteome recovery in ancient dental calculus, available only in minute quantities and irreplaceable after destructive analysis, is of paramount importance. Here, we compare the more traditional ultrafiltration-based and acetone precipitation approaches with the newer paramagnetic bead approach in order to test the influence of demineralization acid on recovered proteome complexity obtained from specimens as well as the sequence coverages matched for significant proteins. We found that a protocol utilizing EDTA combined with paramagnetic beads increased proteome complexity, in some cases doubling the number of unique peptides and number of proteins matched, compared to protocols involving the use of HCl and either acetone precipitation or ultrafiltration. Although the increase in the number of proteins was almost exclusively of bacterial origin, a development that has implications for the study of diseases within these ancient populations, an increase in the peptide number for the dairy proteins β-lactoglobulin and casein was also observed reflecting an increase in sequence coverage for these dietary proteins of interest. We also consider structural explanations for the discrepancies observed between these two key dietary proteins preserved in archaeological dental calculus.}, }
@article {pmid33595467, year = {2021}, author = {Shivaji, S}, title = {A systematic review of gut microbiome and ocular inflammatory diseases: Are they associated?.}, journal = {Indian journal of ophthalmology}, volume = {69}, number = {3}, pages = {535-542}, doi = {10.4103/ijo.IJO_1362_20}, pmid = {33595467}, issn = {1998-3689}, abstract = {The primary focus of this review was to establish the possible association of dysbiotic changes in the gut bacterial microbiomes with both intestinal and extra-intestinal diseases with emphasis on ocular diseases such as bacterial keratitis, fungal keratitis, uveitis, age-related macular degeneration, and ocular mucosal diseases. For this particular purpose, a systematic search was conducted using PubMed and Google Scholar for publications related to gut microbiome and human health (using the keywords: gut microbiome, ocular disease, dysbiosis, keratitis, uveitis, and AMD). The predictions are that microbiome studies would help to unravel dysbiotic changes in the gut bacterial microbiome at the taxonomic and functional level and thus form the basis to mitigate inflammatory diseases of the eye by using nutritional supplements or fecal microbiota transplantation.}, }
@article {pmid33595107, year = {2021}, author = {Wang, C}, title = {Sex-specific metabolic changes induced by high fructose corn syrup during adolescence: Novel evidence from metabolomic and microbiome analyses in mice.}, journal = {The Journal of physiology}, volume = {}, number = {}, pages = {}, doi = {10.1113/JP281388}, pmid = {33595107}, issn = {1469-7793}, }
@article {pmid33594816, year = {2021}, author = {Tian, P and Bastiaanssen, TFS and Song, L and Jiang, B and Zhang, X and Zhao, J and Zhang, H and Chen, W and Cryan, JF and Wang, G}, title = {Unravelling the Microbial Mechanisms Underlying the Psychobiotic Potential of a Bifidobacterium breve Strain.}, journal = {Molecular nutrition &amp; food research}, volume = {}, number = {}, pages = {e2000704}, doi = {10.1002/mnfr.202000704}, pmid = {33594816}, issn = {1613-4133}, abstract = {SCOPE: The antidepressant-like effect of psychobiotics has been observed in both pre-clinical and clinical studies, but the molecular mechanisms of action are largely unclear. To address this, the psychobiotic strain Bifidobacterium breve CCFM1025 was investigated for its genomic features, metabolic features, and gut microbial and metabolic modulation effect.<br><br>METHODS AND RESULTS: Unlike Bifidobacterium breve FHLJDQ3M5, CCFM1025 significantly decreased the chronically stressed mice's depressive-like behaviors and neurological abnormalities. CCFM1025 has more genes encoding glycoside hydrolases when comparing to FHLJDQ3M5's genome, which means CCFM1025 has a superior carbohydrate utilization capacity and living adaptivity in the gut. CCFM1025 also produced higher levels of neuromodulatory metabolites, including hypoxanthine, tryptophan, and nicotinate. The administration of CCFM1025 reshaped the gut microbiome of chronically stressed mice. It resulted in higher cecal xanthine, tryptophan, short-chain fatty acid levels, and enhanced fatty acid and tryptophan biosynthesis capability in the gut-brain interaction (identified by in silico analyses) than FHLJDQ3M5-treated mice.<br><br>CONCLUSIONS: Genomic and metabolic features involving glycoside hydrolases and neuromodulatory metabolites may determine the antidepressant-like effect of Bifidobacterium breve CCFM1025. Psychobiotics' characterization in this manner may provide guidelines for developing novel psychopharmacological agents in the future. This article is protected by copyright. All rights reserved.}, }
@article {pmid33594693, year = {2021}, author = {Brandl, C and Bucci, L and Schett, G and Zaiss, MM}, title = {Crossing the barriers: Revisiting the gut feeling in rheumatoid arthritis.}, journal = {European journal of immunology}, volume = {}, number = {}, pages = {}, doi = {10.1002/eji.202048876}, pmid = {33594693}, issn = {1521-4141}, abstract = {To avoid autoimmunity, it is essential to keep the balance between the defence against pathogens and the maintenance of tolerance to self-antigens. Mucosal inflammation may lead to breakdown of tolerance and activation of autoreactive cells. Growing evidence suggests a major contribution of gut microbiota to the onset of chronic, autoimmune inflammatory diseases, including rheumatoid arthritis (RA). RA patients show significant differences in the composition of gut microbiota compared to healthy controls, and in murine arthritis models certain bacteria can induce inflammatory Th17 responses or autoantibody production. The gut microbiota plays an important role in regulating the balance between immunogenic and tolerogenic immune responses. The intestinal barrier is the site of the body where most host-microbiota interaction takes place. Certain microbiota or their metabolites can cause a break in homeostasis by affecting the intestinal barrier integrity and permeability. However, an intact intestinal barrier is essential to separate the intestinal epithelium from toxins, microorganisms and antigens in the gut lumen. This review will focus on the correlation between a leaky gut and the onset of arthritis. Furthermore, it will be discussed how targeting the intestinal barrier function by dietary changes might provide an opportunity to modulate the development of RA. This article is protected by copyright. All rights reserved.}, }
@article {pmid33594547, year = {2021}, author = {Katsoula, A and Vasileiadis, S and Karamanoli, K and Vokou, D and Karpouzas, DG}, title = {Factors Structuring the Epiphytic Archaeal and Fungal Communities in a Semi-arid Mediterranean Ecosystem.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33594547}, issn = {1432-184X}, support = {-//State Scholarship Foundation of Greece/ ; -//European Social Fund (ESF) and National Resources/ ; -//General Secretariat of Research and Technology, Greece/ ; }, abstract = {The phyllosphere microbiome exerts a strong effect on plants' productivity, and its composition is determined by various factors. To date, most phyllosphere studies have focused on bacteria, while fungi and especially archaea have been overlooked. We studied the effects of plant host and season on the abundance and diversity of the epiphytic archaeal and fungal communities in a typical semi-arid Mediterranean ecosystem. We collected leaves in two largely contrasting seasons (summer and winter) from eight perennial species of varying attributes which could be grouped into the following: (i) high-canopy, evergreen sclerophyllοus shrubs with leathery leaves, and low-canopy, either semi-deciduous shrubs or non-woody perennials with non-leathery leaves, and (ii) aromatic and non-aromatic plants. We determined the abundance of epiphytic Crenarchaea, total fungi, Alternaria and Cladosporium (main airborne fungi) via q-PCR and the structure of the epiphytic archaeal and fungal communities via amplicon sequencing. We observed a strong seasonal effect with all microbial groups examined showing higher abundance in summer. Plant host and season were equally important determinants of the composition of the fungal community consisted mostly of Ascomycota, with Hypocreales dominating in winter and Capnodiales and Pleosporales in summer. In contrast, the archaeal community showed plant host driven patterns dominated by the Soil Crenarchaeotic Group (SCG) and Aenigmarchaeota. Plant habit and aromatic nature exhibited filtering effects only on the epiphytic fungal communities. Our study provides a first in-depth analysis of the key determinants shaping the phyllosphere archaeal and fungal communities of a semi-arid Mediterranean ecosystem.}, }
@article {pmid33594519, year = {2021}, author = {Souders, CL and Zubcevic, J and Martyniuk, CJ}, title = {Tumor Necrosis Factor Alpha and the Gastrointestinal Epithelium: Implications for the Gut-Brain Axis and Hypertension.}, journal = {Cellular and molecular neurobiology}, volume = {}, number = {}, pages = {}, pmid = {33594519}, issn = {1573-6830}, support = {1R56HL136692-01//National Institute of Health/ ; R21AT010192/NH/NIH HHS/United States ; Graduate Student Fellowship//University of Florida/ ; }, abstract = {The colonic epithelium is the site of production and transport of many vasoactive metabolites and neurotransmitters that can modulate the immune system, affect cellular metabolism, and subsequently regulate blood pressure. As an important interface between the microbiome and its host, the colon can contribute to the development of hypertension. In this critical review, we highlight the role of colonic inflammation and microbial metabolites on the gut brain axis in the pathology of hypertension, with special emphasis on the interaction between tumor necrosis factor α (TNFα) and short chain fatty acid (SCFA) metabolites. Here, we review the current literature and identify novel pathways in the colonic epithelium related to hypertension. A network analysis on transcriptome data previously generated in spontaneously hypertensive rats (SHR) and Wistar-Kyoto (WKY) rats reveals differences in several pathways associated with inflammation involving TNFα (NF-κB and STAT Expression Targets) as well as oxidative stress. We also identify down-regulation of networks associated with gastrointestinal function, cardiovascular function, enteric nervous system function, and cholinergic and adrenergic transmission. The analysis also uncovered transcriptome responses related to glycolysis, butyrate oxidation, and mitochondrial function, in addition to gut neuropeptides that serve as modulators of blood pressure and metabolic function. We present a model for the role of TNFα in regulating bacterial metabolite transport and neuropeptide signaling in the gastrointestinal system, highlighting the complexity of host-microbiota interactions in hypertension.}, }
@article {pmid33594506, year = {2021}, author = {Lee, S and Jang, EJ and Jo, J and Park, SJ and Ryu, HG}, title = {Long-term impacts of appendectomy associated with increased incidence of inflammatory bowel disease, infection, and colorectal cancer.}, journal = {International journal of colorectal disease}, volume = {}, number = {}, pages = {}, pmid = {33594506}, issn = {1432-1262}, abstract = {PURPOSE: Although the appendix has been suggested to play a role in maintaining the gut microbiome and immune system, the ramifications of appendectomy on the development inflammatory bowel disease, sepsis, and colorectal cancer are yet to be determined. The purpose of this study was to evaluate the potential long-term impacts of appendectomy, with a focus on inflammatory bowel disease, infection, and colorectal cancer, using the National Healthcare Insurance Service (NHIS) database of Korea.<br><br>METHODS: The National Healthcare Insurance Service database in Korea was used for analysis. Adult patients who received appendectomy between 2005 and 2013 were identified. The control group consisted of patients who did not receive appendectomy were matched by baseline characteristics including comorbidities and frequency of healthcare resource utilization. The primary outcome was the incidence-rate ratio (IRR) of Crohn's disease, ulcerative colitis, Clostridium difficile infection, sepsis, and colorectal cancer after appendectomy or the index date.<br><br>RESULTS: We identified 914,208 patients who underwent appendectomy, and after matching with control patients, a total of 486,844 patients were included for analysis. Patients who underwent appendectomy showed a significantly higher incidence of Crohn's disease (IRR 4.40, 95% confidence interval (CI) 3.78-5.13) and ulcerative colitis (IRR 1.78, 95% CI 1.63-1.93) compared to the control group during the 5-year follow-up period. The associations between appendectomy and Clostridium difficile infection, sepsis, and colorectal cancer were all found to be significant.<br><br>CONCLUSION: Patients who underwent appendectomy may be at increased risk for developing Crohn's disease, ulcerative colitis, Clostridium difficile infection, sepsis, and colorectal cancer.}, }
@article {pmid33594458, year = {2021}, author = {Yao, T and Wang, Z and Liang, X and Liu, C and Yu, Z and Han, X and Liu, R and Liu, Y and Liu, C and Chen, L}, title = {Signatures of vaginal microbiota by 16S rRNA gene: potential bio-geographical application in Chinese Han from three regions of China.}, journal = {International journal of legal medicine}, volume = {}, number = {}, pages = {}, pmid = {33594458}, issn = {1437-1596}, support = {2020A1515010938//the Natural Science Foundation of Guangdong Province/ ; 2019030016//the Science and Technology Program of Guangzhou, China/ ; KF1914//the Opening Fund of Shanghai Key Laboratory of Forensic Medicine (Institute of Forensic Science, Ministry of Justice, China)/ ; }, abstract = {The human microbiome is expected to be a new and promising tool for classification of human epithelial materials. Vaginal fluids are one of the most common biological samples in forensic sexual assault cases, and its identification is crucial to accurately determine the nature of the case. With the development of molecular biology technologies, the concept of vaginal microflora in different physiological states, ethnic groups, and geography is constantly improved. In this study, we conducted high-throughput sequencing of the V3-V4 hypervariable regions of the 16S rRNA gene in vaginal samples from Henan, Guangdong, and Xinjiang populations, in an attempt to reveal more information about the vaginal microflora in different regions. The results showed that the bio-geographical factors might affect the relative abundance of some vaginal microflora, but there was no significant difference in the composition of dominant bacteria in the vagina, which was mainly composed of Lactobacillus and Gardnerella. However, prediction models based on the random forest algorithm suggested that we might be able to distinguish vaginal fluids from populations of different regions according to the species-level OTUs in low abundance. It is promising that microbiome-based methods could provide more personal information when being attempted to trace the origin of body fluids.}, }
@article {pmid33594006, year = {2021}, author = {Aasmets, O and Lüll, K and Lang, JM and Pan, C and Kuusisto, J and Fischer, K and Laakso, M and Lusis, AJ and Org, E}, title = {Machine Learning Reveals Time-Varying Microbial Predictors with Complex Effects on Glucose Regulation.}, journal = {mSystems}, volume = {6}, number = {1}, pages = {}, pmid = {33594006}, issn = {2379-5077}, abstract = {The incidence of type 2 diabetes (T2D) has been increasing globally, and a growing body of evidence links type 2 diabetes with altered microbiota composition. Type 2 diabetes is preceded by a long prediabetic state characterized by changes in various metabolic parameters. We tested whether the gut microbiome could have predictive potential for T2D development during the healthy and prediabetic disease stages. We used prospective data of 608 well-phenotyped Finnish men collected from the population-based Metabolic Syndrome in Men (METSIM) study to build machine learning models for predicting continuous glucose and insulin measures in a shorter (1.5 year) and longer (4 year) period. Our results show that the inclusion of the gut microbiome improves prediction accuracy for modeling T2D-associated parameters such as glycosylated hemoglobin and insulin measures. We identified novel microbial biomarkers and described their effects on the predictions using interpretable machine learning techniques, which revealed complex linear and nonlinear associations. Additionally, the modeling strategy carried out allowed us to compare the stability of model performance and biomarker selection, also revealing differences in short-term and long-term predictions. The identified microbiome biomarkers provide a predictive measure for various metabolic traits related to T2D, thus providing an additional parameter for personal risk assessment. Our work also highlights the need for robust modeling strategies and the value of interpretable machine learning.IMPORTANCE Recent studies have shown a clear link between gut microbiota and type 2 diabetes. However, current results are based on cross-sectional studies that aim to determine the microbial dysbiosis when the disease is already prevalent. In order to consider the microbiome as a factor in disease risk assessment, prospective studies are needed. Our study is the first study that assesses the gut microbiome as a predictive measure for several type 2 diabetes-associated parameters in a longitudinal study setting. Our results revealed a number of novel microbial biomarkers that can improve the prediction accuracy for continuous insulin measures and glycosylated hemoglobin levels. These results make the prospect of using the microbiome in personalized medicine promising.}, }
@article {pmid33594005, year = {2021}, author = {Marotz, C and Morton, JT and Navarro, P and Coker, J and Belda-Ferre, P and Knight, R and Zengler, K}, title = {Quantifying Live Microbial Load in Human Saliva Samples over Time Reveals Stable Composition and Dynamic Load.}, journal = {mSystems}, volume = {6}, number = {1}, pages = {}, pmid = {33594005}, issn = {2379-5077}, abstract = {Evaluating microbial community composition through next-generation sequencing has become increasingly accessible. However, metagenomic sequencing data sets provide researchers with only a snapshot of a dynamic ecosystem and do not provide information about the total microbial number, or load, of a sample. Additionally, DNA can be detected long after a microorganism is dead, making it unsafe to assume that all microbial sequences detected in a community came from living organisms. By combining relic DNA removal by propidium monoazide (PMA) with microbial quantification with flow cytometry, we present a novel workflow to quantify live microbial load in parallel with metagenomic sequencing. We applied this method to unstimulated saliva samples, which can easily be collected longitudinally and standardized by passive collection time. We found that the number of live microorganisms detected in saliva was inversely correlated with salivary flow rate and fluctuated by an order of magnitude throughout the day in healthy individuals. In an acute perturbation experiment, alcohol-free mouthwash resulted in a massive decrease in live bacteria, which would have been missed if we did not consider dead cell signal. While removing relic DNA from saliva samples did not greatly impact the microbial composition, it did increase our resolution among samples collected over time. These results provide novel insight into the dynamic nature of host-associated microbiomes and underline the importance of applying scale-invariant tools in the analysis of next-generation sequencing data sets.IMPORTANCE Human microbiomes are dynamic ecosystems often composed of hundreds of unique microbial taxa. To detect fluctuations over time in the human oral microbiome, we developed a novel workflow to quantify live microbial cells with flow cytometry in parallel with next-generation sequencing, and applied this method to over 150 unstimulated, timed saliva samples. Microbial load was inversely correlated with salivary flow rate and fluctuated by an order of magnitude within a single participant throughout the day. Removing relic DNA improved our ability to distinguish samples over time and revealed that the percentage of sequenced bacteria in a given saliva sample that are alive can range from nearly 0% up to 100% throughout a typical day. These findings highlight the dynamic ecosystem of the human oral microbiome and the benefit of removing relic DNA signals in longitudinal microbiome study designs.}, }
@article {pmid33594001, year = {2021}, author = {Schneider, AN and Sundh, J and Sundström, G and Richau, K and Delhomme, N and Grabherr, M and Hurry, V and Street, NR}, title = {Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce.}, journal = {mSystems}, volume = {6}, number = {1}, pages = {}, pmid = {33594001}, issn = {2379-5077}, abstract = {The health, growth, and fitness of boreal forest trees are impacted and improved by their associated microbiomes. Microbial gene expression and functional activity can be assayed with RNA sequencing (RNA-Seq) data from host samples. In contrast, phylogenetic marker gene amplicon sequencing data are used to assess taxonomic composition and community structure of the microbiome. Few studies have considered how much of this structural and taxonomic information is included in transcriptomic data from matched samples. Here, we described fungal communities using both host-derived RNA-Seq and fungal ITS1 DNA amplicon sequencing to compare the outcomes between the methods. We used a panel of root and needle samples from the coniferous tree species Picea abies (Norway spruce) growing in untreated (nutrient-deficient) and nutrient-enriched plots at the Flakaliden forest research site in boreal northern Sweden. We show that the relationship between samples and alpha and beta diversity indicated by the fungal transcriptome is in agreement with that generated by the ITS data, while also identifying a lack of taxonomic overlap due to limitations imposed by current database coverage. Furthermore, we demonstrate how metatranscriptomics data additionally provide biologically informative functional insights. At the community level, there were changes in starch and sucrose metabolism, biosynthesis of amino acids, and pentose and glucuronate interconversions, while processing of organic macromolecules, including aromatic and heterocyclic compounds, was enriched in transcripts assigned to the genus CortinariusIMPORTANCE A deeper understanding of microbial communities associated with plants is revealing their importance for plant health and productivity. RNA extracted from plant field samples represents the host and other organisms present. Typically, gene expression studies focus on the plant component or, in a limited number of studies, expression in one or more associated organisms. However, metatranscriptomic data are rarely used for taxonomic profiling, which is currently performed using amplicon approaches. We created an assembly-based, reproducible, and hardware-agnostic workflow to taxonomically and functionally annotate fungal RNA-Seq data obtained from Norway spruce roots, which we compared to matching ITS amplicon sequencing data. While we identified some limitations and caveats, we show that functional, taxonomic, and compositional insights can all be obtained from RNA-Seq data. These findings highlight the potential of metatranscriptomics to advance our understanding of interaction, response, and effect between host plants and their associated microbial communities.}, }
@article {pmid33593974, year = {2021}, author = {Graf, J and Ledala, N and Caimano, MJ and Jackson, E and Gratalo, D and Fasulo, D and Driscoll, MD and Coleman, S and Matson, AP}, title = {High-Resolution Differentiation of Enteric Bacteria in Premature Infant Fecal Microbiomes Using a Novel rRNA Amplicon.}, journal = {mBio}, volume = {12}, number = {1}, pages = {}, pmid = {33593974}, issn = {2150-7511}, abstract = {Identifying and tracking microbial strains as microbiomes evolve are major challenges in the field of microbiome research. We utilized a new sequencing kit that combines DNA extraction with PCR amplification of a large region of the rRNA operon and downstream bioinformatic data analysis. Longitudinal microbiome samples of coadmitted twins from two different neonatal intensive care units (NICUs) were analyzed using an ∼2,500-base amplicon that spans the 16S and 23S rRNA genes and mapped to a new, custom 16S-23S rRNA database. Amplicon sequence variants (ASVs) inferred using DADA2 provided sufficient resolution for the differentiation of rRNA variants from closely related but not previously sequenced Klebsiella, Escherichia coli, and Enterobacter strains, among the first bacteria colonizing the gut of these infants after admission to the NICU. Distinct ASV groups (fingerprints) were monitored between coadmitted twins over time, demonstrating the potential to track the source and spread of both commensals and pathogens. The high-resolution taxonomy obtained from long amplicon sequencing enables the tracking of strains temporally and spatially as microbiomes are established in infants in the hospital environment.IMPORTANCE Achieving strain-level resolution is a major obstacle for source tracking and temporal studies of microbiomes. In this study, we describe a novel deep-sequencing approach that provides species- and strain-level resolution of the neonatal microbiome. Using Klebsiella, E. coli, and Enterobacter as examples, we could monitor their temporal dynamics after antibiotic treatment and in pairs of twins. The strain-level resolution, combined with the greater sequencing depth and decreased cost per read of PacBio Sequel 2, enables this advantageous source- and strain-tracking analysis method to be implemented widely across more complex microbiomes.}, }
@article {pmid33593961, year = {2021}, author = {Molyneaux, PL}, title = {The microbiome in IPF: tissue is not the issue.}, journal = {Thorax}, volume = {76}, number = {3}, pages = {218}, doi = {10.1136/thoraxjnl-2020-216330}, pmid = {33593961}, issn = {1468-3296}, }
@article {pmid33593943, year = {2021}, author = {Andersen, SB and Schluter, J}, title = {A metagenomics approach to investigate microbiome sociobiology.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {10}, pages = {}, pmid = {33593943}, issn = {1091-6490}, }
@article {pmid33593881, year = {2021}, author = {Shaikh, FY and White, JR and Gills, JJ and Hakozaki, T and Richard, C and Routy, B and Okuma, Y and Usyk, M and Pandey, A and Weber, JS and Ahn, J and Lipson, EJ and Naidoo, J and Pardoll, DM and Sears, CL}, title = {A uniform computational approach improved on existing pipelines to reveal microbiome biomarkers of non-response to immune checkpoint inhibitors.}, journal = {Clinical cancer research : an official journal of the American Association for Cancer Research}, volume = {}, number = {}, pages = {}, doi = {10.1158/1078-0432.CCR-20-4834}, pmid = {33593881}, issn = {1557-3265}, abstract = {PURPOSE: While immune checkpoint inhibitors (ICIs) have revolutionized the treatment of cancer by producing durable anti-tumor responses, only 10-30% of treated patients respond and the ability to predict clinical benefit remains elusive. Several studies, small in size and using variable analytical methods, suggest the gut microbiome may be a novel, modifiable biomarker for tumor response rates, but the specific bacteria or bacterial communities putatively impacting ICI responses have been inconsistent across the studied populations.<br><br>EXPERIMENTAL DESIGN: We have re-analyzed the available raw 16S rRNA amplicon and metagenomic sequencing data across five recently published ICI studies (n=303 unique patients) using a uniform computational approach.<br><br>RESULTS: Herein, we identify novel bacterial signals associated with clinical response (R) or nonresponse (NR) and develop an Integrated Microbiome Prediction Index. Unexpectedly, the NR-associated Integrated Index shows the strongest and most consistent signal using a random effects model and in a sensitivity and specificity analysis (p < 0.01). We subsequently tested the Integrated Index using validation cohorts across three distinct and diverse cancers (n=105).<br><br>CONCLUSIONS: Our analysis highlights the development of biomarkers for nonresponse, rather than response, in predicting ICI outcomes and suggests a new approach to identify patients who would benefit from microbiome-based interventions to improve response rates.}, }
@article {pmid33593820, year = {2021}, author = {Ferguson, M and Petkau, K and Shin, M and Galenza, A and Fast, D and Foley, E}, title = {Differential effects of commensal bacteria on progenitor cell adhesion, division symmetry and tumorigenesis in the Drosophila intestine.}, journal = {Development (Cambridge, England)}, volume = {}, number = {}, pages = {}, doi = {10.1242/dev.186106}, pmid = {33593820}, issn = {1477-9129}, abstract = {Microbial factors influence homeostatic and oncogenic growth in the intestinal epithelium. However, we know little about immediate effects of commensal bacteria on stem cell division programs. In this study, we examined effects of commensal Lactobacillus species on homeostatic, and tumorigenic stem cell proliferation in the female Drosophila intestine. We identified Lactobacillus brevis as a potent stimulator of stem cell divisions. In a wildtype midgut, Lactobacillus brevis activates growth regulatory pathways that drive stem cell divisions. In a Notch-deficient background, Lactobacillus brevis-mediated proliferation causes rapid expansion of mutant progenitors, leading to accumulation of large, multi-layered tumors throughout the midgut. Mechanistically, we showed that Lactobacillus brevis disrupts expression and subcellular distribution of progenitor cell integrins, supporting symmetric divisions that expand intestinal stem cell populations. Collectively, our data emphasize the impact of commensal microbes on division and maintenance of the intestinal progenitor compartment.}, }
@article {pmid33593778, year = {2021}, author = {Williams, AJ and Paramsothy, R and Wu, N and Ghaly, S and Leach, S and Paramsothy, S and Corte, C and O'Brien, C and Burke, C and Wark, G and Samocha-Bonet, D and Lambert, K and Ahlenstiel, G and Wasinger, V and Dutt, S and Pavli, P and Grimm, M and Lemberg, D and Connor, S and Leong, R and Hold, G}, title = {Australia IBD Microbiome (AIM) Study: protocol for a multicentre longitudinal prospective cohort study.}, journal = {BMJ open}, volume = {11}, number = {2}, pages = {e042493}, doi = {10.1136/bmjopen-2020-042493}, pmid = {33593778}, issn = {2044-6055}, abstract = {INTRODUCTION: Crohn's disease and ulcerative colitis are common chronic idiopathic inflammatory bowel diseases (IBD), which cause considerable morbidity. Although the precise mechanisms of disease remain unclear, evidence implicates a strong multidirectional interplay between diet, environmental factors, genetic determinants/immune perturbations and the gut microbiota. IBD can be brought into remission using a number of medications, which act by suppressing the immune response. However, none of the available medications address any of the underlying potential mechanisms. As we understand more about how the microbiota drives inflammation, much interest has focused on identifying microbial signals/triggers in the search for effective therapeutic targets. We describe the establishment of the Australian IBD Microbiota (AIM) Study, Australia's first longitudinal IBD bioresource, which will identify and correlate longitudinal microbial and metagenomics signals to disease activity as evaluated by validated clinical instruments, patient-reported surveys, as well as biomarkers. The AIM Study will also gather extensive demographic, clinical, lifestyle and dietary data known to influence microbial composition in order to generate a more complete understanding of the interplay between patients with IBD and their microbiota.<br><br>METHODS: The AIM Study is an Australian multicentre longitudinal prospective cohort study, which will enrol 1000 participants; 500 patients with IBD and 500 healthy controls over a 5-year period. Assessment occurs at 3 monthly intervals over a 24-month period. At each assessment oral and faecal samples are self-collected along with patient-reported outcome measures, with clinical data also collected at baseline, 12 and 24 months. Intestinal tissue will be sampled whenever a colonoscopy is performed. Dietary intake, general health and psychological state will be assessed using validated self-report questionnaires. Samples will undergo metagenomic, transcriptomic, proteomic, metabolomic and culturomic analyses. Omics data will be integrated with clinical data to identify predictive biomarkers of response to therapy, disease behaviour and environmental factors in patients with IBD.<br><br>ETHICS AND DISSEMINATION: Ethical approval for this study has been obtained from the South Eastern Sydney Local Health District Research Ethics Committee (HREC 2019/ETH11443). Findings will be reported at national and international gastroenterology meetings and published in peer-reviewed journals.<br><br>TRIAL REGISTRATION NUMBER: ACTRN12619000911190.}, }
@article {pmid33593727, year = {2021}, author = {Brooks, E and Bhatt, AS}, title = {The Gut Microbiome: A Missing Link in Understanding the Gastrointestinal manifestations of COVID-19?.}, journal = {Cold Spring Harbor molecular case studies}, volume = {}, number = {}, pages = {}, doi = {10.1101/mcs.a006031}, pmid = {33593727}, issn = {2373-2873}, abstract = {Coronavirus disease 2019 (COVID-19), which is caused by infection with SARS-CoV-2, presents with a broad constellation of both respiratory and non-respiratory symptoms, although it is primarily considered a respiratory disease. Gastrointestinal symptoms, including nausea, abdominal pain, vomiting and diarrhea, rank chief among these. When coupled with the presence of viral RNA in fecal samples, the presence of gastrointestinal symptoms raises relevant questions regarding whether SARS-CoV-2 can productively infect the upper or lower gastrointestinal tract. Despite the well-documented prevalence of gastrointestinal symptoms and the high rate of SARS-CoV-2 fecal RNA shedding, the biological, clinical and epidemiological relevance of these findings is unclear. Furthermore, the isolation of replication-competent virus from fecal samples has not been reproducibly and rigorously demonstrated. While SARS-CoV-2 shedding likely occurs in a high proportion of patients, gastrointestinal symptoms affect only a subset of individuals. Herein, we summarize what is known about gastrointestinal symptoms and fecal viral shedding in COVID-19, explore the role of the gut microbiome in other respiratory diseases, speculate on the role of the gut microbiota in COVID-19 and discuss potential future directions. Taking these concepts together, we propose that studying gut microbiota perturbations in COVID-19 will enhance our understanding of the symptomology and pathophysiology of this novel devastating disease.}, }
@article {pmid33593539, year = {2021}, author = {Qu, D and Wang, G and Yu, L and Tian, F and Chen, W and Zhai, Q}, title = {The effects of diet and gut microbiota on the regulation of intestinal mucin glycosylation.}, journal = {Carbohydrate polymers}, volume = {258}, number = {}, pages = {117651}, doi = {10.1016/j.carbpol.2021.117651}, pmid = {33593539}, issn = {1879-1344}, abstract = {Intestinal mucins glycosylation is regulated by host cues and environmental signals from the microbiome and diets. However, the mechanisms responsible for the dialogue between these three factors and mucin glycosylation in the digestive environment of the host are not well understood. In this review, the dynamic alterations of mucin glycosylation induced by immune responses to gut diseases are summarized. The various types of interactions between mucin glycans and gut microbes, including adhesins, glycosidases, metabolic products and surface components, are discussed. The mechanisms that determine how dietary components (fat, fiber, prebiotics, protein, and food additives) affect intestinal mucin glycosylation and maintain mucosal homeostasis are identified. A potential framework for individualized dietary recommendations is proposed for the prevention of abnormal mucin glycosylation driven by immune dysregulation, gut microbiome alterations and other factors. This review may provide a basis for future research on glycosylation-inspired therapies for gut diseases.}, }
@article {pmid33593462, year = {2021}, author = {Valle, MCPR and Vieira, IA and Fino, LC and Gallina, DA and Esteves, AM and da Cunha, DT and Cabral, L and Benatti, FB and Maróstica, MR and Batista, ÂG and Santos, R and Pastore, GM and Sartoratto, A and Sivieri, K and Tizioto, PC and Coutinho, LL and Antunes, AEC}, title = {Immune status, well-being and gut microbiota in military supplemented with synbiotic ice cream and submitted to field training: a randomised clinical trial.}, journal = {The British journal of nutrition}, volume = {}, number = {}, pages = {1-31}, doi = {10.1017/S0007114521000568}, pmid = {33593462}, issn = {1475-2662}, abstract = {Strenuous physical activity, sleep deprivation, and psychological stress are common features of military field training. This study aimed to evaluate the effects of supplementation with a synbiotic ice cream on salivary IgA, gastrointestinal symptoms, well-being indicators, and gut microbiota in young military participants undergoing field training. Sixty-five military completed the study: one group was supplemented for 30 days with synbiotic ice cream containing: 2.1x108 CFU/g for L. acidophilus LA-5 and 2.7x109 CFU/g for B. animalis BB-12 and 2.3g of inulin in the 60g of ice cream at manufacture, and the other with a placebo ice cream. Volunteers were evaluated at pre-supplementation (baseline), post-supplementation, and after a five-day military training. Bifidobacterium and Lactobacillus genera were measured in stool samples and both showed a higher differential abundance post-supplementation and training. Salivary IgA and gastrointestinal symptoms decreased at post-training in both groups (p<0.05; main effect of time); however, supplementation with synbiotic did not mitigate this effect. Tenseness and sleepiness were decreased in the synbiotic-treated group, but not in the placebo group at post-military training (p=0.01 and p=0.009, respectively; group x time effect). The other well-being indicators were not affected by the synbiotic supplementation. In conclusion, 30 days of synbiotic ice cream supplementation containing inulin, L. acidophilus LA-5, and B. animalis BB-12 favourably modulated gut microbiota and improved tenseness and sleepiness in healthy young military undergoing a 5-day field training. These improvements may be relevant to this population as they may influence the decision-making process in an environment of high physical and psychological stress.}, }
@article {pmid33593430, year = {2021}, author = {Langdon, A and Schwartz, DJ and Bulow, C and Sun, X and Hink, T and Reske, KA and Jones, C and Burnham, CD and Dubberke, ER and Dantas, G and , }, title = {Microbiota restoration reduces antibiotic-resistant bacteria gut colonization in patients with recurrent Clostridioides difficile infection from the open-label PUNCH CD study.}, journal = {Genome medicine}, volume = {13}, number = {1}, pages = {28}, pmid = {33593430}, issn = {1756-994X}, support = {1U1CI000033 301/CC/CDC HHS/United States ; R01AI123394//National Institute of Allergy and Infectious Diseases/ ; R01HD092414//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; TL1 TR000449/NH/NIH HHS/United States ; St. Jude Fellowship in Basic Research//Pediatric Infectious Diseases Society/ ; T32 HG000045/HG/NHGRI NIH HHS/United States ; }, abstract = {BACKGROUND: Once antibiotic-resistant bacteria become established within the gut microbiota, they can cause infections in the host and be transmitted to other people and the environment. Currently, there are no effective modalities for decreasing or preventing colonization by antibiotic-resistant bacteria. Intestinal microbiota restoration can prevent Clostridioides difficile infection (CDI) recurrences. Another potential application of microbiota restoration is suppression of non-C. difficile multidrug-resistant bacteria and overall decrease in the abundance of antibiotic resistance genes (the resistome) within the gut microbiota. This study characterizes the effects of RBX2660, a microbiota-based investigational therapeutic, on the composition and abundance of the gut microbiota and resistome, as well as multidrug-resistant organism carriage, after delivery to patients suffering from recurrent CDI.<br><br>METHODS: An open-label, multi-center clinical trial in 11 centers in the USA for the safety and efficacy of RBX2660 on recurrent CDI was conducted. Fecal specimens from 29 of these subjects with recurrent CDI who received either one (N = 16) or two doses of RBX2660 (N = 13) were analyzed secondarily. Stool samples were collected prior to and at intervals up to 6 months post-therapy and analyzed in three ways: (1) 16S rRNA gene sequencing for microbiota taxonomic composition, (2) whole metagenome shotgun sequencing for functional pathways and antibiotic resistome content, and (3) selective and differential bacterial culturing followed by isolate genome sequencing to longitudinally track multidrug-resistant organisms.<br><br>RESULTS: Successful prevention of CDI recurrence with RBX2660 correlated with taxonomic convergence of patient microbiota to the donor microbiota as measured by weighted UniFrac distance. RBX2660 dramatically reduced the abundance of antibiotic-resistant Enterobacteriaceae in the 2 months after administration. Fecal antibiotic resistance gene carriage decreased in direct relationship to the degree to which donor microbiota engrafted.<br><br>CONCLUSIONS: Microbiota-based therapeutics reduce resistance gene abundance and resistant organisms in the recipient gut microbiome. This approach could potentially reduce the risk of infections caused by resistant organisms within the patient and the transfer of resistance genes or pathogens to others.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov, NCT01925417 ; registered on August 19, 2013.}, }
@article {pmid33593429, year = {2021}, author = {Moshkelgosha, S and Verhasselt, HL and Masetti, G and Covelli, D and Biscarini, F and Horstmann, M and Daser, A and Westendorf, AM and Jesenek, C and Philipp, S and Diaz-Cano, S and Banga, JP and Michael, D and Plummer, S and Marchesi, JR and Eckstein, A and Ludgate, M and Berchner-Pfannschmidt, U and , }, title = {Modulating gut microbiota in a mouse model of Graves' orbitopathy and its impact on induced disease.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {45}, pmid = {33593429}, issn = {2049-2618}, support = {GA 612116//FP7 People: Marie-Curie Actions IAPP/ ; }, abstract = {BACKGROUND: Graves' disease (GD) is an autoimmune condition in which autoantibodies to the thyrotropin receptor (TSHR) cause hyperthyroidism. About 50% of GD patients also have Graves' orbitopathy (GO), an intractable disease in which expansion of the orbital contents causes diplopia, proptosis and even blindness. Murine models of GD/GO, developed in different centres, demonstrated significant variation in gut microbiota composition which correlated with TSHR-induced disease heterogeneity. To investigate whether correlation indicates causation, we modified the gut microbiota to determine whether it has a role in thyroid autoimmunity. Female BALB/c mice were treated with either vancomycin, probiotic bacteria, human fecal material transfer (hFMT) from patients with severe GO or ddH2O from birth to immunization with TSHR-A subunit or beta-galactosidase (βgal; age ~ 6 weeks). Incidence and severity of GD (TSHR autoantibodies, thyroid histology, thyroxine level) and GO (orbital fat and muscle histology), lymphocyte phenotype, cytokine profile and gut microbiota were analysed at sacrifice (~ 22 weeks).<br><br>RESULTS: In ddH2O-TSHR mice, 84% had pathological autoantibodies, 67% elevated thyroxine, 77% hyperplastic thyroids and 70% orbital pathology. Firmicutes were increased, and Bacteroidetes reduced relative to ddH2O-βgal; CCL5 was increased. The random forest algorithm at the genus level predicted vancomycin treatment with 100% accuracy but 74% and 70% for hFMT and probiotic, respectively. Vancomycin significantly reduced gut microbiota richness and diversity compared with all other groups; the incidence and severity of both GD and GO also decreased; reduced orbital pathology correlated positively with Akkermansia spp. whilst IL-4 levels increased. Mice receiving hFMT initially inherited their GO donors' microbiota, and the severity of induced GD increased, as did the orbital brown adipose tissue volume in TSHR mice. Furthermore, genus Bacteroides, which is reduced in GD patients, was significantly increased by vancomycin but reduced in hFMT-treated mice. Probiotic treatment significantly increased CD25+ Treg cells in orbital draining lymph nodes but exacerbated induced autoimmune hyperthyroidism and GO.<br><br>CONCLUSIONS: These results strongly support a role for the gut microbiota in TSHR-induced disease. Whilst changes to the gut microbiota have a profound effect on quantifiable GD endocrine and immune factors, the impact on GO cellular changes is more nuanced. The findings have translational potential for novel, improved treatments. Video abstract.}, }
@article {pmid33593386, year = {2021}, author = {Young, C and Wood, HM and Seshadri, RA and Van Nang, P and Vaccaro, C and Melendez, LC and Bose, M and Van Doi, M and Piñero, TA and Valladares, CT and Arguero, J and Balaguer, AF and Thompson, KN and Yan, Y and Huttenhower, C and Quirke, P}, title = {The colorectal cancer-associated faecal microbiome of developing countries resembles that of developed countries.}, journal = {Genome medicine}, volume = {13}, number = {1}, pages = {27}, pmid = {33593386}, issn = {1756-994X}, support = {GCRFNG\100433/AMS_/Academy of Medical Sciences/United Kingdom ; GCRFNG\100433/AMS_/Academy of Medical Sciences/United Kingdom ; 203524/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; 2234//Pathological Society of Great Britain and Ireland/ ; Optimisticc C10674/A27140/CRUK_/Cancer Research UK/United Kingdom ; Optimisticc C10674/A27140/CRUK_/Cancer Research UK/United Kingdom ; }, abstract = {BACKGROUND: The incidence of colorectal cancer (CRC) is increasing in developing countries, yet limited research on the CRC- associated microbiota has been conducted in these areas, in part due to scarce resources, facilities, and the difficulty of fresh or frozen stool storage/transport. Here, we aimed (1) to establish a broad representation of diverse developing countries (Argentina, Chile, India, and Vietnam); (2) to validate a 'resource-light' sample-collection protocol translatable in these settings using guaiac faecal occult blood test (gFOBT) cards stored and, importantly, shipped internationally at room temperature; (3) to perform initial profiling of the collective CRC-associated microbiome of these developing countries; and (4) to compare this quantitatively with established CRC biomarkers from developed countries.<br><br>METHODS: We assessed the effect of international storage and transport at room temperature by replicating gFOBT from five UK volunteers, storing two in the UK, and sending replicates to institutes in the four countries. Next, to determine the effect of prolonged UK storage, DNA extraction replicates for a subset of samples were performed up to 252 days apart. To profile the CRC-associated microbiome of developing countries, gFOBT were collected from 41 treatment-naïve CRC patients and 40 non-CRC controls from across the four institutes, and V4 16S rRNA gene sequencing was performed. Finally, we constructed a random forest (RF) model that was trained and tested against existing datasets from developed countries.<br><br>RESULTS: The microbiome was stably assayed when samples were stored/transported at room temperature and after prolonged UK storage. Large-scale microbiome structure was separated by country and continent, with a smaller effect from CRC. Importantly, the RF model performed similarly to models trained using external datasets and identified similar taxa of importance (Parvimonas, Peptostreptococcus, Fusobacterium, Alistipes, and Escherichia).<br><br>CONCLUSIONS: This study demonstrates that gFOBT, stored and transported at room temperature, represents a suitable method of faecal sample collection for amplicon-based microbiome biomarkers in developing countries and suggests a CRC-faecal microbiome association that is consistent between developed and developing countries.}, }
@article {pmid33593158, year = {2021}, author = {Ponsuksili, S and Oster, M and Reyer, H and Hadlich, F and Trakooljul, N and Rodehutscord, M and Camarinha-Silva, A and Bennewitz, J and Wimmers, K}, title = {Genetic regulation and heritability of miRNA and mRNA expression link to phosphorus utilization and gut microbiome.}, journal = {Open biology}, volume = {11}, number = {2}, pages = {200182}, doi = {10.1098/rsob.200182}, pmid = {33593158}, issn = {2046-2441}, abstract = {Improved utilization of phytates and mineral phosphorus (P) in monogastric animals contributes significantly to preserving the finite resource of mineral P and mitigating environmental pollution. In order to identify pathways and to prioritize candidate genes related to P utilization (PU), the genomic heritability of 77 and 80 trait-dependent expressed miRNAs and mRNAs in 482 Japanese quail were estimated and eQTL (expression quantitative trait loci) were detected. In total, 104 miR-eQTL (microRNA expression quantitative traits loci) were associated with SNP markers (false discovery rate less than 10%) including 41 eQTL of eight miRNAs. Similarly, 944 mRNA-eQTL were identified at the 5% False discovery rate threshold, with 573 being cis-eQTL of 36 mRNAs. High heritabilities of miRNA and mRNA expression coincide with highly significant eQTL. Integration of phenotypic data with transcriptome and microbiome data of the same animals revealed genetic regulated mRNA and miRNA transcripts (SMAD3, CAV1, ENNPP6, ATP2B4, miR-148a-3p, miR-146b-5p, miR-16-5p, miR-194, miR-215-5p, miR-199-3p, miR-1388a-3p) and microbes (Candidatus Arthromitus, Enterococcus) that are associated with PU. The results reveal novel insights into the role of mRNAs and miRNAs in host gut tissue functions, which are involved in PU and other related traits, in terms of the genetic regulation and inheritance of their expression and in association with microbiota components.}, }
@article {pmid33592539, year = {2021}, author = {Li, T and Zhang, T and Gao, H and Liu, R and Gu, M and Yang, Y and Cui, T and Lu, Z and Yin, C}, title = {Tempol ameliorates polycystic ovary syndrome through attenuating intestinal oxidative stress and modulating of gut microbiota composition-serum metabolites interaction.}, journal = {Redox biology}, volume = {41}, number = {}, pages = {101886}, doi = {10.1016/j.redox.2021.101886}, pmid = {33592539}, issn = {2213-2317}, abstract = {Polycystic ovary syndrome (PCOS) is a complex endocrine and metabolic disorder, which is often accompanied by oxidative stress. Tempol, a superoxide dismutase mimetic, protects against several diseases caused by oxidative stress. However, the effect of tempol on PCOS has not been investigated. The present study demonstrated the alleviation of ovarian dysfunction and glucose tolerance in dehydroepiandrosterone (DHEA)-induced PCOS rats treated with tempol. Tempol significantly reduced the intestinal oxidative stress in PCOS rats without affecting the ovarian redox rate. The 16S rDNA sequencing of the intestinal microbiome and non-targeted metabolomics analysis indicated significant differences in gut microbiota composition and serum metabolite profiles between the control and PCOS rats, and most of these differences were reduced after tempol intervention. Tempol alters the gut microbiome by increasing the abundance of genus Ruminococcus_1 and by decreasing the abundance of Ruminococcus_2, Staphylococcus, Ideonella, and Corynebnacterium genera. Tempol also attenuates the reduction of serum bile acid and stachyose levels in PCOS rats, and the serum stachyose level was significantly correlated with the abundance of 15 genera, particularly Ruminococcus_1 and Ruminococcus_2. Moreover, stachyose administration improved ovarian dysfunction in PCOS rats. Thus, our data indicate that tempol ameliorates PCOS phenotype by reducing intestinal oxidative stress, restoring gut dysbiosis, and modulating the interaction between gut microbiota and host metabolite. Therefore, tempol intervention is a potential therapeutic approach for PCOS.}, }
@article {pmid33592479, year = {2021}, author = {Gargouri, M and Karray, F and Chebaane, A and Mhiri, N and Partida-Martínez, LP and Sayadi, S and Mliki, A}, title = {Increasing aridity shapes beta diversity and the network dynamics of the belowground fungal microbiome associated with Opuntia ficus-indica.}, journal = {The Science of the total environment}, volume = {773}, number = {}, pages = {145008}, doi = {10.1016/j.scitotenv.2021.145008}, pmid = {33592479}, issn = {1879-1026}, abstract = {AIMS: The effects of aridity on soil and water-use efficient (WUE) crop species are relatively well known. However, the understanding of its impacts on the dynamics of below-ground microorganisms associated with plant roots is less well understood.<br><br>METHODS: To investigate the influence of increasing aridity on the dynamics of the fungal communities, samples from the root endosphere and rhizosphere associated with the prickly pear cactus trees (Opuntia ficus-indica) growing along the aridity gradient were collected and the internal transcribed spacer (ITS) were sequenced. The diversity and network analyses of fungal taxa were determined along with standard measurements of soil parameters.<br><br>RESULTS: We found that (i) the fungal community exhibited similar alpha diversity and shared a set of core taxa within the rhizosphere and endosphere, but there was significant beta diversity differences; (ii) the relative abundance of major phyla was higher in the rhizosphere than in the endosphere; (iii) arbuscular endomycorrhizal colonization was highest in the humid climate and decreased under lower-arid, and was negatively correlated with increased concentration of Ca2+ in the soil; (iv) increased aridity correlated with increased connectivity of the soil microbial-root fungal networks in the arid soils, producing a highly cohesive network in the upper-arid area; and (v) distinct fungal hubs sculpt the fungal microbiome network structure in the rhizosphere and endosphere within each bioclimatic zone.<br><br>CONCLUSIONS: Our findings highlight the importance of gradient analysis-based correlation network as a powerful approach to understand changes in the diversity, the dynamics, and the structure of fungal communities associated with the rhizosphere-endosphere interaction and led to the identification of microbes at each bioclimatic zone that are potentially involved in promoting the survival, protection, and growth of Opuntia trees. The variability of fungal hubs composition depending on plant compartment and bioclimatic zone will give key implications for the application of rhizospheric fungi and endophytes as microbial inoculants in agriculture, as well as in the conservation and restoration of cacti plants in arid and semi-arid lands against the backdrop of climate change. Overall, this study will enhance our understanding of the microbiomes'dynamic of CAM plants in nature.}, }
@article {pmid33592470, year = {2021}, author = {Moreno, J and López-González, JA and Arcos-Nievas, MA and Suárez-Estrella, F and Jurado, MM and Estrella-González, MJ and López, MJ}, title = {Revisiting the succession of microbial populations throughout composting: A matter of thermotolerance.}, journal = {The Science of the total environment}, volume = {773}, number = {}, pages = {145587}, doi = {10.1016/j.scitotenv.2021.145587}, pmid = {33592470}, issn = {1879-1026}, abstract = {Composting has been traditionally considered a process in which a succession of mesophilic and thermophilic microbial populations occurs due to temperature changes. In order to deepen in this model, 1380 bacterial and fungal strains (the entire culturable microbiota isolated from a composting process) were investigated for their ability to grow across a wide range of temperatures (20 to 60 °C). First, qualitative tests were performed to establish a thermal profile for each strain. Then, quantitative tests allowed ascertaining the extent of growth for each strain at each of the tested temperatures. The identity of the isolates enabled to position them taxonomically and permitted tracking the strains throughout the process. Results showed that 90% of the isolates were classified as thermotolerant (they grew at all tested temperatures). Only 9% and 1% of the studied strains showed to be strictly mesophilic or thermophilic, respectively. Firmicutes exhibited the greatest thermal plasticity, followed by Actinobacteria and Ascomycota. Most of the Proteobacteria and all Basidiomycota strains were also able to grow at all the assayed temperatures. Thermotolerance was clearly demonstrated among the composting microbiota, suggesting that the idea of the succession of mesophilic and thermophilic populations throughout the process might need a reassessment.}, }
@article {pmid33592436, year = {2021}, author = {Ye, L and Liu, G and Yao, T and Lu, J}, title = {Monitoring of antimicrobial resistance genes in the spotted sea bass (Lateolabrax maculatus): Association with the microbiome and its environment in aquaculture ponds.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {276}, number = {}, pages = {116714}, doi = {10.1016/j.envpol.2021.116714}, pmid = {33592436}, issn = {1873-6424}, abstract = {Antimicrobial resistance genes (ARGs) pose a serious threat to environment and human health. However, few studies address the abundance and distribution of ARGs associated with farmed fish and their aquaculture environment. Here we conducted an analysis of the abundance and distribution of gut and gill ARGs by quantitative PCR techniques associated with the spotted sea bass (Lateolabrax maculatus) as well as the bacterial communities in the surrounding environment (water and sediment). For this purpose, we sampled six aquaculture ponds in Zhuhai, Guangdong Province, the largest spotted sea bass cultivation site in China. Predominant ARGs were floR, sul2, and tetM-01 in the gut and tetQ, sul1, and floR in the gills. The copy numbers of sul1, sul2, and cmlA1-01 were significantly higher in the environment. Moreover, significant differences were found among the microbiota of the gut, gills, and environment. The former was more similar to those of the environmental microbial communities compared with other sources. The fish gut and gill microbiota were predominantly populated by Fusobacteria and Actinobacteria, respectively. In contrast, Proteobacteria were dominant in water and sediment. Correlation analysis showed that Fusobacteria and Actinobacteria positively correlated with floR and tetQ, respectively, indicating that these microbes were potential hosts for ARGs. Our results showed that ARGs in farmed fish showed marked difference with their aquaculture environment, thus providing a valuable reference for identifying deleterious ARGs in aquatic fish.}, }
@article {pmid33592204, year = {2021}, author = {Chun, Y and Do, A and Grishina, G and Arditi, Z and Ribeiro, V and Grishin, A and Vicencio, A and Bunyavanich, S}, title = {The nasal microbiome, nasal transcriptome, and pet sensitization.}, journal = {The Journal of allergy and clinical immunology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jaci.2021.01.031}, pmid = {33592204}, issn = {1097-6825}, abstract = {BACKGROUND: Pet allergies are common in children with asthma. Microbiota and host responses may mediate allergen sensitization.<br><br>OBJECTIVE: To uncover host-microbe relationships in pet allergen sensitization via joint examination of the nasal microbiome and nasal transcriptome.<br><br>METHODS: We collected nasal samples from 132 children with asthma for parallel 16S rRNA and RNA sequencing. Specific IgE levels for cat and dog dander were measured. Analyses of the nasal microbiome, nasal transcriptome, and their correlations were performed with respect to pet sensitization status.<br><br>RESULTS: Among the 132 children, 91 (68.9%) were cat sensitized and 96 (72.7%) were dog sensitized. Cat sensitization was associated with lower nasal microbial diversity by Shannon Index (P=0.021) and differential nasal bacterial composition by weighted UniFrac distance (PERMANOVA P=0.035). Corynebacterium sp. and Staphylococcus epidermidis were significantly less abundant, and the metabolic process &quot;fatty acid elongation in mitochondria&quot; was lower in pet sensitized vs. unsensitized children. Correlation networks revealed that the nasal expression levels of 47 genes representing inflammatory processes were negatively correlated with the relative abundances of Corynebacterium sp. and Staphylococcus epidermidis. Thus, these species were not only directly associated with the absence of pet sensitization, but also with the under-expression of host gene expression of inflammatory processes that contribute to allergen sensitization. Causal mediation analyses revealed that the associations between these nasal species and pet sensitization were mediated by nasal gene expression.<br><br>CONCLUSION: Higher abundances of nasal Corynebacterium sp. and Staphylococcus epidermidis are associated with absence of pet sensitization and correlate with lower expression of inflammatory genes.}, }
@article {pmid33591814, year = {2021}, author = {Grinbergs, D and Chilián, J and Padilla, N and Reyes, M and France, A and Gerding, M and Moya-Elizondo, EA}, title = {Endophytic microorganisms associated with reversion of silverleaf disease symptoms in apple.}, journal = {Phytopathology}, volume = {}, number = {}, pages = {}, doi = {10.1094/PHYTO-12-20-0548-R}, pmid = {33591814}, issn = {0031-949X}, abstract = {Silverleaf is caused by the fungus Chondrostereum purpureum, which produces wood necrosis and foliar silvering in woody plants. Field observations and studies in apple have shown the reversion of foliar symptoms. Since plants were clones and received identical agronomical management, it was hypothesized that reversion is driven by endophytic microbiota. Thus, the objectives of this study were to compare healthy, diseased and reverted plants with respect to their physiology, endophytic microbial communities, antagonistic ability of their endophytes against C. purpureum and defense-genes-expression. Water-potential, stomatal-conductance, chlorophyll-content and fluorescence were measured. Endophytic bacterial and fungal DNA were analyzed by DGGE, and communities richness and similarity were calculated. Wood cores were collected and bacterial and fungal endophytes were isolated and confronted with C. purpureum virulent strains in dual-culture assays. Defense-genes-expression were measured by qPCR. Results indicated that there were no differences in physiological parameters between healthy and reverted plants, except for fluorescence, and both type of plants differed from diseased ones. Bacterial and fungal communities richness were similar in healthy and reverted plants, and higher than in diseased ones. Endophytes from reverted and healthy plants showed high antagonism to C. purpureum. Furthermore, NPR1-gene-expression was upregulated in reverted plants, while PAL and PGIP showed higher values in diseased plants. Overall, physiological, molecular and microbial characteristics were similar between healthy and reverted plants, and both differed from diseased ones. Therefore, reversion of symptoms is associated with changes in the endophytic microbiota, which seems to be a promising source of biological control agents against C. purpureum.}, }
@article {pmid33591630, year = {2021}, author = {Norman, G and Shi, C and Westby, MJ and Price, BL and McBain, AJ and Dumville, JC and Cullum, N}, title = {Bacteria and bioburden and healing in complex wounds: A prognostic systematic review.}, journal = {Wound repair and regeneration : official publication of the Wound Healing Society [and] the European Tissue Repair Society}, volume = {}, number = {}, pages = {}, doi = {10.1111/wrr.12898}, pmid = {33591630}, issn = {1524-475X}, support = {IS-BRC-1215-20007//NIHR Manchester Biomedical Research Centre/ ; }, abstract = {The wound microbiome may play an important role in the wound healing process. We conducted the first systematic prognosis review investigating whether aspects of the wound microbiome are independent prognostic factors for the healing of complex wounds. We searched Medline, Embase, CINAHL and the Cochrane Library to February 2019. We included longitudinal studies which assessed the independent association of aspects of wound microbiome with healing of complex wounds while controlling for confounding factors. Two reviewers extracted data and assessed risk of bias and certainty of evidence using the GRADE approach. We synthesised studies narratively due to the clinical and methodological heterogeneity of included studies and sparse data. We identified 28 cohorts from 21 studies with a total of 38,604 participants, including people with diabetes and foot ulcers, open surgical wounds, venous leg ulcers and pressure ulcers. Risk of bias varied from low (2 cohorts) to high (17 cohorts); the great majority of participants were in cohorts at high risk of bias. Most evidence related to the association of baseline clinical wound infection with healing. Clinical infection at baseline may be associated with less likelihood of wound healing in foot ulcers in diabetes (HR from cohort with moderate risk of bias 0.53, 95% CI 0.33 to 0.83) or slower healing in open surgical wounds (HR 0.65, 95% CI 0.51 to 0.83); evidence in other wounds is more limited. Most other associations assessed showed no clear relationship with wound healing; evidence was limited and often sparse; and we documented gaps in the evidence. There is low certainty evidence that a diagnosis of wound infection may be prognostic of poorer healing in foot ulcers in diabetes, and some moderate certainty evidence for this in open surgical wounds. Low certainty evidence means that more research could change these findings.}, }
@article {pmid33591591, year = {2021}, author = {Zhu, Y and Shi, T and Lu, X and Xu, Z and Qu, J and Zhang, Z and Shi, G and Shen, S and Hou, Y and Chen, Y and Wang, T}, title = {Fungal-induced glycolysis in macrophages promotes colon cancer by enhancing innate lymphoid cell secretion of IL-22.}, journal = {The EMBO journal}, volume = {}, number = {}, pages = {e105320}, doi = {10.15252/embj.2020105320}, pmid = {33591591}, issn = {1460-2075}, support = {81772542//National Natural Science Foundation of China (NSFC)/ ; 82072648//National Natural Science Foundation of China (NSFC)/ ; BK20190134//Natural Science Foundation of Jiangsu Province (Jiangsu Natural Science Foundation)/ ; 021414380472//MOE | Fundamental Research Funds for the Central Universities (Fundamental Research Fund for the Central Universities)/ ; //The Open Projects of the Discipline of Chinese Medicine of Nanjing University of Chinese Medicine/ ; ZKX17033//Nanjing Medical Science and Technique Development Foundation/ ; YKK18127//Nanjing Medical Science and Technique Development Foundation/ ; }, abstract = {Incorporation of microbiome data has recently become important for prevention, diagnosis, and treatment of colorectal cancer, and several species of bacteria were shown to be associated with carcinogenesis. However, the role of commensal fungi in colon cancer remains poorly understood. Here, we report that mice lacking the c-type lectin Dectin-3 (Dectin-3-/-) show increased tumorigenesis and Candida albicans burden upon chemical induction. Elevated C. albicans load triggered glycolysis in macrophages and interleukin-7 (IL-7) secretion. IL-7 induced IL-22 production in RORγt+ (group 3) innate lymphoid cells (ILC3s) via aryl hydrocarbon receptor and STAT3. Consistently, IL-22 frequency in tumor tissues of colon cancer patients positively correlated with fungal burden, indicating the relevance of this regulatory axis in human disease. These results establish a C. albicans-driven crosstalk between macrophages and innate lymphoid cells in the intestine and expand our understanding on how commensal mycobiota regulate host immunity and promote tumorigenesis.}, }
@article {pmid33591390, year = {2021}, author = {Cuevas-Sierra, A and Romo-Hualde, A and Aranaz, P and Goni, L and Cuervo, M and Martínez, JA and Milagro, FI and Riezu-Boj, JI}, title = {Diet- and sex-related changes of gut microbiota composition and functional profiles after 4 months of weight loss intervention.}, journal = {European journal of nutrition}, volume = {}, number = {}, pages = {}, pmid = {33591390}, issn = {1436-6215}, support = {CB12/03/30002//Centro de Investigación Biomédica en Red-Fisiopatología de la Obesidad y Nutrición/ ; Obekit-PT024//Departamento de Educación, Gobierno de Navarra/ ; Microbiota-PI035//Departamento de Educación, Gobierno de Navarra/ ; RTI2018-102205-B-I00//Ministerio de Ciencia e Innovación/ ; }, abstract = {PURPOSE: Obesity has been related to intestinal dysbiosis and the modification of gut microbiota composition by dietary strategies becomes a promising strategy to help manage obesity. The aim of the current study was to evaluate the effect of two weight-loss diets on the composition and functional profile of gut microbiota.<br><br>METHODS: 55 men and 124 women with BMI > 25 kg/m2 were randomly assigned to moderately high-protein (MHP) or low-fat (LF) diet. Differences in fecal bacteria abundance (based on 16 s rRNA sequencing) between before and after 4 months of calorie restriction was analyzed using EdgeR tool in MicrobiomeAnalyst platform. Bacterial functional profile was predicted using Tax4Fun and metagenomeSeq analysis. Significant KEGG Orthology (KO) terms were selected for the metabolomic study using chromatography.<br><br>RESULTS: After the intervention, MHP-men showed a significant decrease in Negativicutes, Selenomonadales, Dielma and Dielma fastidiosa. LF-men showed a significant increase in Bacilli, Lactobacillales, Christensenellaceae, Peptococcaceae, and Streptococcaceae, Peptococcus, Streptococcus and Christensenella, Duncaniella dubosii_CP039396_93.49%, Roseburia sp_AB744234_98.96% and Alistipes inops_KJ572413_99.57%. MHP-women increased Pasteurellales, Phascolarctobacterium succinatutens, Ruthenibacterium lactatiformans_LR215981_99.55% and decreased in Phascolarctobacterium succinatutens_NR112902_99.56%. Finally, LF-women presented a significant decrease in Bacteroides clarus and Erysipelothrix inopinata_CP060715_84.4%. Surprisingly, no matching bacterial changes were found between these four groups. A total of 42 KO, 10 metabolic pathways and 107 related metabolites related were found implicated in these bacterial changes. Seven metabolites were confirmed in plasma.<br><br>CONCLUSION: Weight-loss-related-changes in gut microbiome composition and the functional profile occur in a sex- and diet-related manner, showing that women and men could differentially benefit from the consumption of MHP and LF diets.<br><br>TRIAL REGISTRATION: NCT02737267, 10th March 2016 retrospectively registered.}, }
