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Bibliography on: Microbiome

The Electronic Scholarly Publishing Project: Providing world-wide, free access to classic scientific papers and other scholarly materials, since 1993.


ESP: PubMed Auto Bibliography 08 Aug 2022 at 01:41 Created: 


It has long been known that every multicellular organism coexists with large prokaryotic ecosystems — microbiomes — that completely cover its surfaces, external and internal. Recent studies have shown that these associated microbiomes are not mere contamination, but instead have profound effects upon the function and fitness of the multicellular organism. We now know that all MCEs are actually functional composites, holobionts, composed of more prokaryotic cells than eukaryotic cells and expressing more prokaryotic genes than eukaryotic genes. A full understanding of the biology of "individual" eukaryotes will now depend on an understanding of their associated microbiomes.

Created with PubMed® Query: microbiome[tiab] NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)


RevDate: 2022-08-06

Chouayekh H, Farhat-Khemakhem A, Karray F, et al (2022)

Effects of Dietary Supplementation with Bacillus amyloliquefaciens US573 on Intestinal Morphology and Gut Microbiota of European Sea Bass.

Probiotics and antimicrobial proteins [Epub ahead of print].

Probiotics or direct-fed microbials (DFM) have proven strong potential for improving aquaculture sustainability. This study aims to evaluate the effects of dietary supplementation with the DFM Bacillus amyloliquefaciens US573 on growth performance, intestinal morphology, and gut microbiota (GM) of European sea bass. For this purpose, healthy fish were divided into two feeding trials in triplicate of 25 fish in each tank. The fish were fed with a control basal diet or a DFM-supplemented diet for 42 days. Results showed that, while no significant effects on growth performance were observed, the length and abundance of villi were higher in the DFM-fed group. The benefic effects of DFM supplementation included also the absence of cysts formation and the increase in number of goblet cells playing essential role in immune response. Through DNA metabarcoding analysis of GM, 5 phyla and 14 major genera were identified. At day 42, the main microbiome changes in response to B. amyloliquefaciens US573 addition included the significant decrease in abundance of Actinobacteria phylum that perfectly correlates with a decrease in Nocardia genus representatives which represent serious threat in marine and freshwater fish. On the contrary, an obvious dominance of Betaproteobacteria associated with the abundance in Variovorax genus members, known for their ability to metabolize numerous substrates, was recorded. Interestingly, Firmicutes, particularly species affiliated to the genus Sporosarcina with recent promising probiotic potential, were identified as the most abundant. These results suggest that B. amyloliquefaciens US573 can be effectively recommended as health-promoting DFM in European sea bass farming.

RevDate: 2022-08-06

Chen M, Li S, Arora I, et al (2022)

Maternal soybean diet on prevention of obesity-related breast cancer through early-life gut microbiome and epigenetic regulation: Maternal soybean prevention on obesity-related breast cancer.

The Journal of nutritional biochemistry pii:S0955-2863(22)00187-5 [Epub ahead of print].

Overnutrition-induced obesity and metabolic dysregulation are considered major risk factors contributing to breast cancer. The origin of both obesity and breast cancer can retrospect to early development in the human lifespan. Genistein (GE), a natural isoflavone enriched in soybean products, has been proposed to associate with a lower risk of breast cancer and various metabolic disorders. Our study aimed to determine the effects of maternal exposure to soybean dietary GE on prevention of overnutrition-induced breast cancer later in life and explore potential mechanisms in different mouse models. Our results showed that maternal dietary GE treatment improved offspring metabolic functions by significantly attenuating high-fat diet (HFD)-induced body fat accumulation, lipid panel abnormalities and glucose intolerance in mice offspring. Importantly, maternal dietary GE exposure effectively delayed HFD-simulated mammary tumor development in female offspring. Mechanistically, we found that maternal dietary GE may exert its chemopreventive effects through affecting essential regulatory gene expression in control of metabolism, inflammation and tumor development via, at least in part, regulation of offspring gut microbiome, bacterial metabolites and epigenetic profiles. Altogether, our findings indicate that maternal GE consumption is an effective intervention approach leading to early-life prevention of obesity-related metabolic disorders and breast cancer later in life through dynamically influencing the interplay between early-life gut microbiota, key microbial metabolite profiles and offspring epigenome.

RevDate: 2022-08-06

Chen Y, Lin J, Xiao L, et al (2022)

Gut microbiota in systemic lupus erythematosus: A fuse and a solution.

Journal of autoimmunity, 132:102867 pii:S0896-8411(22)00075-0 [Epub ahead of print].

Gut commensals help shape and mold host immune system and deeply influence human health. The disease spectrum of mankind that gut microbiome may associate with is ever-growing, but the mechanisms are still enigmas. Characterized by loss of self-tolerance and sustained self-attack, systemic lupus erythematosus (SLE) is labeled with chronic inflammation, production of autoantibodies and multisystem injury, which so far are mostly incurable. Gut microbiota and their metabolites, now known as important environmental triggers of local/systemic immune responses, have been proposed to be involved in SLE development and progression probably through the following mechanisms: translocation beyond their niches; molecular mimicry to cross-activate immune response targeting self-antigens; epitope spreading to expand autoantibodies spectrum; and bystander activation to promote systemic inflammation. Gut microbiota which varies between individuals may also influence the metabolism and bio-transformation of disease-modifying anti-rheumatic drugs, thus associated with the efficacy and toxicity of these drugs, adding another explanation for heterogenic therapeutic responses. Modulation of gut microbiota via diet, probiotics/prebiotics, antibiotics/phages, fecal microbiota transplantation, or helminth to restore immune tolerance and homeostasis is expected to be a promising neoadjuvant therapy for SLE. We reviewed the advances in this territory and discussed the application prospect of modulating gut microbiota in controlling SLE.

RevDate: 2022-08-06

Reis Ferreira M, Pasto A, Ng T, et al (2022)

The microbiota and radiotherapy for head and neck cancer: What should clinical oncologists know?.

Cancer treatment reviews, 109:102442 pii:S0305-7372(22)00111-6 [Epub ahead of print].

Radiotherapy is a linchpin in head and neck squamous cell carcinoma (HN-SCC) treatment. Modulating tumour and/or normal tissue biology offers opportunities to further develop HN-SCC radiotherapy. The microbiota, which can exhibit homeostatic properties and be a modulator of immunity, has recently received considerable interest from the Oncology community. Microbiota research in head and neck oncology has also flourished. However, available data are difficult to interpret for clinical and radiation oncologists. In this review, we focus on how microbiota research can contribute to the improvement of radiotherapy for HN-SCC, focusing on how current and future research can be translated back to the clinic. We include in-depth discussions about the microbiota, its multiple habitats and relevance to human physiology, mechanistic interactions with HN-SCC, available evidence on microbiota and HNC oncogenesis, efficacy and toxicity of treatment. We discuss clinically-relevant areas such as the role of the microbiota as a predictive and prognostic biomarker, as well as the potential of leveraging the microbiota and its interactions with immunity to improve treatment results. Importantly, we draw parallels with other cancers where research is more mature. We map out future directions of research and explain clinical implications in detail.

RevDate: 2022-08-06

Kunimitsu M, Nakagami G, Minematsu T, et al (2022)

An in vivo critically colonised wound model with dysbiotic wound microbiota.

International wound journal [Epub ahead of print].

In critically colonised wounds, many of the signs of infection are often absent, and delayed healing may be the only clinical sign. The prevention of critical colonisation is important, but its pathophysiology has not yet been elucidated. We have previously reported that dysbiotic microbiota dissimilar to the peri-wound skin microbiota may develop in critically colonised wounds. To investigate the role of dysbiotic microbiota, this study aimed to develop a critically colonised wound model by transplantation of dysbiotic microbiota. To transplant microbiota, a bacterial solution (dysbiosis group) or with Luria-Bertani medium (commensal group) was inoculated to full-thickness wounds of rats. The bacterial solution was prepared by anaerobically culturing bacteria from donor rats on an artificial dermis in Luria-Bertani medium for 72 hours. As a result, the degree of the change in the microbial similarity between pre- and post-transplantation of microbiota was significantly higher in the dysbiosis group (P < .001). No signs of infection were observed in any rat in either group. The wound area in the dysbiosis group was significantly larger (P < .001), and there was a significant infiltration of neutrophils (P < .001). All rats of the dysbiosis group represented the clinical features of critically colonised wounds. Furthermore, there were significantly fewer regulatory T cells in the wounds of the dysbiosis group. This is the first study to develop a novel animal model that represents the clinical features of critically colonised wounds and will be useful in investigating the pathogenesis of critical colonisation via regulatory T cells.

RevDate: 2022-08-05

Gong X, Chen TW, Zhang L, et al (2022)

Gut microbiome reflect adaptation of earthworms to cave and surface environments.

Animal microbiome, 4(1):47.

BACKGROUND: Caves are special natural laboratories for most biota and the cave communities are unique. Establishing population in cave is accompanied with modifications in adaptability for most animals. To date, little is known about the survival mechanisms of soil animals in cave environments, albeit they play vital roles in most terrestrial ecosystems. Here, we investigated whether and how gut microbes would contribute to the adaptation of earthworms by comparing the gut microbiome of two earthworm species from the surface and caves.

RESULTS: Two dominant earthworm species inhabited caves, i.e., Allolobophora chlorotica and Aporrectodea rosea. Compared with the counterparts on the surface, A. rosea significantly decreased population in the cave, while A. chlorotica didn't change. Microbial taxonomic and phylogenetic diversities between the earthworm gut and soil environment were asynchronic with functional diversity, with functional gene diversity been always higher in earthworm gut than in soil, but species richness and phylogenetic diversity lower. In addition, earthworm gut microbiome were characterized by higher rrn operon numbers and lower network complexity than soil microbiota.

CONCLUSIONS: Different fitness of the two earthworm species in cave is likely to coincide with gut microbiota, suggesting interactions between host and gut microbiome are essential for soil animals in adapting to new environments. The functional gene diversity provided by gut microbiome is more important than taxonomic or phylogenetic diversity in regulating host adaptability. A stable and high-efficient gut microbiome, including microbiota and metabolism genes, encoded potential functions required by the animal hosts during the processes of adapting to and establishing in the cave environments. Our study also demonstrates how the applications of microbial functional traits analysis may advance our understanding of animal-microbe interactions that may aid animals to survive in extreme ecosystems.

RevDate: 2022-08-05

Wang C, Segal LN, Hu J, et al (2022)

Microbial risk score for capturing microbial characteristics, integrating multi-omics data, and predicting disease risk.

Microbiome, 10(1):121.

BACKGROUND: With the rapid accumulation of microbiome-wide association studies, a great amount of microbiome data are available to study the microbiome's role in human disease and advance the microbiome's potential use for disease prediction. However, the unique features of microbiome data hinder its utility for disease prediction.

METHODS: Motivated from the polygenic risk score framework, we propose a microbial risk score (MRS) framework to aggregate the complicated microbial profile into a summarized risk score that can be used to measure and predict disease susceptibility. Specifically, the MRS algorithm involves two steps: (1) identifying a sub-community consisting of the signature microbial taxa associated with disease and (2) integrating the identified microbial taxa into a continuous score. The first step is carried out using the existing sophisticated microbial association tests and pruning and thresholding method in the discovery samples. The second step constructs a community-based MRS by calculating alpha diversity on the identified sub-community in the validation samples. Moreover, we propose a multi-omics data integration method by jointly modeling the proposed MRS and other risk scores constructed from other omics data in disease prediction.

RESULTS: Through three comprehensive real-data analyses using the NYU Langone Health COVID-19 cohort, the gut microbiome health index (GMHI) multi-study cohort, and a large type 1 diabetes cohort separately, we exhibit and evaluate the utility of the proposed MRS framework for disease prediction and multi-omics data integration. In addition, the disease-specific MRSs for colorectal adenoma, colorectal cancer, Crohn's disease, and rheumatoid arthritis based on the relative abundances of 5, 6, 12, and 6 microbial taxa, respectively, are created and validated using the GMHI multi-study cohort. Especially, Crohn's disease MRS achieves AUCs of 0.88 (0.85-0.91) and 0.86 (0.78-0.95) in the discovery and validation cohorts, respectively.

CONCLUSIONS: The proposed MRS framework sheds light on the utility of the microbiome data for disease prediction and multi-omics integration and provides a great potential in understanding the microbiome's role in disease diagnosis and prognosis. Video Abstract.

RevDate: 2022-08-05

Correale J, Hohlfeld R, SE Baranzini (2022)

The role of the gut microbiota in multiple sclerosis.

Nature reviews. Neurology [Epub ahead of print].

During the past decade, research has revealed that the vast community of micro-organisms that inhabit the gut - known as the gut microbiota - is intricately linked to human health and disease, partly as a result of its influence on systemic immune responses. Accumulating evidence demonstrates that these effects on immune function are important in neuroinflammatory diseases, such as multiple sclerosis (MS), and that modulation of the microbiome could be therapeutically beneficial in these conditions. In this Review, we examine the influence that the gut microbiota have on immune function via modulation of serotonin production in the gut and through complex interactions with components of the immune system, such as T cells and B cells. We then present evidence from studies in mice and humans that these effects of the gut microbiota on the immune system are important in the development and course of MS. We also consider how strategies for manipulating the composition of the gut microbiota could be used to influence disease-related immune dysfunction and form the basis of a new class of therapeutics. The strategies discussed include the use of probiotics, supplementation with bacterial metabolites, transplantation of faecal matter or defined microbial communities, and dietary intervention. Carefully designed studies with large human cohorts will be required to gain a full understanding of the microbiome changes involved in MS and to develop therapeutic strategies that target these changes.

RevDate: 2022-08-05

Li QS, Wang R, Ma ZY, et al (2022)

Dietary selection of metabolically distinct microorganisms drives hydrogen metabolism in ruminants.

The ISME journal [Epub ahead of print].

Ruminants are important for global food security but emit the greenhouse gas methane. Rumen microorganisms break down complex carbohydrates to produce volatile fatty acids and molecular hydrogen. This hydrogen is mainly converted into methane by archaea, but can also be used by hydrogenotrophic acetogenic and respiratory bacteria to produce useful metabolites. A better mechanistic understanding is needed on how dietary carbohydrates influence hydrogen metabolism and methanogenesis. We profiled the composition, metabolic pathways, and activities of rumen microbiota in 24 beef cattle adapted to either fiber-rich or starch-rich diets. The fiber-rich diet selected for fibrolytic bacteria and methanogens resulting in increased fiber utilization, while the starch-rich diet selected for amylolytic bacteria and lactate utilizers, allowing the maintenance of a healthy rumen and decreasing methane production (p < 0.05). Furthermore, the fiber-rich diet enriched for hydrogenotrophic methanogens and acetogens leading to increased electron-bifurcating [FeFe]-hydrogenases, methanogenic [NiFe]- and [Fe]-hydrogenases and acetyl-CoA synthase, with lower dissolved hydrogen (42%, p < 0.001). In contrast, the starch-rich diet enriched for respiratory hydrogenotrophs with greater hydrogen-producing group B [FeFe]-hydrogenases and respiratory group 1d [NiFe]-hydrogenases. Parallel in vitro experiments showed that the fiber-rich selected microbiome enhanced acetate and butyrate production while decreasing methane production (p < 0.05), suggesting that the enriched hydrogenotrophic acetogens converted some hydrogen that would otherwise be used by methanogenesis. These insights into hydrogen metabolism and methanogenesis improve understanding of energy harvesting strategies, healthy rumen maintenance, and methane mitigation in ruminants.

RevDate: 2022-08-05

Kim K, Lee S, Park SC, et al (2022)

Role of an unclassified Lachnospiraceae in the pathogenesis of type 2 diabetes: a longitudinal study of the urine microbiome and metabolites.

Experimental & molecular medicine [Epub ahead of print].

Recent investigations have revealed that the human microbiome plays an essential role in the occurrence of type 2 diabetes (T2D). However, despite the importance of understanding the involvement of the microbiota throughout the body in T2D, most studies have focused specifically on the intestinal microbiota. Extracellular vesicles (EVs) have been recently found to provide important evidence regarding the mechanisms of T2D pathogenesis, as they act as key messengers between intestinal microorganisms and the host. Herein, we explored microorganisms potentially associated with T2D by tracking changes in microbiota-derived EVs from patient urine samples collected three times over four years. Mendelian randomization analysis was conducted to evaluate the causal relationships among microbial organisms, metabolites, and clinical measurements to provide a comprehensive view of how microbiota can influence T2D. We also analyzed EV-derived metagenomic (N = 393), clinical (N = 5032), genomic (N = 8842), and metabolite (N = 574) data from a prospective longitudinal Korean community-based cohort. Our data revealed that GU174097_g, an unclassified Lachnospiraceae, was associated with T2D (β = -189.13; p = 0.00006), and it was associated with the ketone bodies acetoacetate and 3-hydroxybutyrate (r = -0.0938 and -0.0829, respectively; p = 0.0022 and 0.0069, respectively). Furthermore, a causal relationship was identified between acetoacetate and HbA1c levels (β = 0.0002; p = 0.0154). GU174097_g reduced ketone body levels, thus decreasing HbA1c levels and the risk of T2D. Taken together, our findings indicate that GU174097_g may lower the risk of T2D by reducing ketone body levels.

RevDate: 2022-08-05

Fountain K, Barbon A, Gibbon MJ, et al (2022)

Staphylococcus aureus lineages associated with a free-ranging population of the fruit bat Pteropus livingstonii retained over 25 years in captivity.

Scientific reports, 12(1):13457.

Conservation of endangered species has become increasingly complex, and costly interventions to protect wildlife require a robust scientific evidence base. This includes consideration of the role of the microbiome in preserving animal health. Captivity introduces stressors not encountered in the wild including environmental factors and exposure to exotic species, humans and antimicrobial drugs. These stressors may perturb the microbiomes of wild animals, with negative consequences for their health and welfare and hence the success of the conservation project, and ultimately the risk of release of non-native organisms into native ecosystems. We compared the genomes of Staphylococcus aureus colonising critically endangered Livingstone's fruit bats (Pteropus livingstonii) which have been in a captive breeding programme for 25 years, with those from bats in the endemic founder population free ranging in the Comoros Republic. Using whole genome sequencing, we compared 47 isolates from captive bats with 37 isolates from those free ranging in the Comoros Republic. Our findings demonstrate unexpected resilience in the bacteria carried, with the captive bats largely retaining the same two distinctive lineages carried at the time of capture. In addition, we found evidence of genomic changes which suggest specific adaptations to the bat host.

RevDate: 2022-08-05

Wang Y, Nan X, Zhao Y, et al (2022)

Discrepancies among healthy, subclinical mastitic, and clinical mastitic cows in fecal microbiome and metabolome and serum metabolome.

Journal of dairy science pii:S0022-0302(22)00433-7 [Epub ahead of print].

Mastitis is generally considered a local inflammatory disease caused by the invasion of exogenous pathogens and resulting in the dysbiosis of microbiota and metabolites in milk. However, the entero-mammary pathway theory may establish a possible link between some endogenous gut bacteria and the occurrence and development of mastitis. In the current study, we attempted to investigate differences in the gut microbiota profile and metabolite composition in gut and serum from healthy cows and those with subclinical mastitis and clinical mastitis. Compared with those of healthy cows, the microbial community diversities in the feces of cows with subclinical mastitis (SM) and clinical mastitis (CM) were lower. Lower abundance of Bifidobacterium, Romboutsia, Lachnospiraceae_NK3A20_group, Coprococcus, Prevotellaceae_UCG-003, Ruminococcus, and Alistipes, and higher abundance of the phylum Proteobacteria and the genera Escherichia-Shigella and Streptococcus were observed in CM cows. Klebsiella and Paeniclostridium were significantly enriched in the feces of SM cows. Several similarities were observed in feces and serum metabolites in mastitic cows. Higher levels of proinflammatory lipid products (20-trihydroxy-leukotriene-B4, 13,14-dihydro-15-keto-PGE2, and 9,10-dihydroxylinoleic acids) and lower levels of metabolites involved in secondary bile acids (deoxycholic acid, 12-ketolithocholic acid), energy (citric acid and 3-hydroxyisovalerylcarnitine), and purine metabolism (uric acid and inosine) were identified in both SM and CM cows. In addition, elevated concentrations of IL-1β, IL-6, tumor necrosis factor-α and decreased concentrations of glutathione peroxidase and superoxide dismutase were detected in the serum of SM and CM cows. Higher serum concentrations of triglyceride and total cholesterol and lower concentrations of high-density lipoproteins in mastitic cows might be related to changes in the gut microbiota and metabolites. These findings suggested a significant difference in the profile of feces microbiota and metabolites in cows with different udder health status, which might increase our understanding of bovine mastitis.

RevDate: 2022-08-05

Kong HH (2022)

Sharing is caring? Skin microbiome insights into staphylococci in atopic dermatitis patients and caregivers.

RevDate: 2022-08-05

Jin MK, Yang YT, Zhao CX, et al (2022)

ROS as a key player in quinolone antibiotic stress on Arabidopsis thaliana: From the perspective of photosystem function, oxidative stress and phyllosphere microbiome.

The Science of the total environment pii:S0048-9697(22)04920-8 [Epub ahead of print].

With the increasing use of antibiotics, their ecological impacts have received widespread attention. However, research on the toxicity of quinolone antibiotics is still limited, especially regarding the oxidative stress and phyllosphere of plants. In this study, the toxic effects of enrofloxacin, norfloxacin, and levofloxacin on Arabidopsis thaliana and their underlying mechanisms were investigated. The toxicity of the three quinolone antibiotics decreased in the following order: enrofloxacin > norfloxacin > levofloxacin. Physiological cellular changes, such as plasmolysis and chloroplast swelling, were observed using electron microscopy. Photosynthetic efficiency was inhibited with a decline in the effective photochemical quantum yield of photosystem II (Y(II)) and non-photochemical quenching (NPQ), indicating that quinolone antibiotics might reduce light energy conversion efficiency and excess light energy dissipation. Oxidative stress occurred in A. thaliana after quinolone antibiotic treatment, with an increase in reactive oxygen species (ROS) levels and malondialdehyde (MDA) content. High ROS levels stimulated the over-expression of superoxide-responsive genes for self-protection. Structural equation modeling (SEM) analysis showed that photosynthesis inhibition and cellular damage caused by oxidative stress were critical factors for growth inhibition, suggesting that the antioxidant response activated by ROS might be a potential mechanism. Furthermore, the diversity of the phyllospheric microbial communities decreased after enrofloxacin exposure. Additionally, specific microbes were preferentially recruited to the phyllosphere because of the higher ROS levels.

RevDate: 2022-08-05

Russell BJ, Brown SD, Siguenza N, et al (2022)

Intestinal transgene delivery with native E. coli chassis allows persistent physiological changes.

Cell pii:S0092-8674(22)00843-1 [Epub ahead of print].

Live bacterial therapeutics (LBTs) could reverse diseases by engrafting in the gut and providing persistent beneficial functions in the host. However, attempts to functionally manipulate the gut microbiome of conventionally raised (CR) hosts have been unsuccessful because engineered microbial organisms (i.e., chassis) have difficulty in colonizing the hostile luminal environment. In this proof-of-concept study, we use native bacteria as chassis for transgene delivery to impact CR host physiology. Native Escherichia coli bacteria isolated from the stool cultures of CR mice were modified to express functional genes. The reintroduction of these strains induces perpetual engraftment in the intestine. In addition, engineered native E. coli can induce functional changes that affect physiology of and reverse pathology in CR hosts months after administration. Thus, using native bacteria as chassis to "knock in" specific functions allows mechanistic studies of specific microbial activities in the microbiome of CR hosts and enables LBT with curative intent.

RevDate: 2022-08-05

Podlesny D, Durdevic M, Paramsothy S, et al (2022)

Identification of clinical and ecological determinants of strain engraftment after fecal microbiota transplantation using metagenomics.

Cell reports. Medicine pii:S2666-3791(22)00254-3 [Epub ahead of print].

Fecal microbiota transplantation (FMT) is a promising therapeutic approach for microbiota-associated pathologies, but our understanding of the post-FMT microbiome assembly process and its ecological and clinical determinants is incomplete. Here we perform a comprehensive fecal metagenome analysis of 14 FMT trials, involving five pathologies and >250 individuals, and determine the origins of strains in patients after FMT. Independently of the underlying clinical condition, conspecific coexistence of donor and recipient strains after FMT is uncommon and donor strain engraftment is strongly positively correlated with pre-FMT recipient microbiota dysbiosis. Donor strain engraftment was enhanced through antibiotic pretreatment and bowel lavage and dependent on donor and recipient ɑ-diversity; strains from relatively abundant species were more likely and from predicted oral, oxygen-tolerant, and gram-positive species less likely to engraft. We introduce a general mechanistic framework for post-FMT microbiome assembly in alignment with ecological theory, which can guide development of optimized, more targeted, and personalized FMT therapies.

RevDate: 2022-08-05

Federici S, Kredo-Russo S, Valdés-Mas R, et al (2022)

Targeted suppression of human IBD-associated gut microbiota commensals by phage consortia for treatment of intestinal inflammation.

Cell, 185(16):2879-2898.e24.

Human gut commensals are increasingly suggested to impact non-communicable diseases, such as inflammatory bowel diseases (IBD), yet their targeted suppression remains a daunting unmet challenge. In four geographically distinct IBD cohorts (n = 537), we identify a clade of Klebsiella pneumoniae (Kp) strains, featuring a unique antibiotics resistance and mobilome signature, to be strongly associated with disease exacerbation and severity. Transfer of clinical IBD-associated Kp strains into colitis-prone, germ-free, and colonized mice enhances intestinal inflammation. Stepwise generation of a lytic five-phage combination, targeting sensitive and resistant IBD-associated Kp clade members through distinct mechanisms, enables effective Kp suppression in colitis-prone mice, driving an attenuated inflammation and disease severity. Proof-of-concept assessment of Kp-targeting phages in an artificial human gut and in healthy volunteers demonstrates gastric acid-dependent phage resilience, safety, and viability in the lower gut. Collectively, we demonstrate the feasibility of orally administered combination phage therapy in avoiding resistance, while effectively inhibiting non-communicable disease-contributing pathobionts.

RevDate: 2022-08-05

Zhang Z, Zhang G, F Ju (2022)

Using Culture-Enriched Phenotypic Metagenomics for Targeted High-Throughput Monitoring of the Clinically Important Fraction of the β-Lactam Resistome.

Environmental science & technology [Epub ahead of print].

High bacterial community diversity and complexity greatly challenge the cost-efficient monitoring of clinically prevalent antibiotic-resistant bacteria, which are usually present as rare and important populations involved in the environmental dissemination of clinical resistance. Here, we introduce culture-enriched phenotypic metagenomics that integrates culture enrichment, phenotypic screening, and metagenomic analyses as an emerging standardized methodology for targeted resistome monitoring and apply it to decipher the extended-spectrum β-lactam resistome in a municipal wastewater treatment plant (WWTP) and its receiving river. The results showed that clinically prevalent carbapenemase genes (e.g., the NDM and KPC families) and extended-spectrum β-lactamase genes (e.g., the CTX-M, TEM, and OXA families) were prevalent in the WWTP and showed prominent potential in horizontal dissemination. Strikingly, carbapenem and polymyxin resistance genes co-occurred in the highly virulent nosocomial pathogens Enterobacter kobei and Citrobacter freundii. Overall, this study exemplifies phenotypic metagenomics for high-throughput surveillance of a targeted clinically important fraction of antibiotic resistomes and substantially expands current knowledge on extended-spectrum β-lactam resistance in WWTPs.

RevDate: 2022-08-05

Zhang H, Lang X, Li X, et al (2022)

Effect of Zanthoxylum bungeanum essential oil on rumen enzyme activity, microbiome, and metabolites in lambs.

PloS one, 17(8):e0272310 pii:PONE-D-22-08057.

Antibiotics were once used in animal production to improve productivity and resistance to pathogenic microbiota. However, due to its negative effects, the search for a new class of substances that can replace its efficacy has become one of the urgent problems to be solved. Plant essential oils (EOs) as a natural feed additive can maintain microbiota homeostasis and improve animal performance. However, its specific mechanism of action needs to be further investigated. Therefore, we added different doses of essential oil of Zanthoxylum bungeanum (EOZB) to the diets of Small Tail Han Sheep hybrid male lambs (STH lambs) to evaluate the effect of EOZB on rumen enzyme activity, rumen microbiology, and its metabolites in STH lambs. Twenty STH lambs were randomly divided into four groups (n = 5/group) and provided with the same diet. The dietary treatments were as follows: basal diet (BD) group; BD+EOZB 5 ml/kg group; BD+EOZB 10 ml/kg group; BD+EOZB 15 ml/kg group. We found that EOZB 10 ml/kg helped to increase rumen pectinase (P<0.05) and lipase (P<0.05) activities. Microbial 16S rRNA gene analysis showed that EOZB significantly altered the abundance of rumen microbiota (P<0.05). LC/GC-MS metabolomic analysis showed that the addition of EOZB produced a total of 1073 differential metabolites, with 58 differential metabolites remaining after raising the screening criteria. These differential metabolites were mainly enriched in glycerophospholipid metabolism, choline metabolism in cancer, retrograde endocannabinoid signaling, benzoxazinoid biosynthesis, and protein digestion and absorption. Correlation analysis showed that some rumen microbiota were significantly correlated with differential metabolite and enzyme activities.

RevDate: 2022-08-05

Maybee J, Pearson T, L Elliott (2022)

The Gut-Brain-Microbiome Connection: Can Probiotics Decrease Anxiety and Depression?.

Issues in mental health nursing [Epub ahead of print].

Anxiety and depression are highly prevalent mood disorders worldwide. Complete remission of symptoms is often difficult to achieve, despite following recommended treatment guidelines. Numerous antidepressants and anxiolytics exist, and new drugs are being developed constantly, yet the incidence of common mood disorders continues to rise. Despite the prevalence of these issues, mental health treatment has not evolved much in recent years. An exciting area of research uncovered in the past decade is the gut-brain-microbiome axis, a bi-directional communication pathway. Because the human microbiome is closely related to mood, research is being done to investigate whether probiotic supplementation could potentially affect symptoms of anxiety and depression.

RevDate: 2022-08-05

Vogtmann E, Hua X, Yu G, et al (2022)

The oral microbiome and lung cancer risk: An analysis of 3 prospective cohort studies.

Journal of the National Cancer Institute pii:6656358 [Epub ahead of print].

BACKGROUND: Previous studies suggested associations between the oral microbiome and lung cancer, but studies were predominantly cross-sectional and underpowered.