@article {pmid33590560, year = {2021}, author = {Lee, K and Kaspar, JR and Rojas-Carreño, G and Walker, AR and Burne, RA}, title = {A single system detects and protects the beneficial oral bacterium Streptococcus sp. A12 from a spectrum of antimicrobial peptides.}, journal = {Molecular microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mmi.14703}, pmid = {33590560}, issn = {1365-2958}, abstract = {The commensal bacterium Streptococcus sp. A12 has multiple properties that may promote the stability of health-associated oral biofilms, including overt antagonism of the dental caries pathogen Streptococcus mutans. A LanFEG-type ABC transporter, PcfFEG, confers tolerance to the lantibiotic nisin and enhances the ability of A12 to compete against S. mutans. Here, we investigated the regulation of pcfFEG and adjacent genes for a two-component system, pcfRK, to better understand antimicrobial peptide resistance by A12. Induction of pcfFEG-pcfRK was the primary mechanism to respond rapidly to nisin. In addition to nisin, PcfFEG conferred tolerance by A12 to a spectrum of lantibiotic and non-lantibiotic antimicrobial peptides produced by a diverse collection of S. mutans isolates. Loss of PcfFEG resulted in altered spatio-temporal arrangement of A12 and S.mutans in a dual-species biofilm model. Deletion of PcfFEG or PcfK resulted in constitutive activation of pcfFEG and expression of pcfFEG was inhibited by small peptides in the pcfK mutant. Transcriptional profiling of pcfR or pcfK mutants combined with functional genomics revealed peculiarities in PcfK function and a novel panel of genes responsive to nisin. Collectively, the results provide fundamental insights that strengthen the foundation for design of microbial-based therapeutics to control oral infectious diseases.}, }
@article {pmid33590447, year = {2021}, author = {Parente, CET and Brito, EMS and Caretta, CA and Cervantes-Rodríguez, EA and Fábila-Canto, AP and Vollú, RE and Seldin, L and Malm, O}, title = {Bacterial diversity changes in agricultural soils influenced by poultry litter fertilization.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, pmid = {33590447}, issn = {1678-4405}, support = {426192/2016-8//Conselho Nacional de Desenvolvimento Científico e Tecnológico (BR)/ ; 206/2019//Dirección de Apoyo a la Investigación y al Posgrado - Universidad de Guanajuato/ ; PNPD//Coordination and Improvement of Higher Level of Education Personnel (CAPES)/ ; }, abstract = {Poultry litter is widely applied as agricultural fertilizer and can affect the soil microbiome through nutrient overload and antibiotic contamination. In this study, we assessed changes in soil bacterial diversity using high-throughput sequencing approaches. Four samples in triplicate were studied: soils with short- and long-term fertilization by poultry litter (S1 = 10 months and S2 = 30 years, respectively), a soil inside a poultry shed (S3), and a forest soil used as control (S0). Samples S0, S1, and S2 revealed a relatively high richness, with confirmed operational taxonomic units (OTUs) in the three replicates of each sample ranging from 1243 to 1279, while richness in S3 was about three times lower (466). The most abundant phyla were Proteobacteria, Bacteroidetes, and Actinobacteria. Acidobacteria, Planctomycetes, and Verrucomicrobia were also abundant but highly diminished in S3, while Firmicutes was less abundant in S0. Changes in bacterial communities were very evident at the genera level. The genera Gaiella, Rhodoplanes, Solirubacter, and Sphingomonas were predominant in S0 but strongly decreased in the other soils. Pedobacter and Devosia were the most abundant in S1 and were diminished in S2, while Herbiconiux, Brevundimonas, Proteiniphilum, and Petrimonas were abundant in S2. The most abundant genera in S3 were Deinococcus, Truepera, Rhodanobacter, and Castellaniella. A predictive analysis of the metabolic functions with Tax4Fun2 software suggested the potential presence of enzymes associated with antibiotic resistance as well as with denitrification pathways, indicating that the S3 soil is a potential source of nitrous oxide, a powerful greenhouse gas.}, }
@article {pmid33590248, year = {2019}, author = {Boachon, B and Burdloff, Y and Ruan, JX and Rojo, R and Junker, RR and Vincent, B and Nicolè, F and Bringel, F and Lesot, A and Henry, L and Bassard, JE and Mathieu, S and Allouche, L and Kaplan, I and Dudareva, N and Vuilleumier, S and Miesch, L and André, F and Navrot, N and Chen, XY and Werck-Reichhart, D}, title = {A Promiscuous CYP706A3 Reduces Terpene Volatile Emission from Arabidopsis Flowers, Affecting Florivores and the Floral Microbiome.}, journal = {The Plant cell}, volume = {31}, number = {12}, pages = {2947-2972}, doi = {10.1105/tpc.19.00320}, pmid = {33590248}, issn = {1532-298X}, abstract = {Flowers are essential but vulnerable plant organs, exposed to pollinators and florivores; however, flower chemical defenses are rarely investigated. We show here that two clustered terpene synthase and cytochrome P450 encoding genes (TPS11 and CYP706A3) on chromosome 5 of Arabidopsis (Arabidopsis thaliana) are tightly coexpressed in floral tissues, upon anthesis and during floral bud development. TPS11 was previously reported to generate a blend of sesquiterpenes. By heterologous coexpression of TPS11 and CYP706A3 in yeast (Saccharomyces cerevisiae) and Nicotiana benthamiana, we demonstrate that CYP706A3 is active on TPS11 products and also further oxidizes its own primary oxidation products. Analysis of headspace and soluble metabolites in cyp706a3 and 35S:CYP706A3 mutants indicate that CYP706A3-mediated metabolism largely suppresses sesquiterpene and most monoterpene emissions from opening flowers, and generates terpene oxides that are retained in floral tissues. In flower buds, the combined expression of TPS11 and CYP706A3 also suppresses volatile emissions and generates soluble sesquiterpene oxides. Florivory assays with the Brassicaceae specialist Plutella xylostella demonstrate that insect larvae avoid feeding on buds expressing CYP706A3 and accumulating terpene oxides. Composition of the floral microbiome appears also to be modulated by CYP706A3 expression. TPS11 and CYP706A3 simultaneously evolved within Brassicaceae and form the most versatile functional gene cluster described in higher plants so far.}, }
@article {pmid33589631, year = {2021}, author = {McHugh, AJ and Yap, M and Crispie, F and Feehily, C and Hill, C and Cotter, PD}, title = {Microbiome-based environmental monitoring of a dairy processing facility highlights the challenges associated with low microbial-load samples.}, journal = {NPJ science of food}, volume = {5}, number = {1}, pages = {4}, pmid = {33589631}, issn = {2396-8370}, support = {14/F/883//Department of Agriculture, Food and the Marine (DAFM)/ ; 14/F/883//Department of Agriculture, Food and the Marine (DAFM)/ ; 14/F/883//Department of Agriculture, Food and the Marine (DAFM)/ ; SFI/12/RC/2273//Science Foundation Ireland (SFI)/ ; SFI/16/RC/3835//Science Foundation Ireland (SFI)/ ; SFI/12/RC/2273//Science Foundation Ireland (SFI)/ ; SFI/12/RC/2273//Science Foundation Ireland (SFI)/ ; SFI/12/RC/2273//Science Foundation Ireland (SFI)/ ; SFI/12/RC/2273//Science Foundation Ireland (SFI)/ ; 818368//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; }, abstract = {Efficient and accurate identification of microorganisms throughout the food chain can potentially allow the identification of sources of contamination and the timely implementation of control measures. High throughput DNA sequencing represents a potential means through which microbial monitoring can be enhanced. While Illumina sequencing platforms are most typically used, newer portable platforms, such as the Oxford Nanopore Technologies (ONT) MinION, offer the potential for rapid analysis of food chain microbiomes. Initial assessment of the ability of rapid MinION-based sequencing to identify microbes within a simple mock metagenomic mixture is performed. Subsequently, we compare the performance of both ONT and Illumina sequencing for environmental monitoring of an active food processing facility. Overall, ONT MinION sequencing provides accurate classification to species level, comparable to Illumina-derived outputs. However, while the MinION-based approach provides a means of easy library preparations and portability, the high concentrations of DNA needed is a limiting factor.}, }
@article {pmid33589511, year = {2021}, author = {Bi, Y and Tu, Y and Zhang, N and Wang, S and Zhang, F and Suen, G and Shao, D and Li, S and Diao, Q}, title = {Multiomics analysis reveals the presence of a microbiome in the gut of fetal lambs.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2020-320951}, pmid = {33589511}, issn = {1468-3288}, abstract = {OBJECTIVE: Microbial exposure is critical to neonatal and infant development, growth and immunity. However, whether a microbiome is present in the fetal gut prior to birth remains debated. In this study, lambs delivered by aseptic hysterectomy at full term were used as an animal model to investigate the presence of a microbiome in the prenatal gut using a multiomics approach.<br><br>DESIGN: Lambs were euthanised immediately after aseptic caesarean section and their cecal content and umbilical cord blood samples were aseptically acquired. Cecal content samples were assessed using metagenomic and metatranscriptomic sequencing to characterise any existing microbiome. Both sample types were analysed using metabolomics in order to detect microbial metabolites.<br><br>RESULTS: We detected a low-diversity and low-biomass microbiome in the prenatal fetal gut, which was mainly composed of bacteria belonging to the phyla Proteobacteria, Actinobacteria and Firmicutes. Escherichia coli was the most abundant species in the prenatal fetal gut. We also detected multiple microbial metabolites including short chain fatty acids, deoxynojirimycin, mitomycin and tobramycin, further indicating the presence of metabolically active microbiota. Additionally, bacteriophage phiX174 and Orf virus, as well as antibiotic resistance genes, were detected in the fetal gut, suggesting that bacteriophage, viruses and bacteria carrying antibiotic resistance genes can be transmitted from the mother to the fetus during the gestation period.<br><br>CONCLUSIONS: This study provides strong evidence that the prenatal gut harbours a microbiome and that microbial colonisation of the fetal gut commences in utero.}, }
@article {pmid33589262, year = {2021}, author = {Wu, S and Cui, Z and Chen, X and Zheng, L and Ren, H and Wang, D and Yao, J}, title = {Diet-ruminal microbiome-host crosstalk contributes to differential effects of calf starter and alfalfa hay on rumen epithelial development and pancreatic α-amylase activity in yak calves.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2020-18736}, pmid = {33589262}, issn = {1525-3198}, abstract = {Dietary supplementation of alfalfa hay or calf starter during the preweaning period was beneficial to the gastrointestinal development in dairy calves and lambs. In the present study, we designed 2 experiments using weaning with calf starter and alfalfa hay to investigate the diet-ruminal microbiome-host crosstalk in yak calves by analyzing the ruminal microbiota and rumen epithelial transcriptome. During the preweaning period, supplementation with either alfalfa hay or the starter significantly promoted animal growth and organ development in yak calves, including increases in body weight, body height, body length, chest girth, and development of liver, spleen, and thymus. These improvements could be attributed to increased dry matter intake, rumen fermentation, and development. Butyrate concentration increased in yak calves fed alfalfa hay or the starter, which could further promote ruminal epithelium development. Using 16S rRNA gene amplicon sequencing, we determined that butyrate-producing genera were increased by the supplementation with alfalfa hay or the starter. Transcriptomic analysis of the rumen epithelia revealed that the PI3K-Akt signaling pathway, which is critical in mediating many aspects of cellular function such as cell growth, was upregulated in response to alfalfa hay or the starter supplementation. The starter supplementation also increased the jejunal α-amylase activity, whereas alfalfa hay supplementation reduced the ileal α-amylase activity. Furthermore, the co-supplementation of both the starter and alfalfa hay reduced intestinal α-amylase activity. The starter increased ruminal propionate concentration, whereas alfalfa hay exhibited the opposite trend. The observed opposite effects of the starter and alfalfa hay on rumen propionate concentration corresponded with up- and downregulation, respectively, of the ruminal cholecystokinin involved in pancreatic secretion pathway, and thereby increased and decreased pancreatic α-amylase activity. In conclusion, both alfalfa hay and the starter could promote the growth and ruminal epithelial development of yak calves. The starter and alfalfa hay also differentially affected the intestinal α-amylase activities due to their different chemical components and different effects on ruminal fermentation, especially the ruminal propionate production.}, }
@article {pmid33588951, year = {2021}, author = {Raplee, I and Walker, L and Xu, L and Surathu, A and Chockalingam, A and Stewart, S and Han, X and Rouse, R and Li, Z}, title = {Emergence of nosocomial associated opportunistic pathogens in the gut microbiome after antibiotic treatment.}, journal = {Antimicrobial resistance and infection control}, volume = {10}, number = {1}, pages = {36}, pmid = {33588951}, issn = {2047-2994}, abstract = {INTRODUCTION: According to the Centers for Disease Control's 2015 Hospital Acquired Infection Hospital Prevalence Survey, 1 in 31 hospital patients was infected with at least one nosocomial pathogen while being treated for unrelated issues. Many studies associate antibiotic administration with nosocomial infection occurrence. However, to our knowledge, there is little to no direct evidence of antibiotic administration selecting for nosocomial opportunistic pathogens.<br><br>AIM: This study aims to confirm gut microbiota shifts in an animal model of antibiotic treatment to determine whether antibiotic use favors pathogenic bacteria.<br><br>METHODOLOGY: We utilized next-generation sequencing and in-house metagenomic assembly and taxonomic assignment pipelines on the fecal microbiota of a urinary tract infection mouse model with and without antibiotic treatment.<br><br>RESULTS: Antibiotic therapy decreased the number of detectable species of bacteria by at least 20-fold. Furthermore, the gut microbiota of antibiotic treated mice had a significant increase of opportunistic pathogens that have been implicated in nosocomial infections, like Acinetobacter calcoaceticus/baumannii complex, Chlamydia abortus, Bacteroides fragilis, and Bacteroides thetaiotaomicron. Moreover, antibiotic treatment selected for antibiotic resistant gene enriched subpopulations for many of these opportunistic pathogens.<br><br>CONCLUSIONS: Oral antibiotic therapy may select for common opportunistic pathogens responsible for nosocomial infections. In this study opportunistic pathogens present after antibiotic therapy harbored more antibiotic resistant genes than populations of opportunistic pathogens before treatment. Our results demonstrate the effects of antibiotic therapy on induced dysbiosis and expansion of opportunistic pathogen populations and antibiotic resistant subpopulations of those pathogens. Follow-up studies with larger samples sizes and potentially controlled clinical investigations should be performed to confirm our findings.}, }
@article {pmid33588762, year = {2021}, author = {Chen, Q and He, Z and Zhuo, Y and Li, S and Yang, W and Hu, L and Zhong, H}, title = {Rubidium chloride modulated the fecal microbiota community in mice.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {46}, pmid = {33588762}, issn = {1471-2180}, support = {51774339//National Natural Science Foundation of China/ ; 1053320184188//Fundamental Research Funds for Central Universities of the Central South University (CN)/ ; }, abstract = {BACKGROUND: The microbiota plays an important role in host health. Although rubidium (Rb) has been used to study its effects on depression and cancers, the interaction between microbial commensals and Rb is still unexplored. To gain the knowledge of the relationship between Rb and microbes, 51 mice receiving RbCl-based treatment and 13 untreated mice were evaluated for their characteristics and bacterial microbiome changes.<br><br>RESULTS: The 16S ribosomal RNA gene sequencing of fecal microbiota showed that RbCl generally maintained fecal microbial community diversity, while the shifts in fecal microbial composition were apparent after RbCl exposure. RbCl significantly enhanced the abundances of Rikenellaceae, Alistipes, Clostridium XlVa and sulfate-reducing bacteria including Deltaproteobacteria, Desulfovibrionales, Desulfovibrionaceae and Desulfovibrio, but significantly inhibited the abundances of Tenericutes, Mollicutes, Anaeroplasmatales, Anaeroplasmataceae and Anaeroplasma lineages. With regarding to the archaea, we only observed two less richness archaea Sulfolobus and Acidiplasma at the genus level.<br><br>CONCLUSIONS: Changes of fecal microbes may in part contribute to the anticancer or anti-depressant effects of RbCl. These findings further validate that the microbiome could be a target for therapeutic intervention.}, }
@article {pmid33588733, year = {2021}, author = {Zhao, YF and Wei, DN and Tang, Y}, title = {Gut microbiota regulate astrocytic functions in the brain: possible therapeutic consequences.}, journal = {Current neuropharmacology}, volume = {}, number = {}, pages = {}, doi = {10.2174/1570159X19666210215123239}, pmid = {33588733}, issn = {1875-6190}, abstract = {Astrocytes are essential for maintaining the homeostasis of the central nervous system (CNS). Astrocytic dysfunction has been implicated in the progression of several neurodegenerative and psychiatric diseases; however, a multitude of factors and signals influencing astrocytic activity have not been entirely elucidated. Astrocytes respond to local signals from the brain, but are also indirectly modulated by gut microbiota. Previous studies revealed that most of the CNS diseases triggered by astrocytic dysfunction are closely associated with the dysbiosis of gut microbiome. Emerging data from preclinical and clinical studies suggest that maturation and functioning of astrocytes rely on gut microbiota, which plays a pivotal role in the decrease of astrocytic activation and may alleviate symptoms of brain diseases. Herein, we discuss the most recent advances concerning the complex connections between astrocytes and gut microbiota, which are involved in the immune, neurotransmission and neuroendocrine pathways. Deciphering these pathways will facilitate a better understanding of how perturbed gut microbiota contributes to the dysfunction of astrocytes and open therapeutic opportunities for the treatment of brain diseases.}, }
@article {pmid33588422, year = {2021}, author = {Barra, WF and Sarquis, DP and Khayat, AS and Khayat, BCM and Demachki, S and Anaissi, AKM and Ishak, G and Santos, NPC and Dos Santos, SEB and Burbano, RR and Moreira, FC and de Assumpção, PP}, title = {Gastric Cancer Microbiome.}, journal = {Pathobiology : journal of immunopathology, molecular and cellular biology}, volume = {}, number = {}, pages = {1-14}, doi = {10.1159/000512833}, pmid = {33588422}, issn = {1423-0291}, abstract = {Identifying a microbiome pattern in gastric cancer (GC) is hugely debatable due to the variation resulting from the diversity of the studied populations, clinical scenarios, and metagenomic approach. H. pylori remains the main microorganism impacting gastric carcinogenesis and seems necessary for the initial steps of the process. Nevertheless, an additional non-H. pylori microbiome pattern is also described, mainly at the final steps of the carcinogenesis. Unfortunately, most of the presented results are not reproducible, and there are no consensual candidates to share the H. pylori protagonists. Limitations to reach a consistent interpretation of metagenomic data include contamination along every step of the process, which might cause relevant misinterpretations. In addition, the functional consequences of an altered microbiome might be addressed. Aiming to minimize methodological bias and limitations due to small sample size and the lack of standardization of bioinformatics assessment and interpretation, we carried out a comprehensive analysis of the publicly available metagenomic data from various conditions relevant to gastric carcinogenesis. Mainly, instead of just analyzing the results of each available publication, a new approach was launched, allowing the comprehensive analysis of the total sample amount, aiming to produce a reliable interpretation due to using a significant number of samples, from different origins, in a standard protocol. Among the main results, Helicobacter and Prevotella figured in the &quot;top 6&quot; genera of every group. Helicobacter was the first one in chronic gastritis (CG), gastric cancer (GC), and adjacent (ADJ) groups, while Prevotella was the leader among healthy control (HC) samples. Groups of bacteria are differently abundant in each clinical situation, and bacterial metabolic pathways also diverge along the carcinogenesis cascade. This information may support future microbiome interventions aiming to face the carcinogenesis process and/or reduce GC risk.}, }
@article {pmid33588418, year = {2021}, author = {Barbosa, AM and Gomes-Gonçalves, A and Castro, AG and Torrado, E}, title = {Immune System Efficiency in Cancer and the Microbiota Influence.}, journal = {Pathobiology : journal of immunopathology, molecular and cellular biology}, volume = {}, number = {}, pages = {1-17}, doi = {10.1159/000512326}, pmid = {33588418}, issn = {1423-0291}, abstract = {The immune system plays a critical role in preventing cancer development and progression. However, the complex network of cells and soluble factor that form the tumor microenvironment (TME) can dictate the differentiation of tumor-infiltrating leukocytes and shift the antitumor immune response into promoting tumor growth. With the advent of cancer immunotherapy, there has been a reinvigorated interest in defining how the TME shapes the antitumor immune response. This interest brought to light the microbiome as a novel player in shaping cancer immunosurveillance. Indeed, accumulating evidence now suggests that the microbiome may confer susceptibility or resistance to certain cancers and may influence response to therapeutics, particularly immune checkpoint inhibitors. As we move forward into the age of precision medicine, it is vital that we define the factors that influence the interplay between the triad immune system-microbiota-cancer. This knowledge will contribute to improve the therapeutic response to current approaches and will unravel novel targets for immunotherapy.}, }
@article {pmid33588407, year = {2021}, author = {Tay, CJX and Ta, LDH and Ow Yeong, YX and Yap, GC and Chu, JJH and Lee, BW and Tham, EH}, title = {Role of Upper Respiratory Microbiota and Virome in Childhood Rhinitis and Wheeze: Collegium Internationale Allergologicum Update 2021.}, journal = {International archives of allergy and immunology}, volume = {}, number = {}, pages = {1-12}, doi = {10.1159/000513325}, pmid = {33588407}, issn = {1423-0097}, abstract = {There is emerging evidence that the respiratory microbiota influences airway health, and there has been intense research interest in its role in respiratory infections and allergic airway disorders. This review aims to summarize current knowledge of nasal microbiome and virome and their associations with childhood rhinitis and wheeze. The healthy infant nasal microbiome is dominated by Corynebacteriaceae and Staphylococcaceae. In contrast, infants who subsequently develop respiratory disorders are depleted of these microbes and are instead enriched with Proteobacteria spp. Although human rhinovirus and human respiratory syncytial virus are well-documented major viral pathogens that trigger rhinitis and wheezing disorders in infants, recent limited data indicate that bacteriophages may have a role in respiratory health. Future work investigating the interplay between commensal microbiota, virome, and host immunological responses is an important step toward understanding the dynamics of the nasal community in order to develop a strategical approach to combat these common childhood respiratory disorders.}, }
@article {pmid33587919, year = {2021}, author = {Honarbakhsh, M and Ericsson, A and Zhong, G and Isoherranen, N and Zhu, C and Bromberg, Y and Van Buiten, C and Malta, K and Joseph, L and Sampath, H and Lakey, A and Storch, J and Vetriani, C and Chikindas, ML and Breslin, P and Quadro, L}, title = {Impact of vitamin A transport and storage on intestinal retinoid homeostasis and functions.}, journal = {Journal of lipid research}, volume = {}, number = {}, pages = {100046}, doi = {10.1016/j.jlr.2021.100046}, pmid = {33587919}, issn = {1539-7262}, abstract = {Lecithin:retinol acyltransferase (LRAT) and retinol-binding protein (RBP) enable vitamin A storage and transport, respectively, maintaining tissue homeostasis of retinoids (vitamin A derivatives). The precarious vitamin A status of the Lrat-/-Rbp-/- mice rapidly deteriorates upon dietary vitamin A restriction, leading to signs of severe vitamin A deficiency (VAD). As retinoids impact gut morphology and functions, VAD is often linked to intestinal pathological conditions and microbial dysbiosis. Thus, we investigated the contribution of vitamin A storage and transport to intestinal retinoid homeostasis and functionalities. We showed the occurrence of intestinal VAD in Lrat-/-Rbp-/- mice, demonstrating the critical role of both pathways in preserving gut retinoid homeostasis. Moreover, in the mutant colon, VAD resulted in compromised intestinal barrier as manifested by reduced mucins and antimicrobial defense, leaky gut, increased inflammation and oxidative stress, and altered mucosal immunocytokine profiles. These perturbations were accompanied by fecal dysbiosis, revealing that the vitamin A status (sufficient vs. deficient), rather than the amount of dietary vitamin A per se, is likely a major initial discriminant of the intestinal microbiome. Our data also pointed to a specific fecal taxonomic profile and distinct microbial functionalities associated with VAD. Overall, our findings revealed the suitability of the Lrat-/-Rbp-/- mice as a model to study intestinal dysfunctions and dysbiosis promoted by changes in tissue retinoid homeostasis induced by the host vitamin A status and/or intake.}, }
@article {pmid33587815, year = {2021}, author = {Habiyaremye, JD and Herrmann, S and Reitz, T and Buscot, F and Goldmann, K}, title = {Balance between geographic, soil, and host tree parameters to shape soil microbiomes associated to clonal oak varies across soil zones along a European North-South transect.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.15433}, pmid = {33587815}, issn = {1462-2920}, abstract = {Tree root-associated microbiomes are shaped by geographic, soil physico-chemical, and host tree parameters. However, their respective impacts on microbiome variations in soils across larger spatial scales remain weakly studied. We out-planted saplings of oak clone DF159 (Quercus robur L.) as phytometer in four grassland field sites along a European North-South transect. After four years, we first compared the soil microbiomes of the tree root zone (RZ) and the tree root-free zone (RFZ). After, we separately considered the total microbiomes of both zones, besides the microbiome with significant affinity to the RZ, and compared their variability along the transect. Variations within the microbiome of the tree RFZ were shaped by geographic and soil physico-chemical changes, whereby bacteria responded more than fungi. Variations within both microbiomes of the tree RZ depended on the host tree and abiotic parameters. Based on perMANOVA and Mantel correlation tests, impacts of site specificities and geographic distance strongly decreased for the tree RZ affine microbiome. This pattern was more pronounced for fungi than bacteria. Shaping the microbiome of the soil zones in root proximity might be a mechanism mediating the acclimation of oaks to a wide range of environmental conditions across geographic regions. This article is protected by copyright. All rights reserved.}, }
@article {pmid33587780, year = {2021}, author = {Jose, PA and Ben-Yosef, M and Lahuatte, P and Causton, CE and Heimpel, GE and Jurkevitch, E and Yuval, B}, title = {Shifting microbiomes complement life stage transitions and diet of the bird parasite Philornis downsi from the Galapagos Islands.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.15435}, pmid = {33587780}, issn = {1462-2920}, abstract = {Domestication disconnects an animal from its natural environment and diet, imposing changes in the attendant microbial community. We examine these changes in Philornis downsi (Muscidae), an invasive parasitic fly of land birds in the Galapagos Islands. Using a 16S rDNA profiling approach we studied the microbiome of larvae and adults of wild and laboratory-reared populations. These populations diverged in their microbiomes, significantly more so in larval than in adult flies. In field collected second-instar larvae, Klebsiella (70.3%) was the most abundant taxon, while in the laboratory Ignatzschineria and Providencia made up 89.2% of the community. In adults Gilliamella and Dysgonomonas were key members of the core microbiome of field derived females and males but had no or very low representation in the laboratory. Adult flies harbor sex-specific microbial consortia in their gut, as male core microbiomes were significantly dominated by Klebsiella. Thus P. downsi microbiomes are dynamic and shift correspondingly with life cycle and diet. Sex-specific foraging behavior of adult flies and nest conditions, which are absent in the laboratory, may contribute to shaping distinct larval, and adult male and female microbiomes. We discuss these findings in the context of microbe-host co-evolution and the implications for control measures. This article is protected by copyright. All rights reserved.}, }
@article {pmid33587265, year = {2021}, author = {Xiang, H and Chen, S and Zhang, H and Zhu, X and Wang, D and Liu, H and Wang, J and Yin, T and Liu, L and Kong, M and Zhang, J and Li, H and Turner, S and Zhao, X}, title = {Removal of roosters alters the domestic phenotype and microbial and genetic profile of hens.}, journal = {Science China. Life sciences}, volume = {}, number = {}, pages = {}, pmid = {33587265}, issn = {1869-1889}, abstract = {Hens are raised apart from roosters in modern poultry production, a substantial change from their natural social structure. We compared productivity, injuries, behavior, physiology, microbiome and transcriptome of hens housed with (R+) or without (R-) roosters to quantify the effects of this change in social structure. Hens were raised free-range from 70 to 280 days when 30 birds per treatment were assigned to battery cages until Day 315 (R+C vs. R-C), while 30 birds per treatment remained in free-range pens (R+F vs. R-F). Response to a novel environment and object, behavioral time budgets, cecum microbiome, blood composition and transcriptomic sequencing of thigh muscle and spleen were analyzed. Hens housed without roosters showed better survival, consumed less food, produced more eggs and had better feed conversion. R+F hens clustered around the rooster and were less mobile in the novel environment and object tests. R+F hens displayed the richest microbiome, and the presence of roosters resulted in differentially expressed genes related to muscle development, cellular processes, environmental information processing and immune function. Removing roosters from housed hens intensified desirable characteristics favored by domestication probably operating by deprivation of mating behavior and reduced fear, along with altered microbial and genetic function.}, }
@article {pmid33587112, year = {2021}, author = {Balbín-Suárez, A and Jacquiod, S and Rohr, AD and Liu, B and Flachowsky, H and Winkelmann, T and Beerhues, L and Nesme, J and Sørensen, SJ and Vetterlein, D and Smalla, K}, title = {Root exposure to apple replant disease soil triggers local defense response and rhizoplane microbiome dysbiosis.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiab031}, pmid = {33587112}, issn = {1574-6941}, abstract = {A soil column split-root experiment was designed to investigate the ability of apple replant disease (ARD) causing agents to spread in soil. 'M26' apple rootstocks grew into a top layer of Control soil, followed by a barrier-free split-soil layer (Control soil/ARD soil). We observed a severely reduced root growth, concomitant with enhanced gene expression of phytoalexin biosynthetic genes and phytoalexin content in roots from ARD soil, indicating a pronounced local plant defense response. Amplicon sequencing (bacteria, archaea, fungi) revealed local shifts in diversity and composition of microorganisms in the rhizoplane of roots from ARD soil. An enrichment of OTUs affiliated to potential ARD fungal pathogens (Ilyonectria and Nectria sp.) and bacteria frequently associated with ARD (Streptomyces, Variovorax) was noted. In conclusion, our integrated study supports the idea of ARD being local and not spreading into surrounding soil, as only the roots in ARD soil were affected in terms of growth, phytoalexin biosynthetic gene expression, phytoalexin production, and altered microbiome structure. This study further reinforces the microbiological nature of ARD, being likely triggered by a disturbed soil microbiome enriched with low mobility ARD-causing agents that induce a strong plant defense and rhizoplane microbiome dysbiosis, concurring with root damage.}, }
@article {pmid33586839, year = {2021}, author = {Hu, YJ and Wang, J and Harwell, JI and Wake, M}, title = {Association of in utero antibiotic exposure on childhood ear infection trajectories: Results from a national birth cohort study.}, journal = {Journal of paediatrics and child health}, volume = {}, number = {}, pages = {}, doi = {10.1111/jpc.15371}, pmid = {33586839}, issn = {1440-1754}, support = {//MCRI Lifecourse Postdoctoral Fellowship/ ; 1046518//National Health and Medical Research Council (NHMRC) Senior Research Fellowship/ ; 1160906//NHMRC Principal Research Fellowship/ ; //Research at the Murdoch Children's Research Institute (MCRI) Victorian Government's Operational Infrastructure Support Program/ ; }, abstract = {AIM: Most prescribed medicines during pregnancy are antibiotics, with unknown effects on a fetus and on the infant's acquired microbiome. This study investigates associations between in utero antibiotic exposure and ear infection trajectories over the first decade of life, hypothesising effects on early or persistent, rather than later-developing, ear infections.<br><br>METHODS: Design and participants: The Longitudinal Study of Australian Children birth cohort recruited a nationally-representative sample of 5107 infants in 2004.<br><br>MEASURES: Mothers reported antibiotic use in pregnancy when a child was 3-21 months old (wave 1), and ongoing problems with ear infection every 2 years spanning ages 0-1 to 10-11 years (waves 1-6).<br><br>ANALYSIS: Latent class models identified ear infection trajectories, and univariable and multivariable multinomial logistic regression determined odds of adverse trajectories by antibiotic exposure.<br><br>RESULTS: A total of 4500 (88.1% of original sample) children contributed (mean baseline age 0.7 years; 51.3% boys); 10.4% of mothers reported antibiotic use in pregnancy. Four probability trajectories for ear infection emerged: 'consistently low' (86.2%), 'moderate to low' (5.6%), 'low to moderate' (6.7%) and 'consistently high' (1.4%). Antibiotic use in pregnancy was associated with children following 'consistently high' (adjusted odds ratio 2.04, 95% confidence interval 1.08-3.88, P = 0.03) and 'moderate to low' (adjusted odds ratio 1.78, 95% confidence interval 1.25-2.53, P = 0.001) trajectories.<br><br>CONCLUSIONS: Antibiotic use in pregnancy is associated with an increased risk of persistent and early childhood ear infections. This highlights the wisdom of cautious antibiotic use during pregnancy, and the need for the study of potential mechanisms underlying these associations.}, }
@article {pmid33586672, year = {2021}, author = {Yu, M and Pal, S and Paterson, CW and Li, JY and Tyagi, AM and Adams, J and Coopersmith, CM and Weitzmann, MN and Pacifici, R}, title = {Ovariectomy induces bone loss via microbial-dependent trafficking of intestinal TNF+ T cells and Th17 cells.}, journal = {The Journal of clinical investigation}, volume = {131}, number = {4}, pages = {}, doi = {10.1172/JCI143137}, pmid = {33586672}, issn = {1558-8238}, abstract = {Estrogen deficiency causes a gut microbiome-dependent expansion of BM Th17 cells and TNF-α-producing T cells. The resulting increased BM levels of IL-17a (IL-17) and TNF stimulate RANKL expression and activity, causing bone loss. However, the origin of BM Th17 cells and TNF+ T cells is unknown. Here, we show that ovariectomy (ovx) expanded intestinal Th17 cells and TNF+ T cells, increased their S1P receptor 1-mediated (S1PR1-mediated) egress from the intestine, and enhanced their subsequent influx into the BM through CXCR3- and CCL20-mediated mechanisms. Demonstrating the functional relevance of T cell trafficking, blockade of Th17 cell and TNF+ T cell egress from the gut or their influx into the BM prevented ovx-induced bone loss. Therefore, intestinal T cells are a proximal target of sex steroid deficiency relevant for bone loss. Blockade of intestinal T cell migration may represent a therapeutic strategy for the treatment of postmenopausal bone loss.}, }
@article {pmid33586659, year = {2021}, author = {Polak-Witka, K and Constantinou, A and Schwarzer, R and Helmuth, J and Wiessner, A and Hadam, S and Kanti, V and Rancan, F and Andruck, A and Richter, C and Moter, A and Edelmann, A and Rudnicka, L and Blume-Peytavi, U and Vogt, A}, title = {Identification of anti-microbial peptides and traces of microbial DNA in infrainfundibular compartments of human scalp terminal hair follicles.}, journal = {European journal of dermatology : EJD}, volume = {}, number = {}, pages = {}, doi = {10.1684/ejd.2020.3948}, pmid = {33586659}, issn = {1952-4013}, abstract = {BACKGROUND: The upper follicular compartment, a well-known reservoir of cutaneous microbiota, constitutes a space for intensive cross-barrier dialogue. The lower follicle comprises the bulb and bulge, structures with relative immune-privileged status, crucial for physiological cycling, and widely considered to be microbial-free.<br><br>OBJECTIVES: Following our initial immunohistochemical screening for regulatory cytokines and defensin expression in anagen hair follicles, we aimed to confirm our results with a follow-up ELISA investigation. We postulated that exposure to microbial components may trigger expression, and thus opted to investigate microbial presence in this area.<br><br>MATERIALS &amp; METHODS: We performed immunohistochemical staining for selected cytokines and antimicrobial peptides, and Gram and Giemsa staining on tissue sections from healthy individuals. Based on ELISA analyses, we confirmed a marked presence of IL-17A- and HBD2 in infrainfundibular compartments from plucked anagen hair follicles of 12 individuals (six females, six males; frontal and occipital scalp sites). 16S rRNA sequencing on microbial DNA extracted from lower follicles, as well as fluorescence in situ hybridization (FISH) were applied to explore bacterial presence in the infrainfundibular compartments.<br><br>RESULTS: 16S rRNA sequencing yielded reproducible data of bacterial presence in infrainfundibular compartments of plucked scalp follicles; Lawsonella clevelandensis, Staphylococcaceae and Propionibacteriaceae were the most abundant bacteria. Also, FISH revealed biofilm structures formed by Cutibacterium acnes (formerly Propionibacterium acnes) and Staphylococcus sp. below the infundibulum.<br><br>CONCLUSION: As the skin microbiome largely influences the local immune system, the presence of bacteria in proximity to follicular immune-privileged areas may be of relevance to hair cycling in health and disease.}, }
@article {pmid33586656, year = {2021}, author = {Sakamoto, R and Kajihara, I and Mijiddorj, T and Otsuka-Maeda, S and Sawamura, S and Nishimura, Y and Kanemaru, H and Kanazawa-Yamada, S and Nakamura, K and Honda, N and Makino, K and Aoi, J and Igata, T and Makino, T and Masuguchi, S and Fukushima, S and Morinaga, J and Komohara, Y and Ihn, H}, title = {Existence of Staphylococcus aureus correlates with the progression of extramammary Paget's disease: potential involvement of interleukin-17 and M2-like macrophage polarization.}, journal = {European journal of dermatology : EJD}, volume = {}, number = {}, pages = {}, doi = {10.1684/ejd.2021.3972}, pmid = {33586656}, issn = {1952-4013}, abstract = {BACKGROUND: The microbiome plays an important role in the tumour microenvironment (TME).<br><br>OBJECTIVES: In this study, we investigated the clinical significance of the microbiota in extramammary Paget's disease (EMPD).<br><br>MATERIALS &amp; METHODS: Patients with EMPD, treated between March 2007 and September 2019 at Kumamoto University Hospital, were investigated retrospectively. Inclusion criteria included: histological diagnosis of EMPD, inspection of the bacterial culture of the cancer lesion using swab sampling, and availability of sufficient tissue in paraffin blocks for immunohistochemistry. For the latter, primary antibodies against IL-17, CD163 and ionized calcium-binding adapter molecule 1 (Iba1) were used.<br><br>RESULTS: Bacterial cultures of the cancer lesion revealed that Staphylococcus aureus (S. aureus) was highly prevalent in EMPD patients, with dermal invasion or lymph node metastasis, compared to patients without these findings. Furthermore, the number of IL-17-positive cells and CD163-positive M2-like macrophages (pro-tumour macrophages) were increased in EMPD tissues with S. aureus. Moreover, the number of IL-17-producing cells in EMPD tissues positively correlated with the accumulation of CD163-positive M2-like macrophages. In addition, the percentage of CD163-positive cells within Iba-1-positive macrophages (total macrophages) was also significantly elevated in EMPD tissues with S. aureus.<br><br>CONCLUSION: Based on these findings, S. aureus may exacerbate the pathological condition of EMPD via the accumulation of IL-17 and M2-like macrophages.}, }
@article {pmid33585949, year = {2021}, author = {van Lanen, AS and de Bree, A and Greyling, A}, title = {Efficacy of a low-FODMAP diet in adult irritable bowel syndrome: a systematic review and meta-analysis.}, journal = {European journal of nutrition}, volume = {}, number = {}, pages = {}, pmid = {33585949}, issn = {1436-6215}, abstract = {PURPOSE: This review provides an updated overview of observational and intervention studies investigating the effect of a low-FODMAP (fermentable oligo-, di- and monosaccharides, and polyols) diet (LFD) on gastrointestinal (GI) symptoms, quality of life (QoL), nutritional adequacy, and gut microbiome in irritable bowel syndrome (IBS) patients.<br><br>METHODS: We systematically searched available literature until October 2020 for studies that investigated the effect of LFDs on GI symptoms, QoL, nutritional adequacy, and the gut microbiome in IBS patients. The data were represented as standardized mean differences (SMD) for IBS severity, and as mean differences (MD) for IBS-QoL. Meta-analyses were performed for the quantitative analyses using random effects models with inverse variance weighing.<br><br>RESULTS: Twelve papers (nine parallel trials, three crossover studies) were included for the meta-analysis. The LFD reduced IBS severity by a moderate-to-large extent as compared to a control diet (SMD - 0.66, 95% CI - 0.88, - 0.44, I2 = 54%). When analyzing only studies that used the validated IBS-SSS questionnaire, a mean reduction of 45 points (95% CI - 77, - 14; I2 = 89%) was observed. Subgroup analyses on adherence, age, intervention duration, IBS subtype, outcome measure, and risk of bias revealed no significantly different results. The LFD also increased IBS-QoL scores, when compared with a control diet (MD 4.93; 95% CI 1.77, 8.08; I2 = 42%).<br><br>CONCLUSIONS: The low-FODMAP diet reduces GI symptoms and improves quality of life in IBS subjects as compared to control diets. Future work is required to obtain definitive answers regarding potential long-term effects of such diets on nutritional adequacy and the gut microbiome.<br><br>PROSPERO REGISTRATION NUMBER: CRD42020175157.}, }
@article {pmid33585820, year = {2021}, author = {Pearson, CF and Jeffery, R and ,  and Thornton, EE}, title = {Mucosal immune responses in COVID19 - a living review.}, journal = {Oxford open immunology}, volume = {2}, number = {1}, pages = {iqab002}, pmid = {33585820}, issn = {2633-6960}, abstract = {COVID-19 was initially characterized as a disease primarily of the lungs, but it is becoming increasingly clear that the SARS-CoV2 virus is able to infect many organs and cause a broad pathological response. The primary infection site is likely to be a mucosal surface, mainly the lungs or the intestine, where epithelial cells can be infected with virus. Although it is clear that virus within the lungs can cause severe pathology, driven by an exaggerated immune response, infection within the intestine generally seems to cause minor or no symptoms. In this review, we compare the disease processes between the lungs and gastrointestinal tract, and what might drive these different responses. As the microbiome is a key part of mucosal barrier sites, we also consider the effect that microbial species may play on infection and the subsequent immune responses. Because of difficulties obtaining tissue samples, there are currently few studies focused on the local mucosal response rather than the systemic response, but understanding the local immune response will become increasingly important for understanding the mechanisms of disease in order to develop better treatments.}, }
@article {pmid33585724, year = {2021}, author = {Silkiss, RZ and Paap, MK and Ugradar, S}, title = {Increased incidence of chalazion associated with face mask wear during the COVID-19 pandemic.}, journal = {American journal of ophthalmology case reports}, volume = {22}, number = {}, pages = {101032}, pmid = {33585724}, issn = {2451-9936}, abstract = {Purpose: To determine whether the incidence of chalazion increased significantly in the San Francisco Bay Area and Los Angeles County following the widespread adoption of face mask wear in response to the COVID-19 pandemic.<br><br>Methods: This is a retrospective multicenter study of two ophthalmology institutions: a private Oculoplastics practice in San Francisco and the Oculoplastics division of the Stein Eye Institute at the University of California, Los Angeles. All patients seen during the studied time periods with a diagnosis of chalazion or hordeolum were identified through review of electronic medical records and included in the study. Incidence was determined for each month between January and August 2020, and compared to data from prior years via ANOVA to evaluate for changes after the onset of the pandemic.<br><br>Results: In San Francisco, the incidence of chalazion rose significantly in June through August of 2020 when compared to the same interval in 2016, 2017, 2018, and 2019. In Los Angeles, the rise in chalazion incidence in 2020 was also statistically significant when compared to data from the years 2018 and 2019.<br><br>Conclusion: Importance: Widespread mask wear does appear to correspond to an increased incidence of chalazion. This risk may be minimized, while still maintaining the protective benefits of mask wear, by taking the proactive measures discussed to decrease mask induced eye dryness and changes in the eyelid microbiome.}, }
@article {pmid33585532, year = {2020}, author = {Nestel, N and Hvass, JD and Bahl, MI and Hansen, LH and Krych, L and Nielsen, DS and Dragsted, LO and Roager, HM}, title = {The Gut Microbiome and Abiotic Factors as Potential Determinants of Postprandial Glucose Responses: A Single-Arm Meal Study.}, journal = {Frontiers in nutrition}, volume = {7}, number = {}, pages = {594850}, pmid = {33585532}, issn = {2296-861X}, abstract = {The gut microbiome has combined with other person-specific information, such as blood parameters, dietary habits, anthropometrics, and physical activity been found to predict personalized postprandial glucose responses (PPGRs) to various foods. Yet, the contributions of specific microbiome taxa, measures of fermentation, and abiotic factors in the colon to glycemic control remain elusive. We tested whether PPGRs 60 min after a standardized breakfast was associated with gut microbial α-diversity (primary outcome) and explored whether postprandial responses of glucose and insulin were associated with specific microbiome taxa, colonic fermentation as reflected by fecal short-chain fatty acids (SCFAs), and breath hydrogen and methane exhalation, as well as abiotic factors including fecal pH, fecal water content, fecal energy density, intestinal transit time (ITT), and stool consistency. A single-arm meal trial was conducted. A total of 31 healthy (24 female and seven male) subjects consumed a standardized evening meal and a subsequent standardized breakfast (1,499 kJ) where blood was collected for analysis of postprandial glucose and insulin responses. PPGRs to the same breakfast varied across the healthy subjects. The largest inter-individual variability in PPGRs was observed 60 min after the meal but was not associated with gut microbial α-diversity. In addition, no significant associations were observed between postprandial responses and specific taxa of the gut microbiome, measures of colonic fermentation, ITT, or other abiotic factors. However, fasting glucose concentrations were negatively associated with ITT, and fasting insulin was positively associated with fasting breath hydrogen. In conclusion, the gut microbiome, measures of colonic fermentation, and abiotic factors were not shown to be significantly associated with variability in postprandial responses, suggesting that contributions of the gut microbiome, colonic fermentation, and abiotic factors to PPGRs may be subtle in healthy adults.}, }
@article {pmid33585285, year = {2020}, author = {Stavropoulou, E and Kantartzi, K and Tsigalou, C and Konstantinidis, T and Voidarou, C and Konstantinidis, T and Bezirtzoglou, E}, title = {Unraveling the Interconnection Patterns Across Lung Microbiome, Respiratory Diseases, and COVID-19.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {619075}, pmid = {33585285}, issn = {2235-2988}, abstract = {Albeit the lungs were thought to be sterile, recent scientific data reported a microbial microbiota in the lungs of healthy individuals. Apparently, new developments in technological approachesincluding genome sequencing methodologies contributed in the identification of the microbiota and shed light on the role of the gut and lung microbiomes in the development of respiratory diseases. Moreover, knowledge of the human microbiome in health may act as a tool for evaluating characteristic shifts in the case of disease. This review paper discusses the development of respiratory disease linked to the intestinal dysbiosis which influences the lung immunity and microbiome. The gastrointestinal-lung dialogue provides interesting aspects in the pathogenesis of the respiratory diseases. Lastly, we were further interested on the role of this interconnection in the progression and physiopathology of newly emergedCOVID-19.}, }
@article {pmid33585283, year = {2020}, author = {Tejesvi, MV and Tapiainen, T and Vänni, P and Uhari, M and Suokas, M and Lantto, U and Koivunen, P and Renko, M}, title = {Tonsil Mycobiome in PFAPA (Periodic Fever, Aphthous Stomatitis, Pharyngitis, Adenitis) Syndrome: A Case-Control Study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {616814}, pmid = {33585283}, issn = {2235-2988}, abstract = {Periodic fever, aphthous stomatitis, pharyngitis and adenitis syndrome (PFAPA) is the most common periodic fever syndrome in children with unknown etiology, effectively treated with tonsillectomy. Earlier we have shown that tonsil microbiome is different in patients with PFAPA as compared to that in controls. Recently, fungal microbiome, mycobiome, has been linked to the pathogenesis of inflammatory diseases. We now investigated the role of mycobiome of tonsils in PFAPA. Random forest classification, a machine learning approach, was used for the analysis of mycobiome data. We examined tonsils from 30 children with PFAPA and 22 control children undergoing tonsillectomy for non-infectious reasons. We identified 103 amplicon sequence variants, mainly from two fungal phyla, Ascomycota and Basidiomycota. The mean relative abundance of Candida albicans in the tonsil mycobiome was 11% (95% CI: 19 to 27%) in cases and 3.4 % (95% CI: -0.8% to 8%) in controls, p =0.104. Mycobiome data showed no statistical difference in differentiating between PFAPA cases and controls compared to a random chance classifier (area under the curve (AUC) = 0.47, SD = 0.05, p = 0.809). In conclusion, in this controlled study, tonsillar mycobiome in children with PFAPA syndrome did not differ from that of the controls.}, }
@article {pmid33585276, year = {2020}, author = {Saito, S and Aoki, Y and Tamahara, T and Goto, M and Matsui, H and Kawashima, J and Danjoh, I and Hozawa, A and Kuriyama, S and Suzuki, Y and Fuse, N and Kure, S and Yamashita, R and Tanabe, O and Minegishi, N and Kinoshita, K and Tsuboi, A and Shimizu, R and Yamamoto, M}, title = {Oral Microbiome Analysis in Prospective Genome Cohort Studies of the Tohoku Medical Megabank Project.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {604596}, pmid = {33585276}, issn = {2235-2988}, abstract = {A baseline oral microbiome study of the Tohoku Medical Megabank Organization (TMM) was planned to characterize the profile of the oral microbiome in the Japanese population. The study also aimed to clarify risk factors for multifactorial diseases by integrated analysis of the oral microbiome and host genome/omics information. From 2013 to 2016, we collected three types of oral biospecimens, saliva, supragingival plaque, and tongue swab, from a total of 25,101 participants who had a dental examination in TMM. In this study, we used two independent cohorts; the Community-Based Cohort and Birth and Three-Generation Cohort as discovery and validation cohorts, respectively, and we selected participants examined by a single dentist. We found through the 16S ribosomal RNA gene sequencing analysis of 834 participants of the Community-Based Cohort Study that there are differences in the microbial composition and community structure between saliva and plaque. The species diversities in both saliva and plaque were increased in correlation with the severity of periodontal disease. These results were nicely reproduced in the analysis of 455 participants of the Birth and Three-Generation Cohort Study. In addition, strong positive and negative associations of microbial taxa in both plaque and saliva with periodontitis-associated biofilm formation were detected by co-occurrence network analysis. The classes Actinobacteria and Bacilli, including oral health-associated bacterial species, showed a positive correlation in saliva. These results revealed differences in microbial composition and community structure between saliva and plaque and a correlation between microbial species and the severity of periodontal disease. We expect that the large database of the oral microbiome in the TMM biobank will help in the discovery of novel targets for the treatment and prevention of oral diseases, as well as for the discovery of therapeutic and/or preventive targets of systemic diseases.}, }
@article {pmid33584958, year = {2020}, author = {Del Rosso, JQ}, title = {SARECYCLINE AND THE NARROW-SPECTRUM TETRACYCLINE CONCEPT: Currently Available Data and Potential Clinical Relevance in Dermatology.}, journal = {The Journal of clinical and aesthetic dermatology}, volume = {13}, number = {10}, pages = {45-48}, pmid = {33584958}, issn = {1941-2789}, abstract = {Oral tetracyclines are commonly prescribed in dermatology, especially for acne. The most commonly used oral agents for acne treatment over the past several years are doxycycline and minocycline based on their overall efficacy and safety. Available for over five decades as immediate-release formulations, both of these agents exhibit broad-spectrum antibiotic activity and are primarily FDA-approved for treatment of a variety of cutaneous infections. In 2018, oral sarecycline was FDA-approved for the treatment of acne, which is the only disease state for which it was evaluated based on a narrower antibiotic spectrum of activity. This article reviews the overall antibiotic properties of commonly used oral tetracyclines with a focus on explaining the narrow spectrum of activity exhibited by sarecycline. Specifically, sarecycline has high activity against Cutibacterium acnes, the organism correlated with acne pathogenesis, as well as Staphylococci and Streptococci, with a low potential for emergence of resistant mutant bacteria based on in-vitro testing. The narrow-spectrum antibiotic designation of sarecycline relates to its negligible or low activity against many gram-negative and anaerobic bacteria. This article serves to review available data to date to assist clinicians in determining potential clinical relevance related to oral antibiotic use for acne.}, }
@article {pmid33584781, year = {2021}, author = {Baccelli, I and Bertini, L and Hickman, R and Leon-Reyes, A and Proietti, S}, title = {Editorial: Novel Plant Molecules Regulating the Interaction With Pathogenic and Beneficial Fungi.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {644546}, pmid = {33584781}, issn = {1664-462X}, }
@article {pmid33584660, year = {2020}, author = {Czolk, R and Klueber, J and Sørensen, M and Wilmes, P and Codreanu-Morel, F and Skov, PS and Hilger, C and Bindslev-Jensen, C and Ollert, M and Kuehn, A}, title = {IgE-Mediated Peanut Allergy: Current and Novel Predictive Biomarkers for Clinical Phenotypes Using Multi-Omics Approaches.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {594350}, pmid = {33584660}, issn = {1664-3224}, abstract = {Food allergy is a collective term for several immune-mediated responses to food. IgE-mediated food allergy is the best-known subtype. The patients present with a marked diversity of clinical profiles including symptomatic manifestations, threshold reactivity and reaction kinetics. In-vitro predictors of these clinical phenotypes are evasive and considered as knowledge gaps in food allergy diagnosis and risk management. Peanut allergy is a relevant disease model where pioneer discoveries were made in diagnosis, immunotherapy and prevention. This review provides an overview on the immune basis for phenotype variations in peanut-allergic individuals, in the light of future patient stratification along emerging omic-areas. Beyond specific IgE-signatures and basophil reactivity profiles with established correlation to clinical outcome, allergenomics, mass spectrometric resolution of peripheral allergen tracing, might be a fundamental approach to understand disease pathophysiology underlying biomarker discovery. Deep immune phenotyping is thought to reveal differential cell responses but also, gene expression and gene methylation profiles (eg, peanut severity genes) are promising areas for biomarker research. Finally, the study of microbiome-host interactions with a focus on the immune system modulation might hold the key to understand tissue-specific responses and symptoms. The immune mechanism underlying acute food-allergic events remains elusive until today. Deciphering this immunological response shall enable to identify novel biomarker for stratification of patients into reaction endotypes. The availability of powerful multi-omics technologies, together with integrated data analysis, network-based approaches and unbiased machine learning holds out the prospect of providing clinically useful biomarkers or biomarker signatures being predictive for reaction phenotypes.}, }
@article {pmid33584634, year = {2021}, author = {Distaso, MA and Bargiela, R and Brailsford, FL and Williams, GB and Wright, S and Lunev, EA and Toshchakov, SV and Yakimov, MM and Jones, DL and Golyshin, PN and Golyshina, OV}, title = {Corrigendum: High Representation of Archaea Across All Depths in Oxic and Low-pH Sediment Layers Underlying an Acidic Stream.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {633015}, doi = {10.3389/fmicb.2021.633015}, pmid = {33584634}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2020.576520.].}, }
@article {pmid33584627, year = {2021}, author = {Wang, Z and Yu, Y and Li, X and Xiao, H and Zhang, P and Shen, W and Wan, F and He, J and Tang, S and Tan, Z and Wu, D and Yao, H}, title = {Fermented Soybean Meal Replacement in the Diet of Lactating Holstein Dairy Cows: Modulated Rumen Fermentation and Ruminal Microflora.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {625857}, pmid = {33584627}, issn = {1664-302X}, abstract = {This study was conducted to examine the influences of replacing soybean meal (SBM) with fermented soybean meal (FSBM) in the diet of lactating Holstein cattle on rumen fermentation and ruminal bacterial microbiome. Twenty-four lactating Chinese Holstein dairy cattle were assigned to each of the two treatments in a completely randomized design: the SBM group [the basal total mixed ration (TMR) diet containing 5.77% SBM] and the FSBM group (the experimental TMR diet containing 5.55% FSBM). This trial lasted for 54 days (14 days for adjustment and 40 days for data and sample collection), and samples of rumen liquid were collected on 34 d and 54 d, respectively. The results showed that replacing SBM with FSBM significantly increased the molar percentages of propionate (P < 0.01) and valerate (P < 0.05), but reduced the total volatile fatty acid (TVFA) concentration (P < 0.05), butyrate molar proportion (P < 0.05), and the acetate to propionate ratio (P < 0.01). The copy numbers of total bacteria (P < 0.05), Fibrobacter succinogenes (P < 0.01), Selenomonas ruminantium (P < 0.01), and Prevotella spp. (P < 0.05) in the FSBM group were greater, while the density of Prevotella ruminicola (P < 0.05) was lower than those in the SBM treatment. Additionally, Succiniclasticum ruminis and Saccharofermentans acetigenes were significantly enriched (P < 0.05) in the rumen fluid of FSBM-fed cows, despite the fact that there was no remarkable difference in the Alpha diversity indexes, structure and KEGG pathway abundances of the bacterial community across the two treatments. It could hence be concluded that the substitution of FSBM for SBM modulated rumen fermentation and rumen bacterial microbiota in lactating Holstein dairy cows. Further research is required to elucidate the relevant mechanisms of FSBM, and provide more insights into the application of FSBM in dairy cattle.}, }
@article {pmid33584614, year = {2021}, author = {Wu, L and Luo, Y}, title = {Bacterial Quorum-Sensing Systems and Their Role in Intestinal Bacteria-Host Crosstalk.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {611413}, pmid = {33584614}, issn = {1664-302X}, abstract = {Quorum-sensing (QS) system is a rapidly developing field in which we are gradually expanding our understanding about how bacteria communicate with each other and regulate their activities in bacterial sociality. In addition to collectively modifying bacterial behavior, QS-related autoinducers may also be embedded in the crosstalk between host and parasitic microbes. In this review, we summarize current studies on QS in the intestinal microbiome field and its potential role in maintaining homeostasis under physiological conditions. Additionally, we outline the canonical autoinducers and their related QS signal-response systems by which several pathogens interact with the host under pathological conditions, with the goal of better understanding intestinal bacterial sociality and facilitating novel antimicrobial therapeutic strategies.}, }
@article {pmid33584612, year = {2021}, author = {Ramon, E and Belanche-Muñoz, L and Molist, F and Quintanilla, R and Perez-Enciso, M and Ramayo-Caldas, Y}, title = {kernInt: A Kernel Framework for Integrating Supervised and Unsupervised Analyses in Spatio-Temporal Metagenomic Datasets.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {609048}, pmid = {33584612}, issn = {1664-302X}, abstract = {The advent of next-generation sequencing technologies allowed relative quantification of microbiome communities and their spatial and temporal variation. In recent years, supervised learning (i.e., prediction of a phenotype of interest) from taxonomic abundances has become increasingly common in the microbiome field. However, a gap exists between supervised and classical unsupervised analyses, based on computing ecological dissimilarities for visualization or clustering. Despite this, both approaches face common challenges, like the compositional nature of next-generation sequencing data or the integration of the spatial and temporal dimensions. Here we propose a kernel framework to place on a common ground the unsupervised and supervised microbiome analyses, including the retrieval of microbial signatures (taxa importances). We define two compositional kernels (Aitchison-RBF and compositional linear) and discuss how to transform non-compositional beta-dissimilarity measures into kernels. Spatial data is integrated with multiple kernel learning, while longitudinal data is evaluated by specific kernels. We illustrate our framework through a single point soil dataset, a human dataset with a spatial component, and a previously unpublished longitudinal dataset concerning pig production. The proposed framework and the case studies are freely available in the kernInt package at https://github.com/elies-ramon/kernInt.}, }
@article {pmid33584593, year = {2020}, author = {Schreuder, J and Velkers, FC and Bossers, A and Bouwstra, RJ and de Boer, WF and van Hooft, P and Stegeman, JA and Jurburg, SD}, title = {Temporal Dynamics of Cloacal Microbiota in Adult Laying Chickens With and Without Access to an Outdoor Range.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {626713}, pmid = {33584593}, issn = {1664-302X}, abstract = {Associations between animal health and performance, and the host's microbiota have been recently established. In poultry, changes in the intestinal microbiota have been linked to housing conditions and host development, but how the intestinal microbiota respond to environmental changes under farm conditions is less well understood. To gain insight into the microbial responses following a change in the host's immediate environment, we monitored four indoor flocks of adult laying chickens three times over 16 weeks, during which two flocks were given access to an outdoor range, and two were kept indoors. To assess changes in the chickens' microbiota over time, we collected cloacal swabs of 10 hens per flock and performed 16S rRNA gene amplicon sequencing. The poultry house (i.e., the stable in which flocks were housed) and sampling time explained 9.2 and 4.4% of the variation in the microbial community composition of the flocks, respectively. Remarkably, access to an outdoor range had no detectable effect on microbial community composition, the variability of microbiota among chickens of the same flock, or microbiota richness, but the microbiota of outdoor flocks became more even over time. Fluctuations in the composition of the microbiota over time within each poultry house were mainly driven by turnover in rare, rather than dominant, taxa and were unique for each flock. We identified 16 amplicon sequence variants that were differentially abundant over time between indoor and outdoor housed chickens, however none were consistently higher or lower across all chickens of one housing type over time. Our study shows that cloacal microbiota community composition in adult layers is stable following a sudden change in environment, and that temporal fluctuations are unique to each flock. By exploring microbiota of adult poultry flocks within commercial settings, our study sheds light on how the chickens' immediate environment affects the microbiota composition.}, }
@article {pmid33584587, year = {2020}, author = {Fan, R and Burghardt, JP and Huang, J and Xiong, T and Czermak, P}, title = {Purification of Crude Fructo-Oligosaccharide Preparations Using Probiotic Bacteria for the Selective Fermentation of Monosaccharide Byproducts.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {620626}, pmid = {33584587}, issn = {1664-302X}, abstract = {Probiotics are microbes that promote health when consumed in sufficient amounts. They are present in many fermented foods or can be provided directly as supplements. Probiotics utilize non-digestible prebiotic oligosaccharides for growth in the intestinal tract, contributing to a healthy microbiome. The oligosaccharides favored by probiotics are species-dependent, as shown by the selective utilization of substrates in mixed sugar solutions such as crude fructo-oligosaccharides (FOS). Enzymatically produced crude FOS preparations contain abundant monosaccharide byproducts, residual sucrose, and FOS varying in chain length. Here we investigated the metabolic profiles of four probiotic bacteria during the batch fermentation of crude FOS under controlled conditions. We found that Bacillus subtilis rapidly utilized most of the monosaccharides but little sucrose or FOS. We therefore tested the feasibility of a microbial fed-batch fermentation process for the purification of FOS from crude preparations, which increased the purity of FOS from 59.2 to 82.5% with a final concentration of 140 g·l-1. We also tested cell immobilization in alginate beads as a means to remove monosaccharides from crude FOS. This encapsulation concept establishes the basis for new synbiotic formulations that combine probiotic microbes and prebiotic oligosaccharides.}, }
@article {pmid33584584, year = {2020}, author = {Taîbi, A and Rivallan, R and Broussolle, V and Pallet, D and Lortal, S and Meile, JC and Constancias, F}, title = {Terroir Is the Main Driver of the Epiphytic Bacterial and Fungal Communities of Mango Carposphere in Reunion Island.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {619226}, pmid = {33584584}, issn = {1664-302X}, abstract = {The diversity of both bacterial and fungal communities associated with mango surface was explored using a metabarcoding approach targeting fungal ITS2 and bacterial 16S (V3-V4) genomic regions. Fruits were collected in Reunion Island from two different orchards according to a sampling method which allowed the effect of several pre-harvest factors such as geographical location (terroir), cultivars, fruit parts, tree position in the plot, fruit position on the tree (orientation and height), as well as the harvest date to be investigated. A total of 4,266,546 fungal and 2,049,919 bacterial reads were recovered then respectively assigned to 3,153 fungal and 24,087 to bacterial amplicon sequence variants (ASVs). Alpha and beta diversity, as well as differential abundance analyses revealed variations in both bacterial and fungal communities detected on mango surfaces depended upon the studied factor. Results indicated that Burkholderiaceae (58.8%), Enterobacteriaceae (5.2%), Pseudomonadaceae (4.8%), Sphingomonadaceae (4.1%), Beijerinckiaceae (3.5%), and Microbacteriaceae (3.1%) were the dominant bacterial families across all samples. The majority of fungal sequences were assigned to Mycosphaerellaceae (34.5%), Cladosporiaceae (23.21%), Aureobasidiaceae (13.09%), Pleosporaceae (6.92%), Trichosphaeriaceae (5.17%), and Microstromatales_fam_Incertae_sedis (4.67%). For each studied location, mango fruit from each cultivar shared a core microbiome, and fruits of the same cultivar harvested in two different locations shared about 80% fungal and bacterial family taxa. The various factors tested in this study affected bacterial and fungal taxa differently, suggesting that some taxa could act as geographical (terroir) markers and in some cases as cultivar fingerprints. The ranking of the factors investigated in the present study showed that in decreasing order of importance: the plot (terroir), cultivar, fruit parts, harvest date and the position of the fruits are respectively the most impacting factors of the microbial flora, when compared to the orientation and the fruit position (height) on the tree. Overall, these findings provided insights on both bacterial and fungal diversity associated with the mango surface, their patterns from intra-fruit scale to local scale and the potential parameters shaping the mango microbiota.}, }
@article {pmid33584558, year = {2020}, author = {Oyserman, BO and Cordovez, V and Flores, SS and Leite, MFA and Nijveen, H and Medema, MH and Raaijmakers, JM}, title = {Extracting the GEMs: Genotype, Environment, and Microbiome Interactions Shaping Host Phenotypes.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {574053}, pmid = {33584558}, issn = {1664-302X}, abstract = {One of the fundamental tenets of biology is that the phenotype of an organism (Y) is determined by its genotype (G), the environment (E), and their interaction (GE). Quantitative phenotypes can then be modeled as Y = G + E + GE + e, where e is the biological variance. This simple and tractable model has long served as the basis for studies investigating the heritability of traits and decomposing the variability in fitness. The importance and contribution of microbe interactions to a given host phenotype is largely unclear, nor how this relates to the traditional GE model. Here we address this fundamental question and propose an expansion of the original model, referred to as GEM, which explicitly incorporates the contribution of the microbiome (M) to the host phenotype, while maintaining the simplicity and tractability of the original GE model. We show that by keeping host, environment, and microbiome as separate but interacting variables, the GEM model can capture the nuanced ecological interactions between these variables. Finally, we demonstrate with an in vitro experiment how the GEM model can be used to statistically disentangle the relative contributions of each component on specific host phenotypes.}, }
@article {pmid33584555, year = {2020}, author = {Li, R and Yao, Y and Gao, P and Bu, S}, title = {The Therapeutic Efficacy of Curcumin vs. Metformin in Modulating the Gut Microbiota in NAFLD Rats: A Comparative Study.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {555293}, pmid = {33584555}, issn = {1664-302X}, abstract = {Structural disruption of gut microbiota is closely related to the occurrence of non-alcoholic fatty liver disease (NAFLD). Previous research has demonstrated that both curcumin (CUR) and metformin (MET) have a therapeutic effect against NAFLD and play a role in modulating the gut microbiota. However, there is a lack of direct comparison between the two medications in terms of the therapeutic efficacy and the regulatory effect on gut microbiota. In this study, we administered either CUR or MET to rats with high-fat diet (HFD)-induced obesity to observe changes in body parameters, biochemical parameters, liver, and ileum pathology and gut microbiota, and used next generation sequencing and multivariate analysis to evaluate the structural changes of gut microbiota in a NAFLD rat model before and after CUR and MET intervention. It was found that both CUR and MET attenuated hepatic ectopic fat deposition, alleviated inflammatory factors, and improved intestinal barrier integrity in HFD-fed rats. More importantly, CUR and MET reduced the Firmicutes/Bacteroidetes ratio and reverted the composition of the HFD-disrupted gut microbiota. Both CUR and MET treatments effectively modified the gut microbiome, enriched the abundance of beneficial bacteria and reduced opportunistic pathogens in obese rats. The abundance of Butyricicoccus was increased while the abundance of Dorea was decreased in HFD + CUR group. Besides, some beneficial bacteria such as Prevotella were increased in MET-treated animals. Spearman's correlation analysis showed that Helicobacter, Akkermansia, Desulfovibrio, Romboutsia, Corynebacterium, Lactobacillus, Ruminococcaceae_unclassified, Lachnospiraceae_unclassified, and Clostridiales_unclassified showed significantly positive correlations with TG, TC, LDL-C, GLU, IL-6, IL-1β, and TNF-α, and negative correlations with HDL-C (both p < 0.05). However, Prevotella and Stomatobaculum showed an opposite trend. In summary, CUR and MET showed similar effects in alleviating hepatic steatosis, improving intestinal barrier integrity and modulating gut microbiota in HFD-induced obesity rats, and therefore may prove to be a novel adjunctive therapy for NAFLD.}, }
@article {pmid33584283, year = {2020}, author = {Li, J and Cao, Y and Lu, R and Li, H and Pang, Y and Fu, H and Fang, G and Chen, Q and Liu, B and Wu, J and Zhou, Y and Zhou, J}, title = {Integrated Fecal Microbiome and Serum Metabolomics Analysis Reveals Abnormal Changes in Rats with Immunoglobulin A Nephropathy and the Intervention Effect of Zhen Wu Tang.}, journal = {Frontiers in pharmacology}, volume = {11}, number = {}, pages = {606689}, pmid = {33584283}, issn = {1663-9812}, abstract = {Immunoglobulin A nephropathy (IgAN), an autoimmune renal disease with complicated pathogenesis, is one of the principal reasons for end-stage renal disease in the clinic. Evidence has linked apparent alterations in the components of the microbiome and metabolome to renal disease in rats. However, thus far, there is insufficient evidence that supports the potential relationship between gut microbiome, circulating metabolites, and IgAN. This study was designed to probe the effects of IgAN on intestinal microecology and metabolic phenotypes and to understand the possible underlying mechanisms. Fecal and serum samples were collected from IgAN rats. Composition of the gut microbiota and biochemical changes in the metabolites was analyzed using 16S rDNA sequencing and untargeted metabolomics. The IgAN rats exhibited renal insufficiency and increased concentration of 24-h urine protein, in addition to deposition of IgA and IgG immune complexes in the kidney tissues. There was a disturbance in the balance of gut microbiota in IgAN rats, which was remarkably associated with renal damage. Marked changes in microbial structure and function were accompanied by apparent alterations in 1,403 serum metabolites, associated with the disorder of energy, carbohydrate, and nucleotide metabolisms. Administration of Zhen Wu Tang ameliorated microbial dysbiosis and attenuated the renal damage. Besides, treatment with Zhen Wu Tang modulated the metabolic phenotype perturbation in case of gut microbiota dysbiosis in IgAN rats. In conclusion, these findings provided a comprehensive understanding of the potential relationship between the intestinal microbiota and metabolic phenotypes in rats with IgAN. Elucidation of the intestinal microbiota composition and metabolic signature alterations could identify predictive biomarkers for disease diagnosis and progression, which might contribute to providing therapeutic strategies for IgAN.}, }
@article {pmid33583541, year = {2021}, author = {Shafaei, A and Rees, J and Christophersen, CT and Devine, A and Broadhurst, D and Boyce, MC}, title = {Extraction and quantitative determination of bile acids in feces.}, journal = {Analytica chimica acta}, volume = {1150}, number = {}, pages = {338224}, doi = {10.1016/j.aca.2021.338224}, pmid = {33583541}, issn = {1873-4324}, abstract = {With rapid advances in gut microbiome research, fecal bile acids are increasingly being monitored as potential biomarkers of diet related disease susceptibility. As such, rapid, robust and reliable methods for their analysis are of increasing importance. Herein is described a simple extraction method for the analysis of bile acids in feces suitable for subsequent quantification by liquid chromatography and tandem mass spectrometry. A C18 column separated the analytes with excellent peak shape and retention time repeatability maintained across 800 injections. The intra-day and inter-day precision and accuracy was greater than 80%. Recoveries ranged from 83.58 to 122.41%. The limit of detection and limit of quantification were in the range 2.5-15 nM, respectively. The optimized method involved extracting bile acids from wet feces with minimal clean up. A second aliquot of fecal material was dried and weighed to correct for water content. Extracting from dried feces showed reduced recovery that could be corrected for by spiking the feces with deuterated standards prior to drying. Storage of the extracts and standards in a refrigerated autosampler prior to analysis on the LC-MS is necessary. Multiple freeze-thaws of both extracts and standards lead to poor recoveries for some bile acids. The method was successfully applied to 100 human fecal samples.}, }
@article {pmid33583434, year = {2021}, author = {Hudspith, M and Rix, L and Achlatis, M and Bougoure, J and Guagliardo, P and Clode, PL and Webster, NS and Muyzer, G and Pernice, M and de Goeij, JM}, title = {Subcellular view of host-microbiome nutrient exchange in sponges: insights into the ecological success of an early metazoan-microbe symbiosis.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {44}, pmid = {33583434}, issn = {2049-2618}, support = {715513//H2020 European Research Council/ ; }, abstract = {BACKGROUND: Sponges are increasingly recognised as key ecosystem engineers in many aquatic habitats. They play an important role in nutrient cycling due to their unrivalled capacity for processing both dissolved and particulate organic matter (DOM and POM) and the exceptional metabolic repertoire of their diverse and abundant microbial communities. Functional studies determining the role of host and microbiome in organic nutrient uptake and exchange, however, are limited. Therefore, we coupled pulse-chase isotopic tracer techniques with nanoscale secondary ion mass spectrometry (NanoSIMS) to visualise the uptake and translocation of 13C- and 15N-labelled dissolved and particulate organic food at subcellular level in the high microbial abundance sponge Plakortis angulospiculatus and the low microbial abundance sponge Halisarca caerulea.<br><br>RESULTS: The two sponge species showed significant enrichment of DOM- and POM-derived 13C and 15N into their tissue over time. Microbial symbionts were actively involved in the assimilation of DOM, but host filtering cells (choanocytes) appeared to be the primary site of DOM and POM uptake in both sponge species overall, via pinocytosis and phagocytosis, respectively. Translocation of carbon and nitrogen from choanocytes to microbial symbionts occurred over time, irrespective of microbial abundance, reflecting recycling of host waste products by the microbiome.<br><br>CONCLUSIONS: Here, we provide empirical evidence indicating that the prokaryotic communities of a high and a low microbial abundance sponge obtain nutritional benefits from their host-associated lifestyle. The metabolic interaction between the highly efficient filter-feeding host and its microbial symbionts likely provides a competitive advantage to the sponge holobiont in the oligotrophic environments in which they thrive, by retaining and recycling limiting nutrients. Sponges present a unique model to link nutritional symbiotic interactions to holobiont function, and, via cascading effects, ecosystem functioning, in one of the earliest metazoan-microbe symbioses. Video abstract.}, }
@article {pmid33583433, year = {2021}, author = {Raimundo, I and Silva, R and Meunier, L and Valente, SM and Lago-Lestón, A and Keller-Costa, T and Costa, R}, title = {Functional metagenomics reveals differential chitin degradation and utilization features across free-living and host-associated marine microbiomes.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {43}, pmid = {33583433}, issn = {2049-2618}, support = {PTDC/MAR-BIO/1547/2014//Fundação para a Ciência e a Tecnologia/ ; EXPL/MAR-EST/1664/2013//Fundação para a Ciência e a Tecnologia/ ; SFRH/BD/116642/2016//Fundação para a Ciência e a Tecnologia/ ; CEECIND/00788/2017//Fundação para a Ciência e a Tecnologia/ ; UIDB/04565/2020//Fundação para a Ciência e a Tecnologia/ ; }, abstract = {BACKGROUND: Chitin ranks as the most abundant polysaccharide in the oceans yet knowledge of shifts in structure and diversity of chitin-degrading communities across marine niches is scarce. Here, we integrate cultivation-dependent and -independent approaches to shed light on the chitin processing potential within the microbiomes of marine sponges, octocorals, sediments, and seawater.<br><br>RESULTS: We found that cultivatable host-associated bacteria in the genera Aquimarina, Enterovibrio, Microbulbifer, Pseudoalteromonas, Shewanella, and Vibrio were able to degrade colloidal chitin in vitro. Congruent with enzymatic activity bioassays, genome-wide inspection of cultivated symbionts revealed that Vibrio and Aquimarina species, particularly, possess several endo- and exo-chitinase-encoding genes underlying their ability to cleave the large chitin polymer into oligomers and dimers. Conversely, Alphaproteobacteria species were found to specialize in the utilization of the chitin monomer N-acetylglucosamine more often. Phylogenetic assessments uncovered a high degree of within-genome diversification of multiple, full-length endo-chitinase genes for Aquimarina and Vibrio strains, suggestive of a versatile chitin catabolism aptitude. We then analyzed the abundance distributions of chitin metabolism-related genes across 30 Illumina-sequenced microbial metagenomes and found that the endosymbiotic consortium of Spongia officinalis is enriched in polysaccharide deacetylases, suggesting the ability of the marine sponge microbiome to convert chitin into its deacetylated-and biotechnologically versatile-form chitosan. Instead, the abundance of endo-chitinase and chitin-binding protein-encoding genes in healthy octocorals leveled up with those from the surrounding environment but was found to be depleted in necrotic octocoral tissue. Using cultivation-independent, taxonomic assignments of endo-chitinase encoding genes, we unveiled previously unsuspected richness and divergent structures of chitinolytic communities across host-associated and free-living biotopes, revealing putative roles for uncultivated Gammaproteobacteria and Chloroflexi symbionts in chitin processing within sessile marine invertebrates.<br><br>CONCLUSIONS: Our findings suggest that differential chitin degradation pathways, utilization, and turnover dictate the processing of chitin across marine micro-niches and support the hypothesis that inter-species cross-feeding could facilitate the co-existence of chitin utilizers within marine invertebrate microbiomes. We further identified chitin metabolism functions which may serve as indicators of microbiome integrity/dysbiosis in corals and reveal putative novel chitinolytic enzymes in the genus Aquimarina that may find applications in the blue biotechnology sector. Video abstract.}, }
@article {pmid33583056, year = {2021}, author = {Mukherjee, M and Agache, I}, title = {IL-13 signature in severe adult asthmatics with airway neutrophilia: a new endotype to treat!.}, journal = {Allergy}, volume = {}, number = {}, pages = {}, doi = {10.1111/all.14772}, pmid = {33583056}, issn = {1398-9995}, abstract = {With great interest we read the article by Azim and co-workers[1] published in this issue of Allergy. To understand the inflammatory component of the peripheral airways of severeasthmatics uncontrolled by high dose inhaled corticosteroids (ICS) the authors examined the bronchoalveolar lavage.}, }
@article {pmid33582841, year = {2021}, author = {Blake, KS and Choi, J and Dantas, G}, title = {Approaches for characterizing and tracking hospital-associated multidrug-resistant bacteria.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {}, number = {}, pages = {}, pmid = {33582841}, issn = {1420-9071}, support = {R01AI123394//National Institute of Allergy and Infectious Diseases/ ; R01HD092414//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; R01AT009741/AT/NCCIH NIH HHS/United States ; R01OH011578/OH/NIOSH CDC HHS/United States ; W81XWH1810225//Congressionally Directed Medical Research Programs/ ; }, abstract = {Hospital-associated infections are a major concern for global public health. Infections with antibiotic-resistant pathogens can cause empiric treatment failure, and for infections with multidrug-resistant bacteria which can overcome antibiotics of &quot;last resort&quot; there exists no alternative treatments. Despite extensive sanitization protocols, the hospital environment is a potent reservoir and vector of antibiotic-resistant organisms. Pathogens can persist on hospital surfaces and plumbing for months to years, acquire new antibiotic resistance genes by horizontal gene transfer, and initiate outbreaks of hospital-associated infections by spreading to patients via healthcare workers and visitors. Advancements in next-generation sequencing of bacterial genomes and metagenomes have expanded our ability to (1) identify species and track distinct strains, (2) comprehensively profile antibiotic resistance genes, and (3) resolve the mobile elements that facilitate intra- and intercellular gene transfer. This information can, in turn, be used to characterize the population dynamics of hospital-associated microbiota, track outbreaks to their environmental reservoirs, and inform future interventions. This review provides a detailed overview of the approaches and bioinformatic tools available to study isolates and metagenomes of hospital-associated bacteria, and their multi-layered networks of transmission.}, }
@article {pmid33581524, year = {2021}, author = {Cordovez, V and Rotoni, C and Dini-Andreote, F and Oyserman, B and Carrión, VJ and Raaijmakers, JM}, title = {Successive plant growth amplifies genotype-specific assembly of the tomato rhizosphere microbiome.}, journal = {The Science of the total environment}, volume = {772}, number = {}, pages = {144825}, doi = {10.1016/j.scitotenv.2020.144825}, pmid = {33581524}, issn = {1879-1026}, abstract = {Plant microbiome assembly is a spatial and dynamic process driven by root exudates and influenced by soil type, plant developmental stage and genotype. Genotype-dependent microbiome assembly has been reported for different crop plant species. Despite the effect of plant genetics on microbiome assembly, the magnitude of host control over its root microbiome is relatively small or, for many plant species, still largely unknown. Here we cultivated modern and wild tomato genotypes for four successive cycles and showed that divergence in microbiome assembly between the two genotypes was significantly amplified over time. Also, we show that the composition of the rhizosphere microbiome of modern and wild plants became more dissimilar from the initial bulk soil and from each other. Co-occurrence analyses further identified amplicon sequence variants (ASVs) associated with early and late successions of the tomato rhizosphere microbiome. Among the members of the Late Successional Rhizosphere microbiome, we observed an enrichment of ASVs belonging to the genera Acidovorax, Massilia and Rhizobium in the wild tomato rhizosphere, whereas the modern tomato rhizosphere was enriched for an ASV belonging to the genus Pseudomonas. Collectively, our approach allowed us to study the dynamics of rhizosphere microbiome over successional cultivation as well as to categorize rhizobacterial taxa for their ability to form transient or long-term associations with their host plants.}, }
@article {pmid33581487, year = {2021}, author = {Daniel, S and Pusadkar, V and McDonald, J and Mirpuri, J and Azad, RK and Goven, A and Lund, AK}, title = {Traffic generated emissions alter the lung microbiota by promoting the expansion of Proteobacteria in C57Bl/6 mice placed on a high-fat diet.}, journal = {Ecotoxicology and environmental safety}, volume = {213}, number = {}, pages = {112035}, doi = {10.1016/j.ecoenv.2021.112035}, pmid = {33581487}, issn = {1090-2414}, abstract = {Air pollution has been documented to contribute to severe respiratory diseases like asthma and chronic obstructive pulmonary disorder (COPD). Although these diseases demonstrate a shift in the lung microbiota towards Proteobacteria, the effects of traffic generated emissions on lung microbiota profiles have not been well-characterized. Thus, we investigated the hypothesis that exposure to traffic-generated emissions can alter lung microbiota and immune defenses. Since a large population of the Western world consumes a diet rich in fats, we sought to investigate the synergistic effects of mixed vehicle emissions and high-fat diet consumption. We exposed 3-month-old male C57Bl/6 mice placed either on regular chow (LF) or a high-fat (HF: 45% kcal fat) diet to mixed emissions (ME: 30 µg PM/m3 gasoline engine emissions+70 µg PM/m3 diesel engine emissions) or filtered air (FA) for 6 h/d, 7 d/wk for 30 days. Levels of pulmonary immunoglobulins IgA, IgG, and IgM were analyzed by ELISA, and lung microbial profiling was done using qPCR and Illumina 16 S sequencing. We observed a significant decrease in lung IgA in the ME-exposed animals, compared to the FA-exposed animals, both fed a HF diet. Our results also revealed a significant decrease in lung IgG in the ME-exposed animals both on the LF diet and HF diet, in comparison to the FA-exposed animals. We also observed an expansion of Enterobacteriaceae belonging to the Proteobacteria phylum in the ME-exposed groups on the HF diet. Collectively, we show that the combined effects of ME and HF diet result in decreased immune surveillance and lung bacterial dysbiosis, which is of significance in lung diseases.}, }
@article {pmid33581337, year = {2021}, author = {Liu, Z and Mi, K and Zech Xu, Z and Zhang, Q and Liu, X}, title = {PM2RA: A Framework for Detecting and Quantifying Relationship Alterations in Microbial Community.}, journal = {Genomics, proteomics &amp; bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.gpb.2020.07.005}, pmid = {33581337}, issn = {2210-3244}, abstract = {The dysbiosis of gut microbiota is associated with the pathogenesis of human disease. However, observing shifts in the microbe abundance cannot fully reveal underlying perturbations. Examining the relationship alteration (RA) in the microbiome between health status provides additional hints about the pathogenesis of human disease, but no methods were designed to detect and quantify the RA between different conditions directly. Here, we present Profile Monitoring for Microbial Relationship Alteration (PM2RA), an analysis framework to identify and quantify the microbial RAs. The performance of PM2RA was evaluated with synthetic data, and showed higher specificity and sensitivity than the co-occurrence-based methods. Analyses of real microbial datasets showed that PM2RA was robust for quantifying microbial RA across different datasets in several diseases. By applying PM2RA, we identified several novel or previously reported microbes implicated in multiple diseases. PM2RA is now implemented as a web-based application available at http://www.pm2ra-xingyinliulab.cn/.}, }
@article {pmid33581320, year = {2021}, author = {Huson, KM and Atcheson, E and Oliver, NAM and Best, P and Barley, JP and Hanna, REB and McNeilly, TN and Fang, Y and Haldenby, S and Paterson, S and Robinson, MW}, title = {Transcriptome and secretome analysis of intra-mammalian life-stages of the emerging helminth pathogen, Calicophoron daubneyi reveals adaptation to a unique host environment.}, journal = {Molecular &amp; cellular proteomics : MCP}, volume = {}, number = {}, pages = {100055}, doi = {10.1074/mcp.RA120.002175}, pmid = {33581320}, issn = {1535-9484}, abstract = {Paramphistomosis, caused by the rumen fluke, Calicophoron daubneyi, is a parasitic infection of ruminant livestock which has seen a rapid rise in prevalence throughout Western Europe in recent years. Following ingestion of metacercariae (parasite cysts) by the mammalian host, newly-excysted juveniles (NEJs) emerge and invade the duodenal submucosa which causes significant pathology in heavy infections. The immature larvae then migrate upwards, along the gastrointestinal tract, and enter the rumen where they mature and begin to produce eggs. Despite their emergence, and sporadic outbreaks of acute disease, we know little about the molecular mechanisms used by C. daubneyi to establish infection, acquire nutrients and to avoid the host immune response. Here, transcriptome analysis of four intra-mammalian life-cycle stages, integrated with secretome analysis of the NEJ and adult parasites (responsible for acute and chronic disease respectively), revealed how the expression and secretion of selected families of virulence factors and immunomodulators are regulated in accordance with fluke development and migration. Our data show that whilst a family of cathepsins B with varying S2 sub-site residues (indicating distinct substrate specificities) are differentially secreted by NEJs and adult flukes, cathepsins L and F are secreted in low abundance by NEJs only. We found that C. daubneyi has an expanded family of aspartic peptidases, which is up-regulated in adult worms, although they are underrepresented in the secretome. The most abundant proteins in adult fluke secretions were helminth defence molecules (HDMs) that likely establish an immune environment permissive to fluke survival and/or neutralise pathogen-associated molecular patterns (PAMPs) such as bacterial lipopolysaccharide in the microbiome-rich rumen. The distinct collection of molecules secreted by C. daubneyi allowed the development of the first coproantigen-based ELISA for paramphistomosis which, importantly, did not recognise antigens from other helminths commonly found as co-infections with rumen fluke.}, }
@article {pmid33581121, year = {2021}, author = {Tobi, M and Talwar, H and McVicker, B}, title = {The Celiac Disease Microbiome Depends on the PC's of the Puzzle.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2021.02.023}, pmid = {33581121}, issn = {1528-0012}, }
@article {pmid33580951, year = {2021}, author = {Medina, D and Greenspan, SE and Carvalho, T and Becker, CG and Toledo, LF}, title = {Co-infecting pathogen lineages have additive effects on host bacterial communities.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiab030}, pmid = {33580951}, issn = {1574-6941}, abstract = {Amphibian skin bacteria may confer protection against the fungus Batrachochytrium dendrobatidis (Bd), but responses of skin bacteria to different Bd lineages are poorly understood. The global panzootic lineage (Bd-GPL) has caused amphibian declines and extinctions globally. However, other lineages are enzootic (Bd-Asia-2/Brazil). Increased contact rates between Bd-GPL and enzootic lineages via globalization pose unknown consequences for host-microbiome-pathogen dynamics. We conducted a laboratory experiment and used 16S rRNA amplicon-sequencing to assess: 1) whether two lineages (Bd-Asia-2/Brazil and Bd-GPL) and their recombinant, in single and mixed infections, differentially affect amphibian skin bacteria; 2) and the changes associated with the transition to laboratory conditions. We determined no clear differences in bacterial diversity among Bd treatments, despite differences in infection intensity. However, we observed an additive effect of mixed infections on bacterial alpha diversity and a potentially antagonistic interaction between Bd genotypes. Additionally, observed changes in community composition suggest a higher ability of Bd-GPL to alter skin bacteria. Lastly, we observed a drastic reduction in bacterial diversity and a change in community structure in laboratory conditions. We provide evidence for complex interactions between Bd genotypes and amphibian skin bacteria during coinfections, and expand on the implications of experimental conditions in ecological studies.}, }
@article {pmid33580950, year = {2021}, author = {Lopes, LD and Hao, J and Schachtman, DP}, title = {Alkaline soil pH affects bulk soil, rhizosphere and root endosphere microbiomes of plants growing in a Sandhills ecosystem.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiab028}, pmid = {33580950}, issn = {1574-6941}, abstract = {Soil pH is a major factor shaping bulk soil microbial communities. However, it is unclear whether the belowground microbial habitats shaped by plants (e.g. rhizosphere and root endosphere) are also affected by soil pH. We investigated this question by comparing the microbial communities associated with plants growing in neutral and strongly alkaline soils in the Sandhills, which is the largest sand dune complex in the northern hemisphere. Bulk soil, rhizosphere and root endosphere DNA were extracted from multiple plant species and analyzed using 16S rRNA amplicon sequencing. Results showed that rhizosphere, root endosphere and bulk soil microbiomes were different in the contrasting soil pH ranges. The strongest impact of plant species on the belowground microbiomes was in alkaline soils, suggesting a greater selective effect under alkali stress. Evaluation of soil chemical components showed that in addition to soil pH, cation exchange capacity also had a strong impact on shaping bulk soil microbial communities. This study extends our knowledge regarding the importance of pH to microbial ecology showing that root endosphere and rhizosphere microbial communities were also influenced by this soil component, and highlights the important role that plants play particularly in shaping the belowground microbiomes in alkaline soils.}, }
@article {pmid33580815, year = {2021}, author = {Kellogg, JA and Reganold, JP and Murphy, KM and Carpenter-Boggs, LA}, title = {A Plant-Fungus Bioassay Supports the Classification of Quinoa (Chenopodium quinoa Willd.) as Inconsistently Mycorrhizal.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33580815}, issn = {1432-184X}, support = {2016-51300-25808//USDA National Institute of Food and Agriculture (US)/ ; n/a//Lundberg Family Farms, Richvale, California (US)/ ; 1014754//USDA National Institute of Food and Agriculture Hatch project (US)/ ; }, abstract = {Quinoa (Chenopodium quinoa Willd.) is becoming an increasingly important food crop. Understanding the microbiome of quinoa and its relationships with soil microorganisms may improve crop yield potential or nutrient use efficiency. Whether quinoa is a host or non-host of a key soil symbiont, arbuscular mycorrhizal fungi (AMF), is suddenly up for debate with recent field studies reporting root colonization and presence of arbuscules. This research seeks to add evidence to the mycorrhizal classification of quinoa as we investigated additional conditions not previously explored in quinoa that may affect root colonization. A greenhouse study used six AMF species, two AMF commercial inoculant products, and a diverse set of 10 quinoa genotypes. Results showed 0 to 3% quinoa root colonization by AMF when grown under greenhouse conditions. Across quinoa genotypes, AMF inoculant affected shoot dry weight (p = 0.066) and height (p = 0.031). Mykos Gold produced greater dry biomass than Claroideoglomus eutunicatum (27% increase), Rhizophagus clarus (26% increase), and within genotype CQ119, the control (21% increase). No treatment increased plant height compared to control, but Funneliformis mosseae increased height compared to C. eutunicatum (25% increase) and Rhizophagus intraradices (25% increase). Although quinoa plants were minimally colonized by AMF, plant growth responses fell along the mutualism-parasitism continuum. Individual AMF treatments increased leaf greenness in quinoa genotypes 49ALC and QQ87, while R. clarus decreased greenness in CQ119 compared to the control. Our research findings support the recommendation to classify quinoa as non-mycorrhizal when no companion plant is present and inconsistently mycorrhizal when conditional colonization occurs.}, }
@article {pmid33580637, year = {2021}, author = {Cox, NJ and Bowyer, RCE and Ni Lochlainn, M and Wells, PM and Roberts, HC and Steves, CJ}, title = {The composition of the gut microbiome differs among community dwelling older people with good and poor appetite.}, journal = {Journal of cachexia, sarcopenia and muscle}, volume = {}, number = {}, pages = {}, doi = {10.1002/jcsm.12683}, pmid = {33580637}, issn = {2190-6009}, support = {//Chronic Disease Research Foundation/ ; WT081878MA/WT_/Wellcome Trust/United Kingdom ; RE160685//NIHR Doctoral Fellowship/ ; //NIHR Applied Research Collaboration (ARC) Wessex/ ; //National Institute of Health Research (NIHR) Southampton Biomedical Research Centre/ ; }, abstract = {BACKGROUND: Anorexia of ageing is common and important in the development of sarcopenia in older individuals. Links have been proposed between the gut microbiota and sarcopenia. Disordered gut function is also recognized in anorexia of ageing, but how this may relate to resident gut microbiota is unexplored. Understanding this relationship may provide a basis for novel interventions for anorexia of ageing and sarcopenia. This study explores compositional differences of the gut microbiota between community dwelling healthy older adults with good or poor appetite, and associated differences in sarcopenia.<br><br>METHODS: We assessed appetite by the Simplified Nutritional Appetite Questionnaire (SNAQ) in members of the TwinsUK cohort aged ≥65 years. Using a pool of 776 individuals with existing microbiome data estimated from 16S rRNA sequencing data, we identified 102 cases (SNAQ score < 14) (95% female, mean age 68 years) matched to controls (SNAQ > 14) on body mass index, gender, age, diet, calorie consumption, frailty, antibiotic use, socio-economic status, and technical variables to minimize confounding microbiota associations. Species abundance and diversity, compositional differences, and paired differences in taxa abundance were compared between cases and controls. Additionally, we compared case and controls for sarcopenia as measured by muscle mass (appendicular lean mass/height2) and strength (chair stand time in seconds).<br><br>RESULTS: Cases with poor appetite had reduced species richness and diversity of their gut microbiome (adjusted OBSERVED: beta = -0.2, P < 0.001; adjusted SHANNON: beta = -0.17, P = 0.0135), significant compositional differences (adjusted non-parametric multivariate analysis of variance, P = 0.0095), and significant differences in taxa abundance including reduction of genus Lachnospira (logFC = -1.015, q = 0.023). In all-female subgroup analysis, cases with poor appetite demonstrated reduction in muscle strength (11.03 s vs. 9.26 s, P = 0.02).<br><br>CONCLUSIONS: This study is the first to observe differences in the composition of gut microbiota between healthy community dwelling older individuals with good and poor appetite. We found female individuals with reduced muscle strength had poor appetite compared with those with normal strength. These associations require further examination to understand causality and mechanisms of interaction, to inform potential strategies targeting the gut microbiota as a novel intervention for anorexia of ageing and sarcopenia.}, }
@article {pmid33580334, year = {2021}, author = {Juby, S and Choyikutty, D and Nayana, AR and Jayachandran, K and Radhakrishnan, EK}, title = {Quinalphos Tolerant Endophytic Bacillus sp. Fcl1 and its Toxicity-Alleviating Effect in Vigna unguiculata.}, journal = {Current microbiology}, volume = {}, number = {}, pages = {}, pmid = {33580334}, issn = {1432-0991}, abstract = {In order to meet the agricultural requirement for the expanding population, pesticides have been used regularly even with their severe threat. The uncontrolled use of these pesticides can cause irreparable damage to both soil and plant-associated microbiome. Therefore, an environment friendly alternative to enhance plant productivity and yield is highly important. Here comes the importance of endophytic microorganisms with multi-plant beneficial mechanisms to protect plants from the biotic and abiotic stress factors. However, their performance can be negatively affected under pesticide exposure. Hence the present study was conducted to analyse the tolerating ability of a Bacillus sp. Fcl1 which was originally isolated from the rhizome of Curcuma longa towards the pesticide quinalphos and also its ability to reduce the quinalphos-induced toxicity in Vigna unguiculata. The results revealed that the viability of endophytic Bacillus sp. Fcl1 depended on the concentration of quinalphos used for the study. Further, Fcl1 supplementation was found to alleviate the quinalphos-induced toxicity in Vigna unguiculata seedlings. The study is environmentally significant due to the pesticide tolerating and alleviating effect of Bacillus sp. Fcl1 in quinalphos-induced plant toxicity. This could suggest the application of microbes of endophytic origin as an efficient bioinoculant for field application even in the presence of pesticide residues.}, }
@article {pmid33580207, year = {2021}, author = {Zhu, X and Tian, X and Ji, L and Zhang, X and Cao, Y and Shen, C and Hu, Y and Wong, JWH and Fang, JY and Hong, J and Chen, H}, title = {A tumor microenvironment-specific gene expression signature predicts chemotherapy resistance in colorectal cancer patients.}, journal = {NPJ precision oncology}, volume = {5}, number = {1}, pages = {7}, pmid = {33580207}, issn = {2397-768X}, support = {81874159//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31371273//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81602518//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81871901//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Studies have shown that tumor microenvironment (TME) might affect drug sensitivity and the classification of colorectal cancer (CRC). Using TME-specific gene signature to identify CRC subtypes with distinctive clinical relevance has not yet been tested. A total of 18 &quot;bulk&quot; RNA-seq datasets (total n = 2269) and four single-cell RNA-seq datasets were included in this study. We constructed a &quot;Signature associated with FOLFIRI resistant and Microenvironment&quot; (SFM) that could discriminate both TME and drug sensitivity. Further, SFM subtypes were identified using K-means clustering and verified in three independent cohorts. Nearest template prediction algorithm was used to predict drug response. TME estimation was performed by CIBERSORT and microenvironment cell populations-counter (MCP-counter) methods. We identified six SFM subtypes based on SFM signature that discriminated both TME and drug sensitivity. The SFM subtypes were associated with distinct clinicopathological, molecular and phenotypic characteristics, specific enrichments of gene signatures, signaling pathways, prognosis, gut microbiome patterns, and tumor lymphocytes infiltration. Among them, SFM-C and -F were immune suppressive. SFM-F had higher stromal fraction with epithelial-to-mesenchymal transition phenotype, while SFM-C was characterized as microsatellite instability phenotype which was responsive to immunotherapy. SFM-D, -E, and -F were sensitive to FOLFIRI and FOLFOX, while SFM-A, -B, and -C were responsive to EGFR inhibitors. Finally, SFM subtypes had strong prognostic value in which SFM-E and -F had worse survival than other subtypes. SFM subtypes enable the stratification of CRC with potential chemotherapy response thereby providing more precise therapeutic options for these patients.}, }
@article {pmid33580056, year = {2020}, author = {Zhao, T and Li, J and Fu, Y and Ye, H and Liu, X and Li, G and Yang, X and Yang, J}, title = {Influence of gut microbiota on mucosal IgA antibody response to the polio vaccine.}, journal = {NPJ vaccines}, volume = {5}, number = {1}, pages = {47}, pmid = {33580056}, issn = {2059-0105}, abstract = {The impact of intestinal microbiota on mucosal antibody response to the polio vaccine is poorly understood. We examined changes in vaccine-induced intestinal mucosal immunity to poliovirus by measuring the immunoglobulin A (IgA) antibody levels in stool samples collected from 107 infants in China, and the samples were collected 14 days after different sequential vaccinations combining inactivated polio vaccine (IPV) with oral poliovirus vaccine (OPV). Gut microbiota were identified using 16S ribosomal RNA sequencing 28 days before, 14 days before, and at the last dose of OPV. Vaccine-induced type 2-specific mucosal IgA showed a decrease after switching from trivalent to bivalent OPV (bOPV) (positive rate of polio type 2-specific mucosal IgA, 16.7%, 11.8%, and 45.9% for IPV + 2bOPV, 2IPV + bOPV, and 2IPV + trivalent OPV groups, respectively). The composition of the gut microbiome was significantly different, a higher abundance of Firmicutes and a lower abundance of Actinobacteria were observed in IgA-negative infant (n = 66) compared with IgA-positive infants (n = 39), and the gut microbiota were more diverse in IgA-negative infants on the day of OPV inoculation. The abundance of Clostridia was concomitant with a significantly lower conversion rate of mucosal IgA responses to the polio vaccine. The composition of the gut microbiome may affect the intestinal mucosal IgA response to the polio vaccine.}, }
@article {pmid33579999, year = {2020}, author = {Wallen, ZD and Appah, M and Dean, MN and Sesler, CL and Factor, SA and Molho, E and Zabetian, CP and Standaert, DG and Payami, H}, title = {Characterizing dysbiosis of gut microbiome in PD: evidence for overabundance of opportunistic pathogens.}, journal = {NPJ Parkinson's disease}, volume = {6}, number = {1}, pages = {11}, pmid = {33579999}, issn = {2373-8057}, support = {R01 NS036960/NS/NINDS NIH HHS/United States ; P50 NS062684/NS/NINDS NIH HHS/United States ; W81XWH1810508//United States Department of Defense | United States Army | Army Medical Command | Medical Research and Materiel Command (U.S. Army Medical Research and Materiel Command)/ ; T32 NS095775/NS/NINDS NIH HHS/United States ; P50 NS108675/NS/NINDS NIH HHS/United States ; }, abstract = {In Parkinson's disease (PD), gastrointestinal features are common and often precede the motor signs. Braak and colleagues proposed that PD may start in the gut, triggered by a pathogen, and spread to the brain. Numerous studies have examined the gut microbiome in PD; all found it to be altered, but found inconsistent results on associated microorganisms. Studies to date have been small (N = 20 to 306) and are difficult to compare or combine due to varied methodology. We conducted a microbiome-wide association study (MWAS) with two large datasets for internal replication (N = 333 and 507). We used uniform methodology when possible, interrogated confounders, and applied two statistical tests for concordance, followed by correlation network analysis to infer interactions. Fifteen genera were associated with PD at a microbiome-wide significance level, in both datasets, with both methods, with or without covariate adjustment. The associations were not independent, rather they represented three clusters of co-occurring microorganisms. Cluster 1 was composed of opportunistic pathogens and all were elevated in PD. Cluster 2 was short-chain fatty acid (SCFA)-producing bacteria and all were reduced in PD. Cluster 3 was carbohydrate-metabolizing probiotics and were elevated in PD. Depletion of anti-inflammatory SCFA-producing bacteria and elevated levels of probiotics are confirmatory. Overabundance of opportunistic pathogens is an original finding and their identity provides a lead to experimentally test their role in PD.}, }
@article {pmid33579688, year = {2021}, author = {Flynn, PJ and D'Amelio, CL and Sanders, JG and Russell, JA and Moreau, CS}, title = {Localization of bacterial communities within gut compartments across Cephalotes turtle ants.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02803-20}, pmid = {33579688}, issn = {1098-5336}, abstract = {Microbial communities within the animal digestive tract often provide important functions for their hosts. The composition of eukaryotes' gut bacteria can be shaped by host diet, vertical bacterial transmission, and physiological variation within the digestive tract. In several ant taxa, recent findings have demonstrated that nitrogen provisioning by symbiotic bacteria makes up for deficiencies in herbivorous diets. Using 16S rRNA amplicon sequencing and qPCR, this study examined bacterial communities at a fine scale across one such animal group, the turtle ant genus Cephalotes We analyzed the composition and colonization density across four portions of the digestive tract to understand how bacterial diversity is structured across gut compartments, potentially allowing for specific metabolic functions of benefit to the host. In addition, we aimed to understand if caste differentiation or host relatedness influences the gut bacterial communities of Cephalotes ants. Microbial communities were found to vary strongly across Cephalotes gut compartments in ways that transcend both caste and host phylogeny. Despite this, caste and host phylogeny still have detectable effects. We demonstrated microbial community divergence across gut compartments, possibly due to the varying function of each gut compartment for digestion.IMPORTANCE Gut compartments play an important role in structuring the microbial community within individual ants. The gut chambers of the turtle ant digestive tract differ remarkably in symbiont abundance and diversity. Furthermore, caste type explains some variation in the microbiome composition. Finally, the evolutionary history of the Cephalotes species structures the microbiome in our study, which elucidates a trend in which related ants maintain related microbiomes, conceivably owing to co-speciation. Amazingly, gut compartment-specific signatures of microbial diversity, relative abundance, composition, and abundance have been conserved over Cephalotes evolutionary history, signifying that this symbiosis has been largely stable for over 50 million years.}, }
@article {pmid33579687, year = {2021}, author = {Weaver, AA and Bolster, D and Madukoma, CS and Mattingly, AE and Morales-Soto, N and Shrout, JD}, title = {Transient surface hydration impacts biogeography and intercellular interactions of non-motile bacteria.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.03067-20}, pmid = {33579687}, issn = {1098-5336}, abstract = {There are many hydrated surface niches that are neither static nor continuously flowing that are colonized by microbes such as bacteria. Such periodic hydrodynamic regimes are distinct from aquatic systems where microbial dissemination is reasonably predicted by assuming continuous flow or static systems where motile microbes largely control their own fate. Here we show how non-motile bacteria exhibit rapid, dispersive bursts of movement over surfaces using transient confluent hydration from the environment, which we term &quot;surface hydrodispersion&quot; where cells traverse thousands of cell lengths within minutes. The fraction of the population disseminated by surface hydrodispersion is small-on order of 1 cell per million. Thus, surface hydrodispersion can promote isolated distribution of single cells, which is unlike other characterized active and passive surface motilities. We describe this translocation using a continuous time random walk modeling approach and find in computational simulations that transient fluid accumulation, dilution, and gravitational pull are the contributing factors. Surface hydrodispersion, consistent with advection, is unlike simple colony expansion as it dramatically alters spatial relationships, shown here with Staphylococcus aureus, which becomes increasingly virulent when isolated from Corynebacterium striatum Surface hydrodispersion of non-motile bacteria exploiting transient fluid availability and gravity is a mechanism that can result in sporadic and sudden shifts in microbial community behavior. To better understand how this movement can impact biogeography on the millimeter scale, this work describes a system for study of primary factors behind this movement as well as a stochastic model describing this dispersal.Importance: Understanding the dynamics within microbiome communities is a challenge. Knowledge of phylogeny and spatial arrangement has led to increased understanding of numerous polymicrobial communities yet, these snapshots do not convey the dynamics of populations over time. The actual biogeography of any microbiome controls the potential interactions, governing any possible antagonistic or synergistic behavior. Accordingly, a shift in biogeography can enable new behavior. Little is known about the movement mechanisms of &quot;non-motile&quot; microbes. Here we characterize a universal means of movement we term hydrodispersion where non-motile bacteria are transported thousands of cell lengths in minutes. We show that only a small fraction of the population is translocated by hydrodispersion and describe this movement further using a random-walk mathematical model approach in silico We demonstrate the importance of hydrodispersion by showing that Staphylococcus aureus can separate from a coculture inoculation with Corynebacterium striatum thus permitting transition to a more virulent state.}, }
@article {pmid33579685, year = {2021}, author = {Mancabelli, L and Mancino, W and Lugli, GA and Milani, C and Viappiani, A and Anzalone, R and Longhi, G and van Sinderen, D and Ventura, M and Turroni, F}, title = {Comparative genome analyses of Lactobacillus crispatus isolated from different ecological niches reveal an environmental adaptation of this species to the human vaginal environment.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02899-20}, pmid = {33579685}, issn = {1098-5336}, abstract = {Vaginal microbiota is defined as the community of bacteria residing in the human vaginal tract. Recent studies have demonstrated that the vaginal microbiota is dominated by members of the Lactobacillus genus, whose relative abundance and microbial taxa composition are dependent on the healthy status of this human body site. Particularly, among members of this genus, the high prevalence of Lactobacillus crispatus is commonly associated with a healthy vaginal environment. In the current study, we assessed the microbial composition of 94 healthy vaginal microbiome samples through shotgun metagenomics analyses. Based on our results we observed that L. crispatus was the most representative species and correlated negatively with bacteria involved in vaginal infections. Therefore, we isolated fifteen L. crispatus strains from different environments in which this species is abounding, ranging from vaginal swabs of healthy women to chicken fecal samples. The genomes of these strains were decoded and their genetic content was analyzed and correlated with their physiological features. An extensive comparative genomic analysis encompassing all publicly available genome sequences of L. crispatus and combined with those decoded in this study, revealed a genetic adaptation of strains to their ecological niche. In addition, in vitro growth experiments involving all isolated L. crispatus strains together with a synthetic vaginal microbiota reveal how this species is able to modulate the composition of the vaginal microbial consortia at strain level. Overall, our findings suggest that L. crispatus plays an important ecological role in reducing the complexity of the vaginal microbiota by depleting pathogenic bacteria.Importance The vaginal microbiota is defined as the community of bacteria residing in the human vaginal tract. Recent studies have demonstrated that the high prevalence of Lactobacillus crispatus species is commonly associated with a healthy vaginal environment. In the current study, we assessed the microbial composition of 94 public healthy vaginal samples through shotgun metagenomics analyses. Results showed that L. crispatus was the most representative species and correlated negatively with bacteria involved in vaginal infections. Moreover, we isolated and sequenced the genome of new L. crispatus strains from different environments and the comparative genomics analysis revealed a genetic adaptation of strains to their ecological niche. In addition, in-vitro growth experiments display the capability of this species to modulate the composition of the vaginal microbial consortia. Overall, our findings suggest an ecological role exploited by L. crispatus in reducing the complexity of the vaginal microbiota toward a depletion of pathogenic bacteria.}, }
@article {pmid33579683, year = {2021}, author = {Warda, AK and Clooney, AG and Ryan, F and de Almeida Bettio, PH and Di Benedetto, G and Ross, RP and Hill, C}, title = {A postbiotic consisting of heat-treated lactobacilli has a bifidogenic effect in pure culture and in human fermented faecal communities.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02459-20}, pmid = {33579683}, issn = {1098-5336}, abstract = {The gut microbiota has a significant impact on host health. Dietary interventions using probiotics, prebiotics and postbiotics have the potential to alter microbiota composition and function. Other therapeutic interventions such as antibiotics and faecal microbiota transplantation have also been shown to significantly alter the microbiota and its metabolites. Supplementation of a faecal fermentation model of the human gut with a postbiotic product Lactobacillus LB led to changes in microbiome composition (i.e. increase in beneficial bifidobacteria) and associated metabolic changes (i.e. increased acid production). Lactobacillus LB is a heat-treated preparation of cellular biomass and a fermentate generated by Limosilactobacillus fermentum CNCM MA65/4E-1b (formerly known as Lactobacillus fermentum CNCM MA65/4E-1b) and Lactobacillus delbrueckii ssp. delbrueckii CNCM MA65/4E-2z, medically relevant strains used to produce antidiarrheal preparations. In pure culture, Lactobacillus LB also stimulates the growth of a range of bifidobacterial species and strains. Lactobacillus LB-like preparations generated using other Lactobacillaceae, including commercially available probiotic bacteria, did not have the same impact on a model strain (Bifidobacterium longum subsp. infantis ATCC 15697). This bifidogenic activity is heat- and enzyme-stable and cannot be attributed to lactose, which is a major constituent of Lactobacillus LB. Lfermentum CNCM MA65/4E-1b is largely responsible for the observed activity and there is a clear role for compounds smaller than 1 kDa.Importance In general, disruptions to the gut microbiota are associated with multiple disorders in humans. The presence of high levels of Bifidobacterium spp. in the human gut is commonly considered to be beneficial. Bifidobacteria can be supplemented in the diet (as probiotics) or those bifidobacteria already present in the gut can be stimulated by the consumption of prebiotics such as inulin. We demonstrate that Lactobacillus LB (a product consisting of two heat-killed lactic acid bacteria and their metabolites) can stimulate the growth of bifidobacteria in human fermented faecal communities and in pure culture. Given the heat-treatment applied during the production process, there is no risk of the lactic acid bacteria colonising (or causing bacteraemia) in vulnerable consumers (infants, immunocompromised, etc). Lactobacillus LB has the potential to affect human health by selectively promoting the growth of beneficial bacteria.}, }
@article {pmid33579645, year = {2021}, author = {Sharpton, TJ and Combrink, L and Arnold, HK and Gaulke, CA and Kent, M}, title = {Erratum to &quot;Harnessing the gut microbiome in the fight against anthelminthic drug resistance&quot; [Curr. Opin. Microbiol. 53 (February) (2020) 26-34].}, journal = {Current opinion in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.mib.2021.01.003}, pmid = {33579645}, issn = {1879-0364}, }
@article {pmid33579424, year = {2021}, author = {Golonka, RM and Vijay-Kumar, M}, title = {Atypical immunometabolism and metabolic reprogramming in liver cancer: Deciphering the role of gut microbiome.}, journal = {Advances in cancer research}, volume = {149}, number = {}, pages = {171-255}, doi = {10.1016/bs.acr.2020.10.004}, pmid = {33579424}, issn = {2162-5557}, abstract = {Hepatocellular carcinoma (HCC) is the fourth leading cause of cancer-related mortality worldwide. Much recent research has delved into understanding the underlying molecular mechanisms of HCC pathogenesis, which has revealed to be heterogenous and complex. Two major hallmarks of HCC include: (i) a hijacked immunometabolism and (ii) a reprogramming in metabolic processes. We posit that the gut microbiota is a third component in an entanglement triangle contributing to HCC progression. Besides metagenomic studies highlighting the diagnostic potential in the gut microbiota profile, recent research is pinpointing the gut microbiota as an instigator, not just a mere bystander, in HCC. In this chapter, we discuss mechanistic insights on atypical immunometabolism and metabolic reprogramming in HCC, including the examination of tumor-associated macrophages and neutrophils, tumor-infiltrating lymphocytes (e.g., T-cell exhaustion, regulatory T-cells, natural killer T-cells), the Warburg effect, rewiring of the tricarboxylic acid cycle, and glutamine addiction. We further discuss the potential involvement of the gut microbiota in these characteristics of hepatocarcinogenesis. An immediate highlight is that microbiota metabolites (e.g., short chain fatty acids, secondary bile acids) can impair anti-tumor responses, which aggravates HCC. Lastly, we describe the rising 'new era' of immunotherapies (e.g., immune checkpoint inhibitors, adoptive T-cell transfer) and discuss for the potential incorporation of gut microbiota targeted therapeutics (e.g., probiotics, fecal microbiota transplantation) to alleviate HCC. Altogether, this chapter invigorates for continuous research to decipher the role of gut microbiome in HCC from its influence on immunometabolism and metabolic reprogramming.}, }
@article {pmid33579330, year = {2021}, author = {Schwartz, DJ and Langdon, AE and Dantas, G}, title = {Correction to: Understanding the impact of antibiotic perturbation on the human microbiome.}, journal = {Genome medicine}, volume = {13}, number = {1}, pages = {26}, pmid = {33579330}, issn = {1756-994X}, }
@article {pmid33579191, year = {2021}, author = {Lkhagva, E and Chung, HJ and Hong, J and Tang, WHW and Lee, SI and Hong, ST and Lee, S}, title = {The regional diversity of gut microbiome along the GI tract of male C57BL/6 mice.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {44}, pmid = {33579191}, issn = {1471-2180}, support = {Grant No. HI18C2039//Korea Health Industry Development Institute/Republic of Korea ; }, abstract = {BACKGROUND: The proliferation and survival of microbial organisms including intestinal microbes are determined by their surrounding environments. Contrary to popular myth, the nutritional and chemical compositions, water contents, O2 contents, temperatures, and pH in the gastrointestinal (GI) tract of a human are very different in a location-specific manner, implying heterogeneity of the microbial composition in a location-specific manner.<br><br>RESULTS: We first investigated the environmental conditions at 6 different locations along the GI tract and feces of ten weeks' old male SPF C57BL/6 mice. As previously known, the pH and water contents of the GI contents at the different locations of the GI tract were very different from each other in a location-specific manner, and none of which were not even similar to those of feces. After confirming the heterogeneous nature of the GI contents in specific locations and feces, we thoroughly analyzed the composition of the microbiome of the GI contents and feces. 16S rDNA-based metagenome sequencing on the GI contents and feces showed the presence of 13 different phyla. The abundance of Firmicutes gradually decreased from the stomach to feces while the abundance of Bacteroidetes gradually increased. The taxonomic α-diversities measured by ACE (Abundance-based Coverage Estimator) richness, Shannon diversity, and Fisher's alpha all indicated that the diversities of gut microbiome at colon and cecum were much higher than that of feces. The diversities of microbiome compositions were lowest in jejunum and ileum while highest in cecum and colon. Interestingly, the diversities of the fecal microbiome were lower than those of the cecum and colon. Beta diversity analyses by NMDS plots, PCA, and unsupervised hierarchical clustering all showed that the microbiome compositions were very diverse in a location-specific manner. Direct comparison of the fecal microbiome with the microbiome of the whole GI tracts by α-and β-diversities showed that the fecal microbiome did not represent the microbiome of the whole GI tract.<br><br>CONCLUSION: The fecal microbiome is different from the whole microbiome of the GI tract, contrary to a baseline assumption of contemporary microbiome research work.}, }
@article {pmid33578998, year = {2021}, author = {Carranza-Naval, MJ and Vargas-Soria, M and Hierro-Bujalance, C and Baena-Nieto, G and Garcia-Alloza, M and Infante-Garcia, C and Del Marco, A}, title = {Alzheimer's Disease and Diabetes: Role of Diet, Microbiota and Inflammation in Preclinical Models.}, journal = {Biomolecules}, volume = {11}, number = {2}, pages = {}, doi = {10.3390/biom11020262}, pmid = {33578998}, issn = {2218-273X}, support = {PI-0008-2017//Subvencion para la Financiacion de la Investigación y la Innovación Biomedica y en Ciencias de la Salud en el Marco de la Iniciativa Territorial Integrada 2014-2020 para la provincia de Cadiz. Consejeria de Salud y Familias. Junta de Andalucia and finance/ ; BFU 2016-75038-R//Programa Estatal de I+D+I orientada a los Retos de la Sociedadfinanced by the Agencia Estatal de Investigación (AEI) and the Fondo Europeo de Desarrollo Regional (FEDER)./ ; }, abstract = {Alzheimer's disease (AD) is the most common cause of dementia. Epidemiological studies show the association between AD and type 2 diabetes (T2DM), although the mechanisms are not fully understood. Dietary habits and lifestyle, that are risk factors in both diseases, strongly modulate gut microbiota composition. Also, the brain-gut axis plays a relevant role in AD, diabetes and inflammation, through products of bacterial metabolism, like short-chain fatty acids. We provide a comprehensive review of current literature on the relation between dysbiosis, altered inflammatory cytokines profile and microglia in preclinical models of AD, T2DM and models that reproduce both diseases as commonly observed in the clinic. Increased proinflammatory cytokines, such as IL-1β and TNF-α, are widely detected. Microbiome analysis shows alterations in Actinobacteria, Bacteroidetes or Firmicutes phyla, among others. Altered α- and β-diversity is observed in mice depending on genotype, gender and age; therefore, alterations in bacteria taxa highly depend on the models and approaches. We also review the use of pre- and probiotic supplements, that by favoring a healthy microbiome ameliorate AD and T2DM pathologies. Whereas extensive studies have been carried out, further research would be necessary to fully understand the relation between diet, microbiome and inflammation in AD and T2DM.}, }
@article {pmid33578973, year = {2021}, author = {Park, S and Lee, JW}, title = {Detection of Coronaviruses Using RNA Toehold Switch Sensors.}, journal = {International journal of molecular sciences}, volume = {22}, number = {4}, pages = {}, doi = {10.3390/ijms22041772}, pmid = {33578973}, issn = {1422-0067}, support = {()//LG Chem's Early Career Faculty Research Program/ ; 2018R1C1B3007409//Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Science and ICT/ ; 20194030202330//Human Resources Program in Energy Technology of the Korea Institute of Energy Technology Evaluation and Planning (KETEP), which granted financial resources from the Ministry of Trade, Industry and Energy/ ; }, abstract = {A rapid, sensitive and simple point-of-care (POC) nucleic acid diagnostic test is needed to prevent spread of infectious diseases. Paper-based toehold reaction, a recently emerged colorimetric POC nucleic acid diagnostic test, has been widely used for pathogen detection and microbiome profiling. Here, we introduce an amplification method called reverse transcription loop-mediated amplification (RT-LAMP) prior to the toehold reaction and modify it to enable more sensitive and faster colorimetric detection of RNA viruses. We show that incorporating the modified RT-LAMP to the toehold reaction detects as few as 120 copies of coronavirus RNA in 70 min. Cross-reactivity test against other coronaviruses indicates this toehold reaction with the modified RT-LAMP is highly specific to the target RNA. Overall, the paper-based toehold switch sensors with the modified RT-LAMP allow fast, sensitive, specific and colorimetric coronavirus detection.}, }
@article {pmid33578802, year = {2021}, author = {Davison, E and Johnston, W and Piela, K and Rosier, BT and Paterson, M and Mira, A and Culshaw, S}, title = {The Subgingival Plaque Microbiome, Systemic Antibodies Against Bacteria and Citrullinated Proteins Following Periodontal Therapy.}, journal = {Pathogens (Basel, Switzerland)}, volume = {10}, number = {2}, pages = {}, doi = {10.3390/pathogens10020193}, pmid = {33578802}, issn = {2076-0817}, support = {20823/VAC_/Versus Arthritis/United Kingdom ; 290246//FP7 People: Marie-Curie Actions/ ; }, abstract = {Periodontitis (PD) shows an association with rheumatoid arthritis (RA) and systemic inflammation. Periodontal pathogens, namely Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans, are proposed to be capable of inducing citrullination of peptides in the gingiva, inducing the formation of anti-citrullinated protein antibodies (ACPAs) within susceptible hosts. Here, we sought to investigate whether periodontal treatment influenced systemic inflammation and antibody titres to P. gingivalis, A. actinomycetemcomitans, Prevotella intermedia and ACPA in 42 systemically health patients with periodontal disease. Subgingival plaque and serum samples were collected from study participants before (baseline) and 90 days after treatment to analyse the abundance of specific bacteria and evaluate anti-bacterial antibodies, C-reactive protein (CRP), tumour necrosis factor α (TNF-α), interleukin 6 (IL-6) and ACPA in serum. Following treatment, all patients showed reduced periodontal inflammation. Despite observing a weak positive correlation between CRP and IL-6 with periodontal inflammation at baseline, we observed no significant reductions in any indicators of systemic inflammation 90 days after treatment. In contrast, anti-P. gingivalis IgG significantly reduced post-treatment (p < 0.001, Wilcoxon signed rank test), although no changes were observed for other antibody titres. Patients who had detectable P. gingivalis in subgingival plaques had significantly higher anti-P. gingivalis IgG and ACPA titres, suggesting a potential association between P. gingivalis colonisation and systemic antibody titres.}, }
@article {pmid33578763, year = {2021}, author = {Frank, J and Gupta, A and Osadchiy, V and Mayer, EA}, title = {Brain-Gut-Microbiome Interactions and Intermittent Fasting in Obesity.}, journal = {Nutrients}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/nu13020584}, pmid = {33578763}, issn = {2072-6643}, abstract = {The obesity epidemic and its metabolic consequences are a major public health problem both in the USA and globally. While the underlying causes are multifactorial, dysregulations within the brain-gut-microbiome (BGM) system play a central role. Normal eating behavior is coordinated by the tightly regulated balance between intestinal, extraintestinal and central homeostatic and hedonic mechanisms, resulting in stable body weight. The ubiquitous availability and marketing of inexpensive, highly palatable and calorie-dense food has played a crucial role in shifting this balance towards hedonic eating through both central (disruptions in dopaminergic signaling) and intestinal (vagal afferent function, metabolic toxemia, systemic immune activation, changes to gut microbiome and metabolome) mechanisms. The balance between homeostatic and hedonic eating behaviors is not only influenced by the amount and composition of the diet, but also by the timing and rhythmicity of food ingestion. Circadian rhythmicity affects both eating behavior and multiple gut functions, as well as the composition and interactions of the microbiome with the gut. Profound preclinical effects of intermittent fasting and time restricted eating on the gut microbiome and on host metabolism, mostly demonstrated in animal models and in a limited number of controlled human trials, have been reported. In this Review, we will discuss the effects of time-restricted eating on the BGM and review the promising effects of this eating pattern in obesity treatment.}, }
@article {pmid33578709, year = {2021}, author = {Velikova, T and Krastev, B and Lozenov, S and Gencheva, R and Peshevska-Sekulovska, M and Nikolaev, G and Peruhova, M}, title = {Antibiotic-Related Changes in Microbiome: The Hidden Villain behind Colorectal Carcinoma Immunotherapy Failure.}, journal = {International journal of molecular sciences}, volume = {22}, number = {4}, pages = {}, doi = {10.3390/ijms22041754}, pmid = {33578709}, issn = {1422-0067}, support = {DO1-275 / 16.12.2019 &quot;INFRAACT&quot; of Bulgarian NRRI 2017-2023//Ministry of Education and Science/ ; }, abstract = {The interplay between drugs and microbiota is critical for successful treatment. An accumulating amount of evidence has identified the significant impact of intestinal microbiota composition on cancer treatment response, particularly immunotherapy. The possible molecular pathways of the interaction between immune checkpoint inhibitors (ICIs) and the microbiome can be used to reverse immunotherapy tolerance in cancer by using various kinds of interventions on the intestinal bacteria. This paper aimed to review the data available on how the antibiotic-related changes in human microbiota during colorectal cancer (CRC) treatment can affect and determine ICI treatment outcomes. We also covered the data that support the potential intimate mechanisms of both local and systemic immune responses induced by changes in the intestinal microbiota. However, further better-powered studies are needed to thoroughly assess the clinical significance of antibiotic-induced alteration of the gut microbiota and its impact on CRC treatment by direct observations of patients receiving antibiotic treatment.}, }
@article {pmid33578353, year = {2021}, author = {Wang, H and Fotidis, IA and Yan, Q and Angelidaki, I}, title = {Feeding strategies of continuous biomethanation processes during increasing organic loading with lipids or glucose for avoiding potential inhibition.}, journal = {Bioresource technology}, volume = {327}, number = {}, pages = {124812}, doi = {10.1016/j.biortech.2021.124812}, pmid = {33578353}, issn = {1873-2976}, abstract = {Anaerobic co-digestion is a promising solution for nutrients balance and improvement of methane production in anaerobic digestion (AD) processes. However, the knowledge about the effects of different co-substrates in manure-based AD, and different feeding strategies, on the process performance and the methanogenic microbiome pathway, are still missing. Therefore, under harsh and slow stepwise increase of organic loading rate (OLR), by addition of lipids and carbohydrates as co-substrates in continuous reactors, this study elucidated their effect on methane production and methanogenic microbiome. The results showed that, when OLR increased by adding lipids, a severe inhibition due to accumulated long-chain fatty acids (LCFA) was observed, while no significant inhibition was obtained by addition of glucose. Additionally, the LCFA inhibition in the reactor fed with lipid was alleviated by slow stepwise feeding strategy that enriched aceticlastic Methanosarcina thermophile and Methanosaeta concilii, and hydrogenotrophic Methanobacterium methanogens.}, }