METHODS: Using a case-cohort design, 1,306 incident lung cancer cases were identified in the Agricultural Health Study, NIH-AARP Diet and Health Study, and Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial. Referent subcohorts were randomly selected by strata of age, sex, and smoking history. DNA was extracted from oral wash specimens using the DSP DNA Virus Pathogen kit, the 16S rRNA gene V4 region was amplified and sequenced, and bioinformatics were conducted using QIIME 2. Hazard ratios (HR) and 95% confidence intervals (CI) were calculated using weighted Cox proportional hazards models.

RESULTS: Higher alpha diversity was associated with lower lung cancer risk (Shannon index HR 0.90; 95% CI: 0.84-0.96). Specific principal component vectors of the microbial communities were also significantly associated with lung cancer risk. After multiple testing adjustment, greater relative abundance of three genera and presence of one genus were associated with greater lung cancer risk, while presence of three genera were associated with lower risk. For example, every standard deviation increase in Streptococcus abundance was associated with 1.14 times the risk of lung cancer (95% CI: 1.06-1.22). Associations were strongest among squamous cell carcinoma cases and former smokers.

CONCLUSIONS: Multiple oral microbial measures were prospectively associated with lung cancer risk in three US cohort studies with associations varying by smoking history and histologic subtype. The oral microbiome may offer new opportunities for lung cancer prevention.

RevDate: 2022-08-05

Anonymous (2022)

Collagen I Homotrimers Promote PDAC Growth and Impact Immunity.

Cancer discovery pii:707459 [Epub ahead of print].

Cancer cell-derived Col1 homotrimers regulate the PDAC microbiome and block T-cell infiltration.

RevDate: 2022-08-05

Hakimjavadi H, George SH, Taub M, et al (2022)

The vaginal microbiome is associated with endometrial cancer grade and histology.

Cancer research communications, 2(6):447-455.

The human microbiome has been strongly correlated with disease pathology and outcomes, yet remains relatively underexplored in patients with malignant endometrial disease. In this study, vaginal microbiome samples were prospectively collected at the time of hysterectomy from 61 racially and ethnically diverse patients from three disease conditions: 1) benign gynecologic disease (controls, n=11), 2) low-grade endometrial carcinoma (n=30), and 3) high-grade endometrial carcinoma (n=20). Extracted DNA underwent shotgun metagenomics sequencing, and microbial α and β diversities were calculated. Hierarchical clustering was used to describe community state types (CST), which were then compared by microbial diversity and grade. Differential abundance was calculated, and machine learning utilized to assess the predictive value of bacterial abundance to distinguish grade and histology. Both α- and β-diversity were associated with patient tumor grade. Four vaginal CST were identified that associated with grade of disease. Different histologies also demonstrated variation in CST within tumor grades. Using supervised clustering algorithms, critical microbiome markers at the species level were used to build models that predicted benign vs carcinoma, high-grade carcinoma versus benign, and high-grade versus low-grade carcinoma with high accuracy. These results confirm that the vaginal microbiome segregates not just benign disease from endometrial cancer, but is predictive of histology and grade. Further characterization of these findings in large, prospective studies is needed to elucidate their potential clinical applications.

RevDate: 2022-08-05

Gu X, Bi N, Wang T, et al (2022)

Probiotic Lactobacillus rhamnosus GR-1 supplementation attenuates Pb-induced learning and memory deficits by reshaping the gut microbiota.

Frontiers in nutrition, 9:934118.

Lead (Pb) exposure during early life has been associated with an increased risk of neurodevelopmental disorders, including learning and memory deficits. The intestinal flora, via the microbiome-gut-brain axis, could play a significant role in the nervous system. However, the effects of probiotics on ameliorating Pb-induced learning and memory deficits are still unclear. In this study, we showed that adolescent Pb exposure (150 ppm) for 2 months impaired spatial learning and memory ability, accompanied by the decreasing diversity of gut microbiota, and the decreasing abundance of Lactobacillus at the genus level. Surprisingly, administration of the Lactobacillus rhamnosus GR-1 (1010 organisms/rat/day), not L. rhamnosus LGG or Lactobacillus reuteri RC-14, reversed learning and memory deficits induced by Pb exposure. Meanwhile, administration of the L. rhamnosus GR-1 increased the diversity of the gut microbiota composition and partially normalized the genus level of Lactobacillus, Parabacteroides, Enterococcus, and Akkermansia in Pb-exposed rats. Notably, supplementation of L. rhamnosus GR-1 decreased the gut permeability of Pb-exposed rats, reduced proinflammatory cytokines [interleukin-1β (IL-1β) and IL-6] expression, and promoted anti-inflammatory cytokines [granulocyte colony-stimulating factor (G-CSF)] expression. Interestingly, neural cell treatment with G-CSF rescued Pb-induced neurotoxicity. In general, L. rhamnosus GR-1 supplementation recovered the Pb-induced loss of intestinal bacteria (Lactobacillus), which may have reversed the damage to learning and memory ability. Collectively, our findings demonstrate an unexpectedly pivotal role of L. rhamnosus GR-1 in Pb-induced cognitive deficits and identify a potential probiotic therapy for cognitive dysfunction during early life.

RevDate: 2022-08-05

Zhu W, Hong Y, Li Y, et al (2022)

Microbial and Transcriptomic Profiling Reveals Diet-Related Alterations of Metabolism in Metabolic Disordered Mice.

Frontiers in nutrition, 9:923377.

Metabolic disorders are the prelude of metabolic diseases, which are mainly due to the high-energy intake and genetic contribution. High-fat diet (HFD) or high-sucrose diet is widely used for inducing metabolic disorders characterized by increased body weight, insulin resistance, hepatic steatosis, and alteration of gut microbiome. However, the triangle relationship among diets, gut microbiome, and host metabolism is poorly understood. In our study, we investigated the dynamic changes in gut microbiota, and host metabolism in mice that were fed with either chow diet, HFD, or chow diet with 30% sucrose in drinking water (HSD) for continued 12 weeks. The gut microbiota was analyzed with 16S rDNA sequencing on feces. Hepatic gene expression profile was tested with transcriptomics analysis on liver tissue. The host metabolism was evaluated by measuring body weight, insulin sensitivity, serum lipids, and expression of proteins involved in lipid metabolism of liver. The results showed that HFD feeding affected body weight, insulin resistance, and hepatic steatosis more significantly than HSD feeding. 16S rRNA gene sequencing showed that HFD rapidly and steadily suppressed species richness, altered microbiota structure and function, and increased the abundance of bacteria responsible for fatty acid metabolism and inflammatory signaling. In contrast, HSD had minor impact on the overall bacteria structure or function but activated microbial bile acid biosynthesis. Fecal microbiota transplantation suggested that some metabolic changes induced by HFD or HSD feeding were transferrable, especially in the weight of white adipose tissue and hepatic triglyceride level that were consistent with the phenotypes in donor mice. Moreover, transcriptomic results showed that HFD feeding significantly inhibited fatty acid degradation and increase inflammation, while HSD increased hepatic de novo lipogenesis and inhibited primary bile acid synthesis alternative pathway. In general, our study revealed the dynamic and diversified impacts of HFD and HSD on gut microbiota and host metabolism.

RevDate: 2022-08-05

Yang Z, Liu X, Wu Y, et al (2022)

Effect of the Microbiome on Intestinal Innate Immune Development in Early Life and the Potential Strategy of Early Intervention.

Frontiers in immunology, 13:936300.

Early life is a vital period for mammals to be colonized with the microbiome, which profoundly influences the development of the intestinal immune function. For neonates to resist pathogen infection and avoid gastrointestinal illness, the intestinal innate immune system is critical. Thus, this review summarizes the development of the intestinal microbiome and the intestinal innate immune barrier, including the intestinal epithelium and immune cells from the fetal to the weaning period. Moreover, the impact of the intestinal microbiome on innate immune development and the two main way of early-life intervention including probiotics and fecal microbiota transplantation (FMT) also are discussed in this review. We hope to highlight the crosstalk between early microbial colonization and intestinal innate immunity development and offer some information for early intervention.

RevDate: 2022-08-05

Onisiforou A, GM Spyrou (2022)

Immunomodulatory effects of microbiota-derived metabolites at the crossroad of neurodegenerative diseases and viral infection: network-based bioinformatics insights.

Frontiers in immunology, 13:843128.

Bidirectional cross-talk between commensal microbiota and the immune system is essential for the regulation of immune responses and the formation of immunological memory. Perturbations of microbiome-immune system interactions can lead to dysregulated immune responses against invading pathogens and/or to the loss of self-tolerance, leading to systemic inflammation and genesis of several immune-mediated pathologies, including neurodegeneration. In this paper, we first investigated the contribution of the immunomodulatory effects of microbiota (bacteria and fungi) in shaping immune responses and influencing the formation of immunological memory cells using a network-based bioinformatics approach. In addition, we investigated the possible role of microbiota-host-immune system interactions and of microbiota-virus interactions in a group of neurodegenerative diseases (NDs): Amyotrophic Lateral Sclerosis (ALS), Multiple Sclerosis (MS), Parkinson's disease (PD) and Alzheimer's disease (AD). Our analysis highlighted various aspects of the innate and adaptive immune response systems that can be modulated by microbiota, including the activation and maturation of microglia which are implicated in the development of NDs. It also led to the identification of specific microbiota components which might be able to influence immune system processes (ISPs) involved in the pathogenesis of NDs. In addition, it indicated that the impact of microbiota-derived metabolites in influencing disease-associated ISPs, is higher in MS disease, than in AD, PD and ALS suggesting a more important role of microbiota mediated-immune effects in MS.

RevDate: 2022-08-05

Al Bataineh MT, Künstner A, Dash NR, et al (2022)

Altered Composition of the Oral Microbiota in Depression Among Cigarette Smokers: A Pilot Study.

Frontiers in psychiatry, 13:902433.

Alterations in the oral microbiota composition may influence mental health. However, linkages between compositional changes in the oral microbiota and their role in mental health among cigarette smokers remain largely unknown. In this study, we used shotgun metagenomics data for the oral microbiome of 105 participants. The data showed Bacteroidota, Fusobacteriota, Firmicutes, Proteobacteria, and Actinobacteria to be the most abundant phyla; Streptococcus, Haemophilus D, and Veillonella are the most abundant genera. Then, we clustered our subjects into avoidance and activation groups based on the behavioral activation for depression scale (BADS). Interestingly, the avoidance group exhibited a higher oral microbiome richness and diversity (alpha diversity). Differential abundance testing between BADS avoidance and activation groups showed the phyla Bacteroidota (effect size 0.5047, q = 0.0037), Campylobacterota (effect size 0.4012, q = 0.0276), Firmicutes A (effect size 0.3646, q = 0.0128), Firmicutes I (effect size 0.3581, q = 0.0268), and Fusobacteriota (effect size 0.6055, q = 0.0018) to be significantly increased in the avoidance group, but Verrucomicrobiota (effect size-0.6544, q = 0.0401), was found to be significantly decreased in the avoidance risk group. Network analysis of the 50 genera displaying the highest variation between both groups identified Campylobacter B, Centipeda, and Veillonella as hub nodes in the avoidance group. In contrast, Haemophilus and Streptococcus were identified as hub nodes in the activation group. Next, we investigated functional profiles of the oral microbiota based on BADS avoidance and activation groups and found Lysine degradations pathway was significantly enriched between both groups (ANCOM-BC, q = 0.0692). Altogether, we provide evidence for the presence of depression-related changes in the oral microbiota of smokers and possible functional contribution. The identified differences provide new information to enrich our understanding of oral microbiota-brain axis interplay and their potential impact on mental health.

RevDate: 2022-08-05

Wang CB, Wang Y, Yao Y, et al (2022)

The gut microbiome contributes to splenomegaly and tissue inflammation in a murine model of primary biliary cholangitis.

Annals of translational medicine, 10(9):507.

Background: Splenomegaly is not just a consequence of numerous chronic and acute conditions but may also contribute to their severity, due to the interaction of the spleen with the gut microbiome. This study aimed to explore the effect of the gut microbiome on splenomegaly.

Methods: We used p40-/-IL-2Rα-/- mice as a murine model of primary biliary cholangitis (PBC) as per our previous study. Splenomegaly was evaluated by spleen weight. Severity of liver inflammation was evaluated by hepatic mononuclear cell (MNCs) number and pathological score. Changes of immune cells in the spleen and liver were detected by flow cytometry. The effects of the gut microbiome on splenomegaly and liver inflammation were observed by combined antibiotic treatment in p40-/-IL-2Rα-/- mice.

Results: A proportion of p40-/-IL-2Rα-/- mice developed splenomegaly. The results revealed that liver mononuclear cells infiltration, histological scores of hepatic inflammation, and bile duct damage were positively correlated with the degree of splenomegaly. Hepatic CD4+ and CD8+ T cells numbers were significantly higher in mice with splenomegaly, and this was particularly observed in activated effector memory CD4+ T and CD8+ T cells. A proportion of some other immune cells including granulocytes, B, natural killer (NK), and CD8+ T effector memory cells were also altered in the enlarged spleen. More importantly, administration of quadruple antibiotics to deplete gut microbiota relieved the splenomegaly of p40-/-IL-2Rα-/- mice, significantly alleviated liver inflammation, and caused a significant reduction of liver and spleen T cell accumulation and activation; however, single antibiotics did not induce these changes.

Conclusions: Splenomegaly was associated with more severe liver inflammation in our PBC murine model, and this effect was reversed by quadruple antibiotic treatment.

RevDate: 2022-08-05

Sainz T, Casas I, González-Esguevillas M, et al (2022)

Nutritional Supplementation to Increase Influenza Vaccine Response in Children Living With HIV: A Pilot Clinical Trial.

Frontiers in pediatrics, 10:919753.

Aims: Vaccine response is poor among children living with HIV. The gut microbiota has been identified as a potential target to improve vaccine immunogenicity, but data are scarce in the context of HIV infection.

Methods: Pilot, double-blind, randomized placebo-controlled trial in which 24 HIV-infected children were randomized to receive a mixture of symbiotics, omega-3/6 fatty acids, and amino acids or placebo for 4 weeks, each in combination with ART, and were then immunized against influenza. Vaccine response and safety of the nutritional supplementation were the primary outcomes.

Results: Eighteen HIV-infected children completed the follow-up period (mean age 11.5 ± 4.14 years, 61% female). The nutritional supplement was safe but did not enhance the response to the influenza vaccine. A 4-fold rise in antibody titers was obtained in only 37.5% of participants in the intervention arm vs. 40% in the placebo. No immunological or inflammatory predictors of vaccine response were identified.

Conclusions: In this exploratory study, a 4-week course of symbiotics did not increase influenza vaccine immunogenicity in HIV-infected children. Larger studies are warranted to address the potential of modulating the microbiome in children living with HIV.

RevDate: 2022-08-05

Tavakoli P, Vollmer-Conna U, Hadzi-Pavlovic D, et al (2022)

The Interplay Between Use of Biological Therapies, Psychological State, and the Microbiome in IBD.

Frontiers in medicine, 9:788992.

Background: This study examines longitudinal bio-psychological dynamics and their interplay in IBD patients undergoing conventional and biological therapies.

Methods: Fifty IBD participants (24 UC, 26 CD) in clinical remission were followed for 12 months. Complete longitudinal datasets, biological samples, validated scores of psychological status were collected monthly for analysis of association. Microbiome analysis was performed to identify microbial dynamics and signatures. Patients were grouped on disease phenotype (CD, UC) and mode of treatment (biological therapies, non-biological treatment). General linear models, mixed models, cluster analysis, and analyses of variance were used to examine the longitudinal trends of the variables and their associations over time. Results were corrected for multiple testing.

Results: Results substantiated different interactions between biological therapy and longitudinal trends of inflammatory biomarkers in remission CD and UC patients as well as significant differences between CD and UC patients in their psychological measures during clinical remission, with UC patients having inferior condition compared to CD. A significant reduction in microbial diversity in CD patients compared to UC was identified. Results characterized considerable differences in longitudinal microbial profile between those taking and not taking biological treatment in UC patients, but not in CD patients.

Conclusion: A different trajectory of interdependence was identified between psychological state, sleep, and microbial dynamics with mode of treatment when compared between CD and UC patients. Further studies should investigate the causal relationships between bio-psychological factors for improved treatment purposes.

RevDate: 2022-08-05

Jourova L, Satka S, Frybortova V, et al (2022)

Butyrate Treatment of DSS-Induced Ulcerative Colitis Affects the Hepatic Drug Metabolism in Mice.

Frontiers in pharmacology, 13:936013 pii:936013.

The development of inflammatory bowel disease (IBD) is associated with alterations in the gut microbiota. There is currently no universal treatment for this disease, thus emphasizing the importance of developing innovative therapeutic approaches. Gut microbiome-derived metabolite butyrate with its well-known anti-inflammatory effect in the gut is a promising candidate. Due to increased intestinal permeability during IBD, butyrate may also reach the liver and influence liver physiology, including hepatic drug metabolism. To get an insight into this reason, the aim of this study was set to clarify not only the protective effects of the sodium butyrate (SB) administration on colonic inflammation but also the effects of SB on hepatic drug metabolism in experimental colitis induced by dextran sodium sulfate (DSS) in mice. It has been shown here that the butyrate pre-treatment can alleviate gut inflammation and reduce the leakiness of colonic epithelium by restoration of the assembly of tight-junction protein Zonula occludens-1 (ZO-1) in mice with DSS-induced colitis. In this article, butyrate along with inflammation has also been shown to affect the expression and enzyme activity of selected cytochromes P450 (CYPs) in the liver of mice. In this respect, CYP3A enzymes may be very sensitive to gut microbiome-targeted interventions, as significant changes in CYP3A expression and activity in response to DSS-induced colitis and/or butyrate treatment have also been observed. With regard to medications used in IBD and microbiota-targeted therapeutic approaches, it is important to deepen our knowledge of the effect of gut inflammation, and therapeutic interventions were followed concerning the ability of the organism to metabolize drugs. This gut-liver axis, mediated through inflammation as well as microbiome-derived metabolites, may affect the response to IBD therapy.

RevDate: 2022-08-05

Ma ZS (2022)

Shared Species Analysis, Augmented by Stochasticity Analysis, Is More Effective Than Diversity Analysis in Detecting Variations in the Gut Microbiomes.

Frontiers in microbiology, 13:914429.

Diversity analysis is a de facto standard procedure for most existing microbiome studies. Nevertheless, diversity metrics can be insensitive to changes in community composition (identities). For example, if species A (e.g., a beneficial microbe) is replaced by equal number of species B (e.g., an opportunistic pathogen), the diversity metric may not change, but the community composition has changed. The shared species analysis (SSA) is a computational technique that can discern changes of community composition by detecting the increase/decrease of shared species between two sets of microbiome samples, and it should be more sensitive than standard diversity analysis in discerning changes in microbiome structures. Here, we investigated the effects of ethnicity and lifestyles in China on the structure of Chinese gut microbiomes by reanalyzing the datasets of a large Chinese cohort with 300+ individuals covering 7 biggest Chinese ethnic groups (>95% Chinese population). We found: (i) Regarding lifestyles, SSA revealed significant differences between 100% of pair-wise comparisons in community compositions across all but phylum taxon levels (phylum level = 29%), but diversity analysis only revealed 14-29% pair-wise differences in community diversity across all four taxon levels. (ii) Regarding ethnicities, SSA revealed 100% pair-wise differences in community compositions across all but phylum (phylum level = 48-62%) levels, but diversity analysis only revealed 5-57% differences in community diversity across all four taxon levels. (iii) Ethnicity seems to have more prevalent effects on community structures than lifestyle does (iv) Community structures of the gut microbiomes are more stable at the phylum level than at the other three levels. (v) SSA is more powerful than diversity analysis in detecting the changes of community structures; furthermore, SSA can produce lists of unique and shared OTUs. (vi) Finally, we performed stochasticity analysis to mechanistically interpret the observed differences revealed by the SSA and diversity analyses.

RevDate: 2022-08-05

Díez López C, Montiel González D, Vidaki A, et al (2022)

Prediction of Smoking Habits From Class-Imbalanced Saliva Microbiome Data Using Data Augmentation and Machine Learning.

Frontiers in microbiology, 13:886201.

Human microbiome research is moving from characterization and association studies to translational applications in medical research, clinical diagnostics, and others. One of these applications is the prediction of human traits, where machine learning (ML) methods are often employed, but face practical challenges. Class imbalance in available microbiome data is one of the major problems, which, if unaccounted for, leads to spurious prediction accuracies and limits the classifier's generalization. Here, we investigated the predictability of smoking habits from class-imbalanced saliva microbiome data by combining data augmentation techniques to account for class imbalance with ML methods for prediction. We collected publicly available saliva 16S rRNA gene sequencing data and smoking habit metadata demonstrating a serious class imbalance problem, i.e., 175 current vs. 1,070 non-current smokers. Three data augmentation techniques (synthetic minority over-sampling technique, adaptive synthetic, and tree-based associative data augmentation) were applied together with seven ML methods: logistic regression, k-nearest neighbors, support vector machine with linear and radial kernels, decision trees, random forest, and extreme gradient boosting. K-fold nested cross-validation was used with the different augmented data types and baseline non-augmented data to validate the prediction outcome. Combining data augmentation with ML generally outperformed baseline methods in our dataset. The final prediction model combined tree-based associative data augmentation and support vector machine with linear kernel, and achieved a classification performance expressed as Matthews correlation coefficient of 0.36 and AUC of 0.81. Our method successfully addresses the problem of class imbalance in microbiome data for reliable prediction of smoking habits.

RevDate: 2022-08-05

Shang P, Wei M, Duan M, et al (2022)

Healthy Gut Microbiome Composition Enhances Disease Resistance and Fat Deposition in Tibetan Pigs.

Frontiers in microbiology, 13:965292.

The gut microbiota is involved in a range of physiological processes in animals, and modulating the microbiome composition is considered a novel target for identifying animal traits. Tibetan pigs show better fat deposition and disease resistance compared to Yorkshire pigs. However, studies investigating the correlation between favorable characteristics in Tibetan pigs and the gut microbial community remain scarce. In the current study, 1,249,822 high-quality sequences were obtained by amplicon sequencing of the colon contents of Tibetan and Yorkshire pigs. We found that at the boundary level, the abundance and relative abundance of colon bacterial community in Tibetan pigs were higher than that in Yorkshire pigs (P > 0.05). Phylum level, Firmicutes were the dominant colonic microflora of Tibetan and Yorkshire pigs, and the ratio of Firmicutes to Bacteroides in Tibetan pigs was slightly higher than in Yorkshire pigs. Actinobacteria and Spirobacteria were significantly higher in Tibetan pigs than in Yorkshire pigs (P < 0.05). At the genus level, the relative abundance of Bifidobacterium, Lactobacillus, and Bacteriologist, which are related to disease resistance, was significantly higher than that in Yorkshire pigs in Yorkshire pigs. In conclusion, the composition and abundance of colonic intestinal microflora in Tibetan pigs were closely related to their superior traits. Bifidobacteria, Ruminococcaceae, and Family-XIII-AD3011-Group are conducive to improving disease resistance in Tibetan pigs. Lactobacillus and Solobacterium were observed to be the main bacterial communities involved in fat deposition in Tibetan pigs. This study will provide a new reference for the development and utilization of Tibetan pigs in future.

RevDate: 2022-08-05

Knobloch S, Skírnisdóttir S, Dubois M, et al (2022)

Impact of Putative Probiotics on Growth, Behavior, and the Gut Microbiome of Farmed Arctic Char (Salvelinus alpinus).

Frontiers in microbiology, 13:912473.

Beneficial bacteria promise to promote the health and productivity of farmed fish species. However, the impact on host physiology is largely strain-dependent, and studies on Arctic char (Salvelinus alpinus), a commercially farmed salmonid species, are lacking. In this study, 10 candidate probiotic strains were subjected to in vitro assays, small-scale growth trials, and behavioral analysis with juvenile Arctic char to examine the impact of probiotic supplementation on fish growth, behavior and the gut microbiome. Most strains showed high tolerance to gastric juice and fish bile acid, as well as high auto-aggregation activity, which are important probiotic characteristics. However, they neither markedly altered the core gut microbiome, which was dominated by three bacterial species, nor detectably colonized the gut environment after the 4-week probiotic treatment. Despite a lack of long-term colonization, the presence of the bacterial strains showed either beneficial or detrimental effects on the host through growth rate enhancement or reduction, as well as changes in fish motility under confinement. This study offers insights into the effect of bacterial strains on a salmonid host and highlights three strains, Carnobacterium divergens V41, Pediococcus acidilactici ASG16, and Lactiplantibacillus plantarum ISCAR-07436, for future research into growth promotion of salmonid fish through probiotic supplementation.

RevDate: 2022-08-05

Alves-Barroco C, Brito PH, Santos-Sanches I, et al (2022)

Phylogenetic analysis and accessory genome diversity reveal insight into the evolutionary history of Streptococcus dysgalactiae.

Frontiers in microbiology, 13:952110.

Streptococcus dysgalactiae (SD) is capable of infecting both humans and animals and causing a wide range of invasive and non-invasive infections. With two subspecies, the taxonomic status of subspecies of SD remains controversial. Subspecies equisimilis (SDSE) is an important human pathogen, while subspecies dysgalactiae (SDSD) has been considered a strictly animal pathogen; however, occasional human infections by this subspecies have been reported in the last few years. Moreover, the differences between the adaptation of SDSD within humans and other animals are still unknown. In this work, we provide a phylogenomic analysis based on the single-copy core genome of 106 isolates from both the subspecies and different infected hosts (animal and human hosts). The accessory genome of this species was also analyzed for screening of genes that could be specifically involved with adaptation to different hosts. Additionally, we searched putatively adaptive traits among prophage regions to infer the importance of transduction in the adaptation of SD to different hosts. Core genome phylogenetic relationships segregate all human SDSE in a single cluster separated from animal SD isolates. The subgroup of bovine SDSD evolved from this later clade and harbors a specialized accessory genome characterized by the presence of specific virulence determinants (e.g., cspZ) and carbohydrate metabolic functions (e.g., fructose operon). Together, our results indicate a host-specific SD and the existence of an SDSD group that causes human-animal cluster infections may be due to opportunistic infections, and that the exact incidence of SDSD human infections may be underestimated due to failures in identification based on the hemolytic patterns. However, more detailed research into the isolation of human SD is needed to assess whether it is a carrier phenomenon or whether the species can be permanently integrated into the human microbiome, making it ready to cause opportunistic infections.

RevDate: 2022-08-04

Jamshidi S, Masoumi SJ, Abiri B, et al (2022)

The effects of synbiotic and/or vitamin D supplementation on gut-muscle axis in overweight and obese women: a study protocol for a double-blind, randomized, placebo-controlled trial.

Trials, 23(1):631.

BACKGROUND: Sarcopenia refers to an age-related loss of skeletal muscle content, strength, and function, leading to a decrease in mobility. Obesity may exacerbate age-related complications such as sarcopenia through inflammatory pathways. In addition, intestinal dysbiosis has been proposed as an emerging contributor to sarcopenia due to the stimulation of the immune system and elevated barrier permeability of the intestine. Targeting microbiome with synbiotic and vitamin D supplementation may modulate the microbiome followed by the enhancement of sarcopenia indices. Thus, the present study aims to evaluate the effect of synbiotic supplementation with or without vitamin D on the intestinal microbiome and its relationship with strength, muscle function, and body composition in middle-aged overweight and obese women.

METHODS: This multi-factorial, double-blind, randomized controlled trial will be conducted on 88 participants in eight weeks. The participants will be allocated into four groups receiving vitamin D placebo (weekly) and synbiotic placebo (daily), vitamin D and synbiotic placebo, vitamin D placebo and symbiotic, and vitamin D and synbiotic. Intestinal microbiome assessment will be done by DNA isolation and real-time polymerase chain reaction (PCR). In addition, anthropometric indices, body composition, muscle strength, and physical performance will be evaluated by standard methods. All measurements will be made at the beginning and end of the study.

DISCUSSION: The previous studies showed that probiotics were involved in reducing inflammation, insulin sensitivity, modulation of atrophy markers such as atherogen-1, and decreasing reactive oxygen indices. In addition, vitamin D was found to improve the intestinal microbiome and facilitate muscle anabolism. The present protocol is novel as it aims to investigate the impact of the co-supplementation of synbiotic and vitamin D on the gut microbiome and sarcopenia indices.

TRIAL REGISTRATION: This trial has been registered in the Iranian Registry of Clinical Trials (IRCT20090822002365N25, date of registration: March 2021).

RevDate: 2022-08-04

Zhang H, Qin S, Zhang X, et al (2022)

Dietary resistant starch alleviates Escherichia coli-induced bone loss in meat ducks by promoting short-chain fatty acid production and inhibiting Malt1/NF-κB inflammasome activation.

Journal of animal science and biotechnology, 13(1):92.

BACKGROUND: Escherichia coli (E. coli) infection in humans and animals usually comes with gut dysbiosis, which is potential culprit to skeletal health, it is still unclear to whether diet interfered gut microbiome changes can be a protective strategy to bone loss development. Here, the effects of resistant starch from raw potato starch (RPS), a type of prebiotic, on E. coli-induced bone loss and gut microbial composition in meat ducks were evaluated.

RESULTS: The results showed that dietary 12% RPS treatment improved bone quality, depressed bone resorption, and attenuated the pro-inflammatory reaction in both ileum and bone marrow. Meanwhile, the 12% RPS diet also increased the abundance of Firmicutes in E. coli-treated birds, along with higher production of short-chain fatty acids (SCFAs) especially propionate and butyrate. Whereas addition of β-acid, an inhibitor of bacterial SCFAs production, to the drinking water of ducks fed 12% RPS diet significantly decreased SCFAs level in cecum content and eliminated RPS-induced tibial mass improvement. Further, treatment with MI-2 to abrogate mucosa-associated lymphoid tissue lymphoma translocation protein 1 (Malt1) activity replicated the protective role of dietary 12% RPS in E. coli-induced bone loss including reduced the inhibition on nuclear factor κB (NF-κB) inflammasome activation, decreased bone resorption, and improved bone quality, which were correlated with comparable and higher regulatory T cells (Treg) frequency in MI-2 and 12% RPS group, respectively.

CONCLUSIONS: These findings suggested that the diet with 12% RPS could alleviate E. coli-induced bone loss in meat ducks by changing the gut microbial composition and promoting concomitant SCFAs production, and consequently inhibiting Malt1/NF-κB inflammasome activation and Treg cells expansion.

RevDate: 2022-08-04

Krawczyk AI, Röttjers L, Fonville M, et al (2022)

Quantitative microbial population study reveals geographical differences in bacterial symbionts of Ixodes ricinus.