@article {pmid33578068, year = {2021}, author = {Núñez, A and García, AM and Moreno, DA and Guantes, R}, title = {Seasonal changes dominate long-term variability of the urban air microbiome across space and time.}, journal = {Environment international}, volume = {150}, number = {}, pages = {106423}, doi = {10.1016/j.envint.2021.106423}, pmid = {33578068}, issn = {1873-6750}, abstract = {Compared to soil or aquatic ecosystems, the atmosphere is still an underexplored environment for microbial diversity. In this study, we surveyed the composition, variability and sources of microbes (bacteria and fungi) in the near surface atmosphere of a highly populated area, spanning ~ 4,000 Km2 around the city center of Madrid (Spain), in different seasonal periods along two years. We found a core of abundant bacterial genera robust across space and time, most of soil origin, while fungi were more sensitive to environmental conditions. Microbial communities showed clear seasonal patterns driven by variability of environmental factors, mainly temperature and accumulated rain, while local sources played a minor role. We also identified taxa in both groups characteristic of seasonal periods, but not of specific sampling sites or plant coverage. The present study suggests that the near surface atmosphere of urban environments contains an ecosystem stable across relatively large spatial and temporal scales, with a rather homogenous composition, modulated by climatic variations. As such, it contributes to our understanding of the long-term changes associated to the human exposome in the air of highly populated areas.}, }
@article {pmid33577897, year = {2021}, author = {Apte, U}, title = {Bile Acids: Connecting Link Between Autophagy and Gut Microbiome.}, journal = {Cellular and molecular gastroenterology and hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jcmgh.2021.01.010}, pmid = {33577897}, issn = {2352-345X}, }
@article {pmid33577896, year = {2021}, author = {Rosas-Salazar, C and Kimura, KS and Shilts, MH and Strickland, BA and Freeman, MH and Wessinger, BC and Gupta, V and Brown, HM and Rajagopala, SV and Turner, JH and Das, SR}, title = {SARS-CoV-2 Infection and Viral Load are Associated with the Upper Respiratory Tract Microbiome.}, journal = {The Journal of allergy and clinical immunology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jaci.2021.02.001}, pmid = {33577896}, issn = {1097-6825}, abstract = {BACKGROUND: Little is known about the relationships between SARS-CoV-2, the respiratory virus responsible for the ongoing COVID-19 pandemic, and the upper respiratory tract (URT) microbiome.<br><br>OBJECTIVE: Our objectives were 1) to compare the URT microbiome between SARS-CoV-2-infected and -uninfected adults, and 2) to examine the association of SARS-CoV-2 viral load with the URT microbiome during COVID-19.<br><br>METHODS: We characterized the URT microbiome using 16S ribosomal RNA sequencing in 59 adults (38 with confirmed, symptomatic, mild-to-moderate COVID-19 and 21 asymptomatic, uninfected controls). In those with COVID-19, we measured SARS-CoV-2 viral load using quantitative reverse transcription PCR. We then examined the association of SARS-CoV-2 infection status and its viral load with the ⍺-diversity, β-diversity, and abundance of bacterial taxa of the URT microbiome. Our main models were all adjusted for age and sex.<br><br>RESULTS: The observed species index was significantly higher in SARS-CoV-2-infected than in -uninfected adults (β linear regression coefficient=7.53, 95%CI=0.17-14.89, p=0.045). In differential abundance testing, 9 amplicon sequence variants (ASVs) were significantly different in both of our comparisons, with Peptoniphilus lacrimalis, Campylobacter hominis, Prevotella 9 copri, and an Anaerococcus unclassified ASV being more abundant in those with SARS-CoV-2 infection and in those with high viral load during COVID-19, whereas Corynebacterium unclassified, Staphylococcus haemolyticus, Prevotella disiens, and 2 Corynebacterium_1 unclassified ASVs were more abundant in those without SARS-CoV-2 infection and in those with low viral load during COVID-19.<br><br>CONCLUSION: Our findings suggest complex associations between SARS-CoV-2 and the URT microbiome in adults. Future studies are needed to examine how these viral-bacterial interactions can impact the clinical progression, severity, and recovery of COVID-19.}, }
@article {pmid33577717, year = {2021}, author = {Morris, NL and Choudhry, MA}, title = {Maintenance of gut barrier integrity after injury: Trust your gut microRNAs.}, journal = {Journal of leukocyte biology}, volume = {}, number = {}, pages = {}, doi = {10.1002/JLB.3RU0120-090RR}, pmid = {33577717}, issn = {1938-3673}, support = {R01 AA015731/NH/NIH HHS/United States ; R01 GM128242/NH/NIH HHS/United States ; T32 AA013527/NH/NIH HHS/United States ; }, abstract = {The gastrointestinal (GI) tract is a highly dynamic structure essential for digestion, nutrient absorption, and providing an interface to prevent gut bacterial translocation. In order to maintain the barrier function, the gut utilizes many defense mechanisms including proliferation, apoptosis, and apical junctional complexes. Disruption of any of these parameters due to injury or disease could negatively impact the intestinal barrier function and homeostasis resulting in increased intestine inflammation, permeability, bacterial dysbiosis, and tissue damage. MicroRNAs are small noncoding RNA sequences that are master regulators of normal cellular homeostasis. These regulatory molecules affect cellular signaling pathways and potentially serve as candidates for providing a mechanism of impaired gut barrier integrity following GI-related pathologic conditions, ethanol exposure, or trauma such as burn injury. MicroRNAs influence cellular apoptosis, proliferation, apical junction complex expression, inflammation, and the microbiome. Due to their widespread functional affiliations, altered expression of microRNAs are associated with many pathologic conditions. This review explores the role of microRNAs in regulation of intestinal barrier integrity. The studies reviewed demonstrate that microRNAs largely impact intestine barrier function and provide insight behind the observed adverse effects following ethanol and burn injury. Furthermore, these studies suggest that microRNAs are excellent candidates for therapeutic intervention or for biomarkers to manage gut barrier integrity following trauma such as burn injury and other GI-related pathologic conditions.}, }
@article {pmid33577626, year = {2020}, author = {Muñoz-Benavent, M and Hartkopf, F and Van Den Bossche, T and Piro, VC and García-Ferris, C and Latorre, A and Renard, BY and Muth, T}, title = {Erratum: gNOMO: a multi-omics pipeline for integrated host and microbiome analysis of non-model organisms.}, journal = {NAR genomics and bioinformatics}, volume = {2}, number = {4}, pages = {lqaa083}, doi = {10.1093/nargab/lqaa083}, pmid = {33577626}, issn = {2631-9268}, abstract = {[This corrects the article DOI: 10.1093/nargab/lqaa058.].}, }
@article {pmid33577089, year = {2021}, author = {Freedman, ZB and McGrew, A and Baiser, B and Besson, M and Gravel, D and Poisot, T and Record, S and Trotta, LB and Gotelli, NJ}, title = {Environment-host-microbial interactions shape the Sarracenia purpurea microbiome at the continental scale.}, journal = {Ecology}, volume = {}, number = {}, pages = {e03308}, doi = {10.1002/ecy.3308}, pmid = {33577089}, issn = {1939-9170}, abstract = {The importance of climate, habitat structure, and higher trophic levels on microbial diversity is only beginning to be understood. Here, we examined the influence of climate variables, plant morphology, and the abundance of aquatic invertebrates on the microbial biodiversity of the northern pitcher plant Sarracenia purpurea. The plant's cup-shaped leaves fill with rainwater and support a miniature, yet full-fledged ecosystem with a diverse microbiome that decomposes captured prey and a small network of shredding and filter-feeding aquatic invertebrates that feed on microbes. We characterized pitcher microbiomes of 108 plants sampled at 36 sites from Florida to Quebec. Structural equation models revealed that annual precipitation and temperature, plant size, and midge abundance had direct effects on microbiome taxonomic and phylogenetic diversity. Climate variables also exerted indirect effects through plant size and midge abundance. Further, spatial structure and climate influenced taxonomic composition, but not phylogenetic composition. Our results suggest that direct effects of midge abundance and climate and indirect effects of climate through its effect on plant-associated factors lead to greater richness of microbial phylotypes in warmer, wetter sites.}, }
@article {pmid33576881, year = {2021}, author = {Peng, C and Xu, X and He, Z and Li, N and Ouyang, Y and Zhu, Y and Lu, N and He, C}, title = {Helicobacter pylori infection worsens impaired glucose regulation in high-fat diet mice in association with an altered gut microbiome and metabolome.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {33576881}, issn = {1432-0614}, support = {81860106//National Natural Science Foundation of China/ ; 81670507//National Natural Science Foundation of China/ ; 81870395//National Natural Science Foundation of China/ ; 20192BBG70037//Jiangxi Provincial Department of Science and Technology (CN)/ ; PY201816//Nanchang University (CN)/ ; }, abstract = {Emerging evidence suggests that Helicobacter pylori infection is associated with metabolic disorders, although the underlying mechanisms are poorly defined. This study aimed to investigate the interaction among H. pylori, a high-fat diet (HFD), and the gut microbiota with glucose regulation and alterations in microbial metabolites. Mice were randomly allocated to H. pylori-infected and noninfected groups fed a chow diet or an HFD. After 4 weeks, two of the HFD groups were given antibiotic cocktails for 8 weeks to eliminate the gut microbiota. The results showed that an HFD significantly promoted increases in body weight, insulin resistance, and glucose intolerance, which were alleviated to normal after antibiotic treatment. H. pylori infection aggravated HFD-induced hyperglycemia, which could not be restored by antibiotics. The perturbation of the gut microbiota was greater in the mice cotreated with H. pylori and an HFD (HFDHp) compared to those administered either H. pylori or an HFD alone, with a loss of diversity, higher abundance of Helicobacter, and lower abundance of Lactobacillus. Furthermore, compared to that of the HFD alone group, the gut microbiota of the HFDHp group was much more susceptible to antibiotic destruction, with extremely lower diversity and dominance of Klebsiella. Fecal metabolome analyses demonstrated that the combination of H. pylori infection and an HFD altered metabolic composition and function, which were linked to glucose dysregulation. H. pylori infection may exacerbate the dysbiosis of the gut microenvironment induced by an HFD, including alterations in the microbiota and metabolites, which weakens the restorative effect of antibiotics and results in the persistence of glucose disorders. KEY POINTS: • The interplay of Hp, HFD, and antibiotics on glucose metabolism was firstly explored. • Hp infection impaired the effect of antibiotics on HFD-induced glucose dysregulation. • Hp infection altered gut microbiota and metabolites which aggravated by HFD.}, }
@article {pmid33576852, year = {2021}, author = {Zhou, G and Tong, H and Cai, L and Huang, H}, title = {Transgenerational Effects on the Coral Pocillopora damicornis Microbiome Under Ocean Acidification.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33576852}, issn = {1432-184X}, support = {41876192//National Natural Science Foundation of China/ ; }, abstract = {Reef-building corals are inhabited by functionally diverse microorganisms which play important roles in coral health and persistence in the Anthropocene. However, our understanding of the complex associations within coral holobionts is largely limited, particularly transgenerational exposure to environmental stress, like ocean acidification. Here we investigated the microbiome development of an ecologically important coral Pocillopora damicornis following transgenerational exposure to moderate and high pCO2 (partial pressure of CO2) levels, using amplicon sequencing and analysis. Our results showed that the Symbiodiniaceae community structures in adult and juvenile had similar patterns, all of which were dominated by Durusdinium spp., previously known as clade D. Conversely, prokaryotic communities varied between adults and juveniles, possibly driven by the effect of host development. Surprisingly, there were no significant changes in both Symbiodiniaceae and prokaryotic communities with different pCO2 treatments, which was independent of the life history stage. This study shows that ocean acidification has no significant effect on P. damicornis microbiome, and warrants further research to test whether transgenerational acclimation exists in coral holobiont to projected future climate change.}, }
@article {pmid33576793, year = {2021}, author = {Ducarmon, QR and Kuijper, EJ and Olle, B}, title = {Opportunities and Challenges in Development of Live Biotherapeutic Products To Fight Infections.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiaa779}, pmid = {33576793}, issn = {1537-6613}, abstract = {Treatment of bacterial infections with broad spectrum antibiotics is a strategy severely limited by the decreased ability of the perturbed resident microbiota to control expansion of antibiotic resistant pathogens. Live Biotherapeutic Products (LBPs) could provide an alternative to antibiotics in infection control by restoring gut colonization resistance and controlling expansion of resistant strains, an important therapeutic need not being addressed with existing anti-infective drug modalities. We review opportunities and challenges in developing LBPs for MDRO colonization and infection control, with a focus on commercial FMT-like products and defined bacterial consortia, and spanning considerations related to availability of models for rational drug candidate selection and dose regimen selection, GMP manufacturing, intellectual property, and commercial viability.}, }
@article {pmid33576711, year = {2021}, author = {Ahlawat, S and Kumar, P and Mohan, H and Goyal, S and Sharma, KK}, title = {Inflammatory bowel disease: tri-directional relationship between microbiota, immune system and intestinal epithelium.}, journal = {Critical reviews in microbiology}, volume = {}, number = {}, pages = {1-20}, doi = {10.1080/1040841X.2021.1876631}, pmid = {33576711}, issn = {1549-7828}, abstract = {Human gut microbiota contributes to host nutrition and metabolism, sustains intestinal cell proliferation and differentiation, and modulates host immune system. The alterations in their composition lead to severe gut disorders, including inflammatory bowel disease (IBD) or inflammatory bowel syndrome (IBS). IBD including ulcerative colitis (UC) and Crohn's disease (CD) are gamut of chronic inflammatory disorders of gut, mediated by complex interrelations among genetic, environmental, and internal factors. IBD has debateable aetiology, however in recent years, exploring the central role of a tri-directional relationship between gut microbiota, mucosal immune system, and intestinal epithelium in pathogenesis is getting the most attention. Increasing incidences and early onset explains the exponential rise in IBD burden on health-care systems. Industrialization, hypersensitivity to allergens, lifestyle, hygiene hypothesis, loss of intestinal worms, and gut microbial composition, explains this shifted rise. Hitherto, the interventions modulating gut microbiota composition, microfluidics-based in vitro gastrointestinal models, non-allergic functional foods, nutraceuticals, and faecal microbiota transplantation (FMT) from healthy donors are some of the futuristic approaches for the disease management.}, }
@article {pmid33576511, year = {2021}, author = {Teo, WL}, title = {The &quot;Maskne&quot; microbiome - pathophysiology and therapeutics.}, journal = {International journal of dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1111/ijd.15425}, pmid = {33576511}, issn = {1365-4632}, abstract = {&quot;Maskne&quot; is a new term coined during the 2020 COVID-19 pandemic. It refers to a subset of acne mechanica, deserving consideration in view of widespread reusable fabric mask-wearing to control the pandemic worldwide. Understanding of underlying pathophysiology directly relates to the novel skin microenvironment and textile-skin friction created by mask-wearing, distinct from nontextile-related acne mechanica previously linked to wearing of headgear. Specifically, the occlusive microenvironment leads to microbiome dysbiosis, which is linked to various dermatological conditions. Additional textile-skin interactions include factors such as breathability, stickiness sensations, moisture saturation, and hygiene maintenance. Increased skin temperatures can trigger sweat/heat-related dermatoses, and ear loops potentially trigger pressure-induced dermatoses. Important therapeutic considerations include increased skin irritation potential of conventional acne treatments under occlusion, exacerbation of chronic dermatoses, that is, perioral dermatitis, rosacea, and eczema, and susceptibility of these same patient groups to heightened discomfort with mask-wearing. Cotton, as the traditional fabric of choice for dermatology patients, has limited benefits in the context of face masks - increased subjective discomfort relates to increased moisture saturation and stickiness, inevitable because of high biofluid load of the nasal and oral orifices. Prolonged textile-skin contact time, directly proportional to the risk of maskne, can be an opportunity for the application of biofunctional textiles.}, }
@article {pmid33576406, year = {2021}, author = {Koppe, L and Beddhu, S and Chauveau, P and Kovesdy, CP and Mafra, D and Joshi, S and Kamyar, KZ and Fouque, D}, title = {Editorial: a call for a better understanding of the role of dietary amino acids and posttranslational protein modifications of microbiome in the progression of CKD.}, journal = {Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association}, volume = {}, number = {}, pages = {}, doi = {10.1093/ndt/gfab033}, pmid = {33576406}, issn = {1460-2385}, }
@article {pmid33576347, year = {2021}, author = {Koch, M and Capurso, L}, title = {[&quot;Probiotic medicine&quot; and certainty of the evidence.].}, journal = {Recenti progressi in medicina}, volume = {112}, number = {1}, pages = {1-3}, doi = {10.1701/3551.35253}, pmid = {33576347}, issn = {2038-1840}, abstract = {These are excellent times for probiotic medicine. We have discovered more than 150,000 genomes of the microbiome, which can be aggregated into 4,930 species. However, the dream of microbiome-based medicine requires a new approach - an ecological and evolutionary understanding of host-microbe interactions, rather than a qualitative analysis of species. Yet researchers still disagree on what constitutes a healthy microbiome or how to define an altered one. There is still uncertainty as to which properties of the microbiome will represent the most informative biomarkers in clinical and epidemiological studies. And little is known about how the microbiomes of different regions of the body, such as the mouth, intestines or skin, interact. It is time to re-establish the foundations for the certainty of evidence in myocrobiome-based medicine. We believe robust new pillars are needed: starting clinical trials whenever possible; extending the role of N-of-1 trials; ending the &quot;one probiotic for every disease&quot; principle; reduce the number of outcomes of each research; search for the replicability of the results (the best test for the validity of an intervention with probiotics is not statistical significance but the replication of the result). Again, we would like to urge probiotic medicine researchers not to publish in &quot;pirate&quot; journals.}, }
@article {pmid33576313, year = {2021}, author = {Wang, T and Shi, C and Luo, H and Zheng, H and Fan, L and Tang, M and Su, Y and Yang, J and Mao, C and Xu, Y}, title = {Neuroinflammation in Parkinson's Disease: Triggers, Mechanisms, and Immunotherapies.}, journal = {The Neuroscientist : a review journal bringing neurobiology, neurology and psychiatry}, volume = {}, number = {}, pages = {1073858421991066}, doi = {10.1177/1073858421991066}, pmid = {33576313}, issn = {1089-4098}, abstract = {Parkinson's disease (PD) is a heterogeneous neurodegenerative disease involving multiple etiologies and pathogenesis, in which neuroinflammation is a common factor. Both preclinical experiments and clinical studies provide evidence for the involvement of neuroinflammation in the pathophysiology of PD, although there are a number of key issues related to neuroinflammatory processes in PD that remain to be addressed. In this review, we highlight the relationship between the common pathological mechanisms of PD and neuroinflammation, including aggregation of α-synuclein, genetic factors, mitochondrial dysfunction, and gut microbiome dysbiosis. We also describe the two positive feedback loops initiated in PD after the immune system is activated, and their role in the pathogenesis of PD. In addition, the interconnections and differences between the central and peripheral immune systems are discussed. Finally, we review the latest progress in immunotherapy research for PD patients, and propose future directions for clinical research.}, }
@article {pmid33576276, year = {2021}, author = {Schmidt, BM}, title = {Emerging Diabetic Foot Ulcer Microbiome Analysis using Cutting Edge Technologies.}, journal = {Journal of diabetes science and technology}, volume = {}, number = {}, pages = {1932296821990097}, doi = {10.1177/1932296821990097}, pmid = {33576276}, issn = {1932-2968}, abstract = {One of the most prevalent complications of diabetes mellitus are diabetic foot ulcers (DFU). Diabetic foot ulcers represent a complex condition placing individuals at-risk for major lower extremity amputations and are an independent predictor of patient mortality. DFU heal poorly when standard of care therapy is applied. In fact, wound healing occurs only approximately 30% within 12 weeks and only 45% regardless of time when standard of care is utilized. Similarly, diabetic foot infections occur in half of all DFU and conventional microbiologic cultures can take several days to process before a result is known. DFU represent a significant challenge in this regard because DFU often demonstrate polymicrobial growth, become resistant to preferred antibiotic therapy, and do not inform providers about long-term prognosis. In addition, conventional culture yields may be affected by the timing of antibiotic administration and collection of tissue for analysis. This may lead to suboptimal antibiotic administration or debilitating amputations. The microbiome of DFU is a new frontier to better understand the interactions between host organisms and pathogenic ones. Newer molecular techniques are readily available to assist in analyzing the constituency of the microbiome of DFU. These emerging techniques have already been used to study the microbiome of DFU and have clinical implications that may alter standard of care practice in the near future. Here emerging molecular techniques that can provide clinicians with rapid DFU-related-information and help prognosticate outcomes in this vulnerable patient population are presented.}, }
@article {pmid33576015, year = {2021}, author = {Oliver, JD and Fountain-Jones, NM}, title = {Interspecies bacterial communication produces a delicate balance between Vibrio cholerae and the chironomid egg mass microbiome.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.15839}, pmid = {33576015}, issn = {1365-294X}, abstract = {The evolution of antimicrobial resistance in bacterial pathogens is considered by the World Health Organization to be one of the ten most concerning public health threats facing humanity (World Health Organization 2020). Bacterial diseases previously controllable by antibiotics are resurging and treatment options are dwindling. Cholera is one such disease. Human pathogenic strains of Vibrio cholerae cause as many as 4 million cases of disease resulting in over 100,000 deaths each year (Ali et al. 2015) and multidrug resistant V. cholerae is now established where pandemic cholera persists. Vibrio cholerae is fundamentally an aquatic species thriving in brackish and estuarial waters. Its environmental prevalence, together with both extracellular and intracellular infection of alternative arthropod and mollusk hosts, produces a highly complex ecological milieu that is not well understood. With the absence of reliable antibiotic-based treatment options, it is necessary to build a better understanding of V. cholerae biology and ecology in order to develop alternative methods for risk modelling and disease control. In this issue of Molecular Ecology, authors Sela, Hammer, and Halpern experimentally investigated a mechanism by which V. cholerae pathogenicity is affected by interspecies quorum sensing involving an array of bacterial species from the microbiome of an alternative arthropod host, the egg mass of a chironomid midge (Diptera: Chironomidae) (Sela, Hammer, and Halpern 2020). Quorum sensing is a mechanism whereby bacteria communicate with each other using autoinducers and is known to be important, for example, in shaping virulence in a variety of pathogenic bacteria. The innovative methodologies they used, both in molecular and protein biology and reductive investigative microbiomics, are helping to develop the tools needed for understanding this understudied ecological system and fighting cholera in a post-antibiotic world.}, }
@article {pmid33575644, year = {2020}, author = {Badri, M and Kurtz, ZD and Bonneau, R and Müller, CL}, title = {Shrinkage improves estimation of microbial associations under different normalization methods.}, journal = {NAR genomics and bioinformatics}, volume = {2}, number = {4}, pages = {lqaa100}, pmid = {33575644}, issn = {2631-9268}, abstract = {Estimation of statistical associations in microbial genomic survey count data is fundamental to microbiome research. Experimental limitations, including count compositionality, low sample sizes and technical variability, obstruct standard application of association measures and require data normalization prior to statistical estimation. Here, we investigate the interplay between data normalization, microbial association estimation and available sample size by leveraging the large-scale American Gut Project (AGP) survey data. We analyze the statistical properties of two prominent linear association estimators, correlation and proportionality, under different sample scenarios and data normalization schemes, including RNA-seq analysis workflows and log-ratio transformations. We show that shrinkage estimation, a standard statistical regularization technique, can universally improve the quality of taxon-taxon association estimates for microbiome data. We find that large-scale association patterns in the AGP data can be grouped into five normalization-dependent classes. Using microbial association network construction and clustering as downstream data analysis examples, we show that variance-stabilizing and log-ratio approaches enable the most taxonomically and structurally coherent estimates. Taken together, the findings from our reproducible analysis workflow have important implications for microbiome studies in multiple stages of analysis, particularly when only small sample sizes are available.}, }
@article {pmid33575609, year = {2020}, author = {Muñoz-Benavent, M and Hartkopf, F and Van Den Bossche, T and Piro, VC and García-Ferris, C and Latorre, A and Renard, BY and Muth, T}, title = {gNOMO: a multi-omics pipeline for integrated host and microbiome analysis of non-model organisms.}, journal = {NAR genomics and bioinformatics}, volume = {2}, number = {3}, pages = {lqaa058}, pmid = {33575609}, issn = {2631-9268}, abstract = {The study of bacterial symbioses has grown exponentially in the recent past. However, existing bioinformatic workflows of microbiome data analysis do commonly not integrate multiple meta-omics levels and are mainly geared toward human microbiomes. Microbiota are better understood when analyzed in their biological context; that is together with their host or environment. Nevertheless, this is a limitation when studying non-model organisms mainly due to the lack of well-annotated sequence references. Here, we present gNOMO, a bioinformatic pipeline that is specifically designed to process and analyze non-model organism samples of up to three meta-omics levels: metagenomics, metatranscriptomics and metaproteomics in an integrative manner. The pipeline has been developed using the workflow management framework Snakemake in order to obtain an automated and reproducible pipeline. Using experimental datasets of the German cockroach Blattella germanica, a non-model organism with very complex gut microbiome, we show the capabilities of gNOMO with regard to meta-omics data integration, expression ratio comparison, taxonomic and functional analysis as well as intuitive output visualization. In conclusion, gNOMO is a bioinformatic pipeline that can easily be configured, for integrating and analyzing multiple meta-omics data types and for producing output visualizations, specifically designed for integrating paired-end sequencing data with mass spectrometry from non-model organisms.}, }
@article {pmid33575595, year = {2020}, author = {Yang, P and Tan, C and Han, M and Cheng, L and Cui, X and Ning, K}, title = {Correlation-Centric Network (CCN) representation for microbial co-occurrence patterns: new insights for microbial ecology.}, journal = {NAR genomics and bioinformatics}, volume = {2}, number = {2}, pages = {lqaa042}, pmid = {33575595}, issn = {2631-9268}, abstract = {Mainstream studies of microbial community focused on critical organisms and their physiology. Recent advances in large-scale metagenome analysis projects initiated new researches in the complex correlations between large microbial communities. Specifically, previous studies focused on the nodes (i.e. species) of the Species-Centric Networks (SCNs). However, little was understood about the change of correlation between network members (i.e. edges of the SCNs) when the network was disturbed. Here, we introduced a Correlation-Centric Network (CCN) to the microbial research based on the concept of edge networks. In CCN, each node represented a species-species correlation, and edge represented the species shared by two correlations. In this research, we investigated the CCNs and their corresponding SCNs on two large cohorts of microbiome. The results showed that CCNs not only retained the characteristics of SCNs, but also contained information that cannot be detected by SCNs. In addition, when the members of microbial communities were decreased (i.e. environmental disturbance), the CCNs fluctuated within a small range in terms of network connectivity. Therefore, by highlighting the important species correlations, CCNs could unveil new insights when studying not only the functions of target species, but also the stabilities of their residing microbial communities.}, }
@article {pmid33575585, year = {2020}, author = {Susin, A and Wang, Y and Lê Cao, KA and Calle, ML}, title = {Variable selection in microbiome compositional data analysis.}, journal = {NAR genomics and bioinformatics}, volume = {2}, number = {2}, pages = {lqaa029}, pmid = {33575585}, issn = {2631-9268}, abstract = {Though variable selection is one of the most relevant tasks in microbiome analysis, e.g. for the identification of microbial signatures, many studies still rely on methods that ignore the compositional nature of microbiome data. The applicability of compositional data analysis methods has been hampered by the availability of software and the difficulty in interpreting their results. This work is focused on three methods for variable selection that acknowledge the compositional structure of microbiome data: selbal, a forward selection approach for the identification of compositional balances, and clr-lasso and coda-lasso, two penalized regression models for compositional data analysis. This study highlights the link between these methods and brings out some limitations of the centered log-ratio transformation for variable selection. In particular, the fact that it is not subcompositionally consistent makes the microbial signatures obtained from clr-lasso not readily transferable. Coda-lasso is computationally efficient and suitable when the focus is the identification of the most associated microbial taxa. Selbal stands out when the goal is to obtain a parsimonious model with optimal prediction performance, but it is computationally greedy. We provide a reproducible vignette for the application of these methods that will enable researchers to fully leverage their potential in microbiome studies.}, }
@article {pmid33575288, year = {2021}, author = {Sheng, L and Jena, PK and Hu, Y and Wan, YY}, title = {Age-specific microbiota in altering host inflammatory and metabolic signaling as well as metabolome based on the sex.}, journal = {Hepatobiliary surgery and nutrition}, volume = {10}, number = {1}, pages = {31-48}, pmid = {33575288}, issn = {2304-3881}, support = {R01 CA222490/CA/NCI NIH HHS/United States ; U01 CA179582/CA/NCI NIH HHS/United States ; }, abstract = {Background: Metabolism is sex-different, and the direct link between gut microbiota and aging-associated metabolic changes needs to be established in both sexes.<br><br>Methods: Gene expression, metabolic and inflammatory signaling, gut microbiota profile, and metabolome were studied during aging and after fecal microbiota transplantation (FMT) in mice of both sexes.<br><br>Results: Our data revealed young female mice and aged male mice were the most insulin sensitive and resistant group, respectively. In addition, aging reduced sex difference in insulin sensitivity. Such age- and sex-dependent metabolic phenotypes were accompanied by shifted gut microbiota profile and altered abundance of bacterial genes that produce butyrate, propionate, and bile acids. After receiving feces from the aged males (AFMT), the most insulin-resistant group, recipients of both sexes had increased hepatic inflammation and serum endotoxin. However, AFMT only increased insulin resistance in female mice and abolished sex difference in insulin sensitivity. Additionally, such changes were accompanied by narrowed sex difference in metabolome. Metabolomics data revealed that age-associated insulin resistance in males was accompanied by increased sugar alcohols and dicarboxylic acids as well as reduced aromatic and branched-chain amino acids. Further, receiving feces from the young females (YFMT), the most insulin-sensitive group, reduced body weight and fasting blood glucose in male recipients and improved insulin sensitivity in females, leading to enhanced sex differences in insulin sensitivity and metabolome.<br><br>Conclusions: Aging systemically affected inflammatory and metabolic signaling based on the sex. Gut microbiome is age and sex-specific, which affects inflammation and metabolism in a sex-dependent manner.}, }
@article {pmid33575282, year = {2021}, author = {Chen, X and Lu, D and Li, Z and Yue, W and Wang, J and Jiang, X and Han, H and Wang, C}, title = {Plant and Animal-Type Feedstuff Shape the Gut Microbiota and Metabolic Processes of the Chinese Mitten Crab Eriocheir sinensis.}, journal = {Frontiers in veterinary science}, volume = {8}, number = {}, pages = {589624}, pmid = {33575282}, issn = {2297-1769}, abstract = {In animals, growth and development are strongly correlated with the gut microbiota and metabolic profiles. In this study, gut microbiome communities, metabolic profiles, and growth performance of Eriocheir sinensis under three dietary feed types based on waterweed plants only, freshwater snails only, and waterweed plants combined with freshwater snails were studied by using 16S rRNA gene sequencing and liquid chromatography-mass spectrometry. Results indicated that different feed types dramatically affected the growth performances of E. sinensis by altering the gut microbiota and metabolic profiles. Aquatic plants, such as waterweeds, played essential roles in shaping gut microbiome communities, and the optimal Bacteroides-to-Firmicutes ratio might strongly promote growth performance. Waterweed plants also helped decrease maleficent Proteobacteria caused by excess animal-type feedstuff, such as freshwater snails, and might have positive roles in antibacterial functions in gut. A diet based on waterweeds only resulted in lipid metabolism disorders, which significantly retarded the growth of E. sinensis. In summary, E. sinensis cultured with a diet of waterweeds and freshwater snails showed superior growth performance due to their healthy gut microbiota and metabolic homeostasis. Our findings unveiled the roles of aquatic plants and animal-type food such as freshwater snail in shaping the gut microbiota and metabolic processes and provided guidance for the aquaculture of E. sinensis in future.}, }
@article {pmid33575223, year = {2020}, author = {Vijaya Chandra, SH and Srinivas, R and Dawson, TL and Common, JE}, title = {Cutaneous Malassezia: Commensal, Pathogen, or Protector?.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {614446}, pmid = {33575223}, issn = {2235-2988}, abstract = {The skin microbial community is a multifunctional ecosystem aiding prevention of infections from transient pathogens, maintenance of host immune homeostasis, and skin health. A better understanding of the complex milieu of microbe-microbe and host-microbe interactions will be required to define the ecosystem's optimal function and enable rational design of microbiome targeted interventions. Malassezia, a fungal genus currently comprising 18 species and numerous functionally distinct strains, are lipid-dependent basidiomycetous yeasts and integral components of the skin microbiome. The high proportion of Malassezia in the skin microbiome makes understanding their role in healthy and diseased skin crucial to development of functional skin health knowledge and understanding of normal, healthy skin homeostasis. Over the last decade, new tools for Malassezia culture, detection, and genetic manipulation have revealed not only the ubiquity of Malassezia on skin but new pathogenic roles in seborrheic dermatitis, psoriasis, Crohn's disease, and pancreatic ductal carcinoma. Application of these tools continues to peel back the layers of Malassezia/skin interactions, including clear examples of pathogenicity, commensalism, and potential protective or beneficial activities creating mutualism. Our increased understanding of host- and microbe-specific interactions should lead to identification of key factors that maintain skin in a state of healthy mutualism or, in turn, initiate pathogenic changes. These approaches are leading toward development of new therapeutic targets and treatment options. This review discusses recent developments that have expanded our understanding of Malassezia's role in the skin microbiome, with a focus on its multiple roles in health and disease as commensal, pathogen, and protector.}, }
@article {pmid33575161, year = {2020}, author = {Mori, DI and Schurr, MJ and Nair, DP}, title = {Selective Inhibition of Streptococci Biofilm Growth via a Hydroxylated Azobenzene Coating.}, journal = {Advanced materials interfaces}, volume = {7}, number = {15}, pages = {}, pmid = {33575161}, issn = {2196-7350}, support = {K25 DE027418/DE/NIDCR NIH HHS/United States ; }, abstract = {Strategies to engineer surfaces that can enable the selective inhibition of bacterial pathogens while preserving beneficial microbes can serve as tools to precisely edit the microbiome. In the oral microbiome, this selectivity is crucial in preventing the proliferation of cariogenic species such as Streptococcus mutans (S. mutans). In this communication, coatings consisting of a covalently tethered hydroxylated azobenzene (OH-AAZO) on glassy acrylic resins are studied and characterized for their ability to selectively prevent the attachment and growth of oral Streptococci biofilms. The coating applied on the surface of glassy resins inhibits the growth and proliferation of cariogenic S. mutans and S. oralis biofilms while A. actinomycetemcomitans, S. aureus, and E. coli biofilms are unaffected by the coating . The antibacterial effect is characterized as a function of both the OH-AAZO concentration in the coatings (≥50 mg mL-1) and the structure of the monomer in the coating. Preliminary mechanistic results suggest that the targeted bactericidal effect against Streptococci species is caused by a disruption of membrane ion potential, inducing cell death.}, }
@article {pmid33574872, year = {2020}, author = {NĘdzi-GÓra, M and WrÓblewska, M and GÓrska, R}, title = {The Effect of Lactobacillus salivarius SGL03 on Clinical and Microbiological Parameters in Periodontal Patients.}, journal = {Polish journal of microbiology}, volume = {69}, number = {4}, pages = {441-451}, pmid = {33574872}, issn = {2544-4646}, abstract = {The destruction of periodontal tissues during periodontitis is the result of the immune-inflammatory reactions to the bacteria of dental biofilm. Probiotics may reduce dysbiosis by the modification of the dental microbiome, which can influence the immune-inflammatory mechanisms. The aim of this study was to estimate the clinical and microbiological parameters, before and after 30 days of application of the dietary supplement containing Lactobacillus salivarius SGL03 or placebo. The study was conducted in 51 patients with stage I or II periodontitis during the maintenance phase of treatment. The clinical parameters and the number of colony forming units (CFU) of bacteria in supragingival plaque were assessed before and after 30 days of the oral once daily administration of the dietary supplement in the form of suspension containing L. salivarius SGL03 or placebo. There were no changes in the PI scores between and within the groups. The value of BOP decreased in both groups. In the study group the significant reduction of the mean pocket depth was revealed (from 2.5 to 2.42, p = 0,027) but without the difference between the groups. There were no significant changes in the number of bacteria within the groups. In the control, but not the study group, positive correlations were observed between the clinical parameters (variables) and the number of bacteria. The use of the dietary supplement containing L. salivarius SGL03 may reduce pocket depth despite the lack of changes in other clinical parameters and the number of bacteria in supragingival plaque.}, }
@article {pmid33574608, year = {2021}, author = {Wang, DD and Nguyen, LH and Li, Y and Yan, Y and Ma, W and Rinott, E and Ivey, KL and Shai, I and Willett, WC and Hu, FB and Rimm, EB and Stampfer, MJ and Chan, AT and Huttenhower, C}, title = {The gut microbiome modulates the protective association between a Mediterranean diet and cardiometabolic disease risk.}, journal = {Nature medicine}, volume = {27}, number = {2}, pages = {333-343}, pmid = {33574608}, issn = {1546-170X}, support = {R01CA202704//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; U54DE023798//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R00DK119412//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; U01CA167552//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; U01CA152904//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01HL060712//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; P30DK046200//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01HL035464//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; K24DK098311//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; }, abstract = {To address how the microbiome might modify the interaction between diet and cardiometabolic health, we analyzed longitudinal microbiome data from 307 male participants in the Health Professionals Follow-Up Study, together with long-term dietary information and measurements of biomarkers of glucose homeostasis, lipid metabolism and inflammation from blood samples. Here, we demonstrate that a healthy Mediterranean-style dietary pattern is associated with specific functional and taxonomic components of the gut microbiome, and that its protective associations with cardiometabolic health vary depending on microbial composition. In particular, the protective association between adherence to the Mediterranean diet and cardiometabolic disease risk was significantly stronger among participants with decreased abundance of Prevotella copri. Our findings advance the concept of precision nutrition and have the potential to inform more effective and precise dietary approaches for the prevention of cardiometabolic disease mediated through alterations in the gut microbiome.}, }
@article {pmid33574140, year = {2021}, author = {Salvado, R and Santos-Minguez, S and Agudo-Conde, C and Lugones-Sanchez, C and Cabo-Laso, A and Mª Hernandez-Sanchez, J and Benito, R and Rodriguez-Sanchez, E and Gomez-Marcos, MA and Hernandez-Rivas, JM and Guimarães Cunha, P and Garcia-Ortiz, L and Investigators, M}, title = {Gut microbiota composition and arterial stiffness measured by pulse wave velocity: case-control study protocol (MIVAS study).}, journal = {BMJ open}, volume = {11}, number = {2}, pages = {e038933}, doi = {10.1136/bmjopen-2020-038933}, pmid = {33574140}, issn = {2044-6055}, abstract = {INTRODUCTION: Intestinal microbiota is arising as a new element in the physiopathology of cardiovascular diseases. A healthy microbiota includes a balanced representation of bacteria with health promotion functions (symbiotes). The aim of this study is to analyse the relationship between intestinal microbiota composition and arterial stiffness.<br><br>METHODS AND ANALYSIS: An observational case-control study will be developed. Cases will be defined by the presence of at least one of the following: carotid-femoral pulse wave velocity (cf-PWV), Cardio-Ankle Vascular Index (CAVI), brachial ankle pulse wave velocity (ba or ba-PWV) above the 90th percentile, for age and sex, of the reference population. Controls will be selected from the same population as cases. The study will be developed in Primary Healthcare Centres. We will select 500 subjects (250 cases and 250 controls), between 45 and 74 years of age. Cases will be selected from a database that combines data from EVA study (Spain) and Guimarães/Vizela study (Portugal).<br><br>MEASUREMENTS: cf-PWV will be measured using the SphygmoCor system, CAVI, ba-PWV and Ankle-Brachial Index will be determined using VaSera device. Gut microbiome composition in faecal samples will be determined by 16S ribosomal RNA sequencing. Lifestyle will be assessed by food frequency questionnaire, adherence to the Mediterranean diet and IPAQ (International Physical Activity Questionnaire). Body composition will be evaluated by bioimpedance.<br><br>ETHICS AND DISSEMINATION: The study has been approved by 'Committee of ethics of research with medicines of the health area of Salamanca' on 14 December 2018 (cod. 2018-11-136) and the 'Ethics committee for health of Guimaraes' (Portugal) on 15 October 2019 (ref: 67/2019). All study participants will sign an informed consent form agreeing to participate in the study, in compliance with the Declaration of Helsinki and the WHO standards for observational studies. The results of this study will allow a better description of gut microbiota in patients with arterial stiffness.<br><br>TRIAL REGISTRATION DETAILS: ClinicalTrials.gov, identifier NCT03900338.}, }
@article {pmid33573975, year = {2021}, author = {Dalle Zotte, A and Singh, Y and Squartini, A and Stevanato, P and Cappellozza, S and Kovitvadhi, A and Subaneg, S and Bertelli, D and Cullere, M}, title = {Effect of a dietary inclusion of full-fat or defatted silkworm pupa meal on the nutrient digestibility and faecal microbiome of fattening quails.}, journal = {Animal : an international journal of animal bioscience}, volume = {}, number = {}, pages = {100112}, doi = {10.1016/j.animal.2020.100112}, pmid = {33573975}, issn = {1751-732X}, abstract = {Silkworm (Bombyx mori L.) pupae are a by-product derived from silk production, which is often treated as waste and thus discarded: this can cause serious environmental problems and a loss of nutrients. Silkworm pupae are a rich source of protein and lipids, and the resulting protein meal can provide promising outcomes as livestock feed, notably for monogastric species. However, one possible issue that needs to be considered is the possible implication of the 1-Deoxynojirimycin (1-DNJ), a bio-compound of the silkworm that impairs glucose absorption, in poultry nutrition. Therefore, the present study evaluated the effect of the dietary inclusion of full-fat or defatted silkworm pupa meal (SWM) on the apparent digestibility of nutrients, feed choice and faecal microbiome in meat-producing quails. For the digestibility trial, a total of thirty-three 27-day-old Japanese quails (Coturnix coturnix japonica) were individually housed in digestibility cages and received three experimental diets: a control diet (control, commercial feed for fattening quails), and two other diets containing the 12.5% of either a full-fat SWM (SWM-FULL) or a defatted SWM (SWM-DEF). Subsequently, twenty-seven 33-day-old quails were simultaneously provided with Control, SWM-FULL and SWM-DEF diets for a 10-day feed choice trial. The results of the digestibility trial showed that the DM intake and excreta production were higher in both SWM groups than in the Control one (P < 0.001). The apparent digestibility of DM, organic matter, CP, ether extract, starch and energy was lower in both SWM groups than in the control group (P < 0.001), suggesting the possible implication of chitin and 1-DNJ. The feed choice test showed that quails preferred the Control diet (P < 0.001). From the microbiome analysis of the excreta, families such as Streptococcaceae (P < 0.05), Rikenellaceae and Eubacteriaceae (P < 0.01) and taxa at species level such as Lactobacillus delbrueckii (P < 0.05), Aneurinibacillus thermoaerophilus and Bacillus thermoamylovorans (P < 0.01) scored higher in SWM-FULL quails than in SWM-DEF and Control treatments. The present study demonstrated that a successful dietary inclusion of SWM for fattening quails needs to overcome the digestive criticalities caused by the of presence specific bio-compounds, namely chitin and 1-DNJ.}, }
@article {pmid33573959, year = {2020}, author = {Gaukroger, CH and Edwards, SA and Walshaw, J and Nelson, A and Adams, IP and Stewart, CJ and Kyriazakis, I}, title = {Shifting sows: longitudinal changes in the periparturient faecal microbiota of primiparous and multiparous sows.}, journal = {Animal : an international journal of animal bioscience}, volume = {}, number = {}, pages = {100135}, doi = {10.1016/j.animal.2020.100135}, pmid = {33573959}, issn = {1751-732X}, abstract = {Knowledge of periparturient longitudinal changes in sow microbiota composition is necessary to fully understand her role in the development of the piglet microbiota, but also to improve gut health and performance of the sow in lactation. Primiparous sows face the challenge of partitioning nutrients to support maternal growth in addition to supporting foetal growth and the demands of lactation. Additional metabolic stress present during the periparturient period may induce changes in the microbiota profile between primiparous and multiparous sows. Using 16S rRNA gene sequencing, the study aimed to characterise the longitudinal changes in the periparturient microbiota and identify differences within the sow microbiota profile associated with parity. Faecal samples from primiparous (n = 13) and multiparous (n = 16) sows were collected at four different time points (day -6, -1, 3 and 8) in relation to farrowing (day 0). Microbiota richness was lowest on day 3 and -1 of the periparturient period (P < 0.05). Microbiota community composition, assessed by weighted and unweighted UniFrac distances, demonstrated longitudinal changes, with day 3 samples clustering away from all other sampling time points (P < 0.05). The relative abundance of several genera segregated gestation from lactation samples including Roseburia, Prevotella 1, Prevotella 2, Christensenellaceae R-7 group, Ruminococcaceae UCG-002 and Ruminococcaceae UCG-010 (P < 0.01). Furthermore, day 3 was characterised by a significant increase in the relative abundance of Escherichia/Shigella, Fusobacterium and Bacteroides, and a decrease in Alloprevotella, Prevotellaceae UCG-003 and Ruminococcus 1 (P < 0.001). Primiparous sows had overall lower periparturient microbiota diversity (P < 0.01) and there was a significant interaction between parity and sampling time point, with primiparous sows having lower microbiota richness on day -6 (P < 0.001). There was a significant interaction between sow parity and sampling time point on microbiota composition on day -6 and -1 (unweighted UniFrac distances; ≤ 0.01) and day 8 (weighted and unweighted UniFrac distances; P < 0.05). Whilst no significant interactions between sow parity and sampling day were observed for genera relative abundances, multiparous sows had a significantly higher relative abundance of Bacteroidetes dgA-11 gut group and Prevotellaceae UCG-004 (P < 0.01). This study demonstrates that the sow microbiota undergoes longitudinal changes, which are collectively related to periparturient changes in the sow environment, diet and physiological changes to support foetal growth, delivery and the onset of lactation, but also sow parity.}, }
@article {pmid33573876, year = {2021}, author = {Ryan, MJ and Schloter, M and Berg, G and Kostic, T and Kinkel, LL and Eversole, K and Macklin, JA and Schelkle, B and Kazou, M and Sarand, I and Singh, BK and Fischer, D and Maguin, E and Ferrocino, I and Lima, N and McClure, RS and Charles, TC and de Souza, RSC and Kiran, GS and Krug, HL and Taffner, J and Roume, H and Selvin, J and Smith, D and Rybakova, D and Sessitsch, A}, title = {Development of Microbiome Biobanks - Challenges and Opportunities: (Trends in Microbiology 29, 89-92; 2021).}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2021.01.009}, pmid = {33573876}, issn = {1878-4380}, }
@article {pmid33573867, year = {2020}, author = {Ciernikova, S and Kasperova, B and Drgona, L and Smolkova, B and Stevurkova, V and Mego, M}, title = {Targeting the gut microbiome: An emerging trend in hematopoietic stem cell transplantation.}, journal = {Blood reviews}, volume = {}, number = {}, pages = {100790}, doi = {10.1016/j.blre.2020.100790}, pmid = {33573867}, issn = {1532-1681}, abstract = {Mounting evidence has demonstrated the critical role of the gut microbiome in different cancer treatment modalities showing intensive crosstalk between microbiota and the host immune system. In cancer patients receiving hematopoietic stem cell transplantation (HSCT), conditioning regimens including chemotherapy, radiotherapy, and immunosuppressive therapy, as well as antimicrobial prophylaxis, result in intestinal barrier disruption and massive changes in microbiota composition. According to clinical studies, a drastic loss of microbial diversity during HSCT is associated with enhanced pro-inflammatory immune response and an increased risk of transplant-related complications such as graft-versus-host disease (GvHD) and mortality. In this review, we outline the current understanding of the role of microbiota diversity in the patient response to cancer therapies and highlight the impact of changes in the gut microbiome on clinical outcomes in post-HSCT patients. Moreover, the therapeutic implications of microbiota modulation by probiotics, prebiotics, and fecal microbiota transplantation (FMT) in hematologic cancer patients receiving HSCT are discussed.}, }
@article {pmid33573862, year = {2021}, author = {Lundy, SD and Sangwan, N and Parekh, NV and Selvam, MKP and Gupta, S and McCaffrey, P and Bessoff, K and Vala, A and Agarwal, A and Sabanegh, ES and Vij, SC and Eng, C}, title = {Functional and Taxonomic Dysbiosis of the Gut, Urine, and Semen Microbiomes in Male Infertility.}, journal = {European urology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.eururo.2021.01.014}, pmid = {33573862}, issn = {1873-7560}, abstract = {BACKGROUND: Little is known about the role of the genitourinary and gastrointestinal microbiota in the pathogenesis of male infertility.<br><br>OBJECTIVE: To compare the taxonomic and functional profiles of the gut, semen, and urine microbiomes of infertile and fertile men.<br><br>We prospectively enrolled 25 men with primary idiopathic infertility and 12 healthy men with proven paternity, and we collected rectal swabs, semen samples, midstream urine specimens, and experimental controls.<br><br>We performed comprehensive semen analysis, 16S rRNA sequencing for quantitative high-resolution taxonomy, and shotgun metagenomics with a median of 140 million reads per sample for functional metabolic pathway profiling.<br><br>RESULTS AND LIMITATIONS: We identified a diverse semen microbiome with modest similarity to the urinary microbiome. Infertile men harbored increased seminal α-diversity and distinct β-diversity, increased seminal Aerococcus, and decreased rectal Anaerococcus. Prevotella abundance was inversely associated with sperm concentration, and Pseudomonas was directly associated with total motile sperm count. Vasectomy appeared to alter the seminal microbiome, suggesting a testicular or epididymal contribution. Anaerobes were highly over-represented in the semen of infertile men with a varicocele, but oxidative stress and leukocytospermia were associated with only subtle differences. Metagenomics data identified significant alterations in the S-adenosyl-L-methionine cycle, which may play a multifaceted role in the pathogenesis of infertility via DNA methylation, oxidative stress, and/or polyamine synthesis.<br><br>CONCLUSIONS: This pilot study represents the first comprehensive investigation into the microbiome in male infertility. These findings provide the foundation for future investigations to explore causality and identify novel microbiome-based diagnostics and therapeutics for men with this complex and emotionally devastating disease.<br><br>PATIENT SUMMARY: We explored the resident populations of bacteria living in the gut, semen, and urine of infertile and fertile men. We found several important bacterial and metabolic pathway differences with the potential to aid in diagnosing and treating male infertility in the future.}, }
@article {pmid33573601, year = {2021}, author = {Alexander, C and Cross, TL and Lee, AH and Ly, LK and Vieson, MD and Ridlon, JM and Nelson, ER and Swanson, KS}, title = {Development of a novel model of cholecystectomy in subsequently ovariectomized mice and characterization of metabolic and gastrointestinal phenotypes: a pilot study.}, journal = {BMC gastroenterology}, volume = {21}, number = {1}, pages = {62}, pmid = {33573601}, issn = {1471-230X}, support = {Hatch Grant ILLU-538-937//U.S. Department of Agriculture/ ; }, abstract = {BACKGROUND: Cholecystectomy (XGB) is the most common abdominal surgery performed in the United States and is associated with an increased post-surgery incidence of metabolic and gastrointestinal (GI) diseases. Two main risk factors for XGB are sex (female) and age (40-50 yr), corresponding with onset of menopause. Post-menopausal estrogen loss alone facilitates metabolic dysfunction, but the effects of XGB on metabolic and GI health have yet to be investigated in this population. Study objectives were to (1) identify possible short-term effects of XGB and (2) develop a novel murine model of XGB in human menopause via subsequent ovariectomy (OVX) and assess longitudinal effects of OVX on metabolism, GI physiology, and GI microbiota in XGB mice.<br><br>METHODS: Female C57BL/6 mice were utilized in two parallel studies (S1&amp;S2). In S1, XGB mice were compared to a non-XGB baseline group after six wk. In S2, mice were XGB at wk0, either sham (SHM) or OVX at wk6, and sacrificed at wk12, wk18, and wk24. Body composition assessment and fresh fecal collections were conducted periodically. Serum and tissues were collected at sacrifice for metabolic and GI health endpoints.<br><br>RESULTS: Compared to baseline, XGB increased hepatic CYP7A1 and decreased HMGCR relative expression, but did not influence BW, fat mass, or hepatic triglycerides after six wk. In S2, XGB/OVX mice had greater BW and fat mass than XGB/SHM. Cecal microbiota alpha diversity metrics were lower in XGB/OVX mice at wk24 compared the XGB/SHM. No consistent longitudinal patterns in fasting serum lipids, fecal microbial diversity, and GI gene expression were observed between S2 groups.<br><br>CONCLUSIONS: In addition to developing a novel, clinically-representative model of XGB and subsequent OVX, our results suggest that OVX resulted in the expected phenotype to some extent, but that XGB may modify or mask some responses and requires further investigation.}, }
@article {pmid33573326, year = {2021}, author = {Lin, YT and Lin, TY and Hung, SC and Liu, PY and Wu, PH and Chuang, YS and Hung, WC and Chiu, YW and Kuo, MC and Wu, CY}, title = {Anti-Acid Drug Treatment Induces Changes in the Gut Microbiome Composition of Hemodialysis Patients.}, journal = {Microorganisms}, volume = {9}, number = {2}, pages = {}, doi = {10.3390/microorganisms9020286}, pmid = {33573326}, issn = {2076-2607}, support = {MOST 106-2314-B-037-054, MOST 107-2314-B-037-104, and MOST 107-2314-B-037-098-MY3//Ministry of Science and Technology, Taiwan/ ; KMUH105-5R15, KMUH106-6R17, KMUH106-6T03, KMUH107-7R16, KMUH107-7R78, KMUH108-8M11, and KMUH108-8R70//Kaohsiung Medical University Hospital, Taiwan/ ; KMU-Q108024 and KMU-Q108027//Kaohsiung Medical University, Taiwan/ ; NSYSUKMU 105-I005 and NSYSUKMU 106-I005//NSYSU-KMU JOINT RESEARCH PROJECT/ ; }, abstract = {Anti-acid drugs, proton pump inhibitor (PPI) and histamine-2 blocker (H2-blocker), are commonly prescribed to treat gastrointestinal disorders. These anti-acid drugs alter gut microbiota in the general population, but their effects are not known in hemodialysis patients. Hence, we investigated the microbiota composition in hemodialysis patients treated with PPIs or H2-blocker. Among 193 hemodialysis patients, we identified 32 H2-blocker users, 23 PPI users, and 138 no anti-acid drug subjects. Fecal samples were obtained to analyze the gut microbiome using 16S RNA amplicon sequencing. Differences in the microbial composition of the H2-blocker users, PPI users, and controls were assessed using linear discriminant analysis effect size and the random forest algorithm. The species richness or evenness (α-diversity) was similar among the three groups, whereas the inter-individual diversity (β-diversity) was different between H2-blocker users, PPI users, and controls. Hemodialysis patients treated with H2-blocker and PPIs had a higher microbial dysbiosis index than the controls, with a significant increase in the genera Provetella 2, Phascolarctobacterium, Christensenellaceae R-7 group, and Eubacterium oxidoreducens group in H2-blocker users, and Streptococcus and Veillonella in PPI users. In addition, compared to the H2-blocker users, there was a significant enrichment of the genera Streptococcus in PPI users, as confirmed by the random forest analysis and the confounder-adjusted regression model. In conclusion, PPIs significantly changed the gut microbiota composition in hemodialysis patients compared to H2-blocker users or controls. Importantly, the Streptococcus genus was significantly increased in PPI treatment. These findings caution against the overuse of PPIs.}, }
@article {pmid33573276, year = {2021}, author = {Nishioka, A and Tobaruela, EC and Fraga, LN and Tomás-Barberán, FA and Lajolo, FM and Hassimotto, NMA}, title = {Stratification of Volunteers According to Flavanone Metabolite Excretion and Phase II Metabolism Profile after Single Doses of 'Pera' Orange and 'Moro' Blood Orange Juices.}, journal = {Nutrients}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/nu13020473}, pmid = {33573276}, issn = {2072-6643}, support = {2013/07914-8//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2020/06467-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 134456/2016-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 141878/2019-3//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, abstract = {Large interindividual variations in the biological response to citrus flavanones have been observed, and this could be associated with high variations in their bioavailability. The aim of this study was to identify the main determinants underlying interindividual differences in citrus flavanone metabolism and excretion. In a randomized cross-over study, non-obese and obese volunteers, aged 19-40 years, ingested single doses of Pera and Moro orange juices, and urine was collected for 24 h. A large difference in the recovery of the urinary flavanone phase II metabolites was observed, with hesperetin-sulfate and hesperetin-sulfo-O-glucuronide being the major metabolites. Subjects were stratified according to their total excretion of flavanone metabolites as high, medium, and low excretors, but the expected correlation with the microbiome was not observed at the genus level. A second stratification was proposed according to phase II flavanone metabolism, whereby participants were divided into two excretion groups: Profiles A and B. Profile B individuals showed greater biotransformation of hesperetin-sulfate to hesperetin-sulfo-O-glucuronide, as well as transformation of flavanone-monoglucuronide to the respective diglucuronides, suggestive of an influence of polymorphisms on UDP-glucuronosyltransferase. In conclusion, this study proposes a new stratification of volunteers based on their metabolic profiles. Gut microbiota composition and polymorphisms of phase II enzymes may be related to the interindividual variability of metabolism.}, }
@article {pmid33573261, year = {2021}, author = {Gavriilidou, A and Mackenzie, TA and Sánchez, P and Tormo, JR and Ingham, C and Smidt, H and Sipkema, D}, title = {Bioactivity Screening and Gene-Trait Matching across Marine Sponge-Associated Bacteria.}, journal = {Marine drugs}, volume = {19}, number = {2}, pages = {}, doi = {10.3390/md19020075}, pmid = {33573261}, issn = {1660-3397}, support = {721421//MarPipe/ ; }, abstract = {Marine sponges harbor diverse microbial communities that represent a significant source of natural products. In the present study, extracts of 21 sponge-associated bacteria were screened for their antimicrobial and anticancer activity, and their genomes were mined for secondary metabolite biosynthetic gene clusters (BGCs). Phylogenetic analysis assigned the strains to four major phyla in the sponge microbiome, namely Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Bioassays identified one extract with anti-methicillin-resistant Staphylococcus aureus (MRSA) activity, and more than 70% of the total extracts had a moderate to high cytotoxicity. The most active extracts were derived from the Proteobacteria and Actinobacteria, prominent for producing bioactive substances. The strong bioactivity potential of the aforementioned strains was also evident in the abundance of BGCs, which encoded mainly beta-lactones, bacteriocins, non-ribosomal peptide synthetases (NRPS), terpenes, and siderophores. Gene-trait matching was performed for the most active strains, aiming at linking their biosynthetic potential with the experimental results. Genetic associations were established for the anti-MRSA and cytotoxic phenotypes based on the similarity of the detected BGCs with BGCs encoding natural products with known bioactivity. Overall, our study highlights the significance of combining in vitro and in silico approaches in the search of novel natural products of pharmaceutical interest.}, }
@article {pmid33572734, year = {2021}, author = {Rueda Ruzafa, L and Cedillo, JL and Hone, AJ}, title = {Nicotinic Acetylcholine Receptor Involvement in Inflammatory Bowel Disease and Interactions with Gut Microbiota.}, journal = {International journal of environmental research and public health}, volume = {18}, number = {3}, pages = {}, doi = {10.3390/ijerph18031189}, pmid = {33572734}, issn = {1660-4601}, abstract = {The gut-brain axis describes a complex interplay between the central nervous system and organs of the gastrointestinal tract. Sensory neurons of dorsal root and nodose ganglia, neurons of the autonomic nervous system, and immune cells collect and relay information about the status of the gut to the brain. A critical component in this bi-directional communication system is the vagus nerve which is essential for coordinating the immune system's response to the activities of commensal bacteria in the gut and to pathogenic strains and their toxins. Local control of gut function is provided by networks of neurons in the enteric nervous system also called the 'gut-brain'. One element common to all of these gut-brain systems is the expression of nicotinic acetylcholine receptors. These ligand-gated ion channels serve myriad roles in the gut-brain axis including mediating fast synaptic transmission between autonomic pre- and postganglionic neurons, modulation of neurotransmitter release from peripheral sensory and enteric neurons, and modulation of cytokine release from immune cells. Here we review the role of nicotinic receptors in the gut-brain axis with a focus on the interplay of these receptors with the gut microbiome and their involvement in dysregulation of gut function and inflammatory bowel diseases.}, }
@article {pmid33572693, year = {2021}, author = {Kang, GU and Jung, DR and Lee, YH and Jeon, SY and Han, HS and Chong, GO and Shin, JH}, title = {Potential Association between Vaginal Microbiota and Cervical Carcinogenesis in Korean Women: A Cohort Study.}, journal = {Microorganisms}, volume = {9}, number = {2}, pages = {}, doi = {10.3390/microorganisms9020294}, pmid = {33572693}, issn = {2076-2607}, support = {918010043SB010//Ministry of Agriculture, Food and Rural Affairs (MAFRA)/ ; }, abstract = {Convincing studies demonstrated that vaginal flora is one of the most impactful key components for the well-being of the genital tract in women. Nevertheless, the potential capability of vaginal-derived bacterial communities as biomarkers to monitor cervical carcinogenesis (CC) has yet to be studied actively compared to those of bacterial vaginosis (BV). We hypothesized that vaginal microbiota might be associated with the progression of CC. In this study, we enrolled 23 participants, including healthy controls (HC group; n = 7), patients with cervical intraepithelial neoplasia (CIN) 2 and 3 (CIN group, n = 8), and patients with invasive cervical cancer (CAN group; n = 8). Amplicon sequencing was performed using the Ion Torrent PGM to characterize the vaginal microbiota. Patients with CIN and CAN presented vaginal microbiota dysbiosis compared with HC. The alpha diversity analysis revealed that CC has a trend to be increased in terms of diversity indexes. Moreover, CC was associated with the abundance of specific microbes, of which Lactobacillus and Gardnerella were the most significantly different between HC and CIN, whereas Streptococcus was differentially abundant in CAN compared with CIN. We then evaluated their diagnostic abilities. Testing in terms of diagnostic ability using the three genera revealed considerably high performance with an area under the receiver-operating characteristic curve of 0.982, 0.953, and 0.922. The current study suggests that the presence of Gardnerella and Streptococcus may be involved in the advancment of CC.}, }
@article {pmid33572538, year = {2021}, author = {Castagnoli, R and Pala, F and Bosticardo, M and Licari, A and Delmonte, OM and Villa, A and Marseglia, GL and Notarangelo, LD}, title = {Gut Microbiota-Host Interactions in Inborn Errors of Immunity.}, journal = {International journal of molecular sciences}, volume = {22}, number = {3}, pages = {}, pmid = {33572538}, issn = {1422-0067}, support = {BENCH-TO-BEDSIDE (BTB) PROJECT; RAG deficiency: From pathophysiology to precise gene correction/NH/NIH HHS/United States ; Division of Intramural Research, NIAID//National Health Research Institutes/ ; }, abstract = {Inborn errors of immunity (IEI) are a group of disorders that are mostly caused by genetic mutations affecting immune host defense and immune regulation. Although IEI present with a wide spectrum of clinical features, in about one third of them various degrees of gastrointestinal (GI) involvement have been described and for some IEI the GI manifestations represent the main and peculiar clinical feature. The microbiome plays critical roles in the education and function of the host's innate and adaptive immune system, and imbalances in microbiota-immunity interactions can contribute to intestinal pathogenesis. Microbial dysbiosis combined to the impairment of immunosurveillance and immune dysfunction in IEI, may favor mucosal permeability and lead to inflammation. Here we review how immune homeostasis between commensals and the host is established in the gut, and how these mechanisms can be disrupted in the context of primary immunodeficiencies. Additionally, we highlight key aspects of the first studies on gut microbiome in patients affected by IEI and discuss how gut microbiome could be harnessed as a therapeutic approach in these diseases.}, }