Microbiome, 10(1):120.

BACKGROUND: Ixodes ricinus ticks vector pathogens that cause serious health concerns. Like in other arthropods, the microbiome may affect the tick's biology, with consequences for pathogen transmission. Here, we explored the bacterial communities of I. ricinus across its developmental stages and six geographic locations by the 16S rRNA amplicon sequencing, combined with quantification of the bacterial load.

RESULTS: A wide range of bacterial loads was found. Accurate quantification of low microbial biomass samples permitted comparisons to high biomass samples, despite the presence of contaminating DNA. The bacterial communities of ticks were associated with geographical location rather than life stage, and differences in Rickettsia abundance determined this association. Subsequently, we explored the geographical distribution of four vertically transmitted symbionts identified in the microbiome analysis. For that, we screened 16,555 nymphs from 19 forest sites for R. helvetica, Rickettsiella spp., Midichloria mitochondrii, and Spiroplasma ixodetis. Also, the infection rates and distributions of these symbionts were compared to the horizontally transmitted pathogens Borrelia burgdorferi sensu lato, Anaplasma phagocytophilum, and Neoehrlichia mikurensis. The infection rates of all vertically transmitted symbionts differed between the study sites, and none of the symbionts was present in all tested ticks suggesting a facultative association with I. ricinus. The proportions in which symbionts occurred in populations of I. ricinus were highly variable, but geographically close study sites expressed similar proportions. These patterns were in contrast to what we observed for horizontally transmitted pathogens. Lastly, nearly 12% of tested nymphs were free of any targeted microorganisms, which is in line with the microbiome analyses.

CONCLUSIONS: Our results show that the microbiome of I. ricinus is highly variable, but changes gradually and ticks originating from geographically close forest sites express similar bacterial communities. This suggests that geography-related factors affect the infection rates of vertically transmitted symbionts in I. ricinus. Since some symbionts, such as R. helvetica can cause disease in humans, we propose that public health investigations consider geographical differences in its infection rates.

RevDate: 2022-08-04

Aira M, Pérez-Losada M, Crandall KA, et al (2022)

Host taxonomy determines the composition, structure, and diversity of the earthworm cast microbiome under homogenous feeding conditions.

FEMS microbiology ecology pii:6655979 [Epub ahead of print].

Host evolutionary history is a key factor shaping the earthworm cast microbiome, although its effect can be shadowed by the earthworm's diet. To untangle dietary from taxon effects, we raised nine earthworm species on a uniform diet of cow manure and compared cast microbiome across species while controlling for diet. Our results showed that, under controlled laboratory conditions, earthworm microbiomes are species-specific, more diverse than that of the controlled diet, and mainly comprised of native bacteria (i.e., not acquired from the diet). Furthermore, diet has a medium to large convergence effect on microbiome composition since earthworms shared 16 to 74% of their bacterial amplicon sequence variants (ASV). The inter-species core microbiome included 10 ASVs, while their intra-species core microbiomes were larger and varied in ASV richness (24-48%) and sequence abundance across earthworm species. This specificity in core microbiomes and variable degree of similarity in bacterial composition suggest that phylosymbiosis could determine earthworm microbiome assembly. However, lack of congruence between the earthworm phylogeny and the microbiome dendrogram suggests that a consistent diet fed over several generations may have weakened potential phylosymbiotic effects. Thus, cast microbiome assembly in earthworms seem to be the result of an interplay among host phylogeny and diet.

RevDate: 2022-08-04

Edwards VL, McComb E, Gleghorn JP, et al (2022)

Three-dimensional models of the cervicovaginal epithelia to study host-microbiome interactions and sexually transmitted infections.

Pathogens and disease pii:6655985 [Epub ahead of print].

Two-dimensional (2D) cell culture systems have historically provided controlled, reproducible means to analyze host-pathogen interactions observed in the human reproductive tract. Although inexpensive, straightforward, and requiring a very short time commitment, these models recapitulate neither the functionality of multi-layered cell types nor the associated microbiome that occurs in a human. Animal models have commonly been used to recreate the complexity of human infections. However, extensive modifications of animal models are required to recreate interactions that resemble those in the human reproductive tract. Three-dimensional (3D) cell culture models have emerged as alternative means of reproducing vital elements of human infections at a fraction of the cost of animal models and on a scale that allows for replicative experiments. Here we describe a new 3D model that utilizes transwells with epithelial cells seeded apically and a basolateral extracellular matrix (ECM)-like layer. The model produced tissues with morphologic and physiological resemblance to human cervical and vaginal epithelia, including mucus levels produced by cervical cells. Infection by Chlamydia trachomatis and Neisseria gonorrhoeae was demonstrated, as well as the growth of bacterial species observed in the human vaginal microbiota. This enabled controlled mechanistic analyses of the interactions between host cells, the vaginal microbiota and STI pathogens.

RevDate: 2022-08-04

Carvalho MJ, Sands K, Thomson K, et al (2022)

Antibiotic resistance genes in the gut microbiota of mothers and linked neonates with or without sepsis from low- and middle-income countries.

Nature microbiology [Epub ahead of print].

Early development of the microbiome has been shown to affect general health and physical development of the infant and, although some studies have been undertaken in high-income countries, there are few studies from low- and middle-income countries. As part of the BARNARDS study, we examined the rectal microbiota of 2,931 neonates (term used up to 60 d) with clinical signs of sepsis and of 15,217 mothers screening for blaCTX-M-15, blaNDM, blaKPC and blaOXA-48-like genes, which were detected in 56.1%, 18.5%, 0% and 4.1% of neonates' rectal swabs and 47.1%, 4.6%, 0% and 1.6% of mothers' rectal swabs, respectively. Carbapenemase-positive bacteria were identified by MALDI-TOF MS and showed a high diversity of bacterial species (57 distinct species/genera) which exhibited resistance to most of the antibiotics tested. Escherichia coli, Klebsiella pneumoniae and Enterobacter cloacae/E. cloacae complex, the most commonly found isolates, were subjected to whole-genome sequencing analysis and revealed close relationships between isolates from different samples, suggesting transmission of bacteria between neonates, and between neonates and mothers. Associations between the carriage of antimicrobial resistance genes (ARGs) and healthcare/environmental factors were identified, and the presence of ARGs was a predictor of neonatal sepsis and adverse birth outcomes.

RevDate: 2022-08-04

Malayil L, Chattopadhyay S, Mongodin EF, et al (2022)

Bacterial communities of hookah tobacco products are diverse and differ across brands and flavors.

Applied microbiology and biotechnology [Epub ahead of print].

Young adults are increasingly using non-cigarette products, such as hookahs, since they are perceived as healthier alternatives to cigarette smoking. However, hookah users are exposed to not only carcinogenic compounds but also microorganisms that may play an active role in the development of both infectious and chronic diseases among users. Nevertheless, existing hookah research in this area has focused only on microorganisms that may be transferred to users through the smoking apparatus and not on bacterial communities associated with hookah tobacco. To address this knowledge gap, we conducted time-series experiments on commercially available hookah brands (Al Fakher (flavors: two apple, mint, and watermelon) and Fumari (flavors: white gummy bear, ambrosia, and mint chocolate chill)) stored under three different temperature and relative humidity conditions over 14 days. To characterize bacterial communities, the total DNA was extracted on days 0, 5, 9, and 14, PCR-amplified for the V3V4 region of the bacterial 16S rRNA gene, sequenced on the Illumina HiSeq platform, and analyzed using R. Diversity (alpha and beta) analyses revealed that the microbiotas of Fumari and Al Fakher products differed significantly and that flavor had a significant effect on the hookah microbiota. Overall, Pseudomonas, Bacillus, Sphingomonas, and Methylobacterium were the predominant bacterial taxa across all products. Additionally, we observed compositional differences between hookah brands across the 14-day incubation. These data suggest that the bacterial communities of hookah tobacco are diverse and differ across brands and flavors, which may have critical implications regarding exposures to specific bacteria among hookah users. KEY POINTS: • Commercial hookah products harbor diverse bacterial communities. • Brands and flavors impact the diversity of these communities. • Research on their viability and transmission to users' respiratory tracts is needed.

RevDate: 2022-08-04

Kim N, Gim JA, Lee BJ, et al (2022)

Crosstalk between mucosal microbiota, host gene expression, and sociomedical factors in the progression of colorectal cancer.

Scientific reports, 12(1):13447.

Various omics-based biomarkers related to the occurrence, progression, and prognosis of colorectal cancer (CRC) have been identified. In this study, we attempted to identify gut microbiome-based biomarkers and detect their association with host gene expression in the initiation and progression of CRC by integrating analysis of the gut mucosal metagenome, RNA sequencing, and sociomedical factors. We performed metagenome and RNA sequencing on colonic mucosa samples from 13 patients with advanced CRC (ACRC), 10 patients with high-risk adenoma (HRA), and 7 normal control (NC) individuals. All participants completed a questionnaire on sociomedical factors. The interaction and correlation between changes in the microbiome and gene expression were assessed using bioinformatic analysis. When comparing HRA and NC samples, which can be considered to represent the process of tumor initiation, 28 genes and five microbiome species were analyzed with correlation plots. When comparing ACRC and HRA samples, which can be considered to represent the progression of CRC, seven bacterial species and 21 genes were analyzed. When comparing ACRC and NC samples, 16 genes and five bacterial species were analyzed, and four correlation plots were generated. A network visualizing the relationship between bacterial and host gene expression in the initiation and progression of CRC indicated that Clostridium spiroforme and Tyzzerella nexilis were hub bacteria in the development and progression of CRC. Our study revealed the interactions of and correlation between the colonic mucosal microbiome and host gene expression to identify potential roles of the microbiome in the initiation and progression of CRC. Our results provide gut microbiome-based biomarkers that may be potential diagnostic markers and therapeutic targets in patients with CRC.

RevDate: 2022-08-05

Jantharadej K, Kongprajug A, Mhuantong W, et al (2022)

Comparative genomic analyses of pathogenic bacteria and viruses and antimicrobial resistance genes in an urban transportation canal.

The Science of the total environment, 848:157652 pii:S0048-9697(22)04750-7 [Epub ahead of print].

Water commuting is a major urban transportation method in Thailand. However, urban boat commuters risk exposure to microbially contaminated bioaerosols or splash. We aimed to investigate the microbial community structures, identify bacterial and viral pathogens, and assess the abundance of antimicrobial resistance genes (ARGs) using next-generation sequencing (NGS) at 10 sampling sites along an 18 km transportation boat route in the Saen Saep Canal, which traverses cultural, commercial, and suburban land-based zones. The shotgun metagenomic (Illumina HiSeq) and 16S rRNA gene amplicon (V4 region) (Illumina MiSeq) sequencing platforms revealed diverse microbial clusters aligned with the zones, with explicit segregation between the cultural and suburban sites. The shotgun metagenomic sequencing further identified bacterial and viral pathogens, and ARGs. The predominant bacterial pathogens (>0.5 % relative abundance) were the Burkholderia cepacia complex, Arcobacter butzleri, Burkholderia vietnamiensis, Klebsiella pneumoniae, and the Enterobacter cloacae complex. The viruses (0.28 %-0.67 % abundance in all microbial sequences) comprised mainly vertebrate viruses and bacteriophages, with encephalomyocarditis virus (33.3 %-58.2 % abundance in viral sequences), hepatitis C virus genotype 1, human alphaherpesvirus 1, and human betaherpesvirus 6A among the human viral pathogens. The 15 ARG types contained 611 ARG subtypes, including those resistant to beta-lactam, which was the most diverse and abundant group (206 subtypes; 17.0 %-27.5 %), aminoglycoside (94 subtypes; 9.6 %-15.3 %), tetracycline (80 subtypes; 15.6 %-20.2 %), and macrolide (79 subtypes; 14.5 %-32.1 %). Interestingly, the abundance of ARGs associated with resistance to beta-lactam, trimethoprim, and sulphonamide, as well as A. butzleri and crAssphage, at the cultural sites was significantly different from the other sites (p < 0.05). We demonstrated the benefits of using NGS to deliver insights into microbial communities, and antimicrobial resistance, both of which pose a risk to human health. Using NGS may facilitate microbial risk mitigation and management for urban water commuters and proximal residents.

RevDate: 2022-08-04

Kim JH, Go GP, Son KH, et al (2022)

Arazyme in combination with dietary carbohydrolases influences odor emission and gut microbiome in growing-finishing pigs.

The Science of the total environment pii:S0048-9697(22)04834-3 [Epub ahead of print].

This study evaluated the effects of supplementing feed with arazyme and dietary carbohydrolases derived from invertebrate gut-associated symbionts on the noxious gas emissions, gut microbiota, and host-microbiome interactions of pigs. Here, 270 and 260 growing pigs were assigned to control and treatment groups, respectively. The tested feed additives contained a mixture of arazyme (2,500,000 Unit/kg) and synergetic enzymes, xylanase (200,000 Unit/kg) and mannanase (200,000 Unit/kg), derived from insect gut-associated symbionts in a 7.5:1:1 ratio. The control group was fed a basal diet and the treatment group was fed the basal diet supplemented with 0.1 % enzyme mixture (v/v) for 2 months. Odorous gases were monitored in ventilated air from tested houses. Fecal samples were collected from steel plate under the cage at the completion of the experiment to determine chemical composition, odor emissions, and bacterial communities. There was a significant decrease in the concentration of NH3 (22.5 vs. 11.2 ppm; P < 0.05), H2S (7.35 vs. 3.74 ppm; P < 0.05), trimethylamine (TMA) (0.066 vs. 0.001 ppm; P < 0.05), and p-cresol (0.004 ppm vs. 0 ppm; P < 0.05) at 56 d in treatment group compared with the control group. Moreover, fecal analysis results showed that exogenous enzyme supplementation caused a reduction in VFAs and indole content with approximately >60 % and 72.7 %, respectively. The result of gas emission analysis showed that NH3 (9.9 vs. 5.3 ppm; P < 0.05) and H2S (5.8 vs. 4.1 ppm; P < 0.05) were significantly reduced in the treatment group compared to the control group. The gut microbiota of the treatment group differed significantly from that of the control group, and the treatment group altered predicted metabolic pathways, including sulfur and nitrogen related metabolism, urea degradation. The results demonstrated that supplementing feed with arazyme with dietary carbohydrolases effectively controls noxious gas emissions and improves health and meat quality of pigs.

RevDate: 2022-08-04

Bulleri F, Pretti C, Bertolino M, et al (2022)

Adding functions to marine infrastructure: Pollutant accumulation, physiological and microbiome changes in sponges attached to floating pontoons inside marinas.

The Science of the total environment pii:S0048-9697(22)04872-0 [Epub ahead of print].

The rate of introduction of man-made habitats in coastal environments is growing at an unprecedented pace, as a consequence of the expansion of urban areas. Floating installations, due to their unique hydrodynamic features, are able to provide great opportunities for enhancing water detoxification through the use of sessile, filtering organisms. We assessed whether the application of sponges to floating pontoons could function as a tool for biomonitoring organic and inorganic pollutants and for improving water quality inside a moderately contaminated marina in the NW Mediterranean. Fragments of two common Mediterranean sponges (Petrosia (Petrosia) ficiformis and Ircinia oros) were fixed to either suspended natural fibre nets beneath a floating pontoon or to metal frames deployed on the sea bottom. We assessed the accumulation of organic and inorganic contaminants in sponge fragments and, in order to provide an insight into their health status, we examined changes in their metabolic and oxidative stress responses and associated microbiomes. Fragments of both sponge species filtered out pollutants from seawater on both support types, but generally showed a better physiological and metabolic status when fixed to nets underneath the pontoon than to bottom frames. P. (P) ficiformis maintained a more efficient metabolism and exhibited a lower physiological stress levels and higher stability of the associated microbiome in comparison with I. oros. Our study suggests that the application of sponges to floating pontoon represents a promising nature-based solution to improve the ecological value of urban environments.

RevDate: 2022-08-04

Bousbaine D, Fisch LI, London M, et al (2022)

A conserved Bacteroidetes antigen induces anti-inflammatory intestinal T lymphocytes.

Science (New York, N.Y.), 377(6606):660-666.

The microbiome contributes to the development and maturation of the immune system. In response to commensal bacteria, intestinal CD4+ T lymphocytes differentiate into functional subtypes with regulatory or effector functions. The development of small intestine intraepithelial lymphocytes that coexpress CD4 and CD8αα homodimers (CD4IELs) depends on the microbiota. However, the identity of the microbial antigens recognized by CD4+ T cells that can differentiate into CD4IELs remains unknown. We identified β-hexosaminidase, a conserved enzyme across commensals of the Bacteroidetes phylum, as a driver of CD4IEL differentiation. In a mouse model of colitis, β-hexosaminidase-specific lymphocytes protected against intestinal inflammation. Thus, T cells of a single specificity can recognize a variety of abundant commensals and elicit a regulatory immune response at the intestinal mucosa.

RevDate: 2022-08-04

Li L, Sohn J, Genco RJ, et al (2022)

Computational approach to modeling microbiome landscapes associated with chronic human disease progression.

PLoS computational biology, 18(8):e1010373 pii:PCOMPBIOL-D-22-00062 [Epub ahead of print].

A microbial community is a dynamic system undergoing constant change in response to internal and external stimuli. These changes can have significant implications for human health. However, due to the difficulty in obtaining longitudinal samples, the study of the dynamic relationship between the microbiome and human health remains a challenge. Here, we introduce a novel computational strategy that uses massive cross-sectional sample data to model microbiome landscapes associated with chronic disease development. The strategy is based on the rationale that each static sample provides a snapshot of the disease process, and if the number of samples is sufficiently large, the footprints of individual samples populate progression trajectories, which enables us to recover disease progression paths along a microbiome landscape by using computational approaches. To demonstrate the validity of the proposed strategy, we developed a bioinformatics pipeline and applied it to a gut microbiome dataset available from a Crohn's disease study. Our analysis resulted in one of the first working models of microbial progression for Crohn's disease. We performed a series of interrogations to validate the constructed model. Our analysis suggested that the model recapitulated the longitudinal progression of microbial dysbiosis during the known clinical trajectory of Crohn's disease. By overcoming restrictions associated with complex longitudinal sampling, the proposed strategy can provide valuable insights into the role of the microbiome in the pathogenesis of chronic disease and facilitate the shift of the field from descriptive research to mechanistic studies.

RevDate: 2022-08-04

Lin B, Ma Y, S Wu (2022)

Multi-Omics and Artificial Intelligence-Guided Data Integration in Chronic Liver Disease: Prospects and Challenges for Precision Medicine.

Omics : a journal of integrative biology [Epub ahead of print].

Chronic liver disease (CLD) is a significant planetary health burden. CLD includes a broad range of liver pathologies from different causes, for example, hepatitis B virus infection, fatty liver disease, hepatocellular carcinoma, and nonalcoholic fatty liver disease or the metabolic associated fatty liver disease. Biomarker and diagnostic discovery, and new molecular targets for precision treatments are timely and sorely needed in CLD. In this context, multi-omics data integration is increasingly being facilitated by artificial intelligence (AI) and attendant digital transformation of systems science. While the digital transformation of multi-omics integrative analyses is still in its infancy, there are noteworthy prospects, hope, and challenges for diagnostic and therapeutic innovation in CLD. This expert review aims at the emerging knowledge frontiers as well as gaps in multi-omics data integration at bulk tissue levels, and those including single cell-level data, gut microbiome data, and finally, those incorporating tissue-specific information. We refer to AI and related digital transformation of the CLD research and development field whenever possible. This review of the emerging frontiers at the intersection of systems science and digital transformation informs future roadmaps to bridge digital technology discovery and clinical omics applications to benefit planetary health and patients with CLD.

RevDate: 2022-08-04

Stallmach A, S Nitschmann (2022)

[SER-109: oral microbiome therapy for recurrent Clostridioides difficile infections : SER-109 versus Placebo in the Treatment of Adults with Recurrent Clostridium Difficile Infection (ECOSPOR III)].

Innere medizin (Heidelberg, Germany), 63(7):805-807.

RevDate: 2022-08-04

Glanville AR, AB Mitchell (2022)

New Tools for Old Problems: Gastroesophageal Reflux Disease and the Lung Allograft Microbiome.

American journal of respiratory and critical care medicine [Epub ahead of print].

RevDate: 2022-08-04

Fang Y, Yang G, Yang J, et al (2022)

Human microbiota colonization and pancreatic ductal carcinoma.

Critical reviews in microbiology [Epub ahead of print].

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive disease with a high mortality rate and a poor prognosis. The human microbiota has been confirmed to participate in oncogenesis and may influence the treatment response to both chemotherapy and immunotherapy. Evidence for the association of the microbiota with PDAC risk, tumorigenesis, treatment response, and survival period is rapidly emerging. The oral microbiota and gut microbiota have the potential to be used in early diagnosis and risk stratification. Intratumor microbiota-targeted intervention strategies may be used as adjuvants to current treatments to improve therapeutic efficacy and overall survival. Here, we summarize the effect and association of the oral, gut and intratumor microbiota on the oncogenesis, progression and treatment of PDAC, as well as the potential of the microbiota to serve as a biomarker for the diagnosis and prognosis of PDAC, as well as a therapeutic target.

RevDate: 2022-08-04

Wodzanowski KA, Hyland SN, Chinthamani S, et al (2022)

Investigating Peptidoglycan Recycling Pathways in Tannerella forsythia with N-Acetylmuramic Acid Bioorthogonal Probes.

ACS infectious diseases [Epub ahead of print].

The human oral microbiome is the second largest microbial community in humans, harboring over 700 bacterial species, which aid in digestion and protect from growth of disease-causing pathogens. One such oral pathogen, Tannerella forsythia, along with other species, contributes to the pathogenesis of periodontitis. T. forsythia is unable to produce its own N-acetylmuramic acid (NAM) sugar, essential for peptidoglycan biosynthesis and therefore must scavenge NAM from other species with which it cohabitates. Here, we explore the recycling potential of T. forsythia for NAM uptake with a bioorthogonal modification into its peptidoglycan, allowing for click-chemistry-based visualization of the cell wall structure. Additionally, we identified NAM recycling enzyme homologues in T. forsythia that are similar to the enzymes found in Pseudomonas putida. These homologues were then genetically transformed into a laboratory safe Escherichia coli strain, resulting in the efficient incorporation of unnatural NAM analogues into the peptidoglycan backbone and its visualization, alone or in the presence of human macrophages. This strain will be useful in further studies to probe NAM recycling and peptidoglycan scavenging pathways of T. forsythia and other cohabiting bacteria.

RevDate: 2022-08-04

Chesnokova MG, Chesnokov VA, Mironov AY, et al (2022)

Analysis of micro-relief of biofilm of yeast Candida albicans of basic plastics by the method of laser modulation interference microscopy.

Klinicheskaia laboratornaia diagnostika, 67(7):407-413.

The development of mycotic colonization of the base surface with further biodegradation of acrylic plastics is currently of undoubted interest. The oral cavity is a favorable ecological niche for colonization by fungi and their subsequent possible invasion into the epithelium of the oral mucosa. The method of modulation interference laser microscopy is of considerable interest to researchers in medicine in the context of obtaining the necessary information about the morphological characteristics of microbial cells and the microbiome community as a whole during the colonization of a certain ecological niche in the human body. Purpose of the study: to analyze the microrelief of the biofilm of yeast-like fungi of the species Candida albicans of base plastics of the hot type of polymerization using the method of laser modulation interference microscopy. An experimental study was carried out in order to study biofilms of yeast-like fungi of the genus Candida on samples of basic plastics, an image of a biofilm of yeast-like fungi of the species Candida albicans was obtained on the surface of a plastic of a hot type of polymerization (polymethyl methacrylate) in the visualization of the phase portrait, a description of its horizontal and vertical bioprofile. As a result of the research, the heterogeneous structure of the biofilm was determined, due to the different density and accumulation of cells along the surface, the characteristics of the surface were established in accordance with the roughness criteria. The microrelief parameters on a separately arbitrarily selected section line allow one to determine the characteristics of the biofilm in the required area and make it possible to judge the nature of its formation in a certain biological niche.

RevDate: 2022-08-04

Yang J, Zhang G, Peng M, et al (2022)

Bionic Regulators Break the Ecological Niche of Pathogenic Bacteria for Modulating Dysregulated Microbiome in Colitis.

Advanced materials (Deerfield Beach, Fla.) [Epub ahead of print].

Therapeutic approaches that reprogram the gut microbiome are promising strategies to alleviate and cure inflammatory bowel disease (IBD). However, abnormal expansion of E. coli during inflammation can promote pathogenic bacteria occupying ecological niches to resist reprogramming of the microbiome. Herein, we develop a bionic regulator (CaWO4 @YCW) to efficiently and precisely regulate the gut microbiome by specifically suppressing the abnormal expansion of E. coli during colitis and boosting probiotic growth. Inspired by the binding of E. coli strains to the mannose-rich yeast cell wall (YCW), we chose YCW as the bionic shell to encapsulate CaWO4 . We demonstrate that the YCW shell endows CaWO4 with superior resistance to the harsh environment of the gastrointestinal tract and adheres to the abnormally expanded E. coli in colitis, specifically as a positioner. Notably, the high expression of calprotectin at the colitis site triggers the release of tungsten ions through calcium deprivation in CaWO4 , thus inhibiting E. coli growth by replacing molybdenum in the molybdopterin cofactor. Moreover, YCW functions as a prebiotic and promotes probiotic growth. Consequently, CaWO4 @YCW can efficiently and precisely reprogram the gut microbiome by eliminating pathogenic bacteria and providing prebiotics, resulting in an extraordinary therapeutic advantage for DSS-induced colitis. This article is protected by copyright. All rights reserved.

RevDate: 2022-08-04

Qin H, Yuan B, Huang W, et al (2022)

Utilizing Gut Microbiota to Improve Hepatobiliary Tumor Treatments: Recent Advances.

Frontiers in oncology, 12:924696.

Hepatobiliary tumors, which include cholangiocarcinoma, hepatocellular carcinoma (HCC), and gallbladder cancer, are common cancers that have high morbidity and mortality rates and poor survival outcomes. In humans, the microbiota is comprised of symbiotic microbial cells (10-100 trillion) that belong to the bacterial ecosystem mainly residing in the gut. The gut microbiota is a complicated group that can largely be found in the intestine and has a dual role in cancer occurrence and progression. Previous research has focused on the crucial functions of the intestinal microflora as the main pathophysiological mechanism in HCC development. Intestinal bacteria produce a broad range of metabolites that exhibit a variety of pro- and anticarcinogenic effects on HCC. Therefore, probiotic alteration of the gut microflora could promote gut flora balance and help prevent the occurrence of HCC. Recent evidence from clinical and translational studies suggests that fecal microbiota transplant is one of the most successful therapies to correct intestinal bacterial imbalance. We review the literature describing the effects and mechanisms of the microbiome in the gut in the context of HCC, including gut bacterial metabolites, probiotics, antibiotics, and the transplantation of fecal microbiota, and discuss the potential influence of the microbiome environment on cholangiocarcinoma and gallbladder cancer. Our findings are expected to reveal therapeutic targets for the prevention of hepatobiliary tumors, and the development of clinical treatment strategies, by emphasizing the function of the gut microbiota.

RevDate: 2022-08-04

Li Z, Zhao Y, Cheng J, et al (2022)

Integrated Plasma Metabolomics and Gut Microbiota Analysis: The Intervention Effect of Jiawei Xiaoyao San on Liver Depression and Spleen Deficiency Liver Cancer Rats.

Frontiers in pharmacology, 13:906256 pii:906256.

Primary liver cancer is the third most common malignancy, and hepatocellular carcinoma is its main subtype, with a high recurrence rate and high mortality. Intestinal microflora and metabolic disorders are present in most HCC patients. Traditional Chinese medicine (TCM) plays an important role in the composition of intestinal microorganisms and the transformation of active metabolites. Many scholars are trying to develop related drugs to assist in the treatment of liver cancer. In the preliminary study of the research group, it was found that the Jiawei Xiaoyao San has a certain therapeutic effect on liver cancer, but the specific mechanism is still unclear. Therefore, this study constructed a liver cancer rat model with liver stagnation and spleen deficiency, to explore the regulatory effect of Jiawei Xiaoyao San on plasma metabolites and intestinal microflora and to find the potential mechanism of Jiawei Xiaoyao San in the treatment of liver cancer. Plasma samples and fecal samples were collected from liver cancer rats with liver depression and spleen deficiency for microbiome 16S rDNA sequencing and metabolic ESI-QTRAP-MS/MS analysis. Various bioinformatics methods were used to analyze the dataset individually and in combination. The analysis and identification of plasma metabolomics showed that the intervention effect of Jiawei Xiaoyao San on liver cancer rats with liver depression and spleen deficiency was related to 11 differential metabolites and signal pathways such as primary bile acid biosynthesis, phenylalanine metabolism, pantothenate and COA biosynthesis, metabolic pathways, cholesterol metabolism, and bile secretion. Combined with fecal microbiological analysis, it was found that Jiawei Xiaoyao San could significantly change the composition of intestinal flora in liver cancer rates, increase beneficial bacteria, and reduce the composition of harmful bacteria. This study provides some experimental basis for the traditional Chinese medicine theory and clinical application of Jiawei Xiaoyao San in the adjuvant treatment of liver cancer. The potential mechanism may be to regulate metabolism and intestinal flora to play the role of regulating liver depression, activating blood, and detoxifying, to achieve the purpose of adjuvant treatment of liver cancer.

RevDate: 2022-08-04

Mancabelli L, Ciociola T, Lugli GA, et al (2022)

Guideline for the analysis of the microbial communities of the human upper airways.

Journal of oral microbiology, 14(1):2103282 pii:2103282.

The recent COVID-19 pandemic prompted a rapid-growing interest in the investigation of the human microbiota of the upper airways. In fact, the resident microbial community of this body district may have an influence on the onset of SARS-CoV-2 infection and its clinical course in terms of presence, symptom severity, and outcomes. However, several microbiological methodologies are available to study the human microbiota, reflecting the extensive fragmentation of methodological approaches. We investigate the impact of two critical steps that can induce biases in the downstream analyses, i.e. sampling method and microbial DNA extraction kit employed. We observed major discrepancies regarding the total amount of prokaryotic DNA that could be retrieved from a biological sample and the proportion between bacterial DNA and human host DNA. Moreover, shotgun DNA sequencing and taxonomic profile reconstruction also revealed correlations between sampling methods and the procedures applied for microbial DNA extraction. Based on all the data collected in this study, we formulate indications regarding the most efficient and reliable methodological procedures for the metagenomic analyses of the upper airways' microbiota to maximize accuracy and reproducibility.