@article {pmid33571903, year = {2021}, author = {Kampouris, ID and Agrawal, S and Orschler, L and Cacace, D and Kunze, S and Berendonk, TU and Klümper, U}, title = {Antibiotic resistance gene load and irrigation intensity determine the impact of wastewater irrigation on antimicrobial resistance in the soil microbiome.}, journal = {Water research}, volume = {193}, number = {}, pages = {116818}, doi = {10.1016/j.watres.2021.116818}, pmid = {33571903}, issn = {1879-2448}, abstract = {Treated wastewater (TWW) irrigation is a useful counter-measure against the depletion of freshwater (FW) resources. However, TWW contains several contaminants of emerging concern, such as antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs). Thus, TWW irrigation might promote the spread of antimicrobial resistance in soil environments. In the present work, we hypothesized that the ARG load and irrigation intensity define the effect of TWW irrigation on ARG spread dynamics in soil. This hypothesis was tested using a multiphase approach: a) comparing soil from a full-scale, commercially operated, TWW irrigated field with non-irrigated soil, b) long-term sampling of the TWW irrigated field over one year with different irrigation intensities and intercepted by irrigation breaks and c) laboratory-scale soil microcosms irrigated with TWW compared to FW. Six ARGs, the integrase gene intI1 and the 16S rRNA were quantified using qPCR. In addition, effects of TWW irrigation on bacterial community composition of microcosm-samples were analysed with 16S rRNA amplicon sequencing. The genes sul1, qnrS, blaOXA-58, tet(M) and intI1 were significantly more abundant in the TWW irrigated field soil, whereas blaCTX--M-32 and blaTEM, the least abundant genes in the TWW irrigation, showed higher abundance in the non-irrigated soil. The relative abundance of sul1, qnrS, blaOXA-58, tet(M) and intI1 correlated with TWW irrigation intensity and decreased during irrigation breaks. Despite the decrease, the levels of these genes remained consistently higher than the non-irrigated soil indicating persistence upon their introduction into the soil. Microcosm experiments verified observations from the field study: TWW irrigation promoted the spread of ARGs and intI1 into soil at far elevated levels compared to FW irrigation. However, the impact of TWW irrigation on 16S rRNA absolute abundance and the soil microbial community composition was negligible. In conclusion, the impact of TWW irrigation depends mainly on the introduced ARG load and the irrigation intensity.}, }
@article {pmid33571753, year = {2021}, author = {Gray, J and Kahl, O and Zintl, A}, title = {What do we still need to know about Ixodes ricinus?.}, journal = {Ticks and tick-borne diseases}, volume = {12}, number = {3}, pages = {101682}, doi = {10.1016/j.ttbdis.2021.101682}, pmid = {33571753}, issn = {1877-9603}, abstract = {In spite of many decades of intensive research on Ixodes ricinus, the castor bean tick of Europe, several important aspects of its basic biology remain elusive, such as the factors determining seasonal development, tick abundance and host specificity, and the importance of water management. Additionally, there are more recent questions about the geographical diversity of tick genotypes and phenotypes, the role of migratory birds in the ecoepidemiology of I. ricinus, the importance of protective immune responses against I. ricinus, particularly in the context of vaccination, and the role of the microbiome in pathogen transmission. Without more detailed knowledge of these issues, it is difficult to assess the likely effects of changes in climate and biodiversity on tick distribution and activity, to predict potential risks arising from new and established tick populations and I. ricinus-borne pathogens, and to improve prevention and control measures. This review aims to discuss the most important outstanding questions against the backdrop of the current state of knowledge of this important tick species.}, }
@article {pmid33571685, year = {2021}, author = {Ngambia Freitas, FS and Njiokou, F and Tsagmo Ngoune, JM and Sempere, G and Berthier, D and Geiger, A}, title = {Modulation of trypanosome establishment in Glossina palpalis palpalis by its microbiome in the Campo sleeping sickness focus, Cameroon.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {90}, number = {}, pages = {104763}, doi = {10.1016/j.meegid.2021.104763}, pmid = {33571685}, issn = {1567-7257}, abstract = {The purpose of this study was to investigate factors involved in vector competence by analyzing whether the diversity and relative abundance of the different bacterial genera inhabiting the fly's gut could be associated with its trypanosome infection status. This was investigated on 160 randomly selected G. p. palpalis flies - 80 trypanosome-infected, 80 uninfected - collected in 5 villages of the Campo trypanosomiasis focus in South Cameroon. Trypanosome species were identified using specific primers, and the V4 region of the 16S rRNA gene of bacteria was targeted for metabarcoding analysis in order to identify the bacteria and determine microbiome composition. A total of 261 bacterial genera were identified of which only 114 crossed two barriers: a threshold of 0.01% relative abundance and the presence at least in 5 flies. The secondary symbiont Sodalis glossinidius was identified in 50% of the flies but it was not considered since its relative abundance was much lower than the 0.01% relative abundance threshold. The primary symbiont Wigglesworthia displayed 87% relative abundance, the remaining 13% were prominently constituted by the genera Spiroplasma, Tediphilus, Acinetobacter and Pseudomonas. Despite a large diversity in bacterial genera and in their abundance observed in micobiome composition, the statistical analyzes of the 160 tsetse flies showed an association with flies' infection status and the sampling sites. Furthermore, tsetse flies harboring Trypanosoma congolense Savanah type displayed a different composition of bacterial flora compared to uninfected flies. In addition, our study revealed that 36 bacterial genera were present only in uninfected flies, which could therefore suggest a possible involvement in flies' refractoriness; with the exception of Cupriavidus, they were however of low relative abundance. Some genera, including Acinetobacter, Cutibacterium, Pseudomonas and Tepidiphilus, although present both in infected and uninfected flies, were found to be associated with uninfected status of tsetse flies. Hence their effective role deserves to be further evaluated in order to determine whether some of them could become targets for tsetse control of fly vector competence and consequently for the control of the disease. Finally, when comparing the bacterial genera identified in tsetse flies collected during 4 epidemiological surveys, 39 genera were found to be common to flies from at least 2 sampling campaigns.}, }
@article {pmid33571595, year = {2021}, author = {Zhang, X and Yao, Z and Sun, X and Zhang, G}, title = {Cross-linked arabinoxylan in a Ca2+-alginate matrix reversed the body weight gain of HFD-fed C57BL/6J mice through modulation of the gut microbiome.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ijbiomac.2021.02.048}, pmid = {33571595}, issn = {1879-0003}, abstract = {Here, we compared the effects of different physical forms of arabinoxylan (AX) - a microsphere of cross-linked arabinoxylan (CAX) in a Ca2+-alginate matrix (MC) and physical mixture of AX and alginate (PM) on gut microbiota and development of obesity in C57BL/6J mice. Supplementation of MC in high fat (HF) diet to mice for 10 weeks significantly reversed the body weight gain induced by the HF diet, along with less fat accumulation in both livers and the epididymal adipose than the PM group. Microbiome analysis showed that MC significantly altered the gut microbiota composition with a noticeable increase of butyrogenic bacteria of Lachnospiraceae. The butyrate produced by MC fermentation and the increased abundance of Lachnospiraceae might be the underlying mechanism of the anti-obesity effect of MC. The results indicated that the physical forms of dietary fiber are closely associated with its health benefits, and MC might be served as a new functional food ingredient to prevent obesity.}, }
@article {pmid33571442, year = {2021}, author = {Rebeck, ON and Dantas, G and Schwartz, DJ}, title = {Improving ICI outcomes with a little help from my microbial friends.}, journal = {Cell host &amp; microbe}, volume = {29}, number = {2}, pages = {155-157}, doi = {10.1016/j.chom.2021.01.012}, pmid = {33571442}, issn = {1934-6069}, abstract = {Gut microbiome composition correlates with responsiveness to immune checkpoint inhibitor therapy. In a recent study in Science, Baruch et al. manipulated gut microbiome composition in patients with refractory metastatic melanoma using fecal microbiota transplants. Fecal microbiota transplant was safe and partially effective in inducing remission in refractory patients.}, }
@article {pmid33571360, year = {2021}, author = {Sindi, AS and Geddes, DT and Wlodek, ME and Muhlhausler, BS and Payne, MS and Stinson, LF}, title = {Can we modulate the breastfed infant gut microbiota through maternal diet?.}, journal = {FEMS microbiology reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsre/fuab011}, pmid = {33571360}, issn = {1574-6976}, abstract = {Initial colonisation of the infant gut is robustly influenced by regular ingestion of human milk, a substance that contains microbes, microbial metabolites, immune proteins, and oligosaccharides. Numerous factors have been identified as potential determinants of the human milk and infant gut microbiota, including maternal diet; however, there is limited data on the influence of maternal diet during lactation on either of these. Here, we review the processes thought to contribute to human milk and infant gut bacterial colonisation and provide a basis for considering the role of maternal dietary patterns during lactation in shaping infant gut microbial composition and function. Although only one observational study has directly investigated the influence of maternal diet during lactation on the infant gut microbiome, data from animal studies suggests that modulation of the maternal gut microbiota, via diet or probiotics, may influence the mammary or milk microbiota. Additionally, evidence from human studies suggests that the maternal diet during pregnancy may affect the gut microbiota of the breastfed infant. Together, there is a plausible hypothesis that maternal diet during lactation may influence the infant gut microbiota. If substantiated in further studies, this may present a potential window of opportunity for modulating the infant gut microbiome in early life.}, }
@article {pmid33571355, year = {2021}, author = {Dos Santos, LF and Souta, JF and Soares, CP and da Rocha, LO and Santos, MLC and Grativol, C and Roesch, LFW and Olivares, FL}, title = {Insights into the structure and role of seed-borne bacteriome during maize germination.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiab024}, pmid = {33571355}, issn = {1574-6941}, abstract = {Seed germination events modulate microbial community composition, which ultimately influences seed to seedling growth performance. Here we evaluate the germinated maize (variety SHS 5050) root bacterial community of disinfected seed (DS) and non-disinfected seed (NDS). Using a gnotobiotic system, sodium hypochlorite (1.25%, 30 min) treated seeds showed a reduction of bacterial population size and an apparent increase of bacterial community diversity associated with a significant selective reduction of Burkholderia related sequences. The shift in the bacterial community composition in DS negatively affects germination speed, seedling growth, and reserve mobilization rates compared with NDS. A synthetic bacterial community (syncom) formed by twelve isolates (9 Burkholderia spp.; 2 Bacillus spp. and 1 Staphylococcus sp.) obtained from natural microbiota maize seeds herein were capable of recovering germination and seedling growth when reintroduced in DS. Overall results showed that changes in bacterial community composition and selective reduction of Burkholderia related members dominance interfere with germination events and initial growth of the maize plantlets. By cultivation-dependent and independent approaches, we deciphered seed-maize microbiome structure, bacterial niches location, and bacterial taxa with relevant roles in seedlings growth performance. A causal relationship between seed microbial community succession and germination performance open opportunities in seed technologies to build-up microbial communities to boost plant growth and health.}, }
@article {pmid33570819, year = {2021}, author = {Ngowi, EE and Wang, YZ and Khattak, S and Khan, NH and Sayed Mohamed Mahmoud, S and Helmy, YASH and Jiang, QY and Li, T and Duan, SF and Ji, XY and Wu, DD}, title = {Impact of the factors shaping gut microbiota on obesity.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jam.15036}, pmid = {33570819}, issn = {1365-2672}, abstract = {Obesity is considered as a risk factor for chronic health diseases such as heart diseases, cancer, and diabetes 2. Reduced physical activities, lifestyle, poor nutritional diet, and genetics are among the risk factors associated with the development of obesity. In recent years, several studies have explored the link between the gut microbiome and the progression of diseases including obesity, with the shift in microbiome abundance and composition being the main focus. The alteration of gut microbiome composition affects both nutrients metabolism and specific gene expressions thereby disturbing body physiology. Specifically, the abundance of fiber-metabolizing microbes is associated with weight loss and that of protein and fat-metabolizing bacteria with weight gain. Various internal and external factors such as genetics, maternal obesity, mode of delivery, breastfeeding, nutrition, antibiotic use, and the chemical compounds present in the environment are known to interfere with the richness of the gut microbiota (GM), thereby influencing weight gain/loss and ultimately the development of obesity. However, the effectiveness of each factor in potentiating the shift in microbes' abundance to result in significant changes that can lead to obesity is not yet clear. In this review, we will highlight the factors involved in shaping gut microbiota, their influence on obesity and possible interventions. Understanding the influence of these factors on the diversity of the GM and how to improve their effectiveness on disease conditions could be key in the treatment of metabolic diseases.}, }
@article {pmid33570760, year = {2021}, author = {Chen, X and Zhang, Z and Han, X and Hao, X and Lu, X and Yan, J and Biswas, A and Dunfield, K and Zou, W}, title = {Impacts of land-use changes on the variability of microbiomes in soil profiles.}, journal = {Journal of the science of food and agriculture}, volume = {}, number = {}, pages = {}, doi = {10.1002/jsfa.11150}, pmid = {33570760}, issn = {1097-0010}, abstract = {BACKGROUND: The conversion of arable land to grassland and/or forested land is a common strategy of restoration, because the development of plant communities can inhibit the erosion of soil, increase biodiversity and improve associated ecosystem services. The vertical profiles of microbial communities, however, have not been well characterized, and their variability after land conversion is not well understood. We assessed the effects of the conversion of arable land (AL) to grassland (GL) and forested land (FL) on bacterial communities as old as 29 years in 0-200 cm profiles of a Chinese Mollisol.<br><br>RESULTS: The soil in AL has been a stable ecosystem, and changes in assembly of soil microbiomes tended to be larger in the topsoil. The soil properties and microbial biodiversity of arable land were larger following revegetation and reforestation. The conversion caused a more complex coupling among microbes, and negative interactions and average connectivity were stronger in the 0-20 cm layers in GL and in the 20-60 cm layers in FL. The land use dramatically influenced the assembly of the microbial communities more in GL than AL and FL. The bacterial diversity was an important component of soil multinutrient cycling in the profiles and that microbial functions were not as affected by changes in land use.<br><br>CONCLUSION: The spatial variation of the microbiomes provided critical information on belowground soil ecology and the ability of the soil to provide crucial ecosystem services. This article is protected by copyright. All rights reserved.}, }
@article {pmid33570667, year = {2021}, author = {Franco-Frías, E and Mercado-Guajardo, V and Merino-Mascorro, A and Pérez-Garza, J and Heredia, N and León, JS and Jaykus, LA and Dávila-Aviña, J and García, S}, title = {Analysis of Bacterial Communities by 16S rRNA Gene Sequencing in a Melon-Producing Agro-environment.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33570667}, issn = {1432-184X}, support = {A1-S-250//Consejo Nacional de Ciencia y Tecnología/ ; 2018-07410, 2019-67017-29642//National Institute of Food and Agriculture/ ; HHSF223201710406P//U.S. Food and Drug Administration/ ; }, abstract = {Cantaloupe melons, which have been responsible of an increasing number of foodborne disease outbreaks, may become contaminated with microbial pathogens during production. However, little information is available on the microbial populations in the cantaloupe farm environment. The purpose of this work was to characterize the bacterial communities present on cantaloupe farms. Fruit, soil, and harvester hand rinsates were collected from two Mexican cantaloupe farms, each visited three times. Microbiome analysis was performed by sequencing 16sRNA and analyzed using qiime2 software. Correlations were determined between sample type and microbial populations. The α and β diversity analysis identified 2777 sequences across all samples. The soil samples had the highest number and diversity of unique species (from 130 to 1329 OTUs); cantaloupe (from 112 to 205 OTUs), and hands (from 67 to 151 OTUs) had similar diversity. Collectively, Proteobacteria was the most abundant phyla (from 42 to 95%), followed by Firmicutes (1-47%), Actinobacteria (< 1 to 23%), and Bacteroidetes (< 1 to 4.8%). The most abundant genera were Acinetobacter (20-58%), Pseudomonas (14.5%), Erwinia (13%), and Exiguobacterium (6.3%). Genera with potential to be pathogenic included Bacillus (4%), Salmonella (0.85%), Escherichia-Shigella (0.38%), Staphylococcus (0.32%), Listeria (0.29%), Clostridium (0.28%), and Cronobacter (0.27%), which were found at lower frequencies. This study provides information on the cantaloupe production microbiome, which can inform future research into critical food safety issues such as antimicrobial resistance, virulence, and genomic epidemiology.}, }
@article {pmid33570553, year = {2021}, author = {Jiang, H and Fang, S and Yang, H and Chen, C}, title = {Identification of the relationship between the gut microbiome and feed efficiency in a commercial pig cohort.}, journal = {Journal of animal science}, volume = {}, number = {}, pages = {}, doi = {10.1093/jas/skab045}, pmid = {33570553}, issn = {1525-3163}, abstract = {Feed efficiency is an economically important trait in pig production. Gut microbiota plays an important role in energy harvest, nutrient metabolism and fermentation of dietary indigestible components. Whether and which gut microbes affect feed efficiency in pigs are largely unknown. Here, a total of 208 healthy Duroc pigs were used as experimental materials. Feces and serum samples were collected at the age of 140d. We first performed 16S rRNA gene and metagenomic sequencing analysis to investigate the relationship between the gut microbiome and porcine residual feed intake (RFI). 16S rRNA gene sequencing analysis detected 21 OTUs showing the tendency to correlation with the RFI (P < 0.01). Metagenomic sequencing further identified that the members of Clostridiales, e.g. Ruminococcus flavefaoiens, Lachnospiraceae bacterium 28-4 and Lachnospiraceae phytofermentans, were enriched in pigs with low RFI (high feed efficiency), while 11 bacterial species including five Prevotella spp., especially, the Prevotella copri, had higher abundance in pigs with high RFI. Functional capacity analysis suggested that the gut microbiome of low RFI pigs had high abundance of the pathways related to amino acid metabolism and biosynthesis, but low abundance of the pathways associated with monosaccharide metabolism and lipopolysaccharide biosynthesis. Serum metabolome and fecal short chain fatty acids (SCFAs) were determined by UPLC-QTOF/MS and gas chromatograph, respectively. Propionic acid in feces and the serum metabolites related to amino acid metabolism were negatively correlated with the RFI. The results from this study may provide potential gut microbial biomarkers that could be used for improving feed efficiency in pig production industry.}, }
@article {pmid33570236, year = {2021}, author = {Mahdavinia, M and Greenfield, LR and Moore, D and Botha, M and Engen, P and Gray, C and Lunjani, N and Hlela, C and Basera, W and Hobane, L and Watkins, A and Mankahla, A and Gaunt, B and Facey-Thomas, H and Landay, A and Keshavarzian, A and Levin, ME}, title = {House dust microbiota and atopic dermatitis; effect of urbanization.}, journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology}, volume = {}, number = {}, pages = {}, doi = {10.1111/pai.13471}, pmid = {33570236}, issn = {1399-3038}, abstract = {BACKGROUND: Previous studies have shown that a child's risk of developing atopic disease is impacted by both genetic and environmental factors. Because small children spend the majority of their time in their homes, exposure to microbial factors in their home environment may be protective or risk factors for development of atopic diseases, such as atopic dermatitis.<br><br>METHODS: Dust samples from the homes of 86 Black South African children 12 to 36 months old were collected for analysis of the bacterial microbiome. This case-control study design included children with and without atopic dermatitis from rural and urban environments.<br><br>RESULTS: Significant differences in bacterial composition and diversity were found when comparing children with and without atopic dermatitis. Furthermore, house dust microbiota was significantly different in rural and urban areas. Differences were best accounted for by higher relative abundance of Ruminococcaceae, Lachnospiraceae and Bacteroidaceae families in rural compared to urban houses. Levels of Ruminococcaceae were also found to be significantly depleted in the house dust of rural children with atopic dermatitis as compared to control children.<br><br>CONCLUSIONS: House dust composition may be an important risk factor for the development of atopic disease, and this association may be driven in part by the gut microbiome. Low levels of the Ruminococcaceae family from Clostridia class in particular may explain the association between urban living and atopy. However, further research is needed to elucidate these links.}, }
@article {pmid33570164, year = {2021}, author = {Koeken, VACM and van Crevel, R and Netea, MG and Li, Y}, title = {Resolving trained immunity with systems biology.}, journal = {European journal of immunology}, volume = {}, number = {}, pages = {}, doi = {10.1002/eji.202048882}, pmid = {33570164}, issn = {1521-4141}, abstract = {Trained immunity is characterized by long-term functional reprogramming of innate immune cells following challenge with pathogens or microbial ligands during infection or vaccination. This cellular reprogramming leads to increased responsiveness upon re-stimulation, and is mediated through epigenetic and metabolic modifications. In this review, we describe how molecular mechanisms underlying trained immunity, for example induced by β-glucan or Bacille Calmette-Guérin (BCG) vaccination, can be investigated by using and integrating different layers of information, including genome, epigenome, transcriptome, proteome, metabolome, microbiome, immune cell phenotyping and function. We also describe the most commonly used experimental and computational techniques. Finally, we provide a number of examples of how a systems biology approach was applied to study trained immunity to understand inter-individual variation or the complex interplay between molecular layers. In conclusion, trained immunity represents an opportunity for regulating innate immune function, and understanding the complex interplay of mechanisms that mediate trained immunity might enable us to employ it as a clinical tool in the future. This article is protected by copyright. All rights reserved.}, }
@article {pmid33569635, year = {2021}, author = {Yang, KL and Lejeune, A and Chang, G and Scher, JU and Koralov, SB}, title = {Microbial-derived antigens and metabolites in spondyloarthritis.}, journal = {Seminars in immunopathology}, volume = {}, number = {}, pages = {}, pmid = {33569635}, issn = {1863-2300}, support = {R01HL125816/NH/NIH HHS/United States ; R01AR070131/NH/NIH HHS/United States ; R01AR073851/NH/NIH HHS/United States ; 21-A0-00-1003713/NPF/National Psoriasis Foundation/United States ; 21-A0-00-1003713/NPF/National Psoriasis Foundation/United States ; LF-OC-20-000351//LEO Foundation/ ; R01AR074500/AR/NIAMS NIH HHS/United States ; }, abstract = {Spondyloarthritis (SpA) is a group of chronic, immune-mediated, inflammatory diseases affecting the bone, synovium, and enthesis. Microbiome, the community of microorganisms that has co-evolved with human hosts, plays a pivotal role in human health and disease. This invisible &quot;essential organ&quot; supplies the host with a myriad of chemicals and molecules. In turn, microbial metabolites can serve as messengers for microbes to communicate with each other and in the cross-talk with host cells. Gut dysbiosis in SpA is associated with altered microbial metabolites, and an accumulated body of research has contributed to the understanding that changes in intestinal microbiota can modulate disease pathogenesis. We review the novel findings from human and animal studies to provide an overview of the contribution of individual microbial metabolites and antigens to SpA.}, }
@article {pmid33569055, year = {2020}, author = {Mölzer, C and Heissigerova, J and Wilson, HM and Kuffova, L and Forrester, JV}, title = {Immune Privilege: The Microbiome and Uveitis.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {608377}, pmid = {33569055}, issn = {1664-3224}, abstract = {Immune privilege (IP), a term introduced to explain the unpredicted acceptance of allogeneic grafts by the eye and the brain, is considered a unique property of these tissues. However, immune responses are modified by the tissue in which they occur, most of which possess IP to some degree. The eye therefore displays a spectrum of IP because it comprises several tissues. IP as originally conceived can only apply to the retina as it contains few tissue-resident bone-marrow derived myeloid cells and is immunologically shielded by a sophisticated barrier - an inner vascular and an outer epithelial barrier at the retinal pigment epithelium. The vascular barrier comprises the vascular endothelium and the glia limitans. Immune cells do not cross the blood-retinal barrier (BRB) despite two-way transport of interstitial fluid, governed by tissue oncotic pressure. The BRB, and the blood-brain barrier (BBB) mature in the neonatal period under signals from the expanding microbiome and by 18 months are fully established. However, the adult eye is susceptible to intraocular inflammation (uveitis; frequency ~200/100,000 population). Uveitis involving the retinal parenchyma (posterior uveitis, PU) breaches IP, while IP is essentially irrelevant in inflammation involving the ocular chambers, uveal tract and ocular coats (anterior/intermediate uveitis/sclerouveitis, AU). Infections cause ~50% cases of AU and PU but infection may also underlie the pathogenesis of immune-mediated &quot;non-infectious&quot; uveitis. Dysbiosis accompanies the commonest form, HLA-B27-associated AU, while latent infections underlie BRB breakdown in PU. This review considers the pathogenesis of uveitis in the context of IP, infection, environment, and the microbiome.}, }
@article {pmid33569053, year = {2020}, author = {Vignesh, R and Swathirajan, CR and Tun, ZH and Rameshkumar, MR and Solomon, SS and Balakrishnan, P}, title = {Could Perturbation of Gut Microbiota Possibly Exacerbate the Severity of COVID-19 via Cytokine Storm?.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {607734}, pmid = {33569053}, issn = {1664-3224}, }
@article {pmid33568789, year = {2021}, author = {Zhou, W and Qi, D and Swaisgood, RR and Wang, L and Jin, Y and Wu, Q and Wei, F and Nie, Y}, title = {Symbiotic bacteria mediate volatile chemical signal synthesis in a large solitary mammal species.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {33568789}, issn = {1751-7370}, support = {QYZDB-SSW-SMC047//Chinese Academy of Sciences Key Project (CAS Key Project)/ ; 2016YFC0503200//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; 31622012//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32000314//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Mammalian chemosignals-or scent marks-are characterized by astounding chemical diversity, reflecting both complex biochemical pathways that produce them and rich information exchange with conspecifics. The microbiome of scent glands was thought to play prominent role in the chemical signal synthesis, with diverse microbiota metabolizing glandular products to produce odorants that may be used as chemosignals. Here, we use gas chromatography-mass spectrometry and metagenomic shotgun sequencing to explore this phenomenon in the anogenital gland secretions (AGS) of the giant panda (Ailuropoda melanoleuca). We find that this gland contains a diverse community of fermentative bacteria with enzymes that support metabolic pathways (e.g., lipid degradation) for the productions of volatile odorants specialized for chemical communication. We found quantitative and qualitative differences in the microbiota between AGS and digestive tract, a finding which was mirrored by differences among chemical compounds that could be used for olfactory communication. Volatile chemical compounds were more diverse and abundant in AGS than fecal samples, and our evidence suggests that metabolic pathways have been specialized for the synthesis of chemosignals for communication. The panda's microbiome is rich with genes coding for enzymes that participate in the fermentation pathways producing chemical compounds commonly deployed in mammalian chemosignals. These findings illuminate the poorly understood phenomena involved in the role of symbiotic bacteria in the production of chemosignals.}, }
@article {pmid33568752, year = {2021}, author = {Rungratanawanich, W and Qu, Y and Wang, X and Essa, MM and Song, BJ}, title = {Advanced glycation end products (AGEs) and other adducts in aging-related diseases and alcohol-mediated tissue injury.}, journal = {Experimental &amp; molecular medicine}, volume = {}, number = {}, pages = {}, pmid = {33568752}, issn = {2092-6413}, support = {Wang//Department of Neurobiology, Harvard Medical School/ ; }, abstract = {Advanced glycation end products (AGEs) are potentially harmful and heterogeneous molecules derived from nonenzymatic glycation. The pathological implications of AGEs are ascribed to their ability to promote oxidative stress, inflammation, and apoptosis. Recent studies in basic and translational research have revealed the contributing roles of AGEs in the development and progression of various aging-related pathological conditions, such as diabetes, cardiovascular complications, gut microbiome-associated illnesses, liver or neurodegenerative diseases, and cancer. Excessive chronic and/or acute binge consumption of alcohol (ethanol), a widely consumed addictive substance, is known to cause more than 200 diseases, including alcohol use disorder (addiction), alcoholic liver disease, and brain damage. However, despite the considerable amount of research in this area, the underlying molecular mechanisms by which alcohol abuse causes cellular toxicity and organ damage remain to be further characterized. In this review, we first briefly describe the properties of AGEs: their formation, accumulation, and receptor interactions. We then focus on the causative functions of AGEs that impact various aging-related diseases. We also highlight the biological connection of AGE-alcohol-adduct formations to alcohol-mediated tissue injury. Finally, we describe the potential translational research opportunities for treatment of various AGE- and/or alcohol-related adduct-associated disorders according to the mechanistic insights presented.}, }
@article {pmid33568354, year = {2021}, author = {}, title = {Stool Swap Overcomes PD-1 Resistance.}, journal = {Cancer discovery}, volume = {}, number = {}, pages = {}, doi = {10.1158/2159-8290.CD-NB2021-0311}, pmid = {33568354}, issn = {2159-8290}, abstract = {Fecal transplants can make immunotherapy-refractory melanomas sensitive to checkpoint blockade, a finding that highlights the potential of manipulating gut bacteria to boost response rates to anti-PD-1 agents. Yet, how best to modulate the microbiome remains a matter of active debate.}, }
@article {pmid33568231, year = {2021}, author = {Moossavi, S and Fehr, K and Khafipour, E and Azad, MB}, title = {Repeatability and reproducibility assessment in a large-scale population-based microbiota study: case study on human milk microbiota.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {41}, pmid = {33568231}, issn = {2049-2618}, support = {//CIHR/Canada ; }, abstract = {BACKGROUND: Quality control including assessment of batch variabilities and confirmation of repeatability and reproducibility are integral component of high throughput omics studies including microbiome research. Batch effects can mask true biological results and/or result in irreproducible conclusions and interpretations. Low biomass samples in microbiome research are prone to reagent contamination; yet, quality control procedures for low biomass samples in large-scale microbiome studies are not well established.<br><br>RESULTS: In this study, we have proposed a framework for an in-depth step-by-step approach to address this gap. The framework consists of three independent stages: (1) verification of sequencing accuracy by assessing technical repeatability and reproducibility of the results using mock communities and biological controls; (2) contaminant removal and batch variability correction by applying a two-tier strategy using statistical algorithms (e.g. decontam) followed by comparison of the data structure between batches; and (3) corroborating the repeatability and reproducibility of microbiome composition and downstream statistical analysis. Using this approach on the milk microbiota data from the CHILD Cohort generated in two batches (extracted and sequenced in 2016 and 2019), we were able to identify potential reagent contaminants that were missed with standard algorithms and substantially reduce contaminant-induced batch variability. Additionally, we confirmed the repeatability and reproducibility of our results in each batch before merging them for downstream analysis.<br><br>CONCLUSION: This study provides important insight to advance quality control efforts in low biomass microbiome research. Within-study quality control that takes advantage of the data structure (i.e. differential prevalence of contaminants between batches) would enhance the overall reliability and reproducibility of research in this field. Video abstract.}, }
@article {pmid33568223, year = {2021}, author = {Xue, MY and Xie, YY and Zhong, YF and Liu, JX and Guan, LL and Sun, HZ}, title = {Ruminal resistome of dairy cattle is individualized and the resistotypes are associated with milking traits.}, journal = {Animal microbiome}, volume = {3}, number = {1}, pages = {18}, pmid = {33568223}, issn = {2524-4671}, support = {31729004//National Natural Science Foundation of China/ ; CARS-36//Agriculture Research System of China/ ; }, abstract = {BACKGROUND: Antimicrobial resistance is one of the most urgent threat to global public health, as it can lead to high morbidity, mortality, and medical costs for humans and livestock animals. In ruminants, the rumen microbiome carries a large number of antimicrobial resistance genes (ARGs), which could disseminate to the environment through saliva, or through the flow of rumen microbial biomass to the hindgut and released through feces. The occurrence and distribution of ARGs in rumen microbes has been reported, revealing the effects of external stimuli (e.g., antimicrobial administrations and diet ingredients) on the antimicrobial resistance in the rumen. However, the host effect on the ruminal resistome and their interactions remain largely unknown. Here, we investigated the ruminal resistome and its relationship with host feed intake and milk protein yield using metagenomic sequencing.<br><br>RESULTS: The ruminal resistome conferred resistance to 26 classes of antimicrobials, with genes encoding resistance to tetracycline being the most predominant. The ARG-containing contigs were assigned to bacterial taxonomy, and the majority of highly abundant bacterial genera were resistant to at least one antimicrobial, while the abundances of ARG-containing bacterial genera showed distinct variations. Although the ruminal resistome is not co-varied with host feed intake, it could be potentially linked to milk protein yield in dairy cows. Results showed that host feed intake did not affect the alpha or beta diversity of the ruminal resistome or the abundances of ARGs, while the Shannon index (R2 = 0.63, P < 0.01) and richness (R2 = 0.67, P < 0.01) of the ruminal resistome were highly correlated with milk protein yield. A total of 128 significantly different ARGs (FDR < 0.05) were identified in the high- and low-milk protein yield dairy cows. We found four ruminal resistotypes that are driven by specific ARGs and associated with milk protein yield. Particularly, cows with low milk protein yield are classified into the same ruminal resistotype and featured by high-abundance ARGs, including mfd and sav1866.<br><br>CONCLUSIONS: The current study uncovered the prevalence of ARGs in the rumen of a cohort of lactating dairy cows. The ruminal resistome is not co-varied with host feed intake, while it could be potentially linked to milk protein yield in dairy cows. Our results provide fundamental knowledge on the prevalence, mechanisms and impact factors of antimicrobial resistance in dairy cattle and are important for both the dairy industry and other food animal antimicrobial resistance control strategies.}, }
@article {pmid33568158, year = {2021}, author = {Menni, C and Louca, P and Berry, SE and Vijay, A and Astbury, S and Leeming, ER and Gibson, R and Asnicar, F and Piccinno, G and Wolf, J and Davies, R and Mangino, M and Segata, N and Spector, TD and Valdes, AM}, title = {High intake of vegetables is linked to lower white blood cell profile and the effect is mediated by the gut microbiome.}, journal = {BMC medicine}, volume = {19}, number = {1}, pages = {37}, pmid = {33568158}, issn = {1741-7015}, support = {212904/Z/18//WT_/Wellcome Trust/United Kingdom ; AIMHY; MR/M016560/1/MRC_/Medical Research Council/United Kingdom ; CDRF-18/2019//Chronic Disease Research Foundation/ ; CDRF- 2018//Chronic Disease Research Foundation/ ; BB/NO12739/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; ERC-STG project MetaPG//H2020 European Research Council/ ; ONCOBIOME-825410 project//Horizon 2020 Framework Programme/ ; MASTER-818368 project//Horizon 2020/ ; 1U01CA230551//National Institute for Health Research/ ; }, abstract = {BACKGROUND: Chronic inflammation, which can be modulated by diet, is linked to high white blood cell counts and correlates with higher cardiometabolic risk and risk of more severe infections, as in the case of COVID-19.<br><br>METHODS: Here, we assessed the association between white blood cell profile (lymphocytes, basophils, eosinophils, neutrophils, monocytes and total white blood cells) as markers of chronic inflammation, habitual diet and gut microbiome composition (determined by sequencing of the 16S RNA) in 986 healthy individuals from the PREDICT-1 nutritional intervention study. We then investigated whether the gut microbiome mediates part of the benefits of vegetable intake on lymphocyte counts.<br><br>RESULTS: Higher levels of white blood cells, lymphocytes and basophils were all significantly correlated with lower habitual intake of vegetables, with vegetable intake explaining between 3.59 and 6.58% of variation in white blood cells after adjusting for covariates and multiple testing using false discovery rate (q < 0.1). No such association was seen with fruit intake. A mediation analysis found that 20.00% of the effect of vegetable intake on lymphocyte counts was mediated by one bacterial genus, Collinsella, known to increase with the intake of processed foods and previously associated with fatty liver disease. We further correlated white blood cells to other inflammatory markers including IL6 and GlycA, fasting and post-prandial glucose levels and found a significant relationship between inflammation and diet.<br><br>CONCLUSION: A habitual diet high in vegetables, but not fruits, is linked to a lower inflammatory profile for white blood cells, and a fifth of the effect is mediated by the genus Collinsella.<br><br>TRIAL REGISTRATION: The ClinicalTrials.gov registration identifier is NCT03479866 .}, }
@article {pmid33567985, year = {2021}, author = {Duncan, K and Carey-Ewend, K and Vaishnava, S}, title = {Spatial analysis of gut microbiome reveals a distinct ecological niche associated with the mucus layer.}, journal = {Gut microbes}, volume = {}, number = {}, pages = {1-21}, doi = {10.1080/19490976.2021.1874815}, pmid = {33567985}, issn = {1949-0984}, support = {R01 DK113265/DK/NIDDK NIH HHS/United States ; }, abstract = {Mucus-associated bacterial communities are critical for determining disease pathology and promoting colonization resistance. Yet the key ecological properties of mucus resident communities remain poorly defined. Using an approach that combines in situ hybridization, laser microdissection and 16s rRNA sequencing of spatially distinct regions of the mouse gut lumen, we discovered that a dense microbial community resembling a biofilm is embedded in the mucus layer. The mucus-associated biofilm-like community excluded bacteria belonging to phylum Proteobacteria. Additionally, it was significantly more diverse and consisted of bacterial species that were unique to it. By employing germ-free mice deficient in T and B lymphocytes we found that formation of biofilm-like structure was independent of adaptive immunity. Instead the integrity of biofilm-like community depended on Gram-positive commensals such as Clostridia. Additionally, biofilm-like community in the mucus lost fewer Clostridia and showed smaller bloom of Proteobacteria compared to the lumen upon antibiotic treatment. When subjected to time-restricted feeding biofilm-like structure significantly enhanced in size and showed enrichment of Clostridia. Taken together our work discloses that mucus-associated biofilm-like community represents a specialized community that is structurally and compositionally distinct that excludes aerobic bacteria while enriching for anaerobic bacteria such as Clostridia, exhibits enhanced stability to antibiotic treatment and that can be modulated by dietary changes.}, }
@article {pmid33567698, year = {2021}, author = {Yao, Q and Li, H and Fan, L and Zhang, Y and Zhao, S and Zheng, N and Wang, J}, title = {Dietary Regulation of the Crosstalk between Gut Microbiome and Immune Response in Inflammatory Bowel Disease.}, journal = {Foods (Basel, Switzerland)}, volume = {10}, number = {2}, pages = {}, doi = {10.3390/foods10020368}, pmid = {33567698}, issn = {2304-8158}, support = {CAAS-ZDXT2019004//Scientific Research Project for Major Achievements of Agricultural Science and Technology Innovation Program/ ; CARS-36//Ministry of Modern Agro-Industry Technology Research System of China/ ; ASTIP-IAS12//Agricultural Science and Technology Innovation Program/ ; }, abstract = {Inflammatory bowel disease (IBD), a chronic, recurring inflammatory response, is a growing global public health issue. It results from the aberrant crosstalk among environmental factors, gut microbiota, the immune system, and host genetics, with microbiota serving as the core of communication for differently-sourced signals. In the susceptible host, dysbiosis, characterized by the bloom of facultative anaerobic bacteria and the decline of community diversity and balance, can trigger an aberrant immune response that leads to reduced tolerance against commensal microbiota. In IBD, such dysbiosis has been profoundly proven in animal models, as well as clinic data analysis; however, it has not yet been conclusively ascertained whether dysbiosis actually promotes the disease or is simply a consequence of the inflammatory disorder. Better insight into the complex network of interactions between food, the intestinal microbiome, and host immune response will, therefore, contribute significantly to the diagnosis, treatment, and management of IBD. In this article, we review the ways in which the mutualistic circle of dietary nutrients, gut microbiota, and the immune system becomes anomalous during the IBD process, and discuss the roles of bacterial factors in shaping the intestinal inflammatory barrier and adjusting immune capacity.}, }
@article {pmid33567279, year = {2021}, author = {Han, C and Song, J and Hu, J and Fu, H and Feng, Y and Mu, R and Xing, Z and Wang, Z and Wang, L and Zhang, J and Wang, C and Dong, L}, title = {Smectite promotes probiotic biofilm formation in the gut for cancer immunotherapy.}, journal = {Cell reports}, volume = {34}, number = {6}, pages = {108706}, doi = {10.1016/j.celrep.2021.108706}, pmid = {33567279}, issn = {2211-1247}, abstract = {Administration of probiotics to regulate the immune system is a potential anti-tumor strategy. However, oral administration of probiotics is ineffective because of the poor inhabitation of exogenous bacteria in host intestines. Here we report that smectite, a type of mineral clay and established anti-diarrhea drug, promotes expansion of probiotics (especially Lactobacillus) in the murine gut and subsequently elicits anti-tumor immune responses. The ion-exchangeable microstructure of smectite preferentially promotes lactic acid bacteria (LABs) to form biofilms on smectite in vitro and in vivo. In mouse models, smectite laden with LAB biofilms (Lactobacillus and Bifidobacterium) inhibits tumor growth (when used alone) and enhances the efficacy of chemotherapy or immunotherapy (when used in combination with either of them) by activating dendritic cells (DCs) via Toll-like receptor 2 (TLR2) signaling. Our findings suggest oral administration of smectite as a promising strategy to enrich probiotics in vivo for cancer immunotherapy.}, }
@article {pmid33567173, year = {2021}, author = {Chervinets, VM and Chervinets, YV and Leont'eva, AV and Kozlova, EA and Stulov, NM and Belyaev, VS and Grigoryants, EO and Mironov, AY}, title = {The microbiome of oral cavity patients with periodontitis, adhesive and biofilm forming properties.}, journal = {Klinicheskaia laboratornaia diagnostika}, volume = {66}, number = {1}, pages = {45-51}, doi = {10.18821/0869-2084-2021-66-1-45-51}, pmid = {33567173}, issn = {0869-2084}, mesh = {*Adhesives ; Adult ; Biofilms ; Humans ; *Microbiota ; Middle Aged ; Periodontal Pocket ; }, abstract = {The microbiome of oral cavity in healthy people and patients with periodontitis was analyzed to determine their adhesive properties and the ability to form biofilms. The study involved 2 groups: healthy, 18 people, and an experimental group, 20 patients with chronic generalized periodontitis moderate severity of the disease. The average age of the studied people was 35-45 years. Material - dental plaque, scraping from the mucous membrane of the back of the tongue, the contents of the periodontal groove and periodontal pocket, as well as oral fluid. The main method of diagnostic was bacteriological. The average adhesion index (AAI) was used to determine adhesion level of microorganisms to epithelial cells of oral cavity's mucous membrane. The microbiota's ability to form biofilm was tested on glass and plastic surface. The microbiota of oral cavity of patients with periodontitis was characterized by decrease in the frequency of bacteria of the genera: Streptococcus, Peptostreptococcus, Peptococcus, and an increase in Staphylococcus aureus, Veillonella spp., Bacillus spp. The microbiota of the oral cavity of patients with generalized periodontitis has a greater ability to adhere to the cells of the mucous membrane than in healthy people, while their ability to form biofilms and exhibit pathogenic properties is enhanced. The biofilm formation of microorganisms in healthy and sick people differs both on glass and on plastic surfaces.}, }
@article {pmid33566862, year = {2021}, author = {Beule, L and Karlovsky, P}, title = {Tree rows in temperate agroforestry croplands alter the composition of soil bacterial communities.}, journal = {PloS one}, volume = {16}, number = {2}, pages = {e0246919}, doi = {10.1371/journal.pone.0246919}, pmid = {33566862}, issn = {1932-6203}, abstract = {BACKGROUND: Tree-based intercropping (agroforestry) has been advocated to reduce adverse environmental impacts of conventional arable cropping. Modern agroforestry systems in the temperate zone are alley-cropping systems that combine rows of fast-growing trees with rows of arable crops. Soil microbial communities in these systems have been investigated intensively; however, molecular studies with high taxonomical resolution are scarce.<br><br>METHODS: Here, we assessed the effect of temperate agroforestry on the abundance, diversity and composition of soil bacterial communities at three paired poplar-based alley cropping and conventional monoculture cropland systems using real-time PCR and Illumina sequencing of bacterial 16S rRNA genes. Two of the three systems grew summer barley (Hordeum vulgare); one system grew maize (Zea mays) in the sampling year. To capture the spatial heterogeneity induced by the tree rows, soil samples in the agroforestry systems were collected along transects spanning from the centre of the tree rows to the centre of the agroforestry crop rows.<br><br>RESULTS: Tree rows of temperate agroforestry systems increased the abundance of soil bacteria while their alpha diversity remained largely unaffected. The composition of the bacterial communities in tree rows differed from those in arable land (crop rows of the agroforestry systems and conventional monoculture croplands). Several bacterial groups in soil showed strong association with either tree rows or arable land, revealing that the introduction of trees into arable land through agroforestry is accompanied by the introduction of a tree row-associated microbiome.<br><br>CONCLUSION: The presence of tree row-associated bacteria in agroforestry increases the overall microbial diversity of the system. We speculate that the increase in biodiversity is accompanied by functional diversification. Differences in plant-derived nutrients (root exudates and tree litter) and management practices (fertilization and tillage) likely account for the differences between bacterial communities of tree rows and arable land in agroforestry systems.}, }
@article {pmid33566386, year = {2021}, author = {Brooks, GA and Arevalo, JA and Osmond, AD and Leija, RG and Curl, CC and Tovar, AP}, title = {Lactate in contemporary biology: A phoenix risen1.}, journal = {The Journal of physiology}, volume = {}, number = {}, pages = {}, doi = {10.1113/JP280955}, pmid = {33566386}, issn = {1469-7793}, abstract = {After a Century, it's time to turn the page on understanding of lactate metabolism and appreciate that lactate shuttling is an important component of intermediary metabolism in vivo. Cell-Cell and intracellular Lactate Shuttles fulfill purposes of energy substrate production and distribution as well as cell signaling under fully aerobic conditions. Recognition of lactate shuttling came first in studies of physical exercise where the roles of driver (producer) and recipient (consumer) cells and tissues were obvious. Moreover, the presence of lactate shuttling as part of postprandial glucose disposal and satiety signaling has been recognized. Mitochondrial respiration creates the physiological sink for lactate disposal in vivo. Repeated lactate exposure from regular exercise results in adaptive processes such as mitochondrial biogenesis and other healthful circulatory and neurological characteristic such as improved physical work capacity, metabolic flexibility, learning, and memory. The importance of lactate and lactate shuttling in healthful living is further emphasized when lactate signaling and shuttling are dysregulated as occur in particular illnesses and injuries. Like a Phoenix, lactate has risen to major importance in 21st Century Biology. This article is protected by copyright. All rights reserved.}, }
@article {pmid33566369, year = {2021}, author = {Lee, W and Hayakawa, T and Kurihara, Y and Hanzawa, M and Sawada, A and Kaneko, A and Morimitsu, Y and Natsume, T and Aisu, S and Ito, T and Honda, T and Hanya, G}, title = {Stomach and colonic microbiome of wild Japanese macaques.}, journal = {American journal of primatology}, volume = {}, number = {}, pages = {e23242}, doi = {10.1002/ajp.23242}, pmid = {33566369}, issn = {1098-2345}, support = {15KK0256//JSPS Promotion of Joint International Research/ ; 19KK0186//JSPS Promotion of Joint International Research/ ; 19K16241//JSPS Grant-in-Aid for Young Scientists/ ; 18K14490//Grant-in-Aid for Young Scientists/ ; 17H01911//MEXT Grant-in-Aid for the Scientific Research/ ; 16J01208//Grant-in-Aid for JSPS Research Fellow/ ; }, abstract = {Within the gastrointestinal tract, the physiochemical microenvironments are highly diversified among the different stages of food digestion. Accordingly, gut microbiome composition and function vary at different gut sites. In this study, we examine and compare the compositional and functional potential between the stomach and colonic microbiome of wild Japanese macaques (Macaca fuscata yakui) living in the evergreen forest of Yakushima Island. We find a significantly lower microbial diversity in the stomach than in the colon, possibly due to the stomach's acidic and aerobic environment, which is suboptimal for microbial survival. According to past studies, the microbial taxa enriched in the stomach are aero- and acid-tolerant. By functional prediction through PICRUSt2, we reveal that the stomach microbiome is more enriched in pathways relating to the metabolism of simple sugars. On the contrary, the colonic microbiota is more enriched with fiber-degrading microbes, such as those from Lachnospiracea, Ruminococcaceae, and Prevotella. Our study shows a clear difference in the microbiome between the stomach and colon of Japanese macaques in both composition and function. This study provides a preliminary look at the alpha diversity and taxonomic composition within the stomach microbiome of Japanese macaques, a hindgut-fermenting nonhuman primate.}, }
@article {pmid33566277, year = {2021}, author = {Smith, A}, title = {Using next-generation sequencing to develop a Shigella species threshold and profile faecal samples from suspected diarrhoea cases.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, pmid = {33566277}, issn = {1874-9356}, abstract = {Globally, it is estimated that there are 2 billion cases of diarrhoeal disease each year, with 525,000 children under the age of 5 years, dying from diarrhoea. This also affects 1 in 5 people in the UK each year. Rapid diagnosis, appropriate treatment and infection control measures are, therefore, particularly important. Currently, Public Health Wales and England Microbiology Division test for five key bacterial gastrointestinal pathogens, i.e. Escherichia coli O157 (VTEC), Shigella dysenteriae, Salmonella spp., Campylobacter spp. and Clostridioides difficile. There is, however, a poor success rate with identification of these pathogens, leaving the patient at risk from untreated infections. This study has developed effective and reliable tools with a high positive outcome for diagnosis of diarrhoeal infection. The study blindly analysed 592 samples, with the most abundant species being Shigella sonnei at 15%, and the top genus Bacteroides at 26%. Campylobacter spp. had an abundance of 4%, Clostridium difficile 3%, and Salmonella spp. 0.2%. There were also significant differences in abundance at genus level, between the Flemish Gut project and diarrhoea samples, with respect to Shigella (0.2%) and Campylobacter (0.1%). The project introduced a novel Shigella spp. (Escherichia) threshold of 5.32% to determine (Escherichia) a healthy or unhealthy community. A DMBiome model was developed to integrate the 5.32% threshold of Shigella spp., the Public Health laboratory tested pathogens, and two emerging enteropathogens. The overall positive outcome was that 89% of all samples were diagnosed with diarrhoea infections, leaving 11% unknown.}, }
@article {pmid33565788, year = {2021}, author = {Wei, X and Mei, C and Li, X and Xie, Y}, title = {The Unique Microbiome and Immunity in Pancreatic Cancer.}, journal = {Pancreas}, volume = {50}, number = {2}, pages = {119-129}, doi = {10.1097/MPA.0000000000001744}, pmid = {33565788}, issn = {1536-4828}, abstract = {ABSTRACT: Microorganisms can help maintain homeostasis in humans by providing nutrition, maintaining hormone balance, and regulating inflammatory responses. In the case of imbalances, these microbes can cause various diseases, even malignancy. Pancreatic cancer (PC) is characterized by high tumor invasiveness, distant metastasis, and insensitivity to traditional chemotherapeutic drugs, and it is confirmed that PC is closely related to microorganisms. Recently, most studies based on clinical samples or case reports discussed the positive or negative relationships between microorganisms and PC. However, the specific mechanisms are blurry, especially the involved immunological pathways, and the roles of beneficial flora have usually been ignored. We reviewed studies published through September 2020 as identified using PubMed, MEDLINE, and Web of Science. We mainly introduced the traits of oral, gastrointestinal, and intratumoral microbes in PC and summarized the roles of these microbes in tumorigenesis and tumoral development through immunological pathways, in addition to illustrating the relationships between metabolic diseases with PC by microorganism. In addition, we identified microorganisms as biomarkers for early diagnosis and immunotherapy. This review will be significant for greater understanding the effect of microorganisms in PC and provide more meaningful guidance for future clinical applications.}, }
@article {pmid33565609, year = {2021}, author = {Ebersole, JL and Kirakodu, SS and Orraca, L and Gonzalez Martinez, J and Gonzalez, OA}, title = {Gingival Transcriptomics of Follicular T Cell Footprints in Progressing Periodontitis.}, journal = {Clinical and experimental immunology}, volume = {}, number = {}, pages = {}, doi = {10.1111/cei.13584}, pmid = {33565609}, issn = {1365-2249}, abstract = {Follicular helper T cells (Tfh) cells have ben identified in the circulation and in tertiary lymphoid structures in chronic inflammation. Gingival tissues with periodontitis reflect chronic inflammation so genomic footprints of Tfh cells should occur in these tissues and may differ related to aging effects. METHODS: Macaca mulatta were used in a ligature-induced periodontitis model [adult group (12-23 years of age); young group (3-7 years)]. Gingival tissue and subgingival microbiome samples were obtained at matched healthy ligature-induced disease, and clinical resolution sites. Microarray analysis examined Tfh genes (n=54) related to microbiome characteristics documented using 16S MiSeq RESULTS: An increase in the major transcription factor of Tfh cells, BCL6, was found with disease in both adult and young animals, while master transcription markers of other T cell subsets were either decreased or showed minimal change. Multiple Tfh related genes, including surface receptors and transcription factors were also significantly increased during disease. Specific microbiome patterns were significantly associated with profiles indicative of an increased presence/function of Tfh cells. Importantly, unique microbial complexes showed distinctive patterns of interaction with Tfh genes differing in health and disease, and with age of the animals CONCLUSIONS: An increase in Tfh cell responsiveness occurred in the progression of periodontitis, affected by age and related to specific microbial complexes in the oral microbiome. The capacity of gingival Tfh cells to contribute to localized B cell activation and active antibody responses, including affinity maturation may be critical for controlling periodontal lesions and contributing to limiting and/or resolving the lesions.}, }
@article {pmid33565193, year = {2021}, author = {Song, T and Guan, X and Wang, X and Qu, S and Zhang, S and Hui, W and Men, L and Chen, X}, title = {Dynamic modulation of gut microbiota improves post-myocardial infarct tissue repair in rats via butyric acid-mediated histone deacetylase inhibition.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {35}, number = {3}, pages = {e21385}, doi = {10.1096/fj.201903129RRR}, pmid = {33565193}, issn = {1530-6860}, support = {81570253//National Natural Science Foundation of China (NSFC)/ ; 2015Z040//Health and Family Planning Commission of Jilin Province/ ; 20180101168JC//Department of Science and Technology of Jilin Province (Jilin Province Science and Technology Department)/ ; }, abstract = {The complex and dynamic population of gut microbiota exerts a marked influence on the host during homeostasis and disease. Imbalance of gut microbiota metabolites may lead to cardiac dysfunction in patients with heart failure, which is related to myocardial infarction(MI) severity. However, the role of gut microbiota in the repair process after MI has rarely been reported. To explore the role of gut microbiota in MI repair and its underlying mechanism, we mixed antibiotics in drinking water to interfere with gut microbiota in rats. Hematoxylin and eosin staining, Sirius red staining, western blotting, and immunohistochemistry were used to detect tissue repair and fibrosis. We found that the expressions of alpha-smooth muscle actin, collagen, and histone deacetylase (HDAC) activities were significantly increased. We detected gut microbiota at different time points after MI using 16S ribosomal RNA sequencing and detected that Prevotellaceae, Clostridiaceae, and Lachnospiraceae were significantly altered among the butyric acid producers. We administered sodium butyrate via drinking water and discovered that sodium butyrate reduced HDAC activities and adverse repair. Therefore, we speculated that gut microbiota influences the acetylation level and tissue repair process after MI by affecting butyric acid production.}, }
@article {pmid33565055, year = {2021}, author = {Kim, J and Park, T and Kim, HJ and An, S and Sul, WJ}, title = {Inferences in microbial structural signatures of acne microbiome and mycobiome.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {}, number = {}, pages = {}, pmid = {33565055}, issn = {1976-3794}, abstract = {Acne vulgaris, commonly known as acne, is the most common skin disorder and a multifactorial disease of the sebaceous gland. Although the pathophysiology of acne is still unclear, bacterial and fungal factors are known to be involved in. This study aimed to investigate whether the microbiomes and mycobiomes of acne patients are distinct from those of healthy subjects and to identify the structural signatures of microbiomes related to acne vulgaris. A total of 33 Korean female subjects were recruited (Acne group, n = 17; Healthy group, n = 16), and microbiome samples were collected swabbing the forehead and right cheek. To characterize the fungal and bacterial communities, 16S rRNA V4-V5 and ITS1 region, respectively, were sequenced and analysed using Qiime2. There were no significant differences in alpha and beta diversities of microbiomes between the Acne and Healthy groups. In comparison with the ratio of Cutibacterium to Staphylococcus, the acne patients had higher abundance of Staphylococcus compared to Cutibacterium than the healthy individuals. In network analysis with the dominant microorganism amplicon sequence variants (ASV) (Cutibacterium, Staphylococcus, Malassezia globosa, and Malassezia restricta) Cutibacterium acnes was identified to have hostile interactions with Staphylococcus and Malassezia globosa. Accordingly, this results suggest an insight into the differences in the skin microbiome and mycobiome between acne patients and healthy controls and provide possible microorganism candidates that modulate the microbiomes associated to acne vulgaris.}, }
@article {pmid33565054, year = {2021}, author = {Gwak, HJ and Lee, SJ and Rho, M}, title = {Application of computational approaches to analyze metagenomic data.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {}, number = {}, pages = {}, pmid = {33565054}, issn = {1976-3794}, abstract = {Microorganisms play a vital role in living systems in numerous ways. In the soil or ocean environment, microbes are involved in diverse processes, such as carbon and nitrogen cycle, nutrient recycling, and energy acquisition. The relation between microbial dysbiosis and disease developments has been extensively studied. In particular, microbial communities in the human gut are associated with the pathophysiology of several chronic diseases such as inflammatory bowel disease and diabetes. Therefore, analyzing the distribution of microorganisms and their associations with the environment is a key step in understanding nature. With the advent of next-generation sequencing technology, a vast amount of metagenomic data on unculturable microbes in addition to culturable microbes has been produced. To reconstruct microbial genomes, several assembly algorithms have been developed by incorporating metagenomic features, such as uneven depth. Since it is difficult to reconstruct complete microbial genomes from metagenomic reads, contig binning approaches were suggested to collect contigs that originate from the same genome. To estimate the microbial composition in the environment, various methods have been developed to classify individual reads or contigs and profile bacterial proportions. Since microbial communities affect their hosts and environments through metabolites, metabolic profiles from metagenomic or metatranscriptomic data have been estimated. Here, we provide a comprehensive review of computational methods that can be applied to investigate microbiomes using metagenomic and metatranscriptomic sequencing data. The limitations of metagenomic studies and the key approaches to overcome such problems are discussed.}, }
@article {pmid33564111, year = {2021}, author = {Jani, AJ and Bushell, J and Arisdakessian, CG and Belcaid, M and Boiano, DM and Brown, C and Knapp, RA}, title = {The amphibian microbiome exhibits poor resilience following pathogen-induced disturbance.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {33564111}, issn = {1751-7370}, support = {IOS-1455873//National Science Foundation (NSF)/ ; }, abstract = {Infectious pathogens can disrupt the microbiome in addition to directly affecting the host. Impacts of disease may be dependent on the ability of the microbiome to recover from such disturbance, yet remarkably little is known about microbiome recovery after disease, particularly in nonhuman animals. We assessed the resilience of the amphibian skin microbial community after disturbance by the pathogen, Batrachochytrium dendrobatidis (Bd). Skin microbial communities of laboratory-reared mountain yellow-legged frogs were tracked through three experimental phases: prior to Bd infection, after Bd infection (disturbance), and after clearing Bd infection (recovery period). Bd infection disturbed microbiome composition and altered the relative abundances of several dominant bacterial taxa. After Bd infection, frogs were treated with an antifungal drug that cleared Bd infection, but this did not lead to recovery of microbiome composition (measured as Unifrac distance) or relative abundances of dominant bacterial groups. These results indicate that Bd infection can lead to an alternate stable state in the microbiome of sensitive amphibians, or that microbiome recovery is extremely slow-in either case resilience is low. Furthermore, antifungal treatment and clearance of Bd infection had the additional effect of reducing microbial community variability, which we hypothesize results from similarity across frogs in the taxa that colonize community vacancies resulting from the removal of Bd. Our results indicate that the skin microbiota of mountain yellow-legged frogs has low resilience following Bd-induced disturbance and is further altered by the process of clearing Bd infection, which may have implications for the conservation of this endangered amphibian.}, }
@article {pmid33563976, year = {2021}, author = {Liu, X and Tang, S and Zhong, H and Tong, X and Jie, Z and Ding, Q and Wang, D and Guo, R and Xiao, L and Xu, X and Yang, H and Wang, J and Zong, Y and Liu, W and Liu, X and Zhang, Y and Brix, S and Kristiansen, K and Hou, Y and Jia, H and Zhang, T}, title = {A genome-wide association study for gut metagenome in Chinese adults illuminates complex diseases.}, journal = {Cell discovery}, volume = {7}, number = {1}, pages = {9}, pmid = {33563976}, issn = {2056-5968}, abstract = {The gut microbiome has been established as a key environmental factor to health. Genetic influences on the gut microbiome have been reported, yet, doubts remain as to the significance of genetic associations. Here, we provide shotgun data for whole genome and whole metagenome from a Chinese cohort, identifying no <20% genetic contribution to the gut microbiota. Using common variants-, rare variants-, and copy number variations-based association analyses, we identified abundant signals associated with the gut microbiome especially in metabolic, neurological, and immunological functions. The controversial concept of enterotypes may have a genetic attribute, with the top two loci explaining 11% of the Prevotella-Bacteroides variances. Stratification according to gender led to the identification of differential associations in males and females. Our two-stage metagenome genome-wide association studies on a total of 1295 individuals unequivocally illustrates that neither microbiome nor GWAS studies could overlook one another in our quest for a better understanding of human health and diseases.}, }