RevDate: 2022-08-04

Parker A, James SA, Purse C, et al (2022)

Absence of Bacteria Permits Fungal Gut-To-Brain Translocation and Invasion in Germfree Mice but Ageing Alone Does Not Drive Pathobiont Expansion in Conventionally Raised Mice.

Frontiers in aging neuroscience, 14:828429.

Age-associated changes in the structure of the intestinal microbiome and in its interaction with the brain via the gut-brain axis are increasingly being implicated in neurological and neurodegenerative diseases. Intestinal microbial dysbiosis and translocation of microbes and microbial products including fungal species into the brain have been implicated in the development of dementias such as Alzheimer's disease. Using germ-free mice, we investigated if the fungal gut commensal, Candida albicans, an opportunistic pathogen in humans, can traverse the gastrointestinal barrier and disseminate to brain tissue and whether ageing impacts on the gut mycobiome as a pre-disposing factor in fungal brain infection. C. albicans was detected in different regions of the brain of colonised germ-free mice in both yeast and hyphal cell forms, often in close association with activated (Iba-1+) microglial cells. Using high-throughput ITS1 amplicon sequencing to characterise the faecal gut fungal composition of aged and young SPF mice, we identified several putative gut commensal fungal species with pathobiont potential although their abundance was not significantly different between young and aged mice. Collectively, these results suggest that although some fungal species can travel from the gut to brain where they can induce an inflammatory response, ageing alone is not correlated with significant changes in gut mycobiota composition which could predispose to these events. These results are consistent with a scenario in which significant disruptions to the gut microbiota or intestinal barrier, beyond those which occur with natural ageing, are required to allow fungal escape and brain infection.

RevDate: 2022-08-04

Xu L, Xiang P, Zhang B, et al (2022)

Host Species Influence the Gut Microbiota of Endemic Cold-Water Fish in Upper Yangtze River.

Frontiers in microbiology, 13:906299.

The fish gut microbiome plays an important role in nutrition absorption and energy metabolism. Studying the gut microbes of cold-water fish is important to understand the dietary adaptation strategies in extreme environments. In this study, the gut samples of Schizothorax wangchiachii (SW, herbivorous), Schizothorax kozlovi (SK, omnivorous), and Percocypris pingi (PP, carnivorous) in the upper Yangtze River were collected, and we sequenced 16S rRNA amplicon to study the potential relationship between gut microbes and host species. The results showed that gut microbial composition and diversity were significantly different between the three cold-water fishes. These fishes had different key taxa in their gut microbes, including bacteria involved in the breakdown of food (e.g., Cetobacterium, Aeromonas, and Clostridium sensu stricto 10). The highest alpha diversity indices (e.g., Chao 1 index) were identified in the herbivore (SW), followed by the carnivore (PP), and the lowest in the omnivore (SK). Non-metric multidimensional scaling (NMDS) results revealed that the gut microbial community of these species was different between host species. The neutral community model (NCM) showed that the microbial community structure of SW was shaped by stochastic processes, and the highest species dispersal was found in SW, followed by PP, and the lowest in SK. The results of niche breadth agreed with these findings. Our results demonstrated that host species influenced the gut microbiome composition, diversity, and microbial community assembly processes of the three cold-water fishes. These findings implied that the variation of gut microbiome composition and function plays a key role in digesting and absorbing nutrients from different foods in cold-water fish.

RevDate: 2022-08-04

Zeng Q, Man X, Dai Y, et al (2022)

Pseudomonas spp. Enriched in Endophytic Community of Healthy Cotton Plants Inhibit Cotton Verticillium Wilt.

Frontiers in microbiology, 13:906732.

The plant microbiome plays a fundamental role in plant growth and health. However, detailed information regarding the plant endophytic microbiome during the infection period of a pathogen is largely unknown. Here, we investigated the microbial community of healthy and diseased cotton plants and the root exudate profiles of susceptible and resistant cultivars utilizing high-throughput sequencing and metabolomics. The results showed that the pathogen infection reduced bacterial diversity and significantly affected the bacterial community composition. The microbiome assembly is shaped predominantly by cultivars. The endophytic microbiome of the infected plants showed greater complexity than the healthy plants in network analysis. The results displayed that a total of 76 compounds were significantly different in the two groups, with 18 compounds showing a higher relative abundance in the resistant cultivars and 58 compounds in the susceptible cultivars. Pathway enrichment analysis showed that pathways related to plant hormone signal transduction, biosynthesis of various secondary metabolites, and biosynthesis and metabolism of amino acids were prominently altered. We also demonstrate that plants inoculated with Pseudomonas sp. strains showed increased resistance to the cotton Verticillium wilt compared with the control plants in pot experiments. Overall, it showed that the pathogen infection affected the community composition, and healthy plants displayed an enriched beneficial microbiome to combat the plant disease. These findings significantly advance our understanding of the endophytic microbiome assembly under the pathogen infection and develop microbiome-based solutions for sustainable crop production systems.

RevDate: 2022-08-04

Di Franca ML, Matturro B, Crognale S, et al (2022)

Microbiome Composition and Dynamics of a Reductive/Oxidative Bioelectrochemical System for Perchloroethylene Removal: Effect of the Feeding Composition.

Frontiers in microbiology, 13:951911.

Chlorinated solvents still represent an environmental concern that requires sustainable and innovative bioremediation strategies. This study describes the microbiome composition of a novel bioelectrochemical system (BES) based on sequential reductive/oxidative dechlorination for complete perchloroethylene (PCE) removal occurring in two separate but sequential chambers. The BES has been tested under various feeding compositions [i.e., anaerobic mineral medium (MM), synthetic groundwater (SG), and real groundwater (RG)] differing in presence of sulfate, nitrate, and iron (III). In addition, the main biomarkers of the dechlorination process have been monitored in the system under various conditions. Among them, Dehalococcoides mccartyi 16S rRNA and reductive dehalogenase genes (tceA, bvcA, and vcrA) involved in anaerobic dechlorination have been quantified. The etnE and etnC genes involved in aerobic dechlorination have also been quantified. The feeding composition affected the microbiome, in particular when the BES was fed with RG. Sulfuricurvum, enriched in the reductive compartment, operated with MM and SG, suggesting complex interactions in the sulfur cycle mostly including sulfur oxidation occurring at the anodic counter electrode (MM) or coupled to nitrate reduction (SG). Moreover, the known Mycobacterium responsible for natural attenuation of VC by aerobic degradation was found abundant in the oxidative compartment fed with RG, which was in line with the high VC removal observed (92 ± 2%). D. mccartyi was observed in all the tested conditions ranging from 8.78E + 06 (with RG) to 2.35E + 07 (with MM) 16S rRNA gene copies/L. tceA was found as the most abundant reductive dehalogenase gene in all the conditions explored (up to 2.46 E + 07 gene copies/L in MM). The microbiome dynamics and the occurrence of biomarkers of dechlorination, along with the kinetic performance of the system under various feeding conditions, suggested promising implications for the scale-up of the BES, which couples reductive with oxidative dechlorination to ensure the complete removal of highly chlorinated ethylene and mobile low-chlorinated by-products.

RevDate: 2022-08-04

Salama ES, Jeon BH, Wang J, et al (2022)

Editorial: Microbial advances towards sustainable environment: Microbiome structure & integrated technologies.

Frontiers in microbiology, 13:971696.

RevDate: 2022-08-04

De D, Nayak T, Chowdhury S, et al (2022)

Insights of Host Physiological Parameters and Gut Microbiome of Indian Type 2 Diabetic Patients Visualized via Metagenomics and Machine Learning Approaches.

Frontiers in microbiology, 13:914124.

Type 2 diabetes (T2D) is a serious public health issue and may also contribute to modification in the structure of the intestinal microbiota, implying a link between T2D and microbial inhabitants in the digestive tract. This work aimed to develop efficient models for identifying essential physiological markers for improved T2D classification using machine learning algorithms. Using amplicon metagenomic approaches, an effort has also been made to understand the alterations in core gut microbial members in Indian T2D patients with respect to their control normal glucose tolerance (NGT). Our data indicate the level of fasting blood glucose (FBG) and glycated hemoglobin (HbA1c) were the most useful physiological indicators while random forest and support vector machine with RBF Kernel were effective predictions models for identifications of T2D. The dominating gut microbial members Allopreotella, Rikenellaceae RC9 gut group, Haemophilus, Ruminococcus torques group, etc. in Indian T2D patients showed a strong association with both FBG and HbA1c. These members have been reported to have a crucial role in gut barrier breakdown, blood glucose, and lipopolysaccharide level escalation, or as biomarkers. While the dominant NGT microbiota (Akkermansia, Ligilactobacillus, Enterobacter, etc.) in the colon has been shown to influence inflammatory immune responses by acting as an anti-inflammatory agent and maintaining the gut barrier. The topology study of co-occurrence network analysis indicates that changes in network complexity in T2D lead to variations in the different gut microbial members compared to NGT. These studies provide a better understanding of the gut microbial diversity in Indian T2D patients and show the way for the development of valuable diagnostics strategies to improve the prediction and modulation of the T2D along with already established methods.

RevDate: 2022-08-04

Tibbs-Cortes LE, Tibbs-Cortes BW, S Schmitz-Esser (2022)

Tardigrade Community Microbiomes in North American Orchards Include Putative Endosymbionts and Plant Pathogens.

Frontiers in microbiology, 13:866930.

The microbiome of tardigrades, a phylum of microscopic animals best known for their ability to survive extreme conditions, is poorly studied worldwide and completely unknown in North America. An improved understanding of tardigrade-associated bacteria is particularly important because tardigrades have been shown to act as vectors of the plant pathogen Xanthomonas campestris in the laboratory. However, the potential role of tardigrades as reservoirs and vectors of phytopathogens has not been investigated further. This study analyzed the microbiota of tardigrades from six apple orchards in central Iowa, United States, and is the first analysis of the microbiota of North American tardigrades. It is also the first ever study of the tardigrade microbiome in an agricultural setting. We utilized 16S rRNA gene amplicon sequencing to characterize the tardigrade community microbiome across four contrasts: location, substrate type (moss or lichen), collection year, and tardigrades vs. their substrate. Alpha diversity of the tardigrade community microbiome differed significantly by location and year of collection but not by substrate type. Our work also corroborated earlier findings, demonstrating that tardigrades harbor a distinct microbiota from their environment. We also identified tardigrade-associated taxa that belong to genera known to contain phytopathogens (Pseudomonas, Ralstonia, and the Pantoea/Erwinia complex). Finally, we observed members of the genera Rickettsia and Wolbachia in the tardigrade microbiome; because these are obligate intracellular genera, we consider these taxa to be putative endosymbionts of tardigrades. These results suggest the presence of putative endosymbionts and phytopathogens in the microbiota of wild tardigrades in North America.

RevDate: 2022-08-04

Thirunavukarasu AJ, Ross AC, RM Gilbert (2022)

Vitamin A, systemic T-cells, and the eye: Focus on degenerative retinal disease.

Frontiers in nutrition, 9:914457.

The first discovered vitamin, vitamin A, exists in a range of forms, primarily retinoids and provitamin carotenoids. The bioactive forms of vitamin A, retinol and retinoic acid, have many critical functions in body systems including the eye and immune system. Vitamin A deficiency is associated with dysfunctional immunity, and presents clinically as a characteristic ocular syndrome, xerophthalmia. The immune functions of vitamin A extend to the gut, where microbiome interactions and nutritional retinoids and carotenoids contribute to the balance of T cell differentiation, thereby determining immune status and contributing to inflammatory disease around the whole body. In the eye, degenerative conditions affecting the retina and uvea are influenced by vitamin A. Stargardt's disease (STGD1; MIM 248200) is characterised by bisretinoid deposits such as lipofuscin, produced by retinal photoreceptors as they use and recycle a vitamin A-derived chromophore. Age-related macular degeneration features comparable retinal deposits, such as drusen featuring lipofuscin accumulation; and is characterised by parainflammatory processes. We hypothesise that local parainflammatory processes secondary to lipofuscin deposition in the retina are mediated by T cells interacting with dietary vitamin A derivatives and the gut microbiome, and outline the current evidence for this. No cures exist for Stargardt's or age-related macular degeneration, but many vitamin A-based therapeutic approaches have been or are being trialled. The relationship between vitamin A's functions in systemic immunology and the eye could be further exploited, and further research may seek to leverage the interactions of the gut-eye immunological axis.

RevDate: 2022-08-04

Dissanayake E, N Shimojo (2016)

Probiotics and Prebiotics in the Prevention and Treatment of Atopic Dermatitis.

Pediatric allergy, immunology, and pulmonology, 29(4):174-180.

Atopic dermatitis (AD) is a highly prevalent condition. Recent evidence suggests a link between the altered gut microbiome and the development of AD. Probiotics and/or prebiotics have been used in the treatment and prevention of AD with the intention of correcting the aberrant gut microbiome. As of now, data from meta-analyses show some promise in the use of probiotics for the prevention of AD with the effect being seen only when administered both prenatally and postnatally. Prebiotics and synbiotics have less compelling evidence to support their effectiveness in AD prevention or treatment, mainly due to the discrepancies of results. Explanations for the variations in the results may come from environmental factors, probiotic/prebiotic factors, and host factors that affect efficacy of the probiotic/prebiotic. More studies are needed to understand the mechanisms of action of probiotics/prebiotics and also to identify their true benefits in the prevention and treatment of AD.

RevDate: 2022-08-04

Murota H, I Katayama (2016)

Lifestyle Guidance for Pediatric Patients with Atopic Dermatitis Based on Age-Specific Physiological Function of Skin.

Pediatric allergy, immunology, and pulmonology, 29(4):196-201.

Clinical features of atopic dermatitis change with age as skin homeostatic mechanisms develop. In some cases, symptoms persist from childhood to adult. In early childhood, the characteristic features of this disease are eczema or exudative papules accompanied by itching. After childhood, lichenified dermatitis preceded by severe itching is the major skin manifestation. Presumably, this difference in clinical symptoms between childhood and adulthood may derive from the age-specific physiological function of skin, such as maintenance of proper stratum corneum, secretion of lipids, and perspiration. The volume and composition of secreted lipids and sweat change with age; these changes affect water retention, skin surface pH, and the microbiome. These physiological activities do not follow a hierarchy, but instead are coordinated to harmonize the maintenance of skin homeostasis. Thus, daily skin care based on the characteristic age-specific physiological function of skin should be considered to manage atopic dermatitis. The usage of moisturizers contributes to reduce skin dryness and the incidence of atopic dermatitis, and is recommended immediately after bathing. A water temperature of 38 to 40 degrees during bathing can be beneficial for barrier recovery, and gentle detergents or soap should be chosen if necessary. After exercise, excess sweat on the skin surface should be rinsed off. Avoidance of perspiration-inducing activities is not necessary. High temperature and humidity on skin surface may cause the development of miliaria and subsequent anhidrosis. Wearing hygroscopic and breathable underwear is recommended.

RevDate: 2022-08-04

Hopp RJ, Allison J, D Brooks (2016)

Fifty Years of Chronic Rhinosinusitis in Children: The Accepted, the Unknown, and Thoughts for the Future.

Pediatric allergy, immunology, and pulmonology, 29(2):61-67.