@article {pmid33563907, year = {2020}, author = {Chen, H and Chen, Z and Shen, L and Wu, X and Ma, X and Lin, D and Zhang, M and Ma, X and Liu, Y and Wang, Z and Zhang, Y and Kuang, Z and Lu, Z and Li, X and Ma, L and Lin, X and Si, L and Chen, X}, title = {Fecal microbiota transplantation from patients with autoimmune encephalitis modulates Th17 response and relevant behaviors in mice.}, journal = {Cell death discovery}, volume = {6}, number = {1}, pages = {75}, pmid = {33563907}, issn = {2058-7716}, support = {81971141//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {The significance of the microbiota-gut-brain axis has been increasingly recognized as a major modulator of autoimmunity. Here, we aim to characterize the gut microbiota of a large cohort of treatment-naïve anti-N-methyl-D-aspartate receptor (anti-NMDAR) encephalitis patients relative to that of healthy controls (HCs). Relative to HCs, anti-NMDAR encephalitis patients had a decreased microbiome alpha-diversity index, marked disturbances of gut microbial composition and intestinal permeability damage. Disturbed microbiota in anti-NMDAR encephalitis patients might be linked with different clinical characteristics. Imputed KEGG analysis revealed perturbations of functional modules in the gut microbiomes of anti-NMDAR encephalitis. Compared to HCs, microbiota-depleted mice receiving fecal microbiota transplantation (FMT) from anti-NMDAR encephalitis patients had hypersensitivity and cognitive impairment. Furthermore, anti-NMDAR encephalitis FMT mice showed altered T cells in the spleen and small intestine lamina propria with an increased Th17 cells. Overall, this study first suggests that the anti-NMDAR encephalitis microbiome itself can influence neurologic, Th17 response and behavioral function. The gut microbiota is a potential therapeutic target for anti-NMDAR encephalitis.}, }
@article {pmid33563787, year = {2021}, author = {de la Cuesta-Zuluaga, J and Spector, TD and Youngblut, ND and Ley, RE}, title = {Genomic Insights into Adaptations of Trimethylamine-Utilizing Methanogens to Diverse Habitats, Including the Human Gut.}, journal = {mSystems}, volume = {6}, number = {1}, pages = {}, pmid = {33563787}, issn = {2379-5077}, abstract = {Archaea of the order Methanomassiliicoccales use methylated amines such as trimethylamine as the substrates for methanogenesis. They form two large phylogenetic clades and reside in diverse environments, from soil to the human gut. Two genera, one from each clade, inhabit the human gut: Methanomassiliicoccus, which has one cultured representative, and &quot;Candidatus Methanomethylophilus,&quot; which has none. Questions remain regarding their distribution across biomes and human populations, their association with other taxa in the gut, and whether host genetics correlate with their abundance. To gain insight into the Methanomassiliicoccales clade, particularly its human-associated members, we performed a genomic comparison of 72 Methanomassiliicoccales genomes and assessed their presence in metagenomes derived from the human gut (n = 4,472, representing 22 populations), nonhuman animal gut (n = 145), and nonhost environments (n = 160). Our analyses showed that all taxa are generalists; they were detected in animal gut and environmental samples. We confirmed two large clades, one enriched in the gut and the other enriched in the environment, with notable exceptions. Genomic adaptations to the gut include genome reduction and genes involved in the shikimate pathway and bile resistance. Genomic adaptations differed by clade, not habitat preference, indicating convergent evolution between the clades. In the human gut, the relative abundance of Methanomassiliicoccales spp. correlated with trimethylamine-producing bacteria and was unrelated to host genotype. Our results shed light on the microbial ecology of this group and may help guide Methanomassiliicoccales-based strategies for trimethylamine mitigation in cardiovascular disease.IMPORTANCEMethanomassiliicoccales are less-known members of the human gut archaeome. Members of this order use methylated amines, including trimethylamine, in methane production. This group has only one cultured representative; how its members adapted to inhabit the mammalian gut and how they interact with other microbes is largely unknown. Using bioinformatics methods applied to DNA from a wide range of samples, we profiled the abundances of these Archaea spp. in environmental and host-associated microbial communities. We observed two groups of Methanomassiliicoccales, one largely host associated and one largely found in environmental samples, with some exceptions. When host associated, these Archaea have smaller genomes and possess genes related to bile resistance and aromatic amino acid precursors. We did not detect Methanomassiliicoccales in all human populations tested, but when present, they were correlated with bacteria known to produce trimethylamine. Due to their metabolism of trimethylamine, these intriguing Archaea may form the basis of novel therapies for cardiovascular disease.}, }
@article {pmid33563782, year = {2021}, author = {Joseph, S and Aduse-Opoku, J and Hashim, A and Hanski, E and Streich, R and Knowles, SCL and Pedersen, AB and Wade, WG and Curtis, MA}, title = {A 16S rRNA Gene and Draft Genome Database for the Murine Oral Bacterial Community.}, journal = {mSystems}, volume = {6}, number = {1}, pages = {}, pmid = {33563782}, issn = {2379-5077}, abstract = {A curated murine oral microbiome database to be used as a reference for mouse-based studies has been constructed using a combination of bacterial culture, 16S rRNA gene amplicon, and whole-genome sequencing. The database comprises a collection of nearly full-length 16S rRNA gene sequences from cultured isolates and draft genomes from representative taxa collected from a range of sources, including specific-pathogen-free laboratory mice, wild Mus musculusdomesticus mice, and formerly wild wood mouse Apodemus sylvaticus At present, it comprises 103 mouse oral taxa (MOT) spanning four phyla-Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes-including 12 novel undescribed species-level taxa. The key observations from this study are (i) the low diversity and predominantly culturable nature of the laboratory mouse oral microbiome and (ii) the identification of three major murine-specific oral bacterial lineages, namely, Streptococcus danieliae (MOT10), Lactobacillus murinus (MOT93), and Gemella species 2 (MOT43), which is one of the novel, still-unnamed taxa. Of these, S. danieliae is of particular interest, since it is a major component of the oral microbiome from all strains of healthy and periodontally diseased laboratory mice, as well as being present in wild mice. It is expected that this well-characterized database should be a useful resource for in vitro experimentation and mouse model studies in the field of oral microbiology.IMPORTANCE Mouse model studies are frequently used in oral microbiome research, particularly to investigate diseases such as periodontitis and caries, as well as other related systemic diseases. We have reported here the details of the development of a curated reference database to characterize the oral microbial community in laboratory and some wild mice. The genomic information and findings reported here can help improve the outcomes and accuracy of host-microbe experimental studies that use murine models to understand health and disease. Work is also under way to make the reference data sets publicly available on a web server to enable easy access and downloading for researchers across the world.}, }
@article {pmid33563781, year = {2021}, author = {Borchert, E and García-Moyano, A and Sanchez-Carrillo, S and Dahlgren, TG and Slaby, BM and Bjerga, GEK and Ferrer, M and Franzenburg, S and Hentschel, U}, title = {Deciphering a Marine Bone-Degrading Microbiome Reveals a Complex Community Effort.}, journal = {mSystems}, volume = {6}, number = {1}, pages = {}, pmid = {33563781}, issn = {2379-5077}, abstract = {The marine bone biome is a complex assemblage of macro- and microorganisms; however, the enzymatic repertoire to access bone-derived nutrients remains unknown. The bone matrix is a composite material made up mainly of organic collagen and inorganic hydroxyapatite. We conducted field experiments to study microbial assemblages that can use organic bone components as nutrient source. Bovine and turkey bones were deposited at 69 m depth in a Norwegian fjord (Byfjorden, Bergen). Metagenomic sequence analysis was used to assess the functional potential of microbial assemblages from bone surface and the bone-eating worm Osedax mucofloris, which is a frequent colonizer of whale falls and known to degrade bone. The bone microbiome displayed a surprising taxonomic diversity revealed by the examination of 59 high-quality metagenome-assembled genomes from at least 23 bacterial families. Over 700 genes encoding enzymes from 12 relevant enzymatic families pertaining to collagenases, peptidases, and glycosidases putatively involved in bone degradation were identified. Metagenome-assembled genomes (MAGs) of the class Bacteroidia contained the most diverse gene repertoires. We postulate that demineralization of inorganic bone components is achieved by a timely succession of a closed sulfur biogeochemical cycle between sulfur-oxidizing and sulfur-reducing bacteria, causing a drop in pH and subsequent enzymatic processing of organic components in the bone surface communities. An unusually large and novel collagen utilization gene cluster was retrieved from one genome belonging to the gammaproteobacterial genus ColwelliaIMPORTANCE Bones are an underexploited, yet potentially profitable feedstock for biotechnological advances and value chains, due to the sheer amounts of residues produced by the modern meat and poultry processing industry. In this metagenomic study, we decipher the microbial pathways and enzymes that we postulate to be involved in bone degradation in the marine environment. We here demonstrate the interplay between different bacterial community members, each supplying different enzymatic functions with the potential to cover an array of reactions relating to the degradation of bone matrix components. We identify and describe a novel gene cluster for collagen utilization, which is a key function in this unique environment. We propose that the interplay between the different microbial taxa is necessary to achieve the complex task of bone degradation in the marine environment.}, }
@article {pmid33563732, year = {2021}, author = {Alhusain, F}, title = {Microbiome: Role and functionality in human nutrition cycle.}, journal = {Saudi medical journal}, volume = {42}, number = {2}, pages = {146-150}, doi = {10.15537/smj.2021.2.25587}, pmid = {33563732}, issn = {0379-5284}, abstract = {Microbes are present almost everywhere on this Earth. Humans harbor microbes in various organs, including skin, gut, mouth, and nose. Among these, the gut region has the highest population of microbes. Gut microbiota is directly linked with homeostasis, and a minor change in their numbers predisposes humans to ailments. Notably, the role of the microbial population in the digestive tract directly contributes to body weight. Sometimes, lifestyle changes or antibiotics intake to manage certain infections are associated with disturbance in the gut microflora. Several scientific studies allude to the obesity linkage with disturbed intestinal microflora. This review mainly focuses on how healthy nutrition contributes towards maintaining normal flora inside the human body. Importantly, the contribution of probiotics and prebiotics in maintaining human healthy body weight is discussed.}, }
@article {pmid33563647, year = {2021}, author = {Williams, LA and Richardson, M and Spector, LG and Marcotte, EL}, title = {Cesarean section is associated with an increased risk of acute lymphoblastic leukemia and hepatoblastoma in children from Minnesota.}, journal = {Cancer epidemiology, biomarkers &amp; prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology}, volume = {}, number = {}, pages = {}, doi = {10.1158/1055-9965.EPI-20-1406}, pmid = {33563647}, issn = {1538-7755}, abstract = {Background In recent decades, Cesarean section (C-section) rates have increased. C-section is hypothesized to negatively impact the developing immune system by altering activation of the hypothalamic-pituitary-adrenal axis and the infant microbiome, among other mechanisms, thereby potentially modulating childhood cancer risk. Methods Using linked birth and cancer registry data from Minnesota (1976-2014), we included individuals aged 0-14 at diagnosis with one of 19 cancers. Cases and controls were frequency matched by birth year. We used logistic regression to estimate odds ratios (OR) and 95% confidence intervals (95% CI) as the measure of association between C-section and cancer. We assessed sex-C-section interactions for each cancer and conducted stratified analyses in ALL for birth year, age at diagnosis, and maternal race. Results There were 3,166 cases and 20,589 controls. One third (n=1,174) of controls born during 2004-2014 were delivered via C-section compared to 42.2% of cases (n=285). C-section was associated with ALL (n=819) (OR: 1.20; 95% CI: 1.01-1.43) and hepatoblastoma (n=50) (OR: 1.89; 95% CI: 1.03-3.48), particularly among females (ALL OR: 1.34; 95% CI: 1.04-1.72; hepatoblastoma OR: 3.87; 95% CI: 1.30-11.57). The risk of ALL was highest during 2005-2014 (OR: 1.62; 95% CI: 1.11-2.34) and among children aged 1-5 years (OR: 1.28; 95% CI: 1.02-1.61). Conclusions C-section was associated with and increased risk of ALL and hepatoblastoma. Impact These associations require investigation to determine causality and rule out confounding by indication or reverse causality. The mechanisms underlying these associations may depend on neonatal immune system processes altered during C-section deliveries.}, }
@article {pmid33563544, year = {2021}, author = {Liwinski, T and Leshem, A and Elinav, E}, title = {Breakthroughs and Bottlenecks in Microbiome Research.}, journal = {Trends in molecular medicine}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.molmed.2021.01.003}, pmid = {33563544}, issn = {1471-499X}, abstract = {Over the past 15 years, the research community has witnessed unprecedented progress in microbiome research. We review this increasing knowledge and first attempts of its clinical application, and also limitations and challenges faced by the research community, in mechanistically understanding host-microbiome interactions and integrating these insights into clinical practice.}, }
@article {pmid33563315, year = {2021}, author = {Wu, G and Zhao, N and Zhang, C and Lam, YY and Zhao, L}, title = {Guild-based analysis for understanding gut microbiome in human health and diseases.}, journal = {Genome medicine}, volume = {13}, number = {1}, pages = {22}, pmid = {33563315}, issn = {1756-994X}, abstract = {To demonstrate the causative role of gut microbiome in human health and diseases, we first need to identify, via next-generation sequencing, potentially important functional members associated with specific health outcomes and disease phenotypes. However, due to the strain-level genetic complexity of the gut microbiota, microbiome datasets are highly dimensional and highly sparse in nature, making it challenging to identify putative causative agents of a particular disease phenotype. Members of an ecosystem seldomly live independently from each other. Instead, they develop local interactions and form inter-member organizations to influence the ecosystem's higher-level patterns and functions. In the ecological study of macro-organisms, members are defined as belonging to the same &quot;guild&quot; if they exploit the same class of resources in a similar way or work together as a coherent functional group. Translating the concept of &quot;guild&quot; to the study of gut microbiota, we redefine guild as a group of bacteria that show consistent co-abundant behavior and likely to work together to contribute to the same ecological function. In this opinion article, we discuss how to use guilds as the aggregation unit to reduce dimensionality and sparsity in microbiome-wide association studies for identifying candidate gut bacteria that may causatively contribute to human health and diseases.}, }
@article {pmid33563119, year = {2021}, author = {Hammer, TJ and Le, E and Moran, NA}, title = {Thermal niches of specialized gut symbionts: the case of social bees.}, journal = {Proceedings. Biological sciences}, volume = {288}, number = {1944}, pages = {20201480}, doi = {10.1098/rspb.2020.1480}, pmid = {33563119}, issn = {1471-2954}, abstract = {Responses to climate change are particularly complicated in species that engage in symbioses, as the niche of one partner may be modified by that of the other. We explored thermal traits in gut symbionts of honeybees and bumblebees, which are vulnerable to rising temperatures. In vitro assays of symbiont strains isolated from 16 host species revealed variation in thermal niches. Strains from bumblebees tended to be less heat-tolerant than those from honeybees, possibly due to bumblebees maintaining cooler nests or inhabiting cooler climates. Overall, however, bee symbionts grew at temperatures up to 44°C and withstood temperatures up to 52°C, at or above the upper thermal limits of their hosts. While heat-tolerant, most strains of the symbiont Snodgrassella grew relatively slowly below 35°C, perhaps because of adaptation to the elevated body temperatures that bees maintain through thermoregulation. In a gnotobiotic bumblebee experiment, Snodgrassella was unable to consistently colonize bees reared at 29°C under conditions that limit thermoregulation. Thus, host thermoregulatory behaviour appears important in creating a warm microenvironment for symbiont establishment. Bee-microbiome-temperature interactions could affect host health and pollination services, and inform research on the thermal biology of other specialized gut symbionts.}, }
@article {pmid33562834, year = {2021}, author = {Crognale, S and Braguglia, CM and Gallipoli, A and Gianico, A and Rossetti, S and Montecchio, D}, title = {Direct Conversion of Food Waste Extract into Caproate: Metagenomics Assessment of Chain Elongation Process.}, journal = {Microorganisms}, volume = {9}, number = {2}, pages = {}, doi = {10.3390/microorganisms9020327}, pmid = {33562834}, issn = {2076-2607}, support = {#2019-2407//Fondazione Cariplo/ ; }, abstract = {In a circular economy strategy, waste resources can be used for the biological production of high added-value substances, such as medium chain fatty acids (MCFAs), thus minimising waste and favouring a sustainable process. This study investigates single-stage fermentation processes for the production of MCFAs in a semi-continuous reactor treating the extract of real food waste (FW), without the addition of external electron donors. Two sequential acidogenic fermentation tests were carried out at an organic loading rate (OLR) of 5 and 15 gCOD L-1d-1 with a hydraulic retention time of 4 days and pH controlled at 6 ± 0.2. The highest level of caproate (4.8 g L-1) was observed at OLR of 15 gCOD L-1d-1 with a microbiome mainly composed by lactate-producing Actinomyces, Atopobium, and Olsenella species and caproate-producing Pseudoramibacter. Metagenomic analysis revealed the presence of key enzymes for the production of lactate, such as lactate dehydrogenase and pyruvate ferredoxin oxidoreductase, as well as several enzymes involved in the reverse β-oxidation pathway, thus suggesting the occurrence of a lactate-based chain elongation process.}, }
@article {pmid33562721, year = {2021}, author = {Banfi, D and Moro, E and Bosi, A and Bistoletti, M and Cerantola, S and Crema, F and Maggi, F and Giron, MC and Giaroni, C and Baj, A}, title = {Impact of Microbial Metabolites on Microbiota-Gut-Brain Axis in Inflammatory Bowel Disease.}, journal = {International journal of molecular sciences}, volume = {22}, number = {4}, pages = {}, doi = {10.3390/ijms22041623}, pmid = {33562721}, issn = {1422-0067}, abstract = {The complex bidirectional communication system existing between the gastrointestinal tract and the brain initially termed the &quot;gut-brain axis&quot; and renamed the &quot;microbiota-gut-brain axis&quot;, considering the pivotal role of gut microbiota in sustaining local and systemic homeostasis, has a fundamental role in the pathogenesis of Inflammatory Bowel Disease (IBD). The integration of signals deriving from the host neuronal, immune, and endocrine systems with signals deriving from the microbiota may influence the development of the local inflammatory injury and impacts also more distal brain regions, underlying the psychophysiological vulnerability of IBD patients. Mood disorders and increased response to stress are frequently associated with IBD and may affect the disease recurrence and severity, thus requiring an appropriate therapeutic approach in addition to conventional anti-inflammatory treatments. This review highlights the more recent evidence suggesting that alterations of the microbiota-gut-brain bidirectional communication axis may concur to IBD pathogenesis and sustain the development of both local and CNS symptoms. The participation of the main microbial-derived metabolites, also defined as &quot;postbiotics&quot;, such as bile acids, short-chain fatty acids, and tryptophan metabolites in the development of IBD-associated gut and brain dysfunction will be discussed. The last section covers a critical evaluation of the main clinical evidence pointing to the microbiome-based therapeutic approaches for the treatment of IBD-related gastrointestinal and neuropsychiatric symptoms.}, }
@article {pmid33562498, year = {2021}, author = {Mullins, AP and Arjmandi, BH}, title = {Health Benefits of Plant-Based Nutrition: Focus on Beans in Cardiometabolic Diseases.}, journal = {Nutrients}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/nu13020519}, pmid = {33562498}, issn = {2072-6643}, abstract = {Cardiovascular disease (CVD) is the leading cause of death worldwide, claiming over 650,000 American lives annually. Typically not a singular disease, CVD often coexists with dyslipidemia, hypertension, type-2 diabetes (T2D), chronic system-wide inflammation, and obesity. Obesity, an independent risk factor for both CVD and T2D, further worsens the problem, with over 42% of adults and 18.5% of youth in the U.S. categorized as such. Dietary behavior is a most important modifiable risk factor for controlling the onset and progression of obesity and related disease conditions. Plant-based eating patterns that include beans and legumes support health and disease mitigation through nutritional profile and bioactive compounds including phytochemical. This review focuses on the characteristics of beans and ability to improve obesity-related diseases and associated factors including excess body weight, gut microbiome environment, and low-grade inflammation. Additionally, there are growing data that link obesity to compromised immune response and elevated risk for complications from immune-related diseases. Body weight management and nutritional status may improve immune function and possibly prevent disease severity. Inclusion of beans as part of a plant-based dietary strategy imparts cardiovascular, metabolic, and colon protective effects; improves obesity, low-grade inflammation, and may play a role in immune-related disease risk management.}, }
@article {pmid33562472, year = {2021}, author = {Anderson, G and Carbone, A and Mazzoccoli, G}, title = {Tryptophan Metabolites and Aryl Hydrocarbon Receptor in Severe Acute Respiratory Syndrome, Coronavirus-2 (SARS-CoV-2) Pathophysiology.}, journal = {International journal of molecular sciences}, volume = {22}, number = {4}, pages = {}, doi = {10.3390/ijms22041597}, pmid = {33562472}, issn = {1422-0067}, abstract = {The metabolism of tryptophan is intimately associated with the differential regulation of diverse physiological processes, including in the regulation of responses to severe acute respiratory syndrome, coronavirus-2 (SARS-CoV-2) infection that underpins the COVID-19 pandemic. Two important products of tryptophan metabolism, viz kynurenine and interleukin (IL)4-inducible1 (IL41)-driven indole 3 pyruvate (I3P), activate the aryl hydrocarbon receptor (AhR), thereby altering the nature of immune responses to SARS-CoV-2 infection. AhR activation dysregulates the initial pro-inflammatory cytokines production driven by neutrophils, macrophages, and mast cells, whilst AhR activation suppresses the endogenous antiviral responses of natural killer cells and CD8+ T cells. Such immune responses become further dysregulated by the increased and prolonged pro-inflammatory cytokine suppression of pineal melatonin production coupled to increased gut dysbiosis and gut permeability. The suppression of pineal melatonin and gut microbiome-derived butyrate, coupled to an increase in circulating lipopolysaccharide (LPS) further dysregulates the immune response. The AhR mediates its effects via alterations in the regulation of mitochondrial function in immune cells. The increased risk of severe/fatal SARS-CoV-2 infection by high risk conditions, such as elderly age, obesity, and diabetes are mediated by these conditions having expression levels of melatonin, AhR, butyrate, and LPS that are closer to those driven by SARS-CoV-2 infection. This has a number of future research and treatment implications, including the utilization of melatonin and nutraceuticals that inhibit the AhR, including the polyphenols, epigallocatechin gallate (EGCG), and resveratrol.}, }
@article {pmid33562292, year = {2021}, author = {Traub, J and Reiss, L and Aliwa, B and Stadlbauer, V}, title = {Malnutrition in Patients with Liver Cirrhosis.}, journal = {Nutrients}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/nu13020540}, pmid = {33562292}, issn = {2072-6643}, abstract = {Liver cirrhosis is an increasing public health threat worldwide. Malnutrition is a serious complication of cirrhosis and is associated with worse outcomes. With this review, we aim to describe the prevalence of malnutrition, pathophysiological mechanisms, diagnostic tools and therapeutic targets to treat malnutrition. Malnutrition is frequently underdiagnosed and occurs-depending on the screening methods used and patient populations studied-in 5-92% of patients. Decreased energy and protein intake, inflammation, malabsorption, altered nutrient metabolism, hypermetabolism, hormonal disturbances and gut microbiome dysbiosis can contribute to malnutrition. The stepwise diagnostic approach includes a rapid prescreen, the use of a specific screening tool, such as the Royal Free Hospital Nutritional Prioritizing Tool and a nutritional assessment by dieticians. General dietary measures-especially the timing of meals-oral nutritional supplements, micronutrient supplementation and the role of amino acids are discussed. In summary malnutrition in cirrhosis is common and needs more attention by health care professionals involved in the care of patients with cirrhosis. Screening and assessment for malnutrition should be carried out regularly in cirrhotic patients, ideally by a multidisciplinary team. Further research is needed to better clarify pathogenic mechanisms such as the role of the gut-liver-axis and to develop targeted therapeutic strategies.}, }
@article {pmid33562070, year = {2021}, author = {Miller, B and Mainali, R and Nagpal, R and Yadav, H}, title = {A Newly Developed Synbiotic Yogurt Prevents Diabetes by Improving the Microbiome-Intestine-Pancreas Axis.}, journal = {International journal of molecular sciences}, volume = {22}, number = {4}, pages = {}, doi = {10.3390/ijms22041647}, pmid = {33562070}, issn = {1422-0067}, support = {R01AG018915/NH/NIH HHS/United States ; R56AG064075/NH/NIH HHS/United States ; R56AG069676/NH/NIH HHS/United States ; P30AG21332/NH/NIH HHS/United States ; W81XWH-19-1-0236//U.S. Department of Defense/ ; UL1TR001420/NH/NIH HHS/United States ; }, abstract = {The prevalence of type 2 diabetes mellitus (T2D) is increasing worldwide, and there are no long-term preventive strategies to stop this growth. Emerging research shows that perturbations in the gut microbiome significantly contribute to the development of T2D, while microbiome modulators may be beneficial for T2D prevention. However, microbiome modulators that are effective, safe, affordable, and able to be administered daily are not yet available. Based on our previous pro- and prebiotic studies, we developed a novel synbiotic yogurt comprised of human-origin probiotics and plant-based prebiotics and investigated its impact on diet- and streptozotocin-induced T2D in mice. We compared the effects of our synbiotic yogurt to those of a commercially available yogurt (control yogurt). Interestingly, we found that the feeding of the synbiotic yogurt significantly reduced the development of hyperglycemia (diabetes) in response to high-fat diet feeding and streptozotocin compared to milk-fed controls. Surprisingly, the control yogurt exacerbated diabetes progression. Synbiotic yogurt beneficially modulated the gut microbiota composition compared to milk, while the control yogurt negatively modulated it by significantly increasing the abundance of detrimental bacteria such as Proteobacteria and Enterobacteriaceae. In addition, the synbiotic yogurt protected pancreatic islet morphology compared to the milk control, while the control yogurt demonstrated worse effects on islets. These results suggest that our newly developed synbiotic yogurt protects against diabetes in mice and can be used as a therapeutic to prevent diabetes progression.}, }
@article {pmid33561742, year = {2021}, author = {Konschak, M and Zubrod, JP and Baudy, P and Fink, P and Pietz, S and Duque A, TS and Bakanov, N and Schulz, R and Bundschuh, M}, title = {Mixture effects of a fungicide and an antibiotic: Assessment and prediction using a decomposer-detritivore system.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {232}, number = {}, pages = {105762}, doi = {10.1016/j.aquatox.2021.105762}, pmid = {33561742}, issn = {1879-1514}, abstract = {Antimicrobials, such as fungicides and antibiotics, pose a risk for microbial decomposers (i.e., bacteria and aquatic fungi) and invertebrate detritivores (i.e., shredders) that play a pivotal role in the ecosystem function of leaf litter breakdown. Although waterborne toxicity and diet-related effects (i.e., dietary exposure and microorganism-mediated alterations in food quality for shredders) of fungicides and antibiotics on decomposer-detritivore systems have been increasingly documented, their joint effect is unknown. We therefore assessed waterborne and dietary effects of an antimicrobial mixture consisting of the fungicide azoxystrobin (AZO) and the antibiotic ciprofloxacin (CIP) on microbial decomposers and the shredder Gammarus fossarum using a tiered approach. We compared effect sizes measured in the present study with model predictions (i.e., independent action) based on published data. During a 7-day feeding activity assay quantifying waterborne toxicity in G. fossarum, the leaf consumption of gammarids was reduced by ∼60 % compared to the control when subjected to the mixture at concentrations of each component causing a 20 % reduction in the same response variable when applied individually. Moreover, the selective feeding of gammarids during the food choice assay indicated alterations in food quality induced by the antimicrobial mixture. The food selection and, in addition, the decrease in microbial leaf decomposition is likely linked to changes in leaf-associated bacteria and fungi. During a long-term assay, energy processing, growth and energy reserves of gammarids were increased in presence of 15 and 500 μg/L of AZO and CIP, respectively, through the dietary pathway. These physiological responses were probably driven by CIP-induced alterations in the gut microbiome or immune system of gammarids. In general, model predictions matched observed effects caused by waterborne exposure on the leaf consumption, energy processing and growth of gammarids during short- and long-term assays, respectively. However, when complex horizontal (bacteria and aquatic fungi) and vertical (leaf-associated microorganisms and shredders) interactions were involved, model predictions partly over- or underestimated mixture effects. Therefore, the present study identifies uncertainties of mixture effect predictions for complex biological systems calling for studies targeting the underlying processes and mechanisms.}, }
@article {pmid33561518, year = {2021}, author = {Wang, M and Liu, P and Kong, L and Xu, N and Lei, H}, title = {Promotive effects of sesamin on proliferation and adhesion of intestinal probiotics and its mechanism of action.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {149}, number = {}, pages = {112049}, doi = {10.1016/j.fct.2021.112049}, pmid = {33561518}, issn = {1873-6351}, abstract = {The effect of sesamin on intestinal flora was studied by in vitro animal fecal anaerobic fermentation system, and were analyzed by 16S rDNA sequencing. Results showed that sesamin modulated the composition of intestinal microorganisms and reshaped gut microbiome. The abundance of probiotics Lactobacillaceae and Bifidobacteriaceae increased, while the abundance of Enterobacteriaceae decreased. The properties of probiotics (Bifidobacterium bifidum and Lactophilus acidophilus) adhesion to epithelial colon cells (NCM460) were assessed by gram staining and plate counting methods. Results showed that sesamin increased the adhesive index of probiotics. Analysis of RT-qPCR, Western blot and immunofluorescence staining indicated that sesamin up-regulated the expression of the adhesive protein (β-cadherin and E-cadherin) of NCM460 cells. In conclusion, sesamin could promote the proliferation and adhesion of intestinal probiotics leading to modulating gut microbiota, which provided basis for sesamin as a food-borne functional factor for improving intestinal health.}, }
@article {pmid33561397, year = {2021}, author = {Simpson, RC and Shanahan, E and Scolyer, RA and Long, GV}, title = {Targeting the Microbiome to Overcome Resistance.}, journal = {Cancer cell}, volume = {39}, number = {2}, pages = {151-153}, doi = {10.1016/j.ccell.2021.01.016}, pmid = {33561397}, issn = {1878-3686}, abstract = {Immune checkpoint inhibition has revolutionized the treatment of many cancers, including melanoma. However, primary and acquired resistance remain key challenges for the field. Promising results from a phase I clinical trial recently published in Science highlight the potential of modulating the microbiome via fecal transplant to overcome resistance to immunotherapy.}, }
@article {pmid33560750, year = {2021}, author = {Wysocki, K}, title = {Genomics of aging: Decreased immune defenses.}, journal = {Journal of the American Association of Nurse Practitioners}, volume = {33}, number = {2}, pages = {100-101}, pmid = {33560750}, issn = {2327-6924}, abstract = {There are multiple factors that contribute to aging. In this second series of Genomics of Aging, decreased immune defenses and the effects of unregulated inflammation on the aging process of cells, and the body as a whole, are reviewed from the perspective of genomics and the microbiome. Healthy lifestyle choices and foods can slow down this aging process, and clinical implications are described here.}, }
@article {pmid33560626, year = {2021}, author = {Mikaelyan, KA and Krylov, KY and Petrova, MV and Shestopalov, AE}, title = {[Intestine morphology and microbiocenosis changes in critically ill patients in neurosurgery].}, journal = {Zhurnal voprosy neirokhirurgii imeni N. N. Burdenko}, volume = {85}, number = {1}, pages = {104-110}, doi = {10.17116/neiro202185011104}, pmid = {33560626}, issn = {0042-8817}, mesh = {Critical Care ; *Critical Illness ; Humans ; Intestines ; *Neurosurgery ; Neurosurgical Procedures ; }, abstract = {In recent years, the effect of critical conditions on intestine and the role of such changes in maintenance and progression of systemic disorders are of particular attention. This issue is relevant in critically ill neurosurgical patients too. Intestine morphology and microbiome changes in these patients represent a wide field for researches in intensive care and prevention of secondary damage to other organs and systems. This review ensures a current approach to the problem of intestine morphology and microbiome changes in critically ill neurosurgical patients. We reviewed the data from clinical studies and experiments reproducing a critical condition in animals. Most publications are indexed in the PubMed, e-library, Google Scholar databases. We also analyzed the data from NEJM, JAMA, Lancet, Critical Care and other issues. The manuscript contains an overview of 44 foreign and 13 domestic references; over 50% of researches were published within the past 5 years. Searching depth was over 50 years.}, }
@article {pmid33560577, year = {2021}, author = {Li, J and Deng, Q and Zhang, Y and Wu, D and Li, G and Liu, J and Zhang, L and Wang, HD}, title = {Three Novel Dietary Phenolic Compounds from Pickled Raphanus Sativus L. Inhibit Lipid Accumulation in Obese Mice by Modulating the Gut Microbiota Composition.}, journal = {Molecular nutrition &amp; food research}, volume = {}, number = {}, pages = {e2000780}, doi = {10.1002/mnfr.202000780}, pmid = {33560577}, issn = {1613-4133}, abstract = {SCOPE: Although pickled radish is widely consumed worldwide, few studies have investigated the nutritional benefits of bioactive compounds extracted from pickled radish. In this study, we investigated the relationship among dietary phenolic compounds, lipid accumulation and gut microbiota.<br><br>METHOD AND RESULTS: Three phenolic compounds 2,6-dihydroxyacetophenone (DHAP), 4-hydroxyphenethyl alcohol (4-HPEA) and 4-hydroxybenzaldehyde (HBA) were extracted from pickled radish. LO2 cells treated with free fatty acid were first used to explore the impact of the above three compounds at different doses on reducing lipid levels. The effects of the three compounds on obesity and the gut microbiota were further investigated in high-fat diet (HFD)-induced KM mice. Results showed that three compounds inhibited the lipid accumulation in LO2 cells. The results of animal experiments revealed that three compounds prevented body weight gain and significantly decreased serum lipid levels. Treatment with DHAP, HPEA and HBA reversed gut microbiome dysbiosis in HFD-induced mice. The three phenolic compounds increased Odoribacter, and decreased Helicobacter and Mucispirillum. Notably, DHAP and HBA reduced the HFD-induced increase in the Firmicutes/Bacteroidetes ratio.<br><br>CONCLUSION: These data suggested that phenolic compounds extracted from pickled radish possess excellent lipid-lowering capacity, providing a theoretical basis for further analysis of the nutritional value of pickled radish. This article is protected by copyright. All rights reserved.}, }
@article {pmid33560463, year = {2021}, author = {Kranz, J and Schneidewind, L and Pilatz, A and Wagenlehner, FRA}, title = {[Antibiotic prophylaxis for endourological interventions considering antibiotic stewardship].}, journal = {Der Urologe. Ausg. A}, volume = {}, number = {}, pages = {}, pmid = {33560463}, issn = {1433-0563}, abstract = {Perioperative antibiotic prophylaxis in endourology is used to reduce or avoid postoperative surgical site infections and complicated urinary tract infections. Special attention is paid to antibiotic stewardship strategies to avoid the continuing selection of antibiotics and multidrug-resistant uropathogens as well as collateral damage to the microbiome. The individual risk profile, the local resistance situation, the expected pathogen spectrum, the pharmacokinetics and the approval of each substance are important aspects to be considered in the indications and selection of perioperative antibiotic prophylaxis. Furthermore, applicable hygiene regulations and the surgical care of an intervention must be observed.}, }
@article {pmid33560341, year = {2021}, author = {Wang, Q and McDermott, TR and Walk, ST}, title = {A Single Microbiome Gene Alters Murine Susceptibility to Acute Arsenic Exposure.}, journal = {Toxicological sciences : an official journal of the Society of Toxicology}, volume = {}, number = {}, pages = {}, doi = {10.1093/toxsci/kfab017}, pmid = {33560341}, issn = {1096-0929}, abstract = {Environmental toxicant exposure contributes to the morbidity and mortality of many human diseases. With respect to arsenic, microbially driven chemical transformations dictate its toxicity and mobility in virtually every environment yet studied, so a general hypothesis is that human gut microbiome determines disease outcome following exposure. However, the complex nature of the gut microbiome and the myriad of potential interactions with human cells/tissues make it challenging to quantify the influence of specific arsenic-active functions-a requisite step in developing effective disease prevention and/or clinical intervention strategies. To control both mammalian and microbial function during toxicant exposure, we genetically defined the gut microbiome of mice using only Escherichia coli strain, AW3110 (ΔarsRBC), or the same strain carrying a single genome copy of the Fucus vesiculosus metallothionein gene (AW3110::fmt); a cysteine-rich peptide that complexes with arsenite, facilitating bioaccumulation and reducing its toxic effects. AW3110::fmt bioaccumulated significantly more arsenic and gnotobiotic mice colonized by this strain excreted significantly more arsenic in stool and accumulated significantly less arsenic in organs. Moreover, AW3110::fmt gnotobiotic mice were protected from acute toxicity exposure (20 ppm AsIII) relative to controls. This study demonstrates-in a highly controlled fashion-that a single microbiome function (arsenic bioaccumulation) encoded by a single gene in a single human gut microbiome bacterium significantly alters mammalian host arsenic exposure. The experimental model described herein allows for a highly controlled and directed assessment of microbiome functions and is useful to quantify the influence of specific microbiome-arsenic interactions that help mitigate human disease.}, }
@article {pmid33559845, year = {2021}, author = {Chaikijurajai, T and Tang, WHW}, title = {Gut Microbiome and Precision Nutrition in Heart Failure: Hype or Hope?.}, journal = {Current heart failure reports}, volume = {}, number = {}, pages = {}, pmid = {33559845}, issn = {1546-9549}, support = {R01HL126827/HL/NHLBI NIH HHS/United States ; }, abstract = {PURPOSE OF REVIEW: Over the past decade, the gut microbiome has been shown to play an important role in the pathogenesis of heart failure (HF) and serves as a mediator that links host genomes and environmental exposure (especially dietary intake) to the development and progression of HF. Given that alterations in gut microbial composition and metabolism are commonly seen in patients with HF, the use of gut microbial metabolites as diagnostic and prognostic biomarkers, as well as novel therapeutic targets for HF, is promising.<br><br>RECENT FINDINGS: Alterations in gut microbial composition and function have bidirectional relationships with HF. Gut microbial metabolites, including short-chain fatty acids, bile acids, trimethylamine N-oxide (TMAO), and amino acid metabolites, have been shown to play a significant role in HF. For example, TMAO has been consistently demonstrated as an independent predictor of worse prognosis in patients with HF, and a potential therapeutic target for cardiac remodeling and HF. However, clinical studies on dietary interventions targeting gut microbial metabolites have demonstrated inconsistent findings, which could be from variations in the study population, gut microbial communities, and study designs. Measurement of gut microbial metabolites can improve risk stratification and potentially identify HF patients who are more likely to respond to personalized pharmacologic or dietary interventions targeting specific pathways associated with the gut microbiome.}, }
@article {pmid33559707, year = {2021}, author = {Fromentin, M and Ricard, JD and Roux, D}, title = {Respiratory microbiome in mechanically ventilated patients: a narrative review.}, journal = {Intensive care medicine}, volume = {}, number = {}, pages = {}, pmid = {33559707}, issn = {1432-1238}, support = {Established Investigator award//European Society of Intensive Care Medicine/ ; Basic Science Award//European Society of Intensive Care Medicine/ ; MSD/SRLF//Société de Réanimation de Langue Française/ ; Young investigator award//Société de Pathologie Infectieuse de Langue Française/ ; }, abstract = {The respiratory microbiome has been less explored than the gut microbiome. Despite the speculated importance of dysbiosis of the microbiome in ventilator-associated pneumonia (VAP) and acute respiratory distress syndrome (ARDS), only few studies have been performed in invasively ventilated ICU patients. And only the results of small cohorts have been published. An overlap exists between bacterial populations observed in the lower respiratory tract and the oropharyngeal tract. The bacterial microbiota is characterized by relatively abundant bacteria difficult to cultivate by standard methods. Under mechanical ventilation, a dysbiosis occurs with a drop overtime in diversity. During VAP development, lung dysbiosis is characterized by a shift towards a dominant bacterial pathogen (mostly Proteobacteria) whereas enrichment of gut-associated bacteria mainly Enterobacteriaceae is the specific feature discriminating ARDS patients. However, the role of this dysbiosis in VAP and ARDS pathogenesis is not yet fully understood. A more in-depth analysis of the interplay between bacteria, virus and fungi and a better understanding of the host-microbiome interaction could provide a more comprehensive view of the role of the microbiome in VAP and ARDS pathogenesis. Priority should be given to validate a consensual and robust methodology for respiratory microbiome research and to conduct longitudinal studies. A deeper understanding of microbial interplay should be a valuable guide for care of ARDS and VAP preventive/therapeutic strategies. We present a review on the current knowledge and expose perspectives and potential clinical applications of respiratory microbiome research in mechanically ventilated patients.}, }
@article {pmid33559398, year = {2021}, author = {Michán, C and Blasco, J and Alhama, J}, title = {High-throughput molecular analyses of microbiomes as a tool to monitor the wellbeing of aquatic environments.}, journal = {Microbial biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1751-7915.13763}, pmid = {33559398}, issn = {1751-7915}, support = {CTM2016-75908-R//Spanish Ministry of Economy and Competitiveness/ ; PID2019-110049RB-I00//Spanish Ministry of Science and Innovation/ ; UCO-FEDER-1262384-R//European Regional Development Fund/ ; //Chelonia Association/ ; }, abstract = {Aquatic environments are the recipients of many sources of environmental stress that trigger both local and global changes. To evaluate the associated risks to organisms and ecosystems more sensitive and accurate strategies are required. The analysis of the microbiome is one of the most promising candidates for environmental diagnosis of aquatic systems. Culture-independent interconnected meta-omic approaches are being increasing used to fill the gaps that classical microbial approaches cannot resolve. Here, we provide a prospective view of the increasing application of these high-throughput molecular technologies to evaluate the structure and functional activity of microbial communities in response to changes and disturbances in the environment, mostly of anthropogenic origin. Some relevant topics are reviewed, such as: (i) the use of microorganisms for water quality assessment, highlighting the incidence of antimicrobial resistance as an increasingly serious threat to global public health; (ii) the crucial role of microorganisms and their complex relationships with the ongoing climate change, and other stress threats; (iii) the responses of the environmental microbiome to extreme pollution conditions, such as acid mine drainage or oil spills. Moreover, protists and viruses, due to their huge impacts on the structure of microbial communities, are emerging candidates for the assessment of aquatic environmental health.}, }
@article {pmid33558755, year = {2021}, author = {Tsai, HH and Schmidt, W}, title = {The enigma of environmental pH sensing in plants.}, journal = {Nature plants}, volume = {}, number = {}, pages = {}, pmid = {33558755}, issn = {2055-0278}, abstract = {Environmental pH is a critical parameter for innumerable chemical reactions, myriad biological processes and all forms of life. The mechanisms that underlie the perception of external pH (pHe) have been elucidated in detail for bacteria, fungi and mammalian cells; however, little information is available on whether and, if so, how pHe is perceived by plants. This is particularly surprising since hydrogen ion activity of the substrate is of paramount significance for plants, governing the availability of mineral nutrients, the structure of the soil microbiome and the composition of natural plant communities. Rapid changes in soil pH require constant readjustment of nutrient acquisition strategies, which is associated with dynamic alterations in gene expression. Referring to observations made in diverse experimental set-ups that unambiguously show that pHe per se affects gene expression, we hypothesize that sensing of pHe in plants is mandatory to prioritize responses to various simultaneously received environmental cues.}, }
@article {pmid33558739, year = {2021}, author = {Onuora, S}, title = {Gut microbiome could predict drug response in RA.}, journal = {Nature reviews. Rheumatology}, volume = {}, number = {}, pages = {}, pmid = {33558739}, issn = {1759-4804}, }
@article {pmid33558654, year = {2021}, author = {Zhang, JD and Liu, J and Zhu, SW and Fang, Y and Wang, B and Jia, Q and Hao, HF and Kao, JY and He, QH and Song, LJ and Liu, F and Zhu, BL and Owyang, C and Duan, LP}, title = {Berberine alleviates visceral hypersensitivity in rats by altering gut microbiome and suppressing spinal microglial activation.}, journal = {Acta pharmacologica Sinica}, volume = {}, number = {}, pages = {}, pmid = {33558654}, issn = {1745-7254}, abstract = {Accumulating evidence shows that agents targeting gut dysbiosis are effective for improving symptoms of irritable bowel syndrome (IBS). However, the potential mechanisms remain unclear. In this study we investigated the effects of berberine on the microbiota-gut-brain axis in two rat models of visceral hypersensitivity, i.e., specific pathogen-free SD rats subjected to chronic water avoidance stress (WAS) and treated with berberine (200 mg· kg-1 ·d-1, ig, for 10 days) as well as germ-free (GF) rats subjected to fecal microbiota transplantation (FMT) from a patient with IBS (designated IBS-FMT) and treated with berberine (200 mg· kg-1 ·d-1, ig, for 2 weeks). Before the rats were sacrificed, visceral sensation and depressive behaviors were evaluated. Then colonic tryptase was measured and microglial activation in the dorsal lumbar spinal cord was assessed. The fecal microbiota was profiled using 16S rRNA sequencing, and short chain fatty acids (SCFAs) were measured. We showed that berberine treatment significantly alleviated chronic WAS-induced visceral hypersensitivity and activation of colonic mast cells and microglia in the dorsal lumbar spinal cord. Transfer of fecal samples from berberine-treated stressed donors to GF rats protected against acute WAS. FMT from a patient with IBS induced visceral hypersensitivity and pro-inflammatory phenotype in microglia, while berberine treatment reversed the microglial activation and altered microbial composition and function and SCFA profiles in stools of IBS-FMT rats. We demonstrated that berberine did not directly influence LPS-induced microglial activation in vitro. In both models, several SCFA-producing genera were enriched by berberine treatment, and positively correlated to the morphological parameters of microglia. In conclusion, activation of microglia in the dorsal lumbar spinal cord was involved in the pathogenesis of IBS caused by dysregulation of the microbiota-gut-brain axis, and the berberine-altered gut microbiome mediated the modulatory effects of the agent on microglial activation and visceral hypersensitivity, providing a potential option for the treatment of IBS.}, }
@article {pmid33558614, year = {2021}, author = {Sharma, L and Nagpal, R and Jackson, CR and Patel, D and Singh, P}, title = {Antibiotic-resistant bacteria and gut microbiome communities associated with wild-caught shrimp from the United States versus imported farm-raised retail shrimp.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {3356}, pmid = {33558614}, issn = {2045-2322}, abstract = {In the United States, farm-raised shrimp accounts for ~ 80% of the market share. Farmed shrimp are cultivated as monoculture and are susceptible to infections. The aquaculture industry is dependent on the application of antibiotics for disease prevention, resulting in the selection of antibiotic-resistant bacteria. We aimed to characterize the prevalence of antibiotic-resistant bacteria and gut microbiome communities in commercially available shrimp. Thirty-one raw and cooked shrimp samples were purchased from supermarkets in Florida and Georgia (U.S.) between March-September 2019. The samples were processed for the isolation of antibiotic-resistant bacteria, and isolates were characterized using an array of molecular and antibiotic susceptibility tests. Aerobic plate counts of the cooked samples (n = 13) varied from < 25 to 6.2 log CFU/g. Isolates obtained (n = 110) were spread across 18 genera, comprised of coliforms and opportunistic pathogens. Interestingly, isolates from cooked shrimp showed higher resistance towards chloramphenicol (18.6%) and tetracycline (20%), while those from raw shrimp exhibited low levels of resistance towards nalidixic acid (10%) and tetracycline (8.2%). Compared to wild-caught shrimp, the imported farm-raised shrimp harbored distinct gut microbiota communities and a higher prevalence of antibiotic-resistance genes in their gut. The presence of antibiotic-resistant strains in cooked shrimps calls for change in processing for their mitigation.}, }
@article {pmid33558598, year = {2021}, author = {Bayal, N and Nagpal, S and Haque, MM and Patole, MS and Shouche, Y and Mande, SC and Mande, SS}, title = {Structural aspects of lesional and non-lesional skin microbiota reveal key community changes in leprosy patients from India.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {3294}, pmid = {33558598}, issn = {2045-2322}, support = {DBT/PR15450/COE/34/46/2016//Department of Biotechnology, Ministry of Science and Technology, India/ ; }, abstract = {Although skin is the primary affected organ in Leprosy, the role of the skin microbiome in its pathogenesis is not well understood. Recent reports have shown that skin of leprosy patients (LP) harbours perturbed microbiota which grants inflammation and disease progression. Herein, we present the results of nested Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) which was initially performed for investigating the diversity of bacterial communities from lesional skin (LS) and non-lesional skin (NLS) sites of LP (n = 11). Further, we performed comprehensive analysis of 16S rRNA profiles corresponding to skin samples from participants (n = 90) located in two geographical locations i.e. Hyderabad and Miraj in India. The genus Staphylococcus was observed to be one of the representative bacteria characterizing healthy controls (HC; n = 30), which in contrast was underrepresented in skin microbiota of LP. Taxa affiliated to phyla Firmicutes and Proteobacteria were found to be signatures of HC and LS, respectively. Observed diversity level changes, shifts in core microbiota, and community network structure support the evident dysbiosis in normal skin microbiota due to leprosy. Insights obtained indicate the need for exploring skin microbiota modulation as a potential therapeutic option for leprosy.}, }
@article {pmid33558514, year = {2021}, author = {Beck, KL and Haiminen, N and Chambliss, D and Edlund, S and Kunitomi, M and Huang, BC and Kong, N and Ganesan, B and Baker, R and Markwell, P and Kawas, B and Davis, M and Prill, RJ and Krishnareddy, H and Seabolt, E and Marlowe, CH and Pierre, S and Quintanar, A and Parida, L and Dubois, G and Kaufman, J and Weimer, BC}, title = {Monitoring the microbiome for food safety and quality using deep shotgun sequencing.}, journal = {NPJ science of food}, volume = {5}, number = {1}, pages = {3}, pmid = {33558514}, issn = {2396-8370}, abstract = {In this work, we hypothesized that shifts in the food microbiome can be used as an indicator of unexpected contaminants or environmental changes. To test this hypothesis, we sequenced the total RNA of 31 high protein powder (HPP) samples of poultry meal pet food ingredients. We developed a microbiome analysis pipeline employing a key eukaryotic matrix filtering step that improved microbe detection specificity to >99.96% during in silico validation. The pipeline identified 119 microbial genera per HPP sample on average with 65 genera present in all samples. The most abundant of these were Bacteroides, Clostridium, Lactococcus, Aeromonas, and Citrobacter. We also observed shifts in the microbial community corresponding to ingredient composition differences. When comparing culture-based results for Salmonella with total RNA sequencing, we found that Salmonella growth did not correlate with multiple sequence analyses. We conclude that microbiome sequencing is useful to characterize complex food microbial communities, while additional work is required for predicting specific species' viability from total RNA sequencing.}, }
@article {pmid33558460, year = {2020}, author = {Kroese, JM and Volgenant, CMC and van Schaardenburg, D and Loos, BG and Crielaard, W and Lobbezoo, F}, title = {Temporomandibular joint function, periodontal health, and oral microbiome in early rheumatoid arthritis and at-risk individuals: a prospective cohort study protocol.}, journal = {BDJ open}, volume = {6}, number = {1}, pages = {7}, pmid = {33558460}, issn = {2056-807X}, abstract = {OBJECTIVES/AIMS: Rheumatoid arthritis (RA) is an autoimmune disease affecting the joints, including the temporomandibular joint (TMJ). Early diagnosis and treatment can alleviate symptoms and prevent progression. Predictors for disease outcome in individuals at risk for RA are therefore valuable. While limited information is available on the prevalence of TMJ involvement in early RA, previous studies suggest that RA, periodontitis and the oral microbiome are interrelated. Predictive factors for RA development may thus be present in the oral cavity. Our two aims are: (1) to assess the prevalence of TMJ involvement in early RA, and (2) to investigate the predictive value of oral factors in RA development.<br><br>MATERIALS AND METHODS: We will include 150 individuals in this multi-center, prospective cohort study: 50 patients with early RA, 50 at-risk individuals, and 50 healthy controls. At baseline, the TMJ, periodontal health, and the oral microbiome will be examined. The general health will be followed over time, on four occasions up to 3 years.<br><br>DISCUSSION: Our results will provide insight into the prevalence and clinical characterization of TMJ involvement in early RA. For at-risk individuals, oral factors can be studied as possible predictors for the development of RA.}, }
@article {pmid33558272, year = {2021}, author = {Xu, K and Gao, X and Xia, G and Chen, M and Zeng, N and Wang, S and You, C and Tian, X and Di, H and Tang, W and Li, P and Wang, H and Zeng, X and Tan, C and Meng, F and Li, H and He, Y and Zhou, H and Yin, J}, title = {Rapid gut dysbiosis induced by stroke exacerbates brain infarction in turn.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2020-323263}, pmid = {33558272}, issn = {1468-3288}, abstract = {OBJECTIVE: Stroke is a leading cause of death and disability worldwide. Neuroprotective approaches have failed in clinical trials, thus warranting therapeutic innovations with alternative targets. The gut microbiota is an important contributor to many risk factors for stroke. However, the bidirectional interactions between stroke and gut microbiota remain largely unknown.<br><br>DESIGN: We performed two clinical cohort studies to capture the gut dysbiosis dynamics after stroke and their relationship with stroke prognosis. Then, we used a middle cerebral artery occlusion model to explore gut dysbiosis post-stroke in mice and address the causative relationship between acute ischaemic stroke and gut dysbiosis. Finally, we tested whether aminoguanidine, superoxide dismutase and tungstate can alleviate post-stroke brain infarction by restoring gut dysbiosis.<br><br>RESULTS: Brain ischaemia rapidly induced intestinal ischaemia and produced excessive nitrate through free radical reactions, resulting in gut dysbiosis with Enterobacteriaceae expansion. Enterobacteriaceae enrichment exacerbated brain infarction by enhancing systemic inflammation and is an independent risk factor for the primary poor outcome of patients with stroke. Administering aminoguanidine or superoxide dismutase to diminish nitrate generation or administering tungstate to inhibit nitrate respiration all resulted in suppressed Enterobacteriaceae overgrowth, reduced systemic inflammation and alleviated brain infarction. These effects were gut microbiome dependent and indicated the translational value of the brain-gut axis in stroke treatment.<br><br>CONCLUSIONS: This study reveals a reciprocal relationship between stroke and gut dysbiosis. Ischaemic stroke rapidly triggers gut microbiome dysbiosis with Enterobacteriaceae overgrowth that in turn exacerbates brain infarction.}, }
@article {pmid33557959, year = {2021}, author = {Wang, Y and Nan, X and Zhao, Y and Jiang, L and Wang, M and Wang, H and Zhang, F and Xue, F and Hua, D and Liu, J and Yao, J and Xiong, B}, title = {Rumen microbiome structure and metabolites activity in dairy cows with clinical and subclinical mastitis.}, journal = {Journal of animal science and biotechnology}, volume = {12}, number = {1}, pages = {36}, pmid = {33557959}, issn = {1674-9782}, abstract = {BACKGROUND: Due to the high prevalence and complex etiology, bovine mastitis (BM) is one of the most important diseases to compromise dairy cow health and milk quality. The shift in milk compositions has been widely investigated during mastitis, but recent studies suggested that gastrointestinal microorganism also has a crucial effect on the inflammation of other peripheral tissues and organs, including the mammary gland. However, research focused on the variation of rumen inner-environment during mastitis is still limited. Therefore, the ruminal microbial profiles, metabolites, and milk compositions in cows with different udder health conditions were compared in the present study. Furthermore, the correlations between udder health status and ruminal conditions were investigated. Based on the somatic cell counts (SCC), California mastitis test (CMT) parameters and clinical symptoms of mastitis, 60 lactating Holstein dairy cows with similar body conditions (excepted for the udder health condition) were randomly divided into 3 groups (n = 20 per group) including the healthy (H) group, the subclinical mastitis (SM) group and the clinical mastitis (CM) group. Lactation performance and rumen fermentation parameters were recorded. And rumen microbiota and metabolites were also analyzed via 16S rRNA amplicon sequencing and untargeted metabolomics, respectively.<br><br>RESULTS: As the degree of mastitis increased, rumen lactic acid (LA) (P < 0.01), acetate, propionate, butyrate, valerate (P < 0.001), and total volatile fatty acids (TVFAs) (P < 0.01) concentrations were significantly decreased. In the rumen of CM cows, the significantly increased bacteria related to intestinal and oral inflammation, such as Lachnospiraceae (FDR-adjusted P = 0.039), Moraxella (FDR-adjusted P = 0.011) and Neisseriaceae (FDR-adjusted P = 0.036), etc., were accompanied by a significant increase in 12-oxo-20-dihydroxy-leukotriene B4 (FDR-adjusted P = 5.97 × 10- 9) and 10beta-hydroxy-6beta-isobutyrylfuranoeremophilane (FDR-adjusted P = 3.88 × 10- 10). Meanwhile, in the rumen of SM cows, the Ruminiclostridium_9 (FDR-adjusted P = 0.042) and Enterorhabdus (FDR-adjusted P = 0.043) were increased along with increasing methenamine (FDR-adjusted P = 6.95 × 10- 6), 5-hydroxymethyl-2-furancarboxaldehyde (5-HMF) (FDR-adjusted P = 2.02 × 10- 6) and 6-methoxymellein (FDR-adjusted P = 2.57 × 10- 5). The short-chain fatty acids (SCFAs)-producing bacteria and probiotics in rumen, including Prevoterotoella_1 (FDR-adjusted P = 0.045) and Bifidobacterium (FDR-adjusted P = 0.035), etc., were significantly reduced, with decreasing 2-phenylbutyric acid (2-PBA) (FDR-adjusted P = 4.37 × 10- 6).<br><br>CONCLUSION: The results indicated that there was a significant shift in the ruminal microflora and metabolites associated with inflammation and immune responses during CM. Moreover, in the rumen of cows affected by SM, the relative abundance of several opportunistic pathogens and the level of metabolites which could produce antibacterial compounds or had a competitive inhibitory effect were all increased.}, }
@article {pmid33557941, year = {2021}, author = {Liu, F and Ye, S and Zhu, X and He, X and Wang, S and Li, Y and Lin, J and Wang, J and Lin, Y and Ren, X and Li, Y and Deng, Z}, title = {Gastrointestinal disturbance and effect of fecal microbiota transplantation in discharged COVID-19 patients.}, journal = {Journal of medical case reports}, volume = {15}, number = {1}, pages = {60}, pmid = {33557941}, issn = {1752-1947}, support = {81970156//National Natural Science foundation of China/ ; 81970118//National Natural Science foundation of China/ ; }, abstract = {BACKGROUND: To investigate the potential beneficial effect of fecal microbiota transplantation (FMT) on gastrointestinal symptoms, gut dysbiosis and immune status in discharged COVID-19 patients.<br><br>CASE PRESENTATION: A total of 11 COVID-19 patients were recruited in April, 2020, about one month on average after they were discharged from the hospital. All subjects received FMT for 4 consecutive days by oral capsule administrations with 10 capsules for each day. In total, 5 out of 11 patients reported to be suffered from gastrointestinal symptoms, which were improved after FMT. After FMT, alterations of B cells were observed, which was characterized as decreased naive B cell (P = 0.012) and increased memory B cells (P = 0.001) and non-switched B cells (P = 0.012).The microbial community richness indicated by operational taxonomic units number, observed species and Chao1 estimator was marginally increased after FMT. Gut microbiome composition of discharged COVID-19 patients differed from that of the general population at both phylum and genera level, which was characterized with a lower proportion of Firmicutes (41.0%) and Actinobacteria (4.0%), higher proportion of Bacteroidetes (42.9%) and Proteobacteria (9.2%). FMT can partially restore the gut dysbiosis by increasing the relative abundance of Actinobacteria (15.0%) and reducing Proteobacteria (2.8%) at the phylum level. At the genera level, Bifidobacterium and Faecalibacterium had significantly increased after FMT.<br><br>CONCLUSIONS: After FMT, altered peripheral lymphocyte subset, restored gut microbiota and alleviated gastrointestinal disorders were observe, suggesting that FMT may serve as a potential therapeutic and rehabilitative intervention for the COVID-19.}, }
@article {pmid33557825, year = {2021}, author = {Omoke, D and Kipsum, M and Otieno, S and Esalimba, E and Sheth, M and Lenhart, A and Njeru, EM and Ochomo, E and Dada, N}, title = {Western Kenyan Anopheles gambiae showing intense permethrin resistance harbour distinct microbiota.}, journal = {Malaria journal}, volume = {20}, number = {1}, pages = {77}, pmid = {33557825}, issn = {1475-2875}, support = {American Committee of Medical Entomology Future Leaders in International Entomology Award//American Society of Tropical Medicine and Hygiene/ ; OPP1210769//Bill and Melinda Gates Foundation/ ; }, abstract = {BACKGROUND: Insecticide resistance poses a growing challenge to malaria vector control in Kenya and around the world. Following evidence of associations between the mosquito microbiota and insecticide resistance, the microbiota of Anopheles gambiae sensu stricto (s.s.) from Tulukuyi village, Bungoma, Kenya, with differing permethrin resistance profiles were comparatively characterized.<br><br>METHODS: Using the CDC bottle bioassay, 133 2-3 day-old, virgin, non-blood fed female F1 progeny of field-caught An. gambiae s.s. were exposed to five times (107.5 µg/ml) the discriminating dose of permethrin. Post bioassay, 50 resistant and 50 susceptible mosquitoes were subsequently screened for kdr East and West mutations, and individually processed for microbial analysis using high throughput sequencing targeting the universal bacterial and archaeal 16S rRNA gene.<br><br>RESULTS: 47 % of the samples tested (n = 133) were resistant, and of the 100 selected for further processing, 99 % were positive for kdr East and 1 % for kdr West. Overall, 84 bacterial taxa were detected across all mosquito samples, with 36 of these shared between resistant and susceptible mosquitoes. A total of 20 bacterial taxa were unique to the resistant mosquitoes and 28 were unique to the susceptible mosquitoes. There were significant differences in bacterial composition between resistant and susceptible individuals (PERMANOVA, pseudo-F = 2.33, P = 0.001), with presence of Sphingobacterium, Lysinibacillus and Streptococcus (all known pyrethroid-degrading taxa), and the radiotolerant Rubrobacter, being significantly associated with resistant mosquitoes. On the other hand, the presence of Myxococcus, was significantly associated with susceptible mosquitoes.<br><br>CONCLUSIONS: This is the first report of distinct microbiota in An. gambiae s.s. associated with intense pyrethroid resistance. The findings highlight differentially abundant bacterial taxa between resistant and susceptible mosquitoes, and further suggest a microbe-mediated mechanism of insecticide resistance in mosquitoes. These results also indicate fixation of the kdr East mutation in this mosquito population, precluding further analysis of its associations with the mosquito microbiota, but presenting the hypothesis that any microbe-mediated mechanism of insecticide resistance would be likely of a metabolic nature. Overall, this study lays initial groundwork for understanding microbe-mediated mechanisms of insecticide resistance in African mosquito vectors of malaria, and potentially identifying novel microbial markers of insecticide resistance that could supplement existing vector surveillance tools.}, }
@article {pmid33557737, year = {2021}, author = {Panza, R and Baldassarre, ME and Di Mauro, A and Cervinara, A and Capozza, M and Laforgia, N}, title = {Infantile functional gastrointestinal disorders and maternal psychological status: a narrative review.}, journal = {Current pediatric reviews}, volume = {}, number = {}, pages = {}, doi = {10.2174/1573396317666210208155106}, pmid = {33557737}, issn = {1875-6336}, abstract = {BACKGROUND: Functional gastrointestinal disorders are often extremely distressing for the infant and parents, leading to infant discomfort and crying, parental anxiety, repeated healthcare consultations, and escalating healthcare costs.<br><br>AIM: In this narrative review we analyzed the relationship between maternal psychological status during pregnancy and postpartum and the main infantile functional gastrointestinal disorders.<br><br>MATERIALS AND METHODS: The narrative reviewwas conducted searching scientific databases for articles reporting on infantile functional gastrointestinal disorders in association with maternal depressive or anxiety disorders.<br><br>RESULTS: seven studies were suitable.<br><br>DISCUSSION: Maternal psychological disorders may be correlated to infantile functional gastrointestinal disorders. Whether it is the excessive crying that favors the onset of maternal psychological disorders or, in contrast, an altered attachment style due to the maternal status that facilitates the onset of functional gastrointestinal disorders in the infant is still an open question. Recent findings revealed that both anxious and depressed mothers are more likely to have an adverse gut microbiome.<br><br>CONCLUSIONS: A healthy interaction of the mother-baby dyad is advantageous in ensuring mental and physical development of the offspring. Gynecologists, general practitioners and pediatricians should be alert for an early identification of mothers at risk with the aim to initiate timely targeted interventions. Further research on the role of microbiota and the possible therapeutic approaches with probiotics is required.}, }
@article {pmid33557667, year = {2021}, author = {Tavella, T and Rampelli, S and Guidarelli, G and Bazzocchi, A and Gasperini, C and Pujos-Guillot, E and Comte, B and Barone, M and Biagi, E and Candela, M and Nicoletti, C and Kadi, F and Battista, G and Salvioli, S and O'Toole, PW and Franceschi, C and Brigidi, P and Turroni, S and Santoro, A}, title = {Elevated gut microbiome abundance of Christensenellaceae, Porphyromonadaceae and Rikenellaceae is associated with reduced visceral adipose tissue and healthier metabolic profile in Italian elderly.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1-19}, doi = {10.1080/19490976.2021.1880221}, pmid = {33557667}, issn = {1949-0984}, abstract = {Aging is accompanied by physiological changes affecting body composition and functionality, including accumulation of fat mass at the expense of muscle mass, with effects upon morbidity and quality of life. The gut microbiome has recently emerged as a key environmental modifier of human health that can modulate healthy aging and possibly longevity. However, its associations with adiposity in old age are still poorly understood. Here we profiled the gut microbiota in a well-characterized cohort of 201 Italian elderly subjects from the NU-AGE study, by 16S rRNA amplicon sequencing. We then tested for association with body composition from dual-energy X-ray absorptiometry (DXA), with a focus on visceral and subcutaneous adipose tissue. Dietary patterns, serum metabolome and other health-related parameters were also assessed. This study identified distinct compositional structures of the elderly gut microbiota associated with DXA parameters, diet, metabolic profiles and cardio-metabolic risk factors.}, }
@article {pmid33557631, year = {2021}, author = {}, title = {Erratum: Microbiome of Catheter Collected Urine in Males with Bladder Cancer According to Disease Stage.}, journal = {The Journal of urology}, volume = {205}, number = {3}, pages = {942}, doi = {10.1097/JU.0000000000001585}, pmid = {33557631}, issn = {1527-3792}, }
@article {pmid33557583, year = {2021}, author = {Han, QQ and Fu, Y and Le, JM and Pilot, A and Cheng, S and Chen, PQ and Wu, H and Wan, GQ and Gu, XF}, title = {Electroacupuncture may alleviate behavioral defects via modulation of gut microbiota in a mouse model of Parkinson's disease.}, journal = {Acupuncture in medicine : journal of the British Medical Acupuncture Society}, volume = {}, number = {}, pages = {964528421990658}, doi = {10.1177/0964528421990658}, pmid = {33557583}, issn = {1759-9873}, abstract = {OBJECTIVE: Parkinson's disease (PD) is a chronic neurodegenerative disease involving non-motor symptoms, of which gastrointestinal disorders are the most common. In light of recent results, intestinal dysfunction may be involved in the pathogenesis of PD. Electroacupuncture (EA) has shown potential effects, although the underlying mechanism remains mostly unknown. We speculated that EA could relieve the behavioral defects of PD, and that this effect would be associated with modulation of the gut microbiota.<br><br>METHODS: Mice were randomly divided into three groups: control, PD + MA (manual acupuncture), and PD + EA. MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine) was used to establish the mouse model of PD. Rotarod performance tests, open field tests, and pole tests were carried out to assess motor deficiencies. Immunohistochemistry was conducted to examine the survival of dopaminergic neurons. 16S ribosomal RNA (rRNA) gene sequencing was applied to investigate the alterations of the gut microbiome. Quantitative real-time polymerase chain reaction (PCR) was performed to characterize the messenger RNA (mRNA) levels of pro-inflammatory and anti-inflammatory cytokines.<br><br>RESULTS: We found that EA was able to alleviate the behavioral defects in the rotarod performance test and pole test, and partially rescue the significant loss of dopaminergic neurons in the substantia nigra (SN) chemically induced by MPTP in mice. Moreover, the PD + MA mice showed a tendency toward decreased intestinal microbial alpha diversity, while EA significantly reversed it. The abundance of Erysipelotrichaceae was significantly increased in PD + MA mice, and the alteration was also reversed by EA. In addition, the pro-inflammatory cytokines interleukin (IL)-6 and tumor necrosis factor (TNF)-α were substantially increased in the SN of PD + MA mice, an effect that was reversed by EA.<br><br>CONCLUSION: These results suggest that EA may alleviate behavioral defects via modulation of gut microbiota and suppression of inflammation in the SN of mice with PD, which provides new insights into the pathogenesis of PD and its treatment.}, }
@article {pmid33557433, year = {2021}, author = {Krauze, M and Cendrowska-Pinkosz, M and Matuseviĉius, P and Stępniowska, A and Jurczak, P and Ognik, K}, title = {The Effect of Administration of a Phytobiotic Containing Cinnamon Oil and Citric Acid on the Metabolism, Immunity, and Growth Performance of Broiler Chickens.}, journal = {Animals : an open access journal from MDPI}, volume = {11}, number = {2}, pages = {}, doi = {10.3390/ani11020399}, pmid = {33557433}, issn = {2076-2615}, abstract = {It was postulated that a phytobiotic preparation containing cinnamon oil and citric acid added to drinking water for chickens in a suitable amount and for a suitable time would beneficially modify the microbiota composition and morphology of the small intestine, thereby improving immunity and growth performance without inducing metabolic disorders. The aim of the study was to establish the dosage and time of administration of such a phytobiotic that would have the most beneficial effect on the intestinal histology and microbiota, production results, and immune and metabolic status of broiler chickens. The experiment was carried out on 980 one-day-old male chickens until the age of 42 days. The chickens were assigned to seven experimental groups of 140 birds each (seven replications of 20 individuals each). The control group (G-C) did not receive the phytobiotic. Groups CT-0.05, CT-0.1, and CT-0.25 received the phytobiotic in their drinking water in the amount of 0.05, 0.1, and 0.2 mL/L, respectively, at days 1-42 of life (continuous application, CT). The birds in groups PT-0.05, PT-0.5, and PT-0.25 received the phytobiotic in the same amounts, but only at days 1-7, 15-21, and 29-35 of life (periodic application, PT). Selected antioxidant and biochemical parameters were determined in the blood of the chickens, as well as parameters of immune status and redox status. The morphology of the intestinal epithelium, composition of the microbiome, and production parameters of chickens receiving the phytobiotic in their drinking water were determined as well. The addition of a phytobiotic containing cinnamon oil and citric acid to the drinking water of broiler chickens at a suitable dosage and for a suitable time can beneficially modify the microbiome composition and morphometry of the small intestine (total number of fungi p < 0.001, total number of aerobic bacteria p < 0.001; and total number of coliform bacteria p < 0.001 was decreased) improving the immunity and growth performance of the chickens (there occurred a villi lengthening p = 0.002 and crypts deepening p = 0.003). Among the three tested dosages (0.05, 0.1, and 0.25 mL/L of water) of the preparation containing cinnamon oil, the dosage of 0.25 mL/L of water administered for 42 days proved to be most beneficial. Chickens receiving the phytobiotic in the amount of 0.25 mL/L had better growth performance, which was linked to the beneficial effect of the preparation on the microbiome of the small intestine, metabolism (the HDL level p = 0.017 was increased; and a decreased level of total cholesterol (TC) p = 0.018 and nonesterified fatty acids (NEFA) p = 0.007, LDL p = 0.041, as well as triacylglycerols (TAG) p = 0.014), and immune (the level of lysozyme p = 0.041 was increased, as well as the percentage of phagocytic cells p = 0.034, phagocytosis index p = 0.038, and Ig-A level p = 0.031) and antioxidant system (the level of LOOH p < 0.001, MDA p = 0.002, and the activity of Catalase (CAT) p < 0.001 were decreased, but the level of ferric reducing ability of plasma (FRAP) p = 0.029, glutathione p = 0.045 and vitamin C p = 0.021 were increased).}, }
@article {pmid33557358, year = {2021}, author = {Chekanov, K and Zaytseva, A and Mamedov, I and Solovchenko, A and Lobakova, E}, title = {The Dynamics of the Bacterial Community of the Photobioreactor-Cultivated Green Microalga Haematococcus lacustris during Stress-Induced Astaxanthin Accumulation.}, journal = {Biology}, volume = {10}, number = {2}, pages = {}, doi = {10.3390/biology10020115}, pmid = {33557358}, issn = {2079-7737}, support = {20-74-10028//Russian Science Foundation/ ; }, abstract = {Haematococcus lacustris is a natural source of a valuable ketocarotenoid astaxanthin. Under autotrophic growth conditions, it exists in the form of a community with bacteria. The close coexistence of these microorganisms raises two questions: how broad their diversity is and how they interact with the microalga. Despite the importance these issues, little is known about microorganisms existing in Haematococcus cultures. For the first time, we characterize the dynamic of the H. lacustris microbiome of the microbiome of Haematococcus (a changeover of the bacterial associated species as function of the time) cultivated autotrophically in a photobioreactor based on 16S rRNA metabarcoding data. We found that Proteobacteria and Bacteroidetes are predominant phyla in the community. The Caulobacter bacterium became abundant during astaxanthin accumulation. These data were supported by microscopy. We discuss possible roles and interactions of the community members. These findings are of potential significance for biotechnology. They provide an insight into possible bacterial contamination in algal biomass and reveal the presence of bacteria essential for the algal growth.}, }
@article {pmid33557302, year = {2021}, author = {Monteleone, AM and Troisi, J and Serena, G and Fasano, A and Dalle Grave, R and Cascino, G and Marciello, F and Calugi, S and Scala, G and Corrivetti, G and Monteleone, P}, title = {The Gut Microbiome and Metabolomics Profiles of Restricting and Binge-Purging Type Anorexia Nervosa.}, journal = {Nutrients}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/nu13020507}, pmid = {33557302}, issn = {2072-6643}, abstract = {Alterations in the gut microbiome and fecal metabolites have been detected in anorexia nervosa (AN), but differences in those profiles between restricting AN (ANR) and binge-purging AN (ANBP) type have not been explored. We made a secondary analysis of our previous data concerning microbiome and metabolomics profiles of 17 ANR women, six ANBP women and 20 healthy controls (HC). Twelve fecal metabolites differentiating ANR patients, ANBP patients and HC were identified. Both patient groups showed decreased intra-individual bacterial richness with respect to healthy controls (HC). Compared to ANR subjects, ANBP patients had a significant increase in relative abundances of Bifidobacterium, Bifidobacteriaceae, Bifidobacteriales, and Eubacteriacae and a significant decrease in relative abundances of Odoribacter, Haemophilus, Pasteurellaceae, and Pasteurellales. The heatmaps of the relationships of selected fecal metabolites with microbial families showed different structures among the three groups, with the heatmap of ANBP patients being drastically different from that of HC, while that of ANR patients resulted more similar to HC. These findings, although preliminary because of the relatively small sample size, confirm the occurrence of different gut dysbiosis in ANR and ANBP and demonstrate different connections between gut microorganisms and fecal metabolites in the two AN types.}, }
@article {pmid33557131, year = {2021}, author = {Przybyl, L and Wozna-Wysocka, M and Kozlowska, E and Fiszer, A}, title = {What, When and How to Measure-Peripheral Biomarkers in Therapy of Huntington's Disease.}, journal = {International journal of molecular sciences}, volume = {22}, number = {4}, pages = {}, doi = {10.3390/ijms22041561}, pmid = {33557131}, issn = {1422-0067}, support = {2015/17/D/NZ5/03443//Narodowe Centrum Nauki/ ; 2015/17/N/NZ2/01916//Narodowe Centrum Nauki/ ; }, abstract = {Among the main challenges in further advancing therapeutic strategies for Huntington's disease (HD) is the development of biomarkers which must be applied to assess the efficiency of the treatment. HD is a dreadful neurodegenerative disorder which has its source of pathogenesis in the central nervous system (CNS) but is reflected by symptoms in the periphery. Visible symptoms include motor deficits and slight changes in peripheral tissues, which can be used as hallmarks for prognosis of the course of HD, e.g., the onset of the disease symptoms. Knowing how the pathology develops in the context of whole organisms is crucial for the development of therapy which would be the most beneficial for patients, as well as for proposing appropriate biomarkers to monitor disease progression and/or efficiency of treatment. We focus here on molecular peripheral biomarkers which could be used as a measurable outcome of potential therapy. We present and discuss a list of wet biomarkers which have been proposed in recent years to measure pre- and postsymptomatic HD. Interestingly, investigation of peripheral biomarkers in HD can unravel new aspects of the disease pathogenesis. This especially refers to inflammatory proteins or specific immune cells which attract scientific attention in neurodegenerative disorders.}, }
@article {pmid33557015, year = {2021}, author = {Kono, M and Nagafuchi, Y and Shoda, H and Fujio, K}, title = {The Impact of Obesity and a High-Fat Diet on Clinical and Immunological Features in Systemic Lupus Erythematosus.}, journal = {Nutrients}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/nu13020504}, pmid = {33557015}, issn = {2072-6643}, abstract = {Systemic lupus erythematosus (SLE) is a chronic autoimmune disease with multiple organ involvement predominantly affecting women of childbearing age. Environmental factors, as well as genetic predisposition, can cause immunological disturbances that manifest as SLE. A habitual high-fat diet and obesity have recently been reported to play a role in the pathogenesis of autoimmune diseases. The frequency of obesity is higher in patients with SLE than in general populations. Vitamin D and adipokines, such as leptin and adiponectin, are possible mediators connecting obesity and SLE. Serum leptin and adiponectin levels are elevated in patients with SLE and can impact innate and adaptive immunity. Vitamin D deficiency is commonly observed in SLE. Because vitamin D can modulate the functionality of various immune cells, we review vitamin D supplementation and its effects on the course of clinical disease in this work. We also discuss high-fat diets coinciding with alterations of the gut microbiome, or dysbiosis. Contingent upon dietary habits, microbiota can be conducive to the maintenance of immune homeostasis. A high-fat diet can give rise to dysbiosis, and patients who are affected by obesity and/or have SLE possess less diverse microbiota. Interestingly, a hypothesis about dysbiosis and the development of SLE has been suggested and reviewed here.}, }
@article {pmid33556972, year = {2021}, author = {Krammer, H and Storr, M and Madisch, A and Riffel, J}, title = {[Treatment of IBS with Lactobacillus plantarum 299v: Therapeutic success increases with length of treatment - real-life data of a non-interventional study in Germany].}, journal = {Zeitschrift fur Gastroenterologie}, volume = {59}, number = {2}, pages = {125-134}, doi = {10.1055/a-1340-0204}, pmid = {33556972}, issn = {1439-7803}, abstract = {INTRODUCTION: The treatment of irritable bowel syndrome (IBS) in clinical practice is frequently challenging. Modulation of the intestinal microbiome as a treatment option is becoming more and more important. The effectiveness of a bacterial strain, Lactobacillus plantarum 299v (LP299V), was previously investigated in placebo-controlled clinical trials in patients with IBS over 4 weeks. The aims of the present non-interventional study were therefore to investigate tolerability and effectiveness of LP299V under everyday conditions and to gain information on long-term treatment.<br><br>METHODS: Data on tolerability and effectiveness of LP299V (1 capsule/day; 1 × 1010 CFU) were prospectively collected in 25 centers in 221 patients with IBS. The maximal treatment duration was 12 weeks. The survey was carried out using symptom diaries and medical assessments. Changes in frequency and severity of symptoms were compared to baseline and defined the primary endpoint.<br><br>RESULTS: During the 12-week treatment, a significant and continuous reduction of overall symptom score (p < 0.05) was observed. In addition, a significant reduction of severity (S) and frequency (H) of individual symptoms, such as abdominal pain (S: - 67 %, H: - 51 %), flatulence (S: - 61 %, H: - 63 %), diarrhea (S: - 70 %, H: - 32 %) and constipation (S: - 79 %, H: - 6 %) was observed. Urgency and feeling of incomplete evacuation were significantly decreased (p < 0.001). Additionally, quality of life increased significantly (mental well-being: + 110 %, influence on everyday life: -67 %, p < 0.01). Self-assessment identified that long-term treatment with LP299V was tolerated well by 94 % of patients.<br><br>CONCLUSION: In real life, LP299V significantly alleviates the global symptoms of IBS in patients. In order to achieve the maximum effect, long-term use of LP299V (as here 12 weeks) appears to be indicated and is well tolerated.}, }
@article {pmid33556916, year = {2021}, author = {Wu, L and Yan, Q and Chen, F and Cao, C and Wang, S}, title = {Bupleuri radix extract ameliorates impaired lipid metabolism in high-fat diet-induced obese mice via gut microbia-mediated regulation of FGF21 signaling pathway.}, journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie}, volume = {135}, number = {}, pages = {111187}, doi = {10.1016/j.biopha.2020.111187}, pmid = {33556916}, issn = {1950-6007}, abstract = {BACKGROUND: Obesity and its comorbidities are associated with abnormal lipid metabolism and gut microbiota dysbiosis. Bupleuri Radix is a medicinal plant used in traditional Chinese medicine with the prevention and treatment of obesity-related diseases. In this study, we aim to validate the regulation of Bupleuri Radix Extract (BupE) on lipid metabolism in obese mice, and try to find out the potential active components and reveal the underlying mechanisms.<br><br>METHODS: Ingredients in BupE, their circulating metabolites in mice and fecal biotransformation products were analyzed by ultra-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (UPLC/Q-TOF-MS). Western blotting, RT-PCR and ELISA were used for tests of objective genes and proteins. 16 s rRNA sequencing was performed to examine intestinal bacteria composition and microbes' functional changes were predicted with PICRUSt software. An absolute quantification method was set up via the construction of recombinant plasmid for the assays of intestinal flora. Specific microbial strains were cultured in anaerobic conditions and oral administrated to mice for intestinal mono-colonization.<br><br>RESULTS: BupE attenuated obesity, liver steatosis, and dyslipidemia in HFD-fed mice by up-regulating the expression of FGF21 in liver and white adipose tissue (WAT) as well as the downstream proteins of FGF21 signal pathway including β-klotho, GLUT1 and PGC-1α, etc. UPLC/Q-TOF-MS fingerprints showed no compounds from BupE or their metabolites or biotransformation products were detected in rodent serum samples. High-throughput pyrosequencing data indicated that BupE reversed obesity-induced constructional and functional alterations of intestinal flora. Two bacterial strains, Bacteroides acidifaciens (B. acidifaciens) and Ruminococcus gnavus (R. gnavus), were separated and identified from the feces of obese mice and by intestinal mono-colonization they were verified to intervene in the anti-obesity effects of BupE on mice.<br><br>CONCLUSION: These data suggest that BupE protects against diet-induced obesity and counteracts metabolic syndrome features consistent with a mechanism involving the gut-liver axis that boosts hepatic FGF21 secretion and consequent down-stream proteins expression relating to lipid metabolism. And in this gut-liver axis, intestinal microbes such as B.acidifaciens and R.gnavus play an indispensable role.}, }
@article {pmid33556826, year = {2021}, author = {Ekhlas, D and Kurisu, F and Kasuga, I and Cernava, T and Berg, G and Liu, M and Furumai, H}, title = {Identification of new eligible indicator organisms for combined sewer overflow via 16S rRNA gene amplicon sequencing in Kanda River, Tokyo.}, journal = {Journal of environmental management}, volume = {284}, number = {}, pages = {112059}, doi = {10.1016/j.jenvman.2021.112059}, pmid = {33556826}, issn = {1095-8630}, abstract = {Fecal indicator bacteria (FIB) are commonly used to evaluate the pollution impact of combined sewer overflows (CSOs) in urban rivers. Although water quality assessment with FIB has a long tradition, recent studies demonstrated that FIB have a low correlation with pathogens and therefore are not accurate enough for the assessment of potential human hazards in water. Consequently, new eligible and more specific indicators have to be identified, which was done in this study via sequencing of genetic markers from total community DNA. To identify potential microbiome-based indicators, microbial communities in samples from an urban river in Tokyo under different climatic conditions (dry and rainy) were compared with the influent and effluent of three domestic wastewater treatment plants (WWTPs) by analyzing 16 S rRNA gene amplicon libraries. In the first part of this study, physicochemical parameters and FIB quantification with selective culture techniques facilitated the identification of samples contaminated with CSO, sewage, or both. This allowed the grouping of samples into CSO-contaminated and non-contaminated samples, an essential step prior to the microbiome comparison between samples. Increased turbidity, ammonia concentrations, and E. coli [up to (9.37 ± 0.95) × 102 CFU/mL after 11.5 mm of rainfall] were observed in CSO-contaminated river samples. Comparison of dry weather (including WWTP samples) and rainy weather samples showed a reduction in microbial diversity in CSO-contaminated samples. Furthermore, the results of this study suggest Bacteroides spp. as a novel indicator of sewage pollution in surface waters.}, }
@article {pmid33556733, year = {2021}, author = {Sun, H and Zhang, Y and Yang, Y and Chen, Y and Jeyakumar, P and Shao, Q and Zhou, Y and Ma, M and Zhu, R and Qian, Q and Fan, Y and Xiang, S and Zhai, N and Li, Y and Zhao, Q and Wang, H}, title = {Effect of biofertilizer and wheat straw biochar application on nitrous oxide emission and ammonia volatilization from paddy soil.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {275}, number = {}, pages = {116640}, doi = {10.1016/j.envpol.2021.116640}, pmid = {33556733}, issn = {1873-6424}, abstract = {Biofertilizer can improve soil quality, especially the microbiome composition, which potentially affect soil nitrogen (N) cycling. However, little is known about the responses of nitrous oxide (N2O) emission and ammonia (NH3) volatilization from biochar-amended paddy soil to the biofertilizer application. Therefore, we conducted a soil column experiment using four 240 kg N ha-1 (equivalent to 1.7 g N pot-1) treatments consisting of biofertilizer (3 t ha-1, equivalent to 21.2 g pot-1), biochar (7.5 t ha-1, equivalent to 63.6 g pot-1), and a mixture of biofertilizer and biochar at the same rate and a control (CK). The results showed that the N2O emissions and NH3 volatilizations were equivalent to 0.15-0.28% and 18.0-31.5% of rice seasonal N applied to the four treatments, respectively. Two treatments with biofertilizer and biochar individual amendment significantly increased (P < 0.05) the N2O emissions to same degree by 30.2%, while co-application of biochar and biofertilizer further increased the N2O emission by 74.4% compared to the control. The higher N2O emission was likely attributed to the increased gene copies of AOA, nirK, and nirS. Applying biofertilizer significantly increased (P < 0.05) NH3 volatilization by 24.7% relative to the control, while applying biochar had no influence on NH3 volatilization. Co-application of biofertilizer and biochar significantly decreased (P < 0.05) NH3 volatilization by 12.3% compared to the control. Overall, the net global warming potential based on NH3 and N2O in current study increased by 13.0-26.0% in both the individual- and co-application of biofertilizer and biochar. Interestingly, both individual- and co-applications of biofertilizer and biochar increased the rice grain yield by 16.5-38.3%. Therefore, applications of biofertilizer and biochar did not increase the GHGI. Particularly, the co-applying of them significantly lowered (P < 0.05) the GHGI by 15.2%. In conclusion, biofertilizer and biochar should be co-applied to achieve the goals of environment protection and food security.}, }
@article {pmid33556539, year = {2021}, author = {Basak, JM and Ferreiro, A and Cohen, LS and Sheehan, PW and Nadarajah, CJ and Kanan, MF and Sukhum, KV and Dantas, G and Musiek, ES}, title = {Bacterial sepsis increases hippocampal fibrillar amyloid plaque load and neuroinflammation in a mouse model of Alzheimer's disease.}, journal = {Neurobiology of disease}, volume = {152}, number = {}, pages = {105292}, doi = {10.1016/j.nbd.2021.105292}, pmid = {33556539}, issn = {1095-953X}, abstract = {BACKGROUND: Sepsis, a leading cause for intensive care unit admissions, causes both an acute encephalopathy and chronic brain dysfunction in survivors. A history of sepsis is also a risk factor for future development of dementia symptoms. Similar neuropathologic changes are associated with the cognitive decline of sepsis and Alzheimer's disease (AD), including neuroinflammation, neuronal death, and synaptic loss. Amyloid plaque pathology is the earliest pathological hallmark of AD, appearing 10 to 20 years prior to cognitive decline, and is present in 30% of people over 65. As sepsis is also more common in older adults, we hypothesized that sepsis might exacerbate amyloid plaque deposition and plaque-related injury, promoting the progression of AD-related pathology.<br><br>METHODS: We evaluated whether the brain's response to sepsis modulates AD-related neurodegenerative changes by driving amyloid deposition and neuroinflammation in mice. We induced polymicrobial sepsis by cecal ligation and puncture (CLP) in APP/PS1-21 mice, a model of AD-related β-amyloidosis. We performed CLP or sham surgery at plaque onset (2 months of age) and examined pathology 2 months after CLP in surviving mice.<br><br>RESULTS: Sepsis significantly increased fibrillar amyloid plaque formation in the hippocampus of APP/PS1-21 mice. Sepsis enhanced plaque-related astrocyte activation and complement C4b gene expression in the brain, both of which may play a role in modulating amyloid formation. CLP also caused large scale changes in the gut microbiome of APP/PS1 mice, which have been associated with a pro-amyloidogenic and neuroinflammatory state.<br><br>CONCLUSIONS: Our results suggest that experimental sepsis can exacerbate amyloid plaque deposition and plaque-related inflammation, providing a potential mechanism for increased dementia in older sepsis survivors.}, }
@article {pmid33556534, year = {2021}, author = {Yang, I and Arthur, RA and Zhao, L and Clark, J and Hu, Y and Corwin, EJ and Lah, J}, title = {The oral microbiome and inflammation in mild cognitive impairment.}, journal = {Experimental gerontology}, volume = {147}, number = {}, pages = {111273}, doi = {10.1016/j.exger.2021.111273}, pmid = {33556534}, issn = {1873-6815}, abstract = {Inflammation and immune mechanisms are believed to play important roles in Alzheimer's disease pathogenesis. Research supports the link between poor oral health and Alzheimer's disease. Periodontal disease and dental caries represent the two most common infections of the oral cavity. This study focused on a precursor to Alzheimer's disease, mild cognitive impairment (MCI). Using 16S rRNA sequencing, we characterized and compared the oral microbiome of 68 older adults who met the criteria for MCI or were cognitively normal, then explored relationships between the oral microbiome, diagnostic markers of MCI, and blood markers of systemic inflammation. Two taxa, Pasteurellacae and Lautropia mirabilis were identified to be differentially abundant in this cohort. Although systemic inflammatory markers did not differentiate the two groups, differences in five cerebrospinal fluid inflammatory mediators were identified and had significant associations with MCI. Because inflammatory markers may reflect CNS changes, pursuing this line of research could provide opportunities for new diagnostic tools and illuminate mechanisms for prevention and mitigation of Alzheimer's disease.}, }
@article {pmid33556439, year = {2021}, author = {Lee, MT and Le, HH and Johnson, EL}, title = {Dietary sphinganine is selectively assimilated by members of the mammalian gut microbiome.}, journal = {Journal of lipid research}, volume = {}, number = {}, pages = {100034}, doi = {10.1194/jlr.RA120000950}, pmid = {33556439}, issn = {1539-7262}, }
@article {pmid33556120, year = {2021}, author = {Peng, X and Xie, J and Li, W and Xie, H and Cai, Y and Ding, X}, title = {Comparison of wild rice (Oryza longistaminata) tissues identifies rhizome-specific bacterial and archaeal endophytic microbiomes communities and network structures.}, journal = {PloS one}, volume = {16}, number = {2}, pages = {e0246687}, pmid = {33556120}, issn = {1932-6203}, abstract = {Compared with root-associated habitats, little is known about the role of microbiota inside other rice organs, especially the rhizome of perennial wild rice, and this information may be of importance for agriculture. Oryza longistaminata is perennial wild rice with various agronomically valuable traits, including large biomass on poor soils, high nitrogen use efficiency, and resistance to insect pests and disease. Here, we compared the endophytic bacterial and archaeal communities and network structures of the rhizome to other compartments of O. longistaminata using 16S rRNA gene sequencing. Diverse microbiota and significant variation in community structure were identified among different compartments of O. longistaminata. The rhizome microbial community showed low taxonomic and phylogenetic diversity as well as the lowest network complexity among four compartments. Rhizomes exhibited less phylogenetic clustering than roots and leaves, but similar phylogenetic clustering with stems. Streptococcus, Bacillus, and Methylobacteriaceae were the major genera in the rhizome. ASVs belonging to the Enhydrobacter, YS2, and Roseburia are specifically present in the rhizome. The relative abundance of Methylobacteriaceae in the rhizome and stem was significantly higher than that in leaf and root. Noteworthy type II methanotrophs were observed across all compartments, including the dominant Methylobacteriaceae, which potentially benefits the host by facilitating CH4-dependent N2 fixation under nitrogen nutrient-poor conditions. Our data offers a robust knowledge of host and microbiome interactions across various compartments and lends guidelines to the investigation of adaptation mechanisms of O. longistaminata in nutrient-poor environments for biofertilizer development in agriculture.}, }
@article {pmid33556098, year = {2021}, author = {Revilla, L and Mayorgas, A and Corraliza, AM and Masamunt, MC and Metwaly, A and Haller, D and Tristán, E and Carrasco, A and Esteve, M and Panés, J and Ricart, E and Lozano, JJ and Salas, A}, title = {Multi-omic modelling of inflammatory bowel disease with regularized canonical correlation analysis.}, journal = {PloS one}, volume = {16}, number = {2}, pages = {e0246367}, pmid = {33556098}, issn = {1932-6203}, abstract = {BACKGROUND: Personalized medicine requires finding relationships between variables that influence a patient's phenotype and predicting an outcome. Sparse generalized canonical correlation analysis identifies relationships between different groups of variables. This method requires establishing a model of the expected interaction between those variables. Describing these interactions is challenging when the relationship is unknown or when there is no pre-established hypothesis. Thus, our aim was to develop a method to find the relationships between microbiome and host transcriptome data and the relevant clinical variables in a complex disease, such as Crohn's disease.<br><br>RESULTS: We present here a method to identify interactions based on canonical correlation analysis. We show that the model is the most important factor to identify relationships between blocks using a dataset of Crohn's disease patients with longitudinal sampling. First the analysis was tested in two previously published datasets: a glioma and a Crohn's disease and ulcerative colitis dataset where we describe how to select the optimum parameters. Using such parameters, we analyzed our Crohn's disease data set. We selected the model with the highest inner average variance explained to identify relationships between transcriptome, gut microbiome and clinically relevant variables. Adding the clinically relevant variables improved the average variance explained by the model compared to multiple co-inertia analysis.<br><br>CONCLUSIONS: The methodology described herein provides a general framework for identifying interactions between sets of omic data and clinically relevant variables. Following this method, we found genes and microorganisms that were related to each other independently of the model, while others were specific to the model used. Thus, model selection proved crucial to finding the existing relationships in multi-omics datasets.}, }
@article {pmid33555368, year = {2021}, author = {Grzesiak, J and Woltyńska, A and Zdanowski, MK and Górniak, D and Świątecki, A and Olech, MA and Aleksandrzak-Piekarczyk, T}, title = {Metabolic fingerprinting of the Antarctic cyanolichen Leptogium puberulum-associated bacterial community (Western Shore of Admiralty Bay, King George Island, Maritime Antarctica).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33555368}, issn = {1432-184X}, support = {2017/25/B/NZ8/01915//Narodowe Centrum Nauki/ ; }, abstract = {Lichens are presently regarded as stable biotopes, small ecosystems providing a safe haven for the development of a diverse and numerous microbiome. In this study, we conducted a functional diversity assessment of the microbial community residing on the surface and within the thalli of Leptogium puberulum, a eurytopic cyanolichen endemic to Antarctica, employing the widely used Biolog EcoPlates which test the catabolism of 31 carbon compounds in a colorimetric respiration assay. Lichen thalli occupying moraine ridges of differing age within a proglacial chronosequence, as well as those growing in sites of contrasting nutrient concentrations, were procured from the diverse landscape of the western shore of Admiralty Bay in Maritime Antarctica. The L. puberulum bacterial community catabolized photobiont- (glucose-containing carbohydrates) and mycobiont-specific carbon compounds (D-Mannitol). The bacteria also had the ability to process degradation products of lichen thalli components (D-cellobiose and N-acetyl-D-glucosamine). Lichen thalli growth site characteristics had an impact on metabolic diversity and respiration intensity of the bacterial communities. While high nutrient contents in lichen specimens from &quot;young&quot; proglacial locations and in those from nitrogen enriched sites stimulated bacterial catabolic activity, in old proglacial locations and in nutrient-lacking sites, a metabolic activity restriction was apparent, presumably due to lichen-specific microbial control mechanisms.}, }
@article {pmid33555188, year = {2021}, author = {Peng, H and Shahidi, F}, title = {Cannabis and Cannabis Edibles: A Review.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.0c07472}, pmid = {33555188}, issn = {1520-5118}, abstract = {Cannabis is an excellent natural source of fiber and various bioactive cannabinoids. So far, at least 120 cannabinoids have been identified, and more novel cannabinoids are gradually being unveiled by detailed cannabis studies. However, cannabinoids in both natural and isolated forms are especially vulnerable to oxygen, heat, and light. Therefore, a diversity of cannabinoids is associated with their chemical instability to a large extent. The research status of structural conversion of cannabinoids is introduced. On the other hand, the use of drug-type cannabis and the phytocannabinoids thereof has been rapidly popularized and plays an indispensable role in both medical therapy and daily recreation. The recent legalization of edible cannabis further extends its application into the food industry. The varieties of legal edible cannabis products in the current commercial market are relatively monotonous due to rigorous restrictions under the framework of Cannabis Regulations and infancy of novel developments. Meanwhile, patents/studies related to the safety and quality assurance systems of cannabis edibles are still rare and need to be developed. Furthermore, along with cannabinoids, many phytochemicals such as flavonoids, lignans, terpenoids, and polysaccharides exist in the cannabis matrix, and these may exhibit prebiotic/probiotic properties and improve the composition of the gut microbiome. During metabolism and excretion, the bioactive phytochemicals of cannabis, mostly the cannabinoids, may be structurally modified during enterohepatic detoxification and gut fermentation. However, the potential adverse effects of both acute and chronic exposure to cannabinoids and their vulnerable groups have been clearly recognized. Therefore, a comprehensive understanding of the chemistry, metabolism, toxicity, commercialization, and regulations regarding cannabinoid edibles is reviewed and updated in this contribution.}, }
@article {pmid33554571, year = {2020}, author = {Moumne, O and Hampe, ME and Montoya-Williams, D and Carson, TL and Neu, J and Francois, M and Rhoton-Vlasak, A and Lemas, DJ}, title = {Implications of the vaginal microbiome and potential restorative strategies on maternal health: a narrative review.}, journal = {Journal of perinatal medicine}, volume = {}, number = {}, pages = {}, doi = {10.1515/jpm-2020-0367}, pmid = {33554571}, issn = {1619-3997}, abstract = {The vaginal microbiome undergoes dramatic shifts before and throughout pregnancy. Although the genetic and environmental factors that regulate the vaginal microbiome have yet to be fully elucidated, high-throughput sequencing has provided an unprecedented opportunity to interrogate the vaginal microbiome as a potential source of next-generation therapeutics. Accumulating data demonstrates that vaginal health during pregnancy includes commensal bacteria such as Lactobacillus that serve to reduce pH and prevent pathogenic invasion. Vaginal microbes have been studied as contributors to several conditions occurring before and during pregnancy, and an emerging topic in women's health is finding ways to alter and restore the vaginal microbiome. Among these restorations, perhaps the most significant effect could be preterm labor (PTL) prevention. Since bacterial vaginosis (BV) is known to increase risk of PTL, and vaginal and oral probiotics are effective as supplemental treatments for BV prevention, a potential therapeutic benefit exists for pregnant women at risk of PTL. A new method of restoration, vaginal microbiome transplants (VMTs) involves transfer of one women's cervicovaginal secretions to another. New studies investigating recurrent BV will determine if VMTs can safely establish a healthy Lactobacillus-dominant vaginal microbiome. In most cases, caution must be taken in attributing a disease state and vaginal dysbiosis with a causal relationship, since the underlying reason for dysbiosis is usually unknown. This review focuses on the impact of vaginal microflora on maternal outcomes before and during pregnancy, including PTL, gestational diabetes, preeclampsia, and infertility. It then reviews the clinical evidence focused on vaginal restoration strategies, including VMTs.}, }
@article {pmid33554105, year = {2021}, author = {Jeevarathinam, AS and Guo, F and Williams, T and Smolen, JA and Hyde, JA and McShane, MJ and de Figueiredo, P and Alge, DL}, title = {Enzyme functionalized microgels enable precise regulation of dissolved oxygen and anaerobe culture.}, journal = {Materials today. Bio}, volume = {9}, number = {}, pages = {100092}, pmid = {33554105}, issn = {2590-0064}, abstract = {Anaerobes are a major constituent of the gut microbiome and profoundly influence the overall health of humans. However, the lack of a simple, cost-effective, and scalable system that mimics the anaerobic conditions of the human gut is hindering research on the gut microbiome and the development of therapeutics. Here, we address this gap by using glucose oxidase and catalase containing gelatin microparticles (GOx-CAT-GMPs) to precisely regulate dissolved oxygen concentration [O2] via GOx-mediated consumption of oxygen. Fluorescence images generated using conjugated polymer afterglow nanoparticles showed that [O2] can be tuned from 257.9 ​± ​6.2 to 0.0 ​± ​4.0 ​μM using GOx-CAT-GMPs. Moreover, when the obligate anaerobe Bacteroides thetaiotaomicron was inoculated in media containing GOx-CAT-GMPs, bacterial growth under ambient oxygen was comparable to control conditions in an anaerobic chamber (5.4 ​× ​105 and 8.8 ​× ​105 colony forming units mL-1, respectively). Finally, incorporating GOx-CAT-GMPs into a bioreactor that permitted continuous radial diffusion of oxygen and glucose generated a gut-mimetic [O2] gradient of 132.4 ​± ​2.6 ​μM in the outer ring of the reactor to 7.9 ​± ​1.7 ​μM at the core. Collectively, these results indicate that GOx-CAT-GMPs are highly effective oxygen-regulating materials. These materials can potentially be leveraged to advance gut microbiome research and fecal microbiota transplantation, particularly in low-resource settings.}, }
@article {pmid33553430, year = {2021}, author = {Peng, J and Wang, JY and Huang, HF and Zheng, TT and Li, J and Wang, LJ and Ma, XC and Xiao, HT}, title = {Adiponectin Deficiency Suppresses Rhabdomyosarcoma Associated with Gut Microbiota Regulation.}, journal = {BioMed research international}, volume = {2021}, number = {}, pages = {8010694}, pmid = {33553430}, issn = {2314-6141}, abstract = {The gut microbiota is very important in the initiation, progression, and dissemination of cancer, and the regulation of microbiota has been employed as a novel strategy to enhance the effect of immunotherapy. Adiponectin (APN), an adipocyte-derived hormone, plays a vital role in regulating the immune response of innate immune cells. The deficiency of APN inhibits rhabdomyosarcoma growth. However, whether this function is associated with regulating gut microbiota remains unknown. To investigate, we performed 16S ribosomal RNA (rRNA) gene sequencing on the fecal microbiome of APN gene knockout mice to determine whether APN deletion affects the gut microbiota. We found APN deficiency alters gut microbial functions involved in metabolism, genetic information processing, and cellular processes. In addition, a decreased abundance of Bacteroides and an increased abundance of Prevotella and Helicobacter were observed in rhabdomyosarcoma-bearing APN knockout mice; these bacteria were associated with the inhibition of rhabdomyosarcoma growth. These findings suggest that gut microbiota may be a potential target of APN deficiency against rhabdomyosarcoma.}, }
@article {pmid33553325, year = {2021}, author = {Wu, H and Tang, D and Zheng, F and Li, S and Zhang, X and Yin, L and Liu, F and Dai, Y}, title = {Identification of a novel interplay between intestinal bacteria and metabolites in Chinese patients with IgA nephropathy via integrated microbiome and metabolome approaches.}, journal = {Annals of translational medicine}, volume = {9}, number = {1}, pages = {32}, pmid = {33553325}, issn = {2305-5839}, abstract = {Background: Immunoglobulin A nephropathy (IgAN) is the most common form of primary glomerulonephritis. The intestinal microbial ecosystem and metabolic network of IgAN have not been systematically analyzed. The present study aims to improve understanding of the gut microbiota and its metabolic capabilities to facilitate the development of diagnostic, therapeutic, and prognostic methods for IgAN.<br><br>Methods: We characterized the gut microbiota and metabolic patterns of fecal and serum samples of IgAN patients and healthy controls from the south of China using 16s ribosomal RNA gene sequencing and liquid chromatography-tandem mass spectrometry, respectively, and bioinformatics approaches.<br><br>Results: We found that the relative abundances of Streptococcus and Enterococcus were higher in IgAN patients, whereas Bacteroidetes and Bacteroides were lower. Changes in the gut microbiota of IgAN affected the metabolism and absorbance of microbiota-associated metabolites, in particular polyunsaturated fatty acids, free amino acid, and oligopeptides, and activated the phenylalanine metabolism pathway, thereby constructing a unique metabolic system of IgAN. We identified six pivotal metabolites, including bilirubin, trimethoprim, stearamide, phenylalanine, cis-9,10-epoxystearic acid, and phosphatidylethanolamine 17:0, that connected the metabolic networks of the gut and blood. Additionally, 5-hydroxyeicosatetraenoic acid and 5-hydroxy-6E,8Z,11Z-eicosatrienoic acid were shown to be associated with the classification of glomerular sclerosis.<br><br>Conclusions: We establish a relational network between microbiota, fecal metabolites, and serum metabolites in IgAN. The core microbiota and metabolites identified have promising value in therapeutic applications.}, }
@article {pmid33553288, year = {2020}, author = {Ahmed, E and Yano, R and Fujimori, M and Kand, D and Hanada, M and Nishida, T and Fukuma, N}, title = {Impacts of Mootral on Methane Production, Rumen Fermentation, and Microbial Community in an in vitro Study.}, journal = {Frontiers in veterinary science}, volume = {7}, number = {}, pages = {623817}, pmid = {33553288}, issn = {2297-1769}, abstract = {Methane mitigation strategies have a two-sided benefit for both environment and efficient livestock production. This preliminary short-term in vitro trial using Mootral (garlic and citrus extracts), a novel natural feed supplement, was conducted to evaluate its efficacy on rumen fermentation characteristics, methane production, and the bacterial and archaeal community. The experiment was performed as a batch culture using rumen fluid collected from sheep, and Mootral was supplemented in three concentrations: 0% (Control), 10%, and 20% of the substrate (50% Grass:50% Concentrate). The rumen fermentation data and alpha diversity of microbial community were analyzed by ordinary one-way analysis of variance. The relative abundance and statistical significance of families and operational taxonomic units (OTUs) among the groups were compared by Kruskal-Wallis H test using Calypso software. After 24-h incubation at 39°C, Mootral in a dose-dependent manner improved the production of total volatile fatty acids and propionate while it reduced the acetate proportion and acetate/propionate ratio. The total produced gas was two times higher in the Mootral-supplemented groups than control (P < 0.01), while the proportion of methane in the produced gas was reduced by 22% (P < 0.05) and 54% (P < 0.01) for 10 and 20% Mootral, respectively. Mootral did not change pH, digestibility, and ammonia-nitrogen. Microbial community analyses showed that Mootral effectively changed the ruminal microbiome. The bacterial community showed an increase of the relative abundance of the propionate-producing family such as Prevotellaceae (P = 0.014) and Veillonellaceae (P = 0.030), while there was a decrease in the relative abundance of some hydrogen-producing bacteria by Mootral supplementation. In the archaeal community, Methanobacteriaceae was decreased by Mootral supplementation compared with control (P = 0.032), while the Methanomassiliicoccaceae family increased in a dose-dependent effect (P = 0.038). The results of the study showed the efficacy of the new mixture to alter the ruminal microbial community, produce more propionate, and reduce microbial groups associated with methane production, thus suggesting that Mootral is a promising natural mixture for methane reduction from ruminants.}, }
@article {pmid33553216, year = {2020}, author = {Stavropoulou, E and Kantartzi, K and Tsigalou, C and Konstantinidis, T and Romanidou, G and Voidarou, C and Bezirtzoglou, E}, title = {Focus on the Gut-Kidney Axis in Health and Disease.}, journal = {Frontiers in medicine}, volume = {7}, number = {}, pages = {620102}, pmid = {33553216}, issn = {2296-858X}, abstract = {The recent new developments in technology with culture-independent techniques including genome sequencing methodologies shed light on the identification of microbiota bacterial species and their role in health and disease. Microbiome is actually reported as an important predictive tool for evaluating characteristic shifts in case of disease. Our present review states the development of different renal diseases and pathologies linked to the intestinal dysbiosis, which impacts on host homeostasis. The gastrointestinal-kidney dialogue provides intriguing features in the pathogenesis of several renal diseases. Without any doubt, investigation of this interconnection consists one of the most cutting-edge areas of research with potential implications on our health.}, }
@article {pmid33553082, year = {2020}, author = {Kombe Kombe, AJ and Li, B and Zahid, A and Mengist, HM and Bounda, GA and Zhou, Y and Jin, T}, title = {Epidemiology and Burden of Human Papillomavirus and Related Diseases, Molecular Pathogenesis, and Vaccine Evaluation.}, journal = {Frontiers in public health}, volume = {8}, number = {}, pages = {552028}, pmid = {33553082}, issn = {2296-2565}, abstract = {Diagnosed in more than 90% of cervical cancers, the fourth deadliest cancer in women, human papillomavirus (HPV) is currently the most common pathogen responsible for female cancers. Moreover, HPV infection is associated with many other diseases, including cutaneous and anogenital warts, and genital and upper aerodigestive tract cancers. The incidence and prevalence of these pathologies vary considerably depending on factors including HPV genotype, regional conditions, the study population, and the anatomical site sampled. Recently, features of the cervicovaginal microbiota are found to be associated with the incidence of HPV-related diseases, presenting a novel approach to identify high-risk women through both blood and cervical samples. Overall, the HPV repartition data show that HPV infection and related diseases are more prevalent in developing countries. Moreover, the available (2-, 4-, and 9-valent) vaccines based on virus-like particles, despite their proven effectiveness and safety, present some limitations in terms of system development cost, transport cold chain, and oncogenic HPV variants. In addition, vaccination programs face some challenges, leading to a considerable burden of HPV infection and related diseases. Therefore, even though the new (9-valent) vaccine seems promising, next-generation vaccines as well as awareness programs associated with HPV vaccination and budget reinforcements for immunization are needed.}, }
@article {pmid33553076, year = {2020}, author = {Elmaghrawy, K and Hussey, S and Moran, GP}, title = {The Oral Microbiome in Pediatric IBD: A Source of Pathobionts or Biomarkers?.}, journal = {Frontiers in pediatrics}, volume = {8}, number = {}, pages = {620254}, pmid = {33553076}, issn = {2296-2360}, abstract = {The oral cavity is continuous with the gastrointestinal tract and in children, oral health may be closely linked with the overall health of the GI tract. In the case of pediatric Crohn's disease (CD), oral manifestations are an important clinical indicator of intestinal disease. Recent studies of the microbiome in IBD suggest that translocation of oral microbes to the gut may be a common feature of the microbial dysbiosis which is a signature of both CD and ulcerative colitis (UC). Murine studies suggest that translocation of oral bacteria and yeasts to the lower GI tract may trigger inflammation in susceptible hosts, providing a mechanistic link to the development of IBD. Conversely, some studies have shown that dysbiosis of the oral microbiome may occur, possibly as a result of inflammatory responses and could represent a useful source of biomarkers of GI health. This review summarizes our current knowledge of the oral microbiome in IBD and presents current hypotheses on the potential role of this community in the pathogenesis of these diseases.}, }
@article {pmid33553067, year = {2020}, author = {Avelar Rodriguez, D and Popov, J and Ratcliffe, EM and Toro Monjaraz, EM}, title = {Functional Constipation and the Gut Microbiome in Children: Preclinical and Clinical Evidence.}, journal = {Frontiers in pediatrics}, volume = {8}, number = {}, pages = {595531}, pmid = {33553067}, issn = {2296-2360}, abstract = {Functional constipation is a common condition in childhood with significant impact on patients' quality of life and on health care resources. Functional constipation is characterized by decreased bowel movements and/or hard stools, which cause significant distress for children and their caregivers. While the term &quot;functional&quot; may imply the absence of organic causes with a focus on behavioral aspects, 40% of children continue to have symptoms beyond conventional management with one in four children continuing to experience constipation into adulthood. The refractory and chronic nature of constipation highlights the importance of considering a range of pathophysiological mechanisms, including the potential role of the gut microbiome. In this review, we provide an overview of preclinical and clinical studies that focus on the potential mechanisms through which the gut microbiome might contribute to the clinical presentation of functional constipation in pediatrics.}, }
@article {pmid33553045, year = {2020}, author = {Mohammadi, SO and Yadegar, A and Kargar, M and Mirjalali, H and Kafilzadeh, F}, title = {The impact of Helicobacter pylori infection on gut microbiota-endocrine system axis; modulation of metabolic hormone levels and energy homeostasis.}, journal = {Journal of diabetes and metabolic disorders}, volume = {19}, number = {2}, pages = {1855-1861}, pmid = {33553045}, issn = {2251-6581}, abstract = {The gut microbiota is a complex ecosystem that is involved in the development and preservation of the immune system, energy homeostasis and nutritional status of the host. The crosstalk between gut microbiota and the host cells modulates host physiology and metabolism through different mechanisms. Helicobacter pylori (H. pylori) is known to reside in the gastric mucosa, induce inflammation, and alter both gastric and intestinal microbiota resulting in a broad spectrum of diseases, in particular metabolic syndrome-related disorders. Infection with H. pylori have been shown to affect production level and physiological regulation of the gut metabolic hormones such as ghrelin and leptin which are involved in food intake, energy expenditure and body mass. In this study, we reviewed and discussed data from the literature and follow-up investigations that links H. pylori infection to alterations of the gut microbiota and metabolic hormone levels, which can exert broad influences on host metabolism, energy homeostasis, behavior, appetite, growth, reproduction and immunity. Also, we discussed the strong potential of fecal microbiota transplantation (FMT) as an innovative and promising investigational treatment option for homeostasis of metabolic hormone levels to overcome H. pylori-associated metabolic syndrome-related disorders.}, }
@article {pmid33552999, year = {2020}, author = {Chen, Q and Ma, X and Li, C and Shen, Y and Zhu, W and Zhang, Y and Guo, X and Zhou, J and Liu, C}, title = {Enteric Phageome Alterations in Patients With Type 2 Diabetes.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {575084}, pmid = {33552999}, issn = {2235-2988}, abstract = {Type 2 diabetes is a complex metabolic disease and has been shown to involve alteration of the gut microbiota. Previous studies have primarily focused on changes in the bacterial microbiome, while ignoring the phage community composition. Extracellular phages can lyse host bacteria and thus influence the microbiota through positive or negative interactions with bacteria. We investigated changes in the extracellular phageome and discussed its role in T2D pathogenesis. We used a sequencing-based approach to identify bacteriophage after isolation of VLPs (virus like particles) from fecal samples. We identified 330 species of phages according to the predicted host bacteria from T2D patients (N=17) and nondiabetic controls (N=29). The phageome characteristics were highly diverse among individuals. In the T2D group, the intestinal phage population was altered, and the abundance of phages specific to Enterobacteriaceae hosts increased markedly. Meanwhile, the abundance of Enterobacteriaceae in the gut was significantly increased, and systemic LPS content elevation was observed in the T2D group. Additionally, a consortia of eight phages was found to distinguish T2D patients from nondiabetic controls with good performance (AUC>0.99).}, }
@article {pmid33552996, year = {2020}, author = {Li, H and Chen, J and Ren, X and Yang, C and Liu, S and Bai, X and Shan, S and Dong, X}, title = {Gut Microbiota Composition Changes in Constipated Women of Reproductive Age.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {557515}, pmid = {33552996}, issn = {2235-2988}, abstract = {Background: Chronic constipation is one of the most prevalent functional gastrointestinal disorders, yet its etiology is multifactorial, and the pathophysiological mechanism is still unclear. Previous studies have shown that the gut microbiota of constipated patients differs from healthy controls; however, many discrepancies exist in the findings, and no clear link has been confirmed between chronic constipation and changes in the gut microbiota. Growing evidence indicates that age, gender, and hormone levels can affect the composition of gut microbiota. The aim of this study is to examine the overall changes in gut microbiota within a specific sub-population of patients, namely, constipated women of reproductive age.<br><br>Methods: We carried out a cross-sectional study comparing the fecal microbial composition of 30 healthy women and 29 constipated women using 16S rRNA gene sequencing. Only women of reproductive age were recruited to reduce the effects of age, gender, and hormone levels on the microbiome, and to prevent conflating the impact of these factors with the effects of constipation.<br><br>Results: There were obvious differences in the gut microbiota in constipated women of reproductive age compared with the healthy controls, manifesting mainly as a significant increase in the abundance of Bacteroides (p < 0.05) and a significant decrease in the abundance of Proteobacteria (p < 0.01). The overall composition of the gut microbiota in each group was different, which was reflected in the ratios of Firmicutes to Bacteroidetes (F/B), which was 1.52 in the constipated group vs. 2.21 in the healthy group. Additionally, there was a significant decrease in butyrate-producing bacteria, like Roseburia and Fusicatenibacter (p < 0.01).<br><br>Conclusion: The overall composition of the gut microbiota changed in constipated women of reproductive age, characterized by a loss in Proteobacteria and an increase in Bacteroidetes. Furthermore, the abundance of some butyrate-producing bacteria also reduced. These changes may reflect the unique interactions between host and some bacteria, or some bacterial metabolic products, which may be important targets for future studies to explore the pathogenesis of constipation.}, }
@article {pmid33552620, year = {2021}, author = {Chen, L and Ren, L and Li, D and Ma, X}, title = {Analysis of microbiomes in three traditional starters and volatile components of the Chinese rice wines.}, journal = {Food science and biotechnology}, volume = {30}, number = {1}, pages = {87-96}, pmid = {33552620}, issn = {2092-6456}, abstract = {To understand the effect of microbial community on the flavor of fermented rice wine, microbiomes in three traditional starters (CMQ, NBQ, and YCQ) from different origins for making Chinese rice wines were evaluated and the volatile components of their rice wines were compared. The results showed that the dominant genera in CMQ were Pantoea, Bacillus, Rhizopus, and Candida, the dominant microorganisms in NBQ were Pediococcus, Lactobacillus, Acetobacter, Weissella, Bacillus, Rhizopus, Candida, and Aspergillus, the dominant microorganisms in YCQ were Pediococcus, Lactobacillus, Leuconostoc, Weissella, Lactococcus, Ochrobactrum, Rhizopus, and Mucor. There were significant differences in sensory properties of the wines brewed by three starters. Although the major aroma components were benzyl alcohol, 2-octanone, benzoic acid, and phenethyl acetate, each rice wine had its own main aroma components include 1-octanol, 1-pentanol, ethyl acetate, etc. The results showed that the different microbial communities in starter results in the significant difference of the aroma components in its fermented rice wine.}, }
@article {pmid33552594, year = {2021}, author = {Fiorenza, S and Turtle, CJ}, title = {Associations between the Gut Microbiota, Immune Reconstitution, and Outcomes of Allogeneic Hematopoietic Stem Cell Transplantation.}, journal = {Immunometabolism}, volume = {3}, number = {1}, pages = {}, pmid = {33552594}, issn = {2084-6835}, support = {R01 HL132350/HL/NHLBI NIH HHS/United States ; }, abstract = {Immune reconstitution following allogeneic hematopoietic stem cell transplantation (allo-HSCT) sets the stage for the goal of a successful transplant-the prevention of disease relapse without graft versus host disease (GVHD) and opportunistic infection. In both epidemiologic studies and in controlled animal studies, it is known that the gut microbiome (GM) can profoundly influence normal innate and adaptive immune development and can be altered by microbial transfer and antibiotics. Following allo-HSCT the GM has been shown to influence clinical outcomes but published associations between the GM and immune reconstitution post-allo-HSCT are lacking. In this viewpoint we propose that the extensive knowledge garnered from studying normal immune development can serve as a framework for studying immune development post-allo-HSCT. We summarize existing studies addressing the effect of the GM on immune ontogeny and draw associations with immune reconstitution and the GM post-allo-HSCT.}, }
@article {pmid33552480, year = {2021}, author = {Albhaisi, SAM and Bajaj, JS}, title = {The Influence of the Microbiome on NAFLD and NASH.}, journal = {Clinical liver disease}, volume = {17}, number = {1}, pages = {15-18}, pmid = {33552480}, issn = {2046-2484}, abstract = {Watch a video presentation of this article Watch an interview with the author.}, }
@article {pmid33552218, year = {2021}, author = {Shirvani-Rad, S and Tabatabaei-Malazy, O and Mohseni, S and Hasani-Ranjbar, S and Soroush, AR and Hoseini-Tavassol, Z and Ejtahed, HS and Larijani, B}, title = {Probiotics as a Complementary Therapy for Management of Obesity: A Systematic Review.}, journal = {Evidence-based complementary and alternative medicine : eCAM}, volume = {2021}, number = {}, pages = {6688450}, pmid = {33552218}, issn = {1741-427X}, abstract = {Background: Considering the observed role of probiotics in modulating gut microbiome, probiotics are discussed to be one potential complementary therapy for obesity management in recent years. The aim of the present study was to systematically review the meta-analyses of controlled trials and investigate the effects of probiotics on obesity.<br><br>Methods: A comprehensive search was conducted on PubMed, Web of Science, and Cochrane Library web databases up to May 2020. Inclusion criteria were meta-analyses of controlled trials which evaluated the impact of probiotics on obesity in English language. Meta-analyses done on pregnant women, children, animal studies, or the effect of prebiotics on anthropometric indices were excluded.<br><br>Results: Within 325 recorded studies, 20 studies met the inclusion criteria consisting of 16676 overweight/obese adults with different underlying disorders such as nonalcoholic fatty liver disease (NAFLD), or polycystic ovary syndrome (PCOS). The length of intervention varied from 2 to 26 weeks. Results of meta-analyses have shown a moderate effect of probiotics on body weight in overweight/obese adults: from -0.526 kg/m2 (95% CI: -0.810, -0.247) to -0.25 kg/m2 (95% CI: -0.33, -0.17). Body mass index (BMI) was changed from -1.46 kg/m2 (95% CI: -2.44, -0.48) to -1.08 kg/m2 (95% CI: -2.05, -0.11) in NAFLD. Probiotics could reduce BMI from -0.36 kg/m2 (95% CI: -0.74, 0.02) to -0.29 kg/m2 (95% CI: -0.54, -0.03) in patients with PCOS.<br><br>Conclusion: It seems that the probiotic products could have beneficial effects as an adjunct therapy for care and management of obesity when used in high dose. However, due to heterogeneity of included studies, it is required to confirm our results by more meta-analyses of clinical trials.}, }
@article {pmid33552122, year = {2020}, author = {Deek, RA and Li, H}, title = {A Zero-Inflated Latent Dirichlet Allocation Model for Microbiome Studies.}, journal = {Frontiers in genetics}, volume = {11}, number = {}, pages = {602594}, pmid = {33552122}, issn = {1664-8021}, support = {R01 GM123056/GM/NIGMS NIH HHS/United States ; R01 GM129781/GM/NIGMS NIH HHS/United States ; }, abstract = {The human microbiome consists of a community of microbes in varying abundances and is shown to be associated with many diseases. An important first step in many microbiome studies is to identify possible distinct microbial communities in a given data set and to identify the important bacterial taxa that characterize these communities. The data from typical microbiome studies are high dimensional count data with excessive zeros due to both absence of species (structural zeros) and low sequencing depth or dropout. Although methods have been developed for identifying the microbial communities based on mixture models of counts, these methods do not account for excessive zeros observed in the data and do not differentiate structural from sampling zeros. In this paper, we introduce a zero-inflated Latent Dirichlet Allocation model (zinLDA) for sparse count data observed in microbiome studies. zinLDA builds on the flexible Latent Dirichlet Allocation model and allows for zero inflation in observed counts. We develop an efficient Markov chain Monte Carlo (MCMC) sampling procedure to fit the model. Results from our simulations show zinLDA provides better fits to the data and is able to separate structural zeros from sampling zeros. We apply zinLDA to the data set from the American Gut Project and identify microbial communities characterized by different bacterial genera.}, }
@article {pmid33552078, year = {2020}, author = {Kong, Q and Lv, Z and Kang, Y and An, Y and Liu, Z and Zhang, J}, title = {Bactericidal Permeability Increasing Protein Deficiency Aggravates Acute Colitis in Mice by Increasing the Serum Levels of Lipopolysaccharide.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {614169}, pmid = {33552078}, issn = {1664-3224}, abstract = {Objective: The objective of this study was to understand the role of bactericidal permeability increasing protein (BPI) in the pathogenesis of experimental murine colitis.<br><br>Methods: We used the Cre-LoxP system to generate BPI knockout (BPI KO) mice. Acute colitis was induced in BPI KO mice and wild-type (WT) mice by subjecting the mice to 5% dextran sulfate sodium (DSS). Mice were observed for symptoms of experimental colitis. The survival of BPI KO mice to infection with Acinetobacter baumannii, a gram-negative bacterium, was also assessed.<br><br>Results: Southern blot, RT-PCR, and western blot results showed that the 2nd and 3rd exons of the murine Bpi gene were knocked out systemically, confirming successful construction of the BPI KO mouse. BPI KO mice subjected to DSS showed increased symptoms of experimental colitis, increased colonic mucosal damage, increased epithelial permeability, elevated levels of serum LPS, and a disrupted fecal microbiome as compared with WT mice. Furthermore, BPI KO mice challenged intraperitoneally with A. baumannii died sooner than WT mice, and the total number of bacteria in the abdominal cavity, spleen, and liver was increased in BPI KO mice as compared to WT mice.<br><br>Conclusions: We successfully generated BPI KO mice. The BPI KO mice developed worse colitis than WT mice by increased colitis symptoms and colonic mucosal damage, elevated levels of serum LPS, and a disrupted microbiome. BPI could be a potential target for treatment of ulcerative colitis in humans.}, }
@article {pmid33552063, year = {2020}, author = {Kahalehili, HM and Newman, NK and Pennington, JM and Kolluri, SK and Kerkvliet, NI and Shulzhenko, N and Morgun, A and Ehrlich, AK}, title = {Dietary Indole-3-Carbinol Activates AhR in the Gut, Alters Th17-Microbe Interactions, and Exacerbates Insulitis in NOD Mice.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {606441}, pmid = {33552063}, issn = {1664-3224}, abstract = {The diet represents one environmental risk factor controlling the progression of type 1 diabetes (T1D) in genetically susceptible individuals. Consequently, understanding which specific nutritional components promote or prevent the development of disease could be used to make dietary recommendations in prediabetic individuals. In the current study, we hypothesized that the immunoregulatory phytochemcial, indole-3-carbinol (I3C) which is found in cruciferous vegetables, will regulate the progression of T1D in nonobese diabetic (NOD) mice. During digestion, I3C is metabolized into ligands for the aryl hydrocarbon receptor (AhR), a transcription factor that when systemically activated prevents T1D. In NOD mice, an I3C-supplemented diet led to strong AhR activation in the small intestine but minimal systemic AhR activity. In the absence of this systemic response, the dietary intervention led to exacerbated insulitis. Consistent with the compartmentalization of AhR activation, dietary I3C did not alter T helper cell differentiation in the spleen or pancreatic draining lymph nodes. Instead, dietary I3C increased the percentage of CD4+RORγt+Foxp3- (Th17 cells) in the lamina propria, intraepithelial layer, and Peyer's patches of the small intestine. The immune modulation in the gut was accompanied by alterations to the intestinal microbiome, with changes in bacterial communities observed within one week of I3C supplementation. A transkingdom network was generated to predict host-microbe interactions that were influenced by dietary I3C. Within the phylum Firmicutes, several genera (Intestinimonas, Ruminiclostridium 9, and unclassified Lachnospiraceae) were negatively regulated by I3C. Using AhR knockout mice, we validated that Intestinimonas is negatively regulated by AhR. I3C-mediated microbial dysbiosis was linked to increases in CD25high Th17 cells. Collectively, these data demonstrate that site of AhR activation and subsequent interactions with the host microbiome are important considerations in developing AhR-targeted interventions for T1D.}, }
@article {pmid33552039, year = {2021}, author = {Klammsteiner, T and Walter, A and Bogataj, T and Heussler, CD and Stres, B and Steiner, FM and Schlick-Steiner, BC and Insam, H}, title = {Impact of Processed Food (Canteen and Oil Wastes) on the Development of Black Soldier Fly (Hermetia illucens) Larvae and Their Gut Microbiome Functions.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {619112}, pmid = {33552039}, issn = {1664-302X}, abstract = {Canteens represent an essential food supply hub for educational institutions, companies, and business parks. Many people in these locations rely on a guaranteed service with consistent quality. It is an ongoing challenge to satisfy the demand for sufficient serving numbers, portion sizes, and menu variations to cover food intolerances and different palates of customers. However, overestimating this demand or fluctuating quality of dishes leads to an inevitable loss of unconsumed food due to leftovers. In this study, the food waste fraction of canteen leftovers was identified as an optimal diet for black soldier fly (Hermetia illucens) larvae based on 50% higher consumption and 15% higher waste reduction indices compared with control chicken feed diet. Although the digestibility of food waste was nearly twice as high, the conversion efficiency of ingested and digested chicken feed remains unparalleled (17.9 ± 0.6 and 37.5 ± 0.9 in CFD and 7.9 ± 0.9 and 9.6 ± 1.0 in FWD, respectively). The oil separator waste fraction, however, inhibited biomass gain by at least 85% and ultimately led to a larval mortality of up to 96%. In addition to monitoring larval development, we characterized physicochemical properties of pre- and post-process food waste substrates. High-throughput amplicon sequencing identified Firmicutes, Proteobacteria, and Bacteroidota as the most abundant phyla, and Morganella, Acinetobacter, and certain Lactobacillales species were identified as indicator species. By using metagenome imputation, we additionally gained insights into the functional spectrum of gut microbial communities. We anticipate that the results will contribute to the development of decentralized waste-management sites that make use of larvae to process food waste as it has become common practice for biogas plants.}, }
@article {pmid33552010, year = {2020}, author = {Stergiadis, S and Cabeza-Luna, I and Mora-Ortiz, M and Stewart, RD and Dewhurst, RJ and Humphries, DJ and Watson, M and Roehe, R and Auffret, MD}, title = {Unravelling the Role of Rumen Microbial Communities, Genes, and Activities on Milk Fatty Acid Profile Using a Combination of Omics Approaches.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {590441}, pmid = {33552010}, issn = {1664-302X}, abstract = {Milk products are an important component of human diets, with beneficial effects for human health, but also one of the major sources of nutritionally undesirable saturated fatty acids (SFA). Recent discoveries showing the importance of the rumen microbiome on dairy cattle health, metabolism and performance highlight that milk composition, and potentially milk SFA content, may also be associated with microorganisms, their genes and their activities. Understanding these mechanisms can be used for the development of cost-effective strategies for the production of milk with less SFA. This work aimed to compare the rumen microbiome between cows producing milk with contrasting FA profile and identify potentially responsible metabolic-related microbial mechanisms. Forty eight Holstein dairy cows were fed the same total mixed ration under the same housing conditions. Milk and rumen fluid samples were collected from all cows for the analysis of fatty acid profiles (by gas chromatography), the abundances of rumen microbiome communities and genes (by whole-genome-shotgun metagenomics), and rumen metabolome (using 500 MHz nuclear magnetic resonance). The following groups: (i) 24 High-SFA (66.9-74.4% total FA) vs. 24 Low-SFA (60.2-66.6%% total FA) cows, and (ii) 8 extreme High-SFA (69.9-74.4% total FA) vs. 8 extreme Low-SFA (60.2-64.0% total FA) were compared. Rumen of cows producing milk with more SFA were characterized by higher abundances of the lactic acid bacteria Lactobacillus, Leuconostoc, and Weissella, the acetogenic Proteobacteria Acetobacter and Kozakia, Mycobacterium, two fungi (Cutaneotrichosporon and Cyphellophora), and at a lesser extent Methanobrevibacter and the protist Nannochloropsis. Cows carrying genes correlated with milk FA also had higher concentrations of butyrate, propionate and tyrosine and lower concentrations of xanthine and hypoxanthine in the rumen. Abundances of rumen microbial genes were able to explain between 76 and 94% on the variation of the most abundant milk FA. Metagenomics and metabolomics analyses highlighted that cows producing milk with contrasting FA profile under the same diet, also differ in their rumen metabolic activities in relation to adaptation to reduced rumen pH, carbohydrate fermentation, and protein synthesis and metabolism.}, }
@article {pmid33552004, year = {2020}, author = {Bach, LL and Ram, A and Ijaz, UZ and Evans, TJ and Lindström, J}, title = {A Longitudinal Study of the Human Oropharynx Microbiota Over Time Reveals a Common Core and Significant Variations With Self-Reported Disease.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {573969}, pmid = {33552004}, issn = {1664-302X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {Our understanding of human microbial communities, in particular in regard to diseases is advancing, yet the basic understanding of the microbiome in healthy subjects over time remains limited. The oropharynx is a key target for colonization by several important human pathogens. To understand how the oropharyngeal microbiome might limit infections, and how intercurrent infections might be associated with its composition, we characterized the oropharyngeal microbiome of 18 healthy adults, sampled weekly over a 40-weeks using culture-independent molecular techniques. We detected nine phyla, 202 genera and 1438 assignments on OTU level, dominated by Firmicutes, Bacteroidetes, and Proteobacteria on phylum level. Individual microbiomes of participants were characterized by levels of high alpha diversity (mean = 204.55 OTUs, sd = 35.64), evenness (19.83, sd = 9.74) and high temporal stability (mean Pearson's correlation between samples of 0.52, sd = 0.060), with greater differences in microbiome community composition between than within individuals. Significant changes in community composition were associated with disease states, suggesting that it is possible to detect specific changes in OTU abundance and community composition during illness. We defined the common core microbiota by varying occurrence and abundance thresholds showing that individual core microbiomes share a substantial number of OTUs across participants, chiefly Streptococci and Veillonella. Our results provide insights into the microbial communities that characterize the healthy human oropharynx, community structure and variability, and provide new approaches to define individual and shared cores. The wider implications of this result include the potential for modeling the general dynamics of oropharynx microbiota both in health and in response to antimicrobial treatments or probiotics.}, }
@article {pmid33551269, year = {2021}, author = {Cunningham, M and Azcarate-Peril, MA and Barnard, A and Benoit, V and Grimaldi, R and Guyonnet, D and Holscher, HD and Hunter, K and Manurung, S and Obis, D and Petrova, MI and Steinert, RE and Swanson, KS and van Sinderen, D and Vulevic, J and Gibson, GR}, title = {Shaping the Future of Probiotics and Prebiotics.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2021.01.003}, pmid = {33551269}, issn = {1878-4380}, abstract = {Recent and ongoing developments in microbiome science are enabling new frontiers of research for probiotics and prebiotics. Novel types, mechanisms, and applications currently under study have the potential to change scientific understanding as well as nutritional and healthcare applications of these interventions. The expansion of related fields of microbiome-targeted interventions, and an evolving landscape for implementation across regulatory, policy, prescriber, and consumer spheres, portends an era of significant change. In this review we examine recent, emerging, and anticipated trends in probiotic and prebiotic science, and create a vision for broad areas of developing influence in the field.}, }
@article {pmid33551026, year = {2021}, author = {Marrs, T and Jo, JH and Perkin, MR and Rivett, DW and Witney, AA and Bruce, KD and Logan, K and Craven, J and Radulovic, S and Versteeg, SA and van Ree, R and McLean, WHI and Strachan, DP and Lack, G and Kong, HH and Flohr, C}, title = {Gut microbiota development during infancy: Impact of introducing allergenic foods.}, journal = {The Journal of allergy and clinical immunology}, volume = {147}, number = {2}, pages = {613-621.e9}, doi = {10.1016/j.jaci.2020.09.042}, pmid = {33551026}, issn = {1097-6825}, abstract = {BACKGROUND: The gut microbiota potentially plays an important role in the immunologic education of the host during early infancy.<br><br>OBJECTIVE: We sought to determine how the infant gut microbiota evolve during infancy, particularly in relation to hygiene-related environmental factors, atopic disorders, and a randomized introduction of allergenic solids.<br><br>METHODS: A total of 1303 exclusively breast-fed infants were enrolled in a dietary randomized controlled trial (Enquiring About Tolerance study) from 3 months of age. In this nested longitudinal study, fecal samples were collected at baseline, with additional sampling of selected cases and controls at 6 and 12 months to study the evolution of their gut microbiota, using 16S ribosomal RNA gene-targeted amplicon sequencing.<br><br>RESULTS: In the 288 baseline samples from exclusively breast-fed infant at 3 months, the gut microbiota was highly heterogeneous, forming 3 distinct clusters: Bifidobacterium-rich, Bacteroides-rich, and Escherichia/Shigella-rich. Mode of delivery was the major discriminating factor. Increased Clostridium sensu stricto relative abundance at 3 months was associated with presence of atopic dermatitis on examination at age 3 and 12 months. From the selected cases and controls with longitudinal samples (n = 70), transition to Bacteroides-rich communities and influx of adult-specific microbes were observed during the first year of life. The introduction of allergenic solids promoted a significant increase in Shannon diversity and representation of specific microbes, such as genera belonging to Prevotellaceae and Proteobacteria (eg, Escherichia/Shigella), as compared with infants recommended to exclusively breast-feed.<br><br>CONCLUSIONS: Specific gut microbiota characteristics of samples from 3-month-old breast-fed infants were associated with cesarean birth, and greater Clostridium sensu stricto abundance was associated with atopic dermatitis. The randomized introduction of allergenic solids from age 3 months alongside breast-feeding was associated with differential dynamics of maturation of the gut microbial communities.}, }
@article {pmid33550882, year = {2021}, author = {Du, J and Zhang, P and Luo, J and Shen, L and Zhang, S and Gu, H and He, J and Wang, L and Zhao, X and Gan, M and Yang, L and Niu, L and Zhao, Y and Tang, Q and Tang, G and Jiang, D and Jiang, Y and Li, M and Jiang, A and Jin, L and Ma, J and Shuai, S and Bai, L and Wang, J and Zeng, B and Wu,  and Li, X and Zhu, L}, title = {Dietary betaine prevents obesity through gut microbiota-drived microRNA-378a family.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1-19}, doi = {10.1080/19490976.2020.1862612}, pmid = {33550882}, issn = {1949-0984}, abstract = {Betaine is a natural compound present in commonly consumed foods and may have a potential role in the regulation of glucose and lipids metabolism. However, the underlying molecular mechanism of its action remains largely unknown. Here, we show that supplementation with betaine contributes to improved high-fat diet (HFD)-induced gut microbiota dysbiosis and increases anti-obesity strains such as Akkermansia muciniphila, Lactobacillus, and Bifidobacterium. In mice lacking gut microbiota, the functional role of betaine in preventing HFD-induced obesity, metabolic syndrome, and inactivation of brown adipose tissues are significantly reduced. Akkermansia muciniphila is an important regulator of betaine in improving microbiome ecology and increasing strains that produce short-chain fatty acids (SCFAs). Increasing two main members of SCFAs including acetate and butyrate can significantly regulate the levels of DNA methylation at host miR-378a promoter, thus preventing the development of obesity and glucose intolerance. However, these beneficial effects are partially abolished by Yin yang (YY1), a common target gene of the miR-378a family. Taken together, our findings demonstrate that betaine can improve obesity and associated MS via the gut microbiota-derived miR-378a/YY1 regulatory axis, and reveal a novel mechanism by which gut microbiota improve host health.}, }
@article {pmid33550862, year = {2021}, author = {Shah, A and Tyagi, S and Saratale, GD and Guzik, U and Hu, A and Sreevathsa, R and Reddy, VD and Rai, V and Mulla, SI}, title = {A comprehensive review on the influence of light on signaling cross-talk and molecular communication against phyto-microbiome interactions.}, journal = {Critical reviews in biotechnology}, volume = {}, number = {}, pages = {1-41}, doi = {10.1080/07388551.2020.1869686}, pmid = {33550862}, issn = {1549-7801}, abstract = {Generally, plant growth, development, and their productivity are mainly affected by their growth rate and also depend on environmental factors such as temperature, pH, humidity, and light. The interaction between plants and pathogens are highly specific. Such specificity is well characterized by plants and pathogenic microbes in the form of a molecular signature such as pattern-recognition receptors (PRRs) and microbes-associated molecular patterns (MAMPs), which in turn trigger systemic acquired immunity in plants. A number of Arabidopsis mutant collections are available to investigate molecular and physiological changes in plants under the presence of different light conditions. Over the past decade(s), several studies have been performed by selecting Arabidopsis thaliana under the influence of red, green, blue, far/far-red, and white light. However, only few phenotypic and molecular based studies represent the modulatory effects in plants under the influence of green and blue lights. Apart from this, red light (RL) actively participates in defense mechanisms against several pathogenic infections. This evolutionary pattern of light sensitizes the pathologist to analyze a series of events in plants during various stress conditions of the natural and/or the artificial environment. This review scrutinizes the literature where red, blue, white, and green light (GL) act as sensory systems that affects physiological parameters in plants. Generally, white and RL are responsible for regulating various defense mechanisms, but, GL also participates in this process with a robust impact! In addition to this, we also focus on the activation of signaling pathways (salicylic acid and jasmonic acid) and their influence on plant immune systems against phytopathogen(s).}, }
@article {pmid33550579, year = {2021}, author = {Javan Balegh Marand, A and Van Koeveringe, GA and Janssen, D and Vahed, N and Vögeli, TA and Heesakkers, J and Hajebrahimi, S and Rahnama'i, MS}, title = {Urinary Microbiome and its Correlation with Disorders of the Genitourinary System.}, journal = {Urology journal}, volume = {}, number = {}, pages = {}, doi = {10.22037/uj.v16i7.5976}, pmid = {33550579}, issn = {1735-546X}, abstract = {PURPOSE: Until recently, the urine of healthy individuals was assumed to be sterile. However, improvement of bacterial detection methods has debunked this assumption. Recent studies have shown that the bladder contains microbiomes, which are not detectable under standard conditions. In this review, we aimed to present an overview of the published literature regarding the relationship between urinary microbiota and functional disorders of the genitourinary system.<br><br>METHODS: We searched Medline, PubMed, Embase, The Cochrane library and Scopus to identify RCTs published, with MeSH and free keywords including microbiota, bladder pain syndrome, prostatitis, kidney stone disease, and bladder cancer until September 2020. Randomized controlled trials investigating microbiome and lower urinary tract symptoms were included. Non-randomized trials, cross-over trials and pooled studies were excluded. The articles were critically appraised by two reviewers.<br><br>CONCLUSION: The urine microbiome is a newly introduced concept, which has attracted the attention of medical researchers. Since its recent introduction, researchers have conducted many fruitful studies on this phenomenon, changing our perspective toward the role of bacteria in the urinary tract and our perception of the genitourinary system health. Patient Summary: A deeper understanding of the urinary microbiome can help us to develop more efficient methods for restoring the microbiota to a healthy composition and providing symptom relief. Modification of the urinary microbiome without antibiotic use can be a possible venue for future research.}, }
@article {pmid33550328, year = {2021}, author = {Tian, Y and Sun, L and Qu, H and Yang, Y and Chen, F}, title = {Removal of nonimpacted third molars alters the periodontal condition of their neighbors clinically, immunologically, and microbiologically.}, journal = {International journal of oral science}, volume = {13}, number = {1}, pages = {5}, pmid = {33550328}, issn = {2049-3169}, abstract = {Considering the adverse effects of nonimpacted third molars (N-M3s) on the periodontal health of adjacent second molars (M2s), the removal of N-M3s may be beneficial to the periodontal health of their neighbors. This study aimed to investigate the clinical, immunological, and microbiological changes of the periodontal condition around M2s following removal of neighboring N-M3s across a 6-month period. Subjects with at least one quadrant containing an intact first molar (M1), M2, and N-M3 were screened and those who met the inclusion criteria and decided to receive N-M3 extraction were recruited in the following investigation. M2 periodontal condition was interrogated before M3 extraction (baseline) and at 3 and 6 months postoperatively. Improvements in clinical periodontal indexes of M2s in response to their adjacent N-M3 removal, along with changes in inflammatory biomarkers among gingival crevicular fluid (GCF) and the composition of subgingival plaque collected from the distal sites of the M2s of the targeted quadrant were parallelly analyzed. Complete data of 26 tooth extraction patients across the follow-up period were successfully obtained and subsequently applied for statistical analysis. Compared to the baseline, the periodontal condition of M2s was significantly changed 6 months after N-M3 removal; specifically, the probing depth of M2s significantly reduced (P < 0.001), the matrix metalloproteinase (MMP)-8 concentration involved in GCF significantly decreased (P = 0.025), and the abundance of the pathogenic genera unidentified Prevotellaceae and Streptococcus significantly decreased (P < 0.001 and P = 0.009, respectively). We concluded that N-M3 removal was associated with superior clinical indexes, decreased GCF inflammatory biomarkers, and reduced pathogenic microbiome distribution within the subgingival plaque. Although the retention or removal of N-M3s continues to be controversial, our findings provide additional evidence that medical decisions should be made as early as possible or at least before the neighboring teeth are irretrievably damaged.}, }
@article {pmid33550293, year = {2021}, author = {Zisimopoulos, A and Klavdianou, O and Theodossiadis, P and Chatziralli, I}, title = {The role of microbiome in age-related macular degeneration: A review of the literature.}, journal = {Ophthalmologica. Journal international d'ophtalmologie. International journal of ophthalmology. Zeitschrift fur Augenheilkunde}, volume = {}, number = {}, pages = {}, doi = {10.1159/000515026}, pmid = {33550293}, issn = {1423-0267}, abstract = {BACKGROUND: Age-related macular degeneration (AMD) is a progressive, multifactorial, degenerative disease and the leading cause of severe visual loss in the elderly population. The exact pathogenesis of AMD remains elusive, being the combination of genetic, environmental, metabolic and functional processes. Better understanding of the disease's pathophysiology leads to new treatment targets. Human microbiome seems to be a potential therapeutic pathway for AMD, as it has been recently proven to play a role in its pathogenesis.<br><br>SUMMARY: This review shed light into the association between microbiome and AMD. Key messages: The current evidence based on the existing literature shows that there are differences in taxonomical and functional profiles in human microbiome between patients with AMD and controls, suggesting that microbiome is implicated in AMD onset and progression, being a link between AMD and nutrition/diet. Additionally, specific bacterial classes have been proposed as potential biomarkers for AMD diagnosis. Further randomized clinical studies with large sample are needed to elucidate the role of microbiome in AMD and to draw more solid conclusions.}, }
@article {pmid33550129, year = {2021}, author = {Zhang, Q and Zhang, Z and Zhou, S and Jin, M and Lu, T and Cui, L and Qian, H}, title = {Macleaya cordata extract, an antibiotic alternative, does not contribute to antibiotic resistance gene dissemination.}, journal = {Journal of hazardous materials}, volume = {412}, number = {}, pages = {125272}, doi = {10.1016/j.jhazmat.2021.125272}, pmid = {33550129}, issn = {1873-3336}, abstract = {The abuse of antibiotics and their associated health risks are receiving global attention. The use of antibiotic additives in fodder has been banned in the European Union since 2006 and in China since 2020. Antibiotic alternatives are being developed, but their risks to the soil ecosystem remain poorly understood. Here, we compared the effects of the antibiotic oxytetracycline (OTC10, 10 mg/kg) with those of a Macleaya cordata extract (MCE, 10 and 100 mg/kg), the major antibiotic substitute. All tested concentrations of MCE and OTC10 exerted slight effects on the soil microbiome, but OTC10 and MCE100 could interfere with the structures and functions of the gut microbiome and might thus affect the soil ecological functions of Enchytraeus crypticus. Furthermore, OTC10 exposure inevitably increased the antibiotic resistance gene (ARG) abundance by 213%, whereas MCE did not induce ARG dissemination, which explains why MCE is considered to be associated with a low ecological risk. Our research provides the first demonstration of the risks posed by antibiotic alternatives to soil animals from the perspective of environmental toxicology and explores the potential development of antibiotic alternatives associated with a low ecological risk from a new perspective.}, }
@article {pmid33549995, year = {2021}, author = {Palacios, MM and Trevathan-Tackett, SM and Malerba, ME and Macreadie, PI}, title = {Effects of a nutrient enrichment pulse on blue carbon ecosystems.}, journal = {Marine pollution bulletin}, volume = {165}, number = {}, pages = {112024}, doi = {10.1016/j.marpolbul.2021.112024}, pmid = {33549995}, issn = {1879-3363}, abstract = {Coastal ecosystems are under increasing pressure from land-derived eutrophication in most developed coastlines worldwide. Here, we tested for 277 days the effects of a nutrient pulse on blue carbon retention and cycling within an Australian temperate coastal system. After 56 days of exposure, saltmarsh and mangrove plots subject to a high-nutrient treatment (~20 g N m-2 yr-1 and ~2 g P m-2 yr-1) had ~23% lower superficial soil carbon stocks. Mangrove plots also experienced a ~33% reduction in the microbe Amplicon Sequence Variant richness and a shift in community structure linked to elevated ammonium concentrations. Live plant cover, tea litter decomposition, and soil carbon fluxes (CO2 and CH4) were not significantly affected by the pulse. Before the end of the experiment, soil carbon- and nitrogen-cycling had returned to control levels, highlighting the significant but short-lived impact that a nutrient pulse can have on the carbon sink capacity of coastal wetlands.}, }
@article {pmid33549909, year = {2021}, author = {Kuo, SZ and Dettmer, K and Annavajhala, MK and Chong, DH and Uhlemann, AC and Abrams, JA and Oefner, PJ and Freedberg, DE}, title = {Associations between urinary 3-indoxyl sulfate, a gut microbiome-derived biomarker, and patient outcomes after intensive care unit admission.}, journal = {Journal of critical care}, volume = {63}, number = {}, pages = {15-21}, doi = {10.1016/j.jcrc.2021.01.005}, pmid = {33549909}, issn = {1557-8615}, abstract = {PURPOSE: 3-indoxyl sulfate (3-IS) is an indole metabolism byproduct produced by commensal gut bacteria and excreted in the urine; low urinary 3-IS has been associated with increased mortality in bone marrow transplant recipients. This study investigated urinary 3-IS and patient outcomes in the ICU.<br><br>MATERIALS AND METHODS: Prospective study that collected urine samples, rectal swabs, and clinical data on 78 adult ICU patients at admission and again 72 h later. Urine was analyzed for 3-IS by mass spectrometry.<br><br>RESULTS: Median urinary 3-IS levels were 17.1 μmol/mmol creatinine (IQR 9.5 to 26.2) at admission and 15.6 (IQR 4.2 to 30.7) 72 h later. 22% of patients had low 3-IS (≤6.9 μmol/mmol) on ICU admission and 28% after 72 h. Low 3-IS at 72 h was associated with fewer ICU-free days (22.5 low versus 26 high, p = 0.03) and with death during one year of follow-up (36% low versus 9% high 3-IS, p < 0.01); there was no detectable difference in 30-day mortality (18% low versus 5% high, p = 0.07).<br><br>CONCLUSIONS: Low urinary 3-IS level 72 h after ICU admission was associated with fewer ICU-free days and with increased one-year but not 30-day mortality. Further studies should investigate urinary 3-IS as an ICU biomarker.}, }
@article {pmid33549678, year = {2021}, author = {Umirah, F and Fen Neoh, C and Ramasamy, K and Meng Lim, S}, title = {Differential gut microbiota composition between type 2 diabetes mellitus patients and healthy controls: a systematic review.}, journal = {Diabetes research and clinical practice}, volume = {}, number = {}, pages = {108689}, doi = {10.1016/j.diabres.2021.108689}, pmid = {33549678}, issn = {1872-8227}, abstract = {AIMS: This systematic review summarised the latest findings on differential composition of gut microbiota in T2DM.<br><br>METHODS: Literature search was performed using electronic databases. Relevant studies were identified, extracted and assessed for risk of bias. The primary outcome of this systematic review was the composition of gut microbiota in healthy controls and T2DM while the secondary outcomes included the correlation of gut microbiota with metabolic parameters.<br><br>RESULTS: Thirteen case-control studies involving 575 T2DM and 840 healthy controls were included. T2DM patients exhibited a marked increase in lactobacilli. Six studies found lactobacilli to predominate the gut of T2DM patients; however, this could be confounded by the types of antihyperglyacemic medications. Conversely, butyrate producers dominate the gut of healthy controls. In T2DM patients, butyrate producers were surprisingly higher in those taking metformin intake than those not taking the drug. Whilst lactobacilli were found to be higher with increased plasma glucose, conflicting correlations were observed between various genera and anthropometric measurements, dietary intake, lipid profiles and inflammatory markers. There were moderate to strong significant positive correlations between the class Clostridia and phylum Firmicutes with pro-inflammatory IFN-γ as well as between Negativicutes and IL-6.<br><br>CONCLUSIONS: Altogether, butyrate-producing bacteria are negatively correlated to glycaemic parameters. Lactobacilli are higher in T2DM patients and Firmicutes is correlated with inflammation.}, }
@article {pmid33549582, year = {2021}, author = {Ranjith, K and Sharma, S and Shivaji, S}, title = {Microbes of the human eye: Microbiome, antimicrobial resistance and biofilm formation.}, journal = {Experimental eye research}, volume = {205}, number = {}, pages = {108476}, doi = {10.1016/j.exer.2021.108476}, pmid = {33549582}, issn = {1096-0007}, abstract = {BACKGROUND: The review focuses on the bacteria associated with the human eye using the dual approach of detecting cultivable bacteria and the total microbiome using next generation sequencing. The purpose of this review was to highlight the connection between antimicrobial resistance and biofilm formation in ocular bacteria.<br><br>METHODS: Pubmed was used as the source to catalogue culturable bacteria and ocular microbiomes associated with the normal eyes and those with ocular diseases, to ascertain the emergence of anti-microbial resistance with special reference to biofilm formation.<br><br>RESULTS: This review highlights the genetic strategies used by microorganisms to evade the lethal effects of anti-microbial agents by tracing the connections between candidate genes and biofilm formation.<br><br>CONCLUSION: The eye has its own microbiome which needs to be extensively studied under different physiological conditions; data on eye microbiomes of people from different ethnicities, geographical regions etc. are also needed to understand how these microbiomes affect ocular health.}, }
@article {pmid33549519, year = {2021}, author = {Einarsson, GG and Ronan, NJ and Mooney, D and McGettigan, C and Mullane, D and NiChroinin, M and Shanahan, F and Murphy, DM and McCarthy, M and McCarthy, Y and Eustace, JA and Gilpin, DF and Elborn, JS and Plant, BJ and Tunney, MM}, title = {Extended-culture and culture-independent molecular analysis of the airway microbiota in cystic fibrosis following CFTR modulation with ivacaftor.}, journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jcf.2020.12.023}, pmid = {33549519}, issn = {1873-5010}, abstract = {BACKGROUND: Treatment with Ivacaftor provides a significant clinical benefit in people with cystic fibrosis (PWCF) with the class III G551D-CFTR mutation. This study determined the effect of CFTR modulation with ivacaftor on the lung microbiota in PWCF.<br><br>METHODS: Using both extended-culture and culture-independent molecular methods, we analysed the lower airway microbiota of 14 PWCF, prior to commencing ivacaftor treatment and at the last available visit within the following year. We determined total bacterial and Pseudomonas aeruginosa densities by both culture and qPCR, assessed ecological parameters and community structure and compared these with biomarkers of inflammation and clinical outcomes.<br><br>RESULTS: Significant improvement in FEV1, BMI, sweat chloride and levels of circulating inflammatory biomarkers were observed POST-ivacaftor treatment. Extended-culture demonstrated a higher density of strict anaerobic bacteria (p = 0.024), richness (p = 1.59*10-4) and diversity (p = 0.003) POST-treatment. No significant difference in fold change was observed by qPCR for either total bacterial 16S rRNA copy number or P. aeruginosa density for oprL copy number with treatment. Culture-independent (MiSeq) analysis revealed a significant increase in richness (p = 0.03) and a trend towards increased diversity (p = 0.07). Moreover, improvement in lung function, richness and diversity displayed an inverse correlation with the main markers of inflammation (p < 0.05).<br><br>CONCLUSIONS: Following treatment with ivacaftor, significant improvements in clinical parameters were seen. Despite modest changes in overall microbial community composition, there was a shift towards a bacterial ecology associated with less severe CF lung disease. Furthermore, a significant correlation was observed between richness and diversity and levels of circulating inflammatory markers.}, }
@article {pmid33549144, year = {2021}, author = {Strati, F and Pujolassos, M and Burrello, C and Giuffrè, MR and Lattanzi, G and Caprioli, F and Troisi, J and Facciotti, F}, title = {Antibiotic-associated dysbiosis affects the ability of the gut microbiota to control intestinal inflammation upon fecal microbiota transplantation in experimental colitis models.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {39}, pmid = {33549144}, issn = {2049-2618}, abstract = {BACKGROUND: The gut microbiota plays a central role in host physiology and in several pathological mechanisms in humans. Antibiotics compromise the composition and functions of the gut microbiota inducing long-lasting detrimental effects on the host. Recent studies suggest that the efficacy of different clinical therapies depends on the action of the gut microbiota. Here, we investigated how different antibiotic treatments affect the ability of the gut microbiota to control intestinal inflammation upon fecal microbiota transplantation in an experimental colitis model and in ex vivo experiments with human intestinal biopsies.<br><br>RESULTS: Murine fecal donors were pre-treated with different antibiotics, i.e., vancomycin, streptomycin, and metronidazole before FMT administration to colitic animals. The analysis of the gut microbiome, fecal metabolome, and the immunophenotyping of colonic lamina propria immune cells revealed that antibiotic pre-treatment significantly influences the capability of the microbiota to control intestinal inflammation. Streptomycin and vancomycin-treated microbiota failed to control intestinal inflammation and were characterized by the blooming of pathobionts previously associated with IBD as well as with metabolites related to the presence of oxidative stress and metabolism of simple sugars. On the contrary, the metronidazole-treated microbiota retained its ability to control inflammation co-occurring with the enrichment of Lactobacillus and of innate immune responses involving iNKT cells. Furthermore, ex vivo cultures of human intestinal lamina propria mononuclear cells and iNKT cell clones from IBD patients with vancomycin pre-treated sterile fecal water showed a Th1/Th17 skewing in CD4+ T-cell populations; metronidazole, on the other hand, induced the polarization of iNKT cells toward the production of IL10.<br><br>CONCLUSIONS: Diverse antibiotic regimens affect the ability of the gut microbiota to control intestinal inflammation in experimental colitis by altering the microbial community structure and microbiota-derived metabolites. Video Abstract.}, }
@article {pmid33549013, year = {2021}, author = {Huang, L and Chen, X and Zhou, L and Xu, Q and Xie, J and Zhan, P and Lv, T and Song, Y}, title = {Antibiotic exposure windows and the efficacy of immune checkpoint blockers in patients with cancer: a meta-analysis.}, journal = {Annals of palliative medicine}, volume = {}, number = {}, pages = {}, doi = {10.21037/apm-20-2076}, pmid = {33549013}, issn = {2224-5839}, abstract = {BACKGROUND: Immune checkpoint blockers (ICBs) improve the survival of patients with cancer, but primary or acquired drug resistance is inevitable. Intestinal microorganisms play an important role in immunotherapy and antitumor response, and antibiotic use can cause changes in intestinal microbial abundance and diversity. At present, the effects of antibiotic exposure on the anticancer activity of immunotherapy remain controversial.<br><br>METHODS: We performed a meta-analysis of relevant studies retrieved from electronic databases to assess the effects of the time window of antibiotic exposure on the efficacy of immune checkpoint inhibitors (ICIs). In accordance with the definition of antibiotic use in different articles, the time window of antibiotic exposure was divided into three groups, namely, Groups 1 (antibiotic use within 2 months before or after ICI), 2 (antibiotic use before ICI), and 3 (antibiotic use anytime during ICI).<br><br>RESULTS: After retrieval from the PubMed and the Embase databases, 39 cohorts were included. In group 1, progression-free survival [PFS; hazard ratio (HR) =1.81, 95% confidence interval (CI): 1.40-2.34] and overall survival (OS; HR =1.81, 95% CI: 1.43-2.28) were prolonged in patients without antibiotic use. In group 2, the subgroup analysis showed that antibiotic use had no effect on PFS (HR =0.90, 95% CI: 0.65-1.26) and OS (HR =1.53, 95% CI: 0.89-2.62) when the exposure window defined as 0-3 months. In Group 3, pooled results indicated that PFS (HR =0.78, 95% CI: 0.65-0.93) was prolonged in patients with antibiotic during immunotherapy, and no difference was observed in the OS data (HR =0.98, 95% CI: 0.78-1.24) between the patients with antibiotic and without antibiotic.<br><br>CONCLUSIONS: Antibiotic use in shortly time (within before or after 2 months) around the initiation of immunotherapy was remarkably related to the efficacy of ICIs. A different scenario could be observed that during the long-term treatment of ICIs, the effect of antibiotic exposure seems to be eliminated.}, }
@article {pmid33548700, year = {2021}, author = {Liu, H and Lin, H and Song, B and Sun, X and Xu, R and Kong, T and Xu, F and Li, B and Sun, W}, title = {Stable-isotope probing coupled with high-throughput sequencing reveals bacterial taxa capable of degrading aniline at three contaminated sites with contrasting pH.}, journal = {The Science of the total environment}, volume = {771}, number = {}, pages = {144807}, doi = {10.1016/j.scitotenv.2020.144807}, pmid = {33548700}, issn = {1879-1026}, abstract = {The biodegradation of aniline is an important process related to the attenuation of aniline pollution at contaminated sites. Aniline contamination could occur in various pH (i.e., acidic, neutral, and alkaline) environments. However, little is known about preferred pH conditions of diverse aniline degraders at different sites. This study investigated the active aniline degraders present under contrasting pH environments using three aniline-contaminated cultures, namely, acidic sludge (ACID-S, pH 3.1), neutral river sediment (NEUS, pH 6.6), and alkaline paddy soil (ALKP, pH 8.7). Here, DNA-based stable isotope probing coupled with high-throughput sequencing revealed that aniline degradation was associated with Armatimonadetes sp., Tepidisphaerales sp., and Rhizobiaceae sp. in ACID-S; Thauera sp., Zoogloea sp., and Acidovorax sp. in NEUS; Delftia sp., Thauera sp., and Nocardioides sp. in ALKP. All the putative aniline-degrading bacteria identified were present in the &quot;core&quot; microbiome of these three cultures; however, only an appropriate pH may facilitate their ability to metabolize aniline. In addition, the biotic interactions between putative aniline-degrading bacteria and non-direct degraders showed different characteristics in three cultures, suggesting aniline-degrading bacteria employ diverse survival strategies in different pH environments. These findings expand our current knowledge regarding the diversity of aniline degraders and the environments they inhabit, and provide guidance related to the bioremediation of aniline contaminated sites with complex pH environments.}, }
@article {pmid33548686, year = {2021}, author = {Rasmussen, TS and Jakobsen, RR and Castro-Mejía, JL and Kot, W and Thomsen, AR and Vogensen, FK and Nielsen, DS and Hansen, AK}, title = {Inter-vendor variance of enteric eukaryotic DNA viruses in specific pathogen free C57BL/6N mice.}, journal = {Research in veterinary science}, volume = {136}, number = {}, pages = {1-5}, doi = {10.1016/j.rvsc.2021.01.022}, pmid = {33548686}, issn = {1532-2661}, abstract = {The laboratory mouse strain C57BL/6 is widely used as an animal model for various applications. It is becoming increasingly clear that the bacterial enteric community highly influences the phenotype. Eukaryotic viruses represent a sparsely investigated member of the enteric microbiome that might also affect the phenotype. We here investigated the presence of enteric eukaryotic DNA viruses (EDVs) in specific pathogen-free (SPF) C57BL/6N mice purchased from three vendors upon arrival and after being fed a low-fat diet (LFD) or high-fat diet (HFD). We detected genetic fragments of EDVs belonging to the viral families of Herpes-, Mimi-, Baculo- and Phycodnaviridae represented by two genera; Chlorovirus and Prasinovirus. The EDVs were detected in the mice upon arrival and persisted for 13 weeks. However, these signals of EDVs were only detected at notable levels in mice fed LFD from 2 out of 3 vendors, which suggested that the enteric composition of these EDVs were affected by both vendor (p < 0.003) and different dietary regimes (p < 0.013). This highlights the need of additional studies assessing the potential function of these EDVs that may influence the mouse phenotype and the reproducibility of animal studies using this C57BL/6N substrain.}, }
@article {pmid33548354, year = {2021}, author = {Gallucci, A and Patterson, KC and Weit, AR and Van Der Pol, WJ and Dubois, LG and Percy, AK and Morrow, CD and Campbell, SL and Olsen, ML}, title = {Microbial community changes in a female rat model of Rett syndrome.}, journal = {Progress in neuro-psychopharmacology &amp; biological psychiatry}, volume = {109}, number = {}, pages = {110259}, doi = {10.1016/j.pnpbp.2021.110259}, pmid = {33548354}, issn = {1878-4216}, abstract = {Rett syndrome (RTT) is an X-linked neurodevelopmental disorder that is predominantly caused by alterations of the methyl-CpG-binding protein 2 (MECP2) gene. Disease severity and the presence of comorbidities such as gastrointestinal distress vary widely across affected individuals. The gut microbiome has been implicated in neurodevelopmental disorders such as Autism Spectrum Disorder (ASD) as a regulator of disease severity and gastrointestinal comorbidities. Although the gut microbiome has been previously characterized in humans with RTT compared to healthy controls, the impact of MECP2 mutation on the composition of the gut microbiome in animal models where the host and diet can be experimentally controlled remains to be elucidated. By evaluating the microbial community across postnatal development as behavioral symptoms appear and progress, we have identified microbial taxa that are differentially abundant across developmental timepoints in a zinc-finger nuclease rat model of RTT compared to WT. We have additionally identified p105 as a key translational timepoint. Lastly, we have demonstrated that fecal SCFA levels are not altered in RTT rats compared to WT rats across development. Overall, these results represent an important step in translational RTT research.}, }
@article {pmid33547890, year = {2021}, author = {Fontaine, SS and Mineo, PM and Kohl, KD}, title = {Changes in the gut microbial community of the eastern newt (Notophthalmus viridescens) across its three distinct life stages.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiab021}, pmid = {33547890}, issn = {1574-6941}, abstract = {Understanding the forces that shape vertebrate gut microbial community assembly and composition throughout development is a major focus of the microbiome field. Here, we utilize the complex life cycle of the eastern newt (Notophthalmus viridescens) as a natural wild model to compare the effects of host and environmental factors on gut microbiome development. We compared bacterial inventories of each of the newt's three physiologically distinct developmental stages to determine if each hosted a unique community, or if the two stages which share an aquatic habitat (larvae and adults) harbored more similar communities than those of the third stage, the terrestrial juvenile eft. Additionally, we assessed how the contribution of selective processes to gut microbial assembly changed through development. We found that structurally, each life stage harbored a distinct community, which may be attributable to host factors. Further, across development, we found that community assembly processes shifted from a predominance of neutral to selective forces. However, habitat may also be important in determining community membership and diversity due the uniqueness of eft communities based on these metrics. Our results are similar to those in other vertebrate taxa, suggesting that gut microbiota assembly processes may be conserved across diverse lineages.}, }
@article {pmid33547877, year = {2021}, author = {Snelson, M and Clarke, RE and Nguyen, TV and Penfold, SA and Forbes, JM and Tan, SM and Coughlan, MT}, title = {Long Term High Protein Diet Feeding Alters the Microbiome and Increases Intestinal Permeability, Systemic Inflammation and Kidney Injury in Mice.}, journal = {Molecular nutrition &amp; food research}, volume = {}, number = {}, pages = {e2000851}, doi = {10.1002/mnfr.202000851}, pmid = {33547877}, issn = {1613-4133}, abstract = {SCOPE: This study evaluated the effects of a chronic high protein diet (HPD) on kidney injury, intestinal permeability and gut microbiota perturbations in a mouse model.<br><br>METHOD AND RESULTS: Mice were fed a diet containing either 20% or 52% energy from protein for 24 weeks; protein displaced an equivalent amount of wheat starch. The HPD did not alter glycaemic control or body weight. The HPD induced kidney injury as evidenced by increases in albuminuria, urinary kidney injury molecule-1, blood urea nitrogen, urinary isoprostanes and renal cortical NF-κB p65 gene expression. HPD decreased intestinal occludin gene expression, increased plasma endotoxin and plasma monocyte chemoattractant protein-1, indicating intestinal leakiness and systemic inflammation. Cecal microbial analysis revealed that HPD feeding did not alter alpha diversity, however, did alter beta diversity, indicating an altered microbial community structure with HPD feeding. Predicted metagenome pathway analysis demonstrated a reduction in branched-chain amino acid synthesis and an increase of the urea cycle with consumption of a HPD.<br><br>CONCLUSION: These results demonstrate that long term HPD consumption in mice causes albuminuria, systemic inflammation, increases in gastrointestinal permeability and is associated with gut microbiome remodelling with an increase in the urea cycle pathway, which may contribute to renal injury. This article is protected by copyright. All rights reserved.}, }
@article {pmid33547768, year = {2021}, author = {Heijnen, NFL and Hagens, LA and Smit, MR and Schultz, MJ and van der Poll, T and Schnabel, RM and van der Horst, ICC and Dickson, RP and Bergmans, DCJJ and Bos, LDJ and , }, title = {Biological subphenotypes of acute respiratory distress syndrome may not reflect differences in alveolar inflammation.}, journal = {Physiological reports}, volume = {9}, number = {3}, pages = {e14693}, doi = {10.14814/phy2.14693}, pmid = {33547768}, issn = {2051-817X}, support = {//Dutch Lung Foundation/ ; K23HL130641//National Institutes for Health/ ; R21AI137669//National Institutes for Health/ ; R01HL144599//National Institutes for Health/ ; //University of Michigan/ ; }, abstract = {Biological subphenotypes have been identified in acute respiratory distress syndrome (ARDS) based on two parsimonious models: the &quot;uninflamed&quot; and &quot;reactive&quot; subphenotype (cluster-model) and &quot;hypo-inflammatory&quot; and &quot;hyper-inflammatory&quot; (latent class analysis (LCA) model). The distinction between the subphenotypes is mainly driven by inflammatory and coagulation markers in plasma. However, systemic inflammation is not specific for ARDS and it is unknown whether these subphenotypes also reflect differences in the alveolar compartment. Alveolar inflammation and dysbiosis of the lung microbiome have shown to be important mediators in the development of lung injury. This study aimed to determine whether the &quot;reactive&quot; or &quot;hyper-inflammatory&quot; biological subphenotype also had higher concentrations of inflammatory mediators and enrichment of gut-associated bacteria in the lung. Levels of alveolar inflammatory mediators myeloperoxidase (MPO), surfactant protein D (SPD), interleukin (IL)-1b, IL-6, IL-10, IL-8, interferon gamma (IFN-ƴ), and tumor necrosis factor-alpha (TNFα) were determined in the mini-BAL fluid. Key features of the lung microbiome were measured: bacterial burden (16S rRNA gene copies/ml), community diversity (Shannon Diversity Index), and community composition. No statistically significant differences between the &quot;uninflamed&quot; and &quot;reactive&quot; ARDS subphenotypes were found in a selected set of alveolar inflammatory mediators and key features of the lung microbiome. LCA-derived subphenotypes and stratification based on cause of ARDS (direct vs. indirect) showed similar profiles, suggesting that current subphenotypes may not reflect the alveolar host response. It is important for future research to elucidate the pulmonary biology within each subphenotype properly, which is arguably a target for intervention.}, }
@article {pmid33547403, year = {2021}, author = {Rampelli, S and Turroni, S and Mallol, C and Hernandez, C and Galván, B and Sistiaga, A and Biagi, E and Astolfi, A and Brigidi, P and Benazzi, S and Lewis, CM and Warinner, C and Hofman, CA and Schnorr, SL and Candela, M}, title = {Components of a Neanderthal gut microbiome recovered from fecal sediments from El Salt.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {169}, pmid = {33547403}, issn = {2399-3642}, abstract = {A comprehensive view of our evolutionary history cannot ignore the ancestral features of our gut microbiota. To provide some glimpse into the past, we searched for human gut microbiome components in ancient DNA from 14 archeological sediments spanning four stratigraphic units of El Salt Middle Paleolithic site (Spain), including layers of unit X, which has yielded well-preserved Neanderthal occupation deposits dating around 50 kya. According to our findings, bacterial genera belonging to families known to be part of the modern human gut microbiome are abundantly represented only across unit X samples, showing that well-known beneficial gut commensals, such as Blautia, Dorea, Roseburia, Ruminococcus, Faecalibacterium and Bifidobacterium already populated the intestinal microbiome of Homo since as far back as the last common ancestor between humans and Neanderthals.}, }
@article {pmid33547384, year = {2021}, author = {Zeng, YL and Qin, L and Wei, WJ and Cai, H and Yu, XF and Zhang, W and Wu, XL and Liu, XB and Chen, WM and You, P and Hong, MZ and Liu, Y and Dong, X and Shia, BC and Niu, JJ and Pan, JS}, title = {Meta-omics characteristics of intestinal microbiota associated to HBeAg seroconversion induced by oral antiviral therapy.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {3253}, pmid = {33547384}, issn = {2045-2322}, support = {81871645//National Natural Science Foundation of China/ ; 61603092//National Natural Science Foundation of China/ ; 81500451//National Natural Science Foundation of China/ ; 81100285//National Natural Science Foundation of China/ ; grant number 2015CB553800//National Basic Research Program of China (973 Program)/ ; }, abstract = {Tenofovir and entecavir are currently designated as the preferred oral antiviral drugs for chronic hepatitis B. However, only less than 40% of patients can achieve HBeAg seroconversion. We aim at investigating the role of intestinal microbiome in HBeAg seroconversion induced by oral antiviral therapy and describe multi-omics characteristics of HBeAg seroconversion associated intestinal flora. In this study, we prospectively collected fecal samples at baseline from the patients with HBeAg positive chronic hepatitis B who would have oral antiviral therapy. 16S rDNA sequencing and metabolomics were performed. We identified HBeAg seroconversion-related microbial signature and constructed prediction model for HBeAg seroconversion. Thirty-seven of these subjects achieved HBeAg seroconversion within 156 weeks after the initiation of oral antiviral therapy, while 41 subjects remained HBeAg positive even after over 156 weeks of therapy. A computational statistical and machine learning approach allowed us to identify a microbial signature for HBeAg seroconversion. Using random forest method, we further constructed a classifier based on the microbial signature, with area under curve being 0.749 for the test set. Patients who achieved HBeAg seroconversion tended to have lower abundance of certain fecal metabolites such as essential amino acids, and several dipeptides. By analyzing the fecal microbiota from the patients with and without HBeAg seroconversion, we showed intestinal microbiome play a critical role in HBeAg seroconversion induced by oral antiviral therapy. We also identified intestinal microbial signature that is associated with HBeAg seroconversion after oral antiviral therapy.}, }
@article {pmid33547360, year = {2021}, author = {Hu, J and Lesseur, C and Miao, Y and Manservisi, F and Panzacchi, S and Mandrioli, D and Belpoggi, F and Chen, J and Petrick, L}, title = {Low-dose exposure of glyphosate-based herbicides disrupt the urine metabolome and its interaction with gut microbiota.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {3265}, pmid = {33547360}, issn = {2045-2322}, support = {P30ES023515/ES/NIEHS NIH HHS/United States ; }, abstract = {Glyphosate-based herbicides (GBHs) can disrupt the host microbiota and influence human health. In this study, we explored the potential effects of GBHs on urinary metabolites and their interactions with gut microbiome using a rodent model. Glyphosate and Roundup (equal molar for glyphosate) were administered at the USA glyphosate ADI guideline (1.75 mg/kg bw/day) to the dams and their pups. The urine metabolites were profiled using non-targeted liquid chromatography-high resolution mass spectrometry (LC-HRMS). Our results found that overall urine metabolite profiles significantly differed between dams and pups and between female and male pups. Specifically, we identified a significant increase of homocysteine, a known risk factor of cardiovascular disease in both Roundup and glyphosate exposed pups, but in males only. Correlation network analysis between gut microbiome and urine metabolome pointed to Prevotella to be negatively correlated with the level of homocysteine. Our study provides initial evidence that exposures to commonly used GBH, at a currently acceptable human exposure dose, is capable of modifying urine metabolites in both rat adults and pups. The link between Prevotella-homocysteine suggests the potential role of GBHs in modifying the susceptibility of homocysteine, which is a metabolite that has been dysregulated in related diseases like cardiovascular disease or inflammation, through commensal microbiome.}, }
@article {pmid33547327, year = {2021}, author = {Opron, K and Begley, LA and Erb-Downward, JR and Freeman, C and Madapoosi, S and Alexis, NE and Barjaktarevic, I and Graham Barr, R and Bleecker, ER and Bowler, RP and Christenson, SA and Comellas, AP and Cooper, CB and Couper, DJ and Doerschuk, CM and Dransfield, MT and Han, MK and Hansel, NN and Hastie, AT and Hoffman, EA and Kaner, RJ and Krishnan, J and O'Neal, WK and Ortega, VE and Paine, R and Peters, SP and Michael Wells, J and Woodruff, PG and Martinez, FJ and Curtis, JL and Huffnagle, GB and Huang, YJ}, title = {Lung microbiota associations with clinical features of COPD in the SPIROMICS cohort.}, journal = {NPJ biofilms and microbiomes}, volume = {7}, number = {1}, pages = {14}, pmid = {33547327}, issn = {2055-5008}, support = {HHSN268200900019C/HL/NHLBI NIH HHS/United States ; U24 HL141762/HL/NHLBI NIH HHS/United States ; R01AI129958//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; R03HL138310//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R01 HL121774/HL/NHLBI NIH HHS/United States ; HHSN268200900015C/HL/NHLBI NIH HHS/United States ; HHSN268200900016C/HL/NHLBI NIH HHS/United States ; U01 HL137880/HL/NHLBI NIH HHS/United States ; HHSN268200900018C/HL/NHLBI NIH HHS/United States ; HHSN268200900013C/HL/NHLBI NIH HHS/United States ; R01HL121774//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R01 AI129958/AI/NIAID NIH HHS/United States ; HHSN268200900014C/HL/NHLBI NIH HHS/United States ; R03 HL138310/HL/NHLBI NIH HHS/United States ; HHSN268200900017C/HL/NHLBI NIH HHS/United States ; HHSN268200900020C/HL/NHLBI NIH HHS/United States ; }, abstract = {Chronic obstructive pulmonary disease (COPD) is heterogeneous in development, progression, and phenotypes. Little is known about the lung microbiome, sampled by bronchoscopy, in milder COPD and its relationships to clinical features that reflect disease heterogeneity (lung function, symptom burden, and functional impairment). Using bronchoalveolar lavage fluid collected from 181 never-smokers and ever-smokers with or without COPD (GOLD 0-2) enrolled in the SubPopulations and InteRmediate Outcome Measures In COPD Study (SPIROMICS), we find that lung bacterial composition associates with several clinical features, in particular bronchodilator responsiveness, peak expiratory flow rate, and forced expiratory flow rate between 25 and 75% of FVC (FEF25-75). Measures of symptom burden (COPD Assessment Test) and functional impairment (six-minute walk distance) also associate with disparate lung microbiota composition. Drivers of these relationships include members of the Streptococcus, Prevotella, Veillonella, Staphylococcus, and Pseudomonas genera. Thus, lung microbiota differences may contribute to airway dysfunction and airway disease in milder COPD.}, }
@article {pmid33547058, year = {2021}, author = {Tunsagool, P and Mhuantong, W and Tangphatsornruang, S and Am-In, N and Chuanchuen, R and Luangtongkum, T and Suriyaphol, G}, title = {Metagenomics of antimicrobial and heavy metal resistance in the cecal microbiome of fattening pigs raised without antibiotics.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02684-20}, pmid = {33547058}, issn = {1098-5336}, abstract = {This study aimed to detect the cecal microbiome, antimicrobial resistance (AMR) and heavy metal resistance genes (MRGs) in fattening pigs raised under antibiotic-free (ABF) conditions compared with ordinary industrial pigs (control, C) using whole-genome shotgun sequencing. ABF pigs showed the enrichment of Prevotella (33%) and Lactobacillus (13%), whereas Escherichia coli (40%), Fusobacterium and Bacteroides (each at 4%) were notably observed in the C group. Distinct clusters of cecal microbiota of ABF and C pigs were revealed; however, microbiota of some C pigs (C1) appeared in the same cluster as ABF and were totally separated from the remaining C pigs (C2). For AMR genes, the highest abundance tet(Q) (35.7%) and mef(A) (12.7%) were markedly observed in the ABF group whereas tet(Q) (26.2%) and tet(W) (10.4%) were shown in the C group. tet(Q) was positively correlated to Prevotella in ABF and C1 samples. In the C2 group, the prominent tet(W) was positively correlated to Fusobacterium and Bacteroides Pigs have never received tetracycline but pregnant sows used chlortetracycline once 7 d before parturition. Chromosomal Cu and Zn resistance genes were also shown in both groups regardless the received Cu and Zn feed additives. A higher abundance of multi-metal resistance genes was observed in the C group (44%) compared with the ABF group (41%). In conclusion, the microbiome clusters in some C pigs were similar to that in ABF pigs. High abundant tetracycline resistance genes interrelated to major bacteria were observed in both ABF and C pigs. MRGs were also observed.IMPORTANCE: Owing to the increased problem of AMR in farm animals, raising farm animals without antibiotics is one method that could solve this problem. Our study showed that only some tetracycline and macrolide resistance genes, tet(Q), tet(W) and mef(A), were markedly abundant in ABF and C groups. The tet(Q) and tet(W) genes interrelated to different predominant bacteria in each group, showing the potential role of major bacteria as reservoirs of AMR genes. In addition, chromosomal Cu and Zn resistance genes were also observed in both pig groups, not depending on the use of Cu and Zn additives in both farms. The association of MRGs and AMR genotypes and phenotypes together with the method to re-sensitize bacteria to antibiotics should be studied further to unveil the cause of high resistance genes and solve the problems.}, }
@article {pmid33547052, year = {2021}, author = {Regen, T and Isaac, S and Amorim, A and Núñez, NG and Hauptmann, J and Shanmugavadivu, A and Klein, M and Sankowski, R and Mufazalov, IA and Yogev, N and Huppert, J and Wanke, F and Witting, M and Grill, A and Gálvez, EJC and Nikolaev, A and Blanfeld, M and Prinz, I and Schmitt-Kopplin, P and Strowig, T and Reinhardt, C and Prinz, M and Bopp, T and Becher, B and Ubeda, C and Waisman, A}, title = {IL-17 controls central nervous system autoimmunity through the intestinal microbiome.}, journal = {Science immunology}, volume = {6}, number = {56}, pages = {}, doi = {10.1126/sciimmunol.aaz6563}, pmid = {33547052}, issn = {2470-9468}, abstract = {Interleukin-17A- (IL-17A) and IL-17F-producing CD4+ T helper cells (TH17 cells) are implicated in the development of chronic inflammatory diseases, such as multiple sclerosis and its animal model, experimental autoimmune encephalomyelitis (EAE). TH17 cells also orchestrate leukocyte invasion of the central nervous system (CNS) and subsequent tissue damage. However, the role of IL-17A and IL-17F as effector cytokines is still confused with the encephalitogenic function of the cells that produce these cytokines, namely, TH17 cells, fueling a long-standing debate in the neuroimmunology field. Here, we demonstrated that mice deficient for IL-17A/F lose their susceptibility to EAE, which correlated with an altered composition of their gut microbiota. However, loss of IL-17A/F in TH cells did not diminish their encephalitogenic capacity. Reconstitution of a wild-type-like intestinal microbiota or reintroduction of IL-17A specifically into the gut epithelium of IL-17A/F-deficient mice reestablished their susceptibility to EAE. Thus, our data demonstrated that IL-17A and IL-17F are not encephalitogenic mediators but rather modulators of intestinal homeostasis that indirectly alter CNS-directed autoimmunity.}, }
@article {pmid33546983, year = {2021}, author = {Mosterd, CM and Kanbay, M and van den Born, BJH and van Raalte, DH and Rampanelli, E}, title = {Intestinal microbiota and diabetic kidney diseases: the Role of microbiota and derived metabolites inmodulation of renal inflammation and disease progression.}, journal = {Best practice &amp; research. Clinical endocrinology &amp; metabolism}, volume = {}, number = {}, pages = {101484}, doi = {10.1016/j.beem.2021.101484}, pmid = {33546983}, issn = {1878-1594}, abstract = {Diabetic kidney disease (DKD) represents a growing public health burden and is the leading cause of end-stage kidney diseases. In recent years, host-gut microbiota interactions have emerged as an integral part for host homeostasis. In the context of nephropathies, mounting evidence supports a bidirectional microbiota-kidney crosstalk, which becomes particularly manifest during progressive kidney dysfunction. Indeed, in chronic kidney disease (CKD), the &quot;healthy&quot; microbiota structure is disrupted and intestinal microbes produce large quantities of uremic solutes responsible for renal damage; on the other hand, the uremic state, fueled by reduced renal clearance, causes shifts in microbial metabolism and composition, hence creating a vicious cycle in which dysbiosis and renal dysfunction are progressively worsened. In this review, we will summarize the evidence from clinical/experimental studies concerning the occurrence of gut dysbiosis in diabetic and non-diabetic CKD, discuss the functional consequences of dysbiosis for CKD progression and debate putative therapeutic interventions targeting the intestinal microbiome.}, }
@article {pmid33546963, year = {2021}, author = {Cheung, SW and Boost, MV and Cho, P}, title = {Effect of povidone iodine contact lens disinfecting solution on orthokeratology lens and lens case contamination and organisms in the microbiome of the conjunctiva.}, journal = {Contact lens &amp; anterior eye : the journal of the British Contact Lens Association}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.clae.2021.01.007}, pmid = {33546963}, issn = {1476-5411}, abstract = {PURPOSE: To compare lens cleaning routines using a povidone iodine-based rigid lens disinfecting solution and its effect on conjunctival colonisation, and lens and lens case contamination.<br><br>METHODS: Participants, aged 6-10 years, receiving orthokeratology treatment were randomised to four lens cleaning routines: with and without the use of daily and/or weekly cleaners, which were performed by their parents. Conjunctival colonisation was compared before lens wear and at 1-, 3-, and 6-month after commencement of lens wear. Contamination of lenses and lens cases was investigated at these times. Organisms were identified using MALDI-TOF mass spectrometry.<br><br>RESULTS: Of the 76 participants who completed the study, conjunctival colonization was present in 24 (32 %) at baseline. Of the remaining 52 participants, 34 consistently yielded no growth. Participants positive at baseline were statistically more likely to be colonized after commencement of lens wear (p = 0.020). Overall, colonization rate was reduced to 15 % (11/72) after 6-month lens wear, which reached significance for initially colonized participants (p < 0.001). Few cultures yielded potential ocular pathogens, with notably no Pseudomonas aeruginosa. Contamination rates of both lenses and lens cases were also low, with few isolations of ocular pathogens. No significant differences were observed between cleaning regimes for conjunctival colonization or contamination of lenses or cases.<br><br>CONCLUSIONS: Disinfection for rigid and ortho-k lens wearers may be effectively achieved with the use of povidone iodine-based solution, apparently regardless of cleaning routine adopted in the current study. The absence of pathogens in the conjunctiva, lenses, and lens cases in the great majority of samples indicates that it can improve the safety of overnight lens wear.}, }
@article {pmid33546876, year = {2021}, author = {Davidson, GL and Raulo, A and Knowles, SCL}, title = {Response to Nguyen et al. 'Laboratory-Inspired Manipulations Hold Value for Wild Microbiome-Behaviour Research'.}, journal = {Trends in ecology &amp; evolution}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tree.2021.01.004}, pmid = {33546876}, issn = {1872-8383}, }
@article {pmid33546771, year = {2021}, author = {Piccinni, MZ and Watts, JEM and Fourny, M and Guille, M and Robson, SC}, title = {The skin microbiome of Xenopus laevis and the effects of husbandry conditions.}, journal = {Animal microbiome}, volume = {3}, number = {1}, pages = {17}, pmid = {33546771}, issn = {2524-4671}, support = {212942/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; BB/R014841/1//Biotechnology and Biological Sciences Research Council (GB)/ ; E3//Research England/ ; E3//Research England/ ; }, abstract = {BACKGROUND: Historically the main source of laboratory Xenopus laevis was the environment. The increase in genetically altered animals and evolving governmental constraints around using wild-caught animals for research has led to the establishment of resource centres that supply animals and reagents worldwide, such as the European Xenopus Resource Centre. In the last decade, centres were encouraged to keep animals in a &quot;low microbial load&quot; or &quot;clean&quot; state, where embryos are surface sterilized before entering the housing system; instead of the conventional, &quot;standard&quot; conditions where frogs and embryos are kept without prior surface treatment. Despite Xenopus laevis having been kept in captivity for almost a century, surprisingly little is known about the frogs as a holobiont and how changing the microbiome may affect resistance to disease. This study examines how the different treatment conditions, &quot;clean&quot; and &quot;standard&quot; husbandry in recirculating housing, affects the skin microbiome of tadpoles and female adults. This is particularly important when considering the potential for poor welfare caused by a change in husbandry method as animals move from resource centres to smaller research colonies.<br><br>RESULTS: We found strong evidence for developmental control of the surface microbiome on Xenopus laevis; adults had extremely similar microbial communities independent of their housing, while both tadpole and environmental microbiome communities were less resilient and showed greater diversity.<br><br>CONCLUSIONS: Our findings suggest that the adult Xenopus laevis microbiome is controlled and selected by the host. This indicates that the surface microbiome of adult Xenopus laevis is stable and defined independently of the environment in which it is housed, suggesting that the use of clean husbandry conditions poses little risk to the skin microbiome when transferring adult frogs to research laboratories. This will have important implications for frog health applicable to Xenopus laevis research centres throughout the world.}, }
@article {pmid33546590, year = {2021}, author = {Vo, D and Singh, SC and Safa, S and Sahoo, D}, title = {Boolean implication analysis unveils candidate universal relationships in microbiome data.}, journal = {BMC bioinformatics}, volume = {22}, number = {1}, pages = {49}, pmid = {33546590}, issn = {1471-2105}, mesh = {Animals ; Bacteria ; *Data Analysis ; Humans ; *Microbiota ; }, abstract = {BACKGROUND: Microbiomes consist of bacteria, viruses, and other microorganisms, and are responsible for many different functions in both organisms and the environment. Past analyses of microbiomes focused on using correlation to determine linear relationships between microbes and diseases. Weak correlations due to nonlinearity between microbe pairs may cause researchers to overlook critical components of the data. With the abundance of available microbiome, we need a method that comprehensively studies microbiomes and how they are related to each other.<br><br>RESULTS: We collected publicly available datasets from human, environment, and animal samples to determine both symmetric and asymmetric Boolean implication relationships between a pair of microbes. We then found relationships that are potentially invariants, meaning they will hold in any microbe community. In other words, if we determine there is a relationship between two microbes, we expect the relationship to hold in almost all contexts. We discovered that around 330,000 pairs of microbes universally exhibit the same relationship in almost all the datasets we studied, thus making them good candidates for invariants. Our results also confirm known biological properties and seem promising in terms of disease diagnosis.<br><br>CONCLUSIONS: Since the relationships are likely universal, we expect them to hold in clinical settings, as well as general populations. If these strong invariants are present in disease settings, it may provide insight into prognostic, predictive, or therapeutic properties of clinically relevant diseases. For example, our results indicate that there is a difference in the microbe distributions between patients who have or do not have IBD, eczema and psoriasis. These new analyses may improve disease diagnosis and drug development in terms of accuracy and efficiency.}, }
@article {pmid33546450, year = {2021}, author = {Trevisi, P and Luise, D and Correa, F and Bosi, P}, title = {Timely Control of Gastrointestinal Eubiosis: A Strategic Pillar of Pig Health.}, journal = {Microorganisms}, volume = {9}, number = {2}, pages = {}, doi = {10.3390/microorganisms9020313}, pmid = {33546450}, issn = {2076-2607}, abstract = {The pig gastrointestinal tract (GIT) is an open ecosystem in which microorganisms and their host are mutually involved and continually adapt to different factors and problems which may or may not be host dependent or due to the production system. The aim of the present review is to highlight the factors affecting the GIT microbial balance in young pigs, focusing on the pre- and post-weaning phases, to define a road map for improving pig health and the production efficiency of the food chain. Birth and weaning body weight, physiological maturation,