Chronic sinusitis is an often-used term in both lay and medical circumstances. In children, it has significant but largely undefined healthcare costs. Chronic rhinosinusitis (CRS) in children has well demarcated time periods and symptoms, although the actual pathway from normal sinus to CRS is not well understood. There is reasonable consensus as to the standards for diagnosis, the selection of a first-round antibiotic, and length of treatment. However, no recent prospective studies of antibiotics are available. Areas of continued speculation include the following: the microbiome of pediatric CRS, the best use of standard imaging, alternative antibiotic selection, ancillary therapy, and treatment of refractory CRS. In addition, older adolescents can present with a more adult-oriented CRS with or without polyps, suggesting a broader spectrum of disease than is commonly recognized. An accounting of the accepted elements of pediatric rhinosinusitis, as well as areas for future research, is emphasized in this review and, where appropriate, suggestions for potential investigations are offered.

RevDate: 2022-08-03

Gaire TN, Odland C, Zhang B, et al (2022)

The impacts of viral infection and subsequent antimicrobials on the microbiome-resistome of growing pigs.

Microbiome, 10(1):118.

BACKGROUND: Antimicrobials are used in food-producing animals for purposes of preventing, controlling, and/or treating infections. In swine, a major driver of antimicrobial use is porcine reproductive and respiratory syndrome (PRRS), which is caused by a virus that predisposes infected animals to secondary bacterial infections. Numerous antimicrobial protocols are used to treat PRRS, but we have little insight into how these treatment schemes impact antimicrobial resistance (AMR) dynamics within the fecal microbiome of commercial swine. The aim of this study was to determine whether different PRRS-relevant antimicrobial treatment protocols were associated with differences in the fecal microbiome and resistome of growing pigs. To accomplish this, we used a metagenomics approach to characterize and compare the longitudinal wean-to-market resistome and microbiome of pigs challenged with PRRS virus and then exposed to different antimicrobial treatments, and a group of control pigs not challenged with PRRS virus and having minimal antimicrobial exposure. Genomic DNA was extracted from pen-level composite fecal samples from each treatment group and subjected to metagenomic sequencing and microbiome-resistome bioinformatic and statistical analysis. Microbiome-resistome profiles were compared over time and between treatment groups.

RESULTS: Fecal microbiome and resistome compositions both changed significantly over time, with a dramatic and stereotypic shift between weaning and 9 days post-weaning (dpw). Antimicrobial resistance gene (ARG) richness and diversity were significantly higher at earlier time points, while microbiome richness and diversity were significantly lower. The post-weaning shift was characterized by transition from a Bacteroides-dominated enterotype to Lactobacillus- and Streptococcus-dominated enterotypes. Both the microbiome and resistome stabilized by 44 dpw, at which point the trajectory of microbiome-resistome maturation began to diverge slightly between the treatment groups, potentially due to physical clustering of the pigs. Challenge with PRRS virus seemed to correspond to the re-appearance of many very rare and low-abundance ARGs within the feces of challenged pigs. Despite very different antimicrobial exposures after challenge with PRRS virus, resistome composition remained largely similar between the treatment groups. Differences in ARG abundance between the groups were mostly driven by temporal changes in abundance that occurred prior to antimicrobial exposures, with the exception of ermG, which increased in the feces of treated pigs, and was significantly more abundant in the feces of these pigs compared to the pigs that did not receive post-PRRS antimicrobials.

CONCLUSIONS: The fecal microbiome-resistome of growing pigs exhibited a stereotypic trajectory driven largely by weaning and physiologic aging of the pigs. Events such as viral illness, antimicrobial exposures, and physical grouping of the pigs exerted significant yet relatively minor influence over this trajectory. Therefore, the AMR profile of market-age pigs is the culmination of the life history of the individual pigs and the populations to which they belong. Disease status alone may be a significant driver of AMR in market-age pigs, and understanding the interaction between disease processes and antimicrobial exposures on the swine microbiome-resistome is crucial to developing effective, robust, and reproducible interventions to control AMR. Video Abstract.

RevDate: 2022-08-03

Anton L, Ferguson B, Friedman ES, et al (2022)

Gardnerella vaginalis alters cervicovaginal epithelial cell function through microbe-specific immune responses.

Microbiome, 10(1):119.

BACKGROUND: The cervicovaginal (CV) microbiome is highly associated with vaginal health and disease in both pregnant and nonpregnant individuals. An overabundance of Gardnerella vaginalis (G. vaginalis) in the CV space is commonly associated with adverse reproductive outcomes including bacterial vaginosis (BV), sexually transmitted diseases, and preterm birth, while the presence of Lactobacillus spp. is often associated with reproductive health. While host-microbial interactions are hypothesized to contribute to CV health and disease, the mechanisms by which these interactions regulate CV epithelial function remain largely unknown.

RESULTS: Using an in vitro co-culture model, we assessed the effects of Lactobacillus crispatus (L. crispatus) and G. vaginalis on the CV epithelial barrier, the immune mediators that could be contributing to decreased barrier integrity and the immune signaling pathways regulating the immune response. G. vaginalis, but not L. crispatus, significantly increased epithelial cell death and decreased epithelial barrier integrity in an epithelial cell-specific manner. A G. vaginalis-mediated epithelial immune response including NF-κB activation and proinflammatory cytokine release was initiated partially through TLR2-dependent signaling pathways. Additionally, investigation of the cytokine immune profile in human CV fluid showed distinctive clustering of cytokines by Gardnerella spp. abundance and birth outcome.

CONCLUSIONS: The results of this study show microbe-specific effects on CV epithelial function. Altered epithelial barrier function through cell death and immune-mediated mechanisms by G. vaginalis, but not L. crispatus, indicates that host epithelial cells respond to bacteria-associated signals, resulting in altered epithelial function and ultimately CV disease. Additionally, distinct immune signatures associated with Gardnerella spp. or birth outcome provide further evidence that host-microbial interactions may contribute significantly to the biological mechanisms regulating reproductive outcomes. Video Abstract.

RevDate: 2022-08-03

Fortmann MI, Dirks J, Goedicke-Fritz S, et al (2022)

Immunization of preterm infants: current evidence and future strategies to individualized approaches.

Seminars in immunopathology [Epub ahead of print].

Preterm infants are at particularly high risk for infectious diseases. As this vulnerability extends beyond the neonatal period into childhood and adolescence, preterm infants benefit greatly from infection-preventive measures such as immunizations. However, there is an ongoing discussion about vaccine safety and efficacy due to preterm infants' distinct immunological features. A significant proportion of infants remains un- or under-immunized when discharged from primary hospital stay. Educating health care professionals and parents, promoting maternal immunization and evaluating the potential of new vaccination tools are important means to reduce the overall burden from infectious diseases in preterm infants. In this narrative review, we summarize the current knowledge about vaccinations in premature infants. We discuss the specificities of early life immunity and memory function, including the role of polyreactive B cells, restricted B cell receptor diversity and heterologous immunity mediated by a cross-reactive T cell repertoire. Recently, mechanistic studies indicated that tissue-resident memory (Trm) cell populations including T cells, B cells and macrophages are already established in the fetus. Their role in human early life immunity, however, is not yet understood. Tissue-resident memory T cells, for example, are diminished in airway tissues in neonates as compared to older children or adults. Hence, the ability to make specific recall responses after secondary infectious stimulus is hampered, a phenomenon that is transcriptionally regulated by enhanced expression of T-bet. Furthermore, the microbiome establishment is a dominant factor to shape resident immunity at mucosal surfaces, but it is often disturbed in the context of preterm birth. The proposed function of Trm T cells to remember benign interactions with the microbiome might therefore be reduced which would contribute to an increased risk for sustained inflammation. An improved understanding of Trm interactions may determine novel targets of vaccination, e.g., modulation of T-bet responses and facilitate more individualized approaches to protect preterm babies in the future.

RevDate: 2022-08-03

Wang Y, Xu J, Chen H, et al (2022)

A balanced gut microbiota is essential to maintain health in captive sika deer.

Applied microbiology and biotechnology [Epub ahead of print].

Certain animals harbor a high proportion of pathogens, particular the zoonotic pathogens, in their gut microbiome but are usually asymptomic; however, their carried pathogens may seriously threaten the public health. By understanding how the microbiome overcomes the negative effects of pathogens to maintain host health, we can develop novel solutions to control animal-mediated pathogen transmission including identification and application of beneficial microbes. Here, we analyzed the gut microbiota of 10 asymptomic captive sika deer individuals by full-length 16S rDNA sequencing. Twenty-nine known pathogens capable of infecting humans were identified, and the accumulated proportions of the identified pathogens were highly variable among individuals (2.33 to 39.94%). The relative abundances of several beneficial bacteria, including Lactobacillus and Bifidobacterium, were found to be positively correlated with the relative abundances of accumulated pathogens. Whole-genome metagenomic analysis revealed that the beneficial- and pathogenic-associated functions, such as genes involved in the synthesis of short chain fatty acids and virulence factors, were also positively correlated in the microbiome, indicating that the beneficial and pathogenic functions were maintained at a relatively balanced ratio. Furthermore, the bacteriophages that target the identified pathogens were found to be positively correlated with the pathogenic content in the microbiome. Several high-quality genomes of beneficial bacteria affiliated with Lactobacillus and Bifidobacterium and bacteriophages were recovered from the metagenomic data. Overall, this study provides novel insights into the interplay between beneficial and pathogenic content to ensure maintenance of a healthy gut microbiome, and also contributes to discovery of novel beneficial microbes and functions that control pathogens. KEY POINTS: • Certain asymptomic captive sika deer individuals harbor relatively high amounts of zoonotic pathogens. • The beneficial microbes and the beneficial functions are balanced with the pathogenic contents in the gut microbiome. • Several high-quality genomes of beneficial bacteria and bacteriophages are recovered by metagenomics.

RevDate: 2022-08-03

Prados-Bo A, Rabassa M, Bosch M, et al (2022)

Online information in Spanish on probiotics, yoghurt, kefir, kombucha, fibre and prebiotics: an analysis of the quality of information and the certainty of the evidence supporting health claims.

BMJ open, 12(8):e063316 pii:bmjopen-2022-063316.

OBJECTIVE: To examine the certainty of the evidence supporting health claims about probiotics, yoghurt, kefir, kombucha, fibre and prebiotics, and to assess the quality of online information in Spanish.

DESIGN: Content analysis.

METHODS: We compiled a data set of 114 web pages by searching six popular search phrases in Spanish relating to probiotics, yoghurt, kefir, kombucha, fibre and prebiotics on and coded them for typology and health claims. We examined the certainty of the evidence for health claims from systematic reviews. Information quality was assessed according to 10 criteria, where a web page: mentions scientific publications and reports their conclusions; quantifies relative and absolute effects; acknowledges some limitations; discusses certainty of evidence; reports the potential harms, alternatives and costs; and does not argue based on personal experiences.

RESULTS: Gastrointestinal health (86.0%), general health (57.9%), cardiovascular health (53.5%) and immune system health (50.9%) were the most widely mentioned topics. Half of claims (52.6%, 70/133) were supported by evidence from systematic reviews. Probiotics had the highest number of claims supported by evidence and kombucha the lowest. The highest certainty was found for antibiotic-associated diarrhoea, necrotising enterocolitis and otitis (moderate) in probiotics and yoghurt, infectious diarrhoea and hepatic encephalopathy (moderate) in prebiotics, and cardiovascular health (high to moderate) and colorectal cancer (moderate) in fibre. On a scale of 0-10, the median information quality score for all web pages was 3. Only 18.4% reported study conclusions, 7.9% quantified the effects, 28.9% acknowledged some limitations in the research and 42.1% reported potential harms.

CONCLUSIONS: Most online health claims for dietary interventions intended for improving health through the gut microbiome are supported by low or very low certainty of evidence. Online information does not align with the evidence and is incomplete or unbalanced.

RevDate: 2022-08-03

Yang J, He P, Zhou M, et al (2022)

Variations in oral microbiome and its predictive functions between tumorous and healthy individuals.

Journal of medical microbiology, 71(8):.

Introduction. The oral cavity is one of the largest reservoirs of microorganisms and many pathogenic bacteria have been shown to be associated with the aetiology of oral cancers.Gap Statement. Owing to the complexity of oral microbial communities and their unclear relationship with oral cancer, identification of specific bacteria which contribute to oral cancer is a key imperative.Aim. To compare and investigate the variations in the composition of the bacterial microbiome and its functions between patients with oral tumorous lesions and healthy subjects.Methodology. Twenty-seven samples from individuals with oral tumours (five oral benign tumours and 22 oral squamous cell carcinomas) and 15 samples from healthy subjects were collected. Genomic DNA was extracted and the V3-V5 region of the 16S rRNA gene was sequenced. Subsequently, bioinformatic assessment was conducted using QIIME2, PICRUSt and linear discriminant analysis effect size analyses (LEfSe).Results. The oral microbiota was composed mainly of the phyla Proteobacteria (31.76 %, 35.00 %), Bacteroidetes (30.13 %, 25.13 %) and Firmicutes (23.92 %, 17.07 %) in tumorous and healthy individuals, respectively. Neisseria, Prevotella, Fusobacterium, Streptococcus, Capnocytophaga, Veillonella, Haemophilus, Prevotella, Porphyromonas and Leptotrichia were the most abundant genera. Alpha diversity in the tumour group was significantly greater than that in the healthy group (P<0.05). Differential analysis of microbes between groups demonstrated a significantly higher number of Neisseria, Veillonella, Streptococcus, Leptotrichia, Lautropia, Sphingopyxis, Sphingobium, Tannerella, Actinomyces and Rothia in healthy controls compared with the tumour group. However, the genera Treponema, Micrococcus, Pseudomonas, Janthinobacterium, Parvimos, Loktanella, Staphylococcus, Acinetobacter, Catonella, Aggregatibacter and Propionibacterium were significantly higher in the tumour group. Pathways related to cancers, cell motility, environmental adaptation, metabolism and signal transduction were enhanced in the tumour group, while functions associated with immune system diseases, replication, repair and translation were significantly enhanced in the healthy group.Conclusion. Variations in the oral microbiota and its functions showed a correlation with oral tumours. The tumour group showed an increased abundance of some multi-drug-resistant and periodontitis-related pathogens. The significantly altered microbiotas may serve as potential biomarkers or inform combination therapy for oral tumours.

RevDate: 2022-08-03

Juárez-Fernández M, Goikoetxea-Usandizaga N, Porras D, et al (2022)

Enhanced mitochondrial activity reshapes a gut microbiota profile that delays NASH progression.

Hepatology (Baltimore, Md.) [Epub ahead of print].

OBJECTIVE: Recent studies suggest that mitochondrial dysfunction promotes progression to non-alcoholic steatohepatitis (NASH) by aggravating the gut-liver status. However, the underlying mechanism remains unclear. Herein, we hypothesized that enhanced mitochondrial activity might reshape a specific microbiota signature that, when transferred to germ-free (GF) mice, could delay NASH progression. Design WT and methylation-controlled J protein knock-out (MCJ-KO) mice were fed for 6 weeks with either control or a choline-deficient, L-amino acid-defined, high-fat diet (CDA-HFD). One mouse of each group acted as a donor of caecal microbiota to GF mice, who also underwent the CDA-HFD model for 3 weeks. Hepatic injury, intestinal barrier, gut microbiome and the associated faecal metabolome were then studied.

RESULTS: Following 6 weeks of CDA-HFD, the absence of MCJ, an inhibitor of mitochondrial complex I activity, reduced hepatic injury and improved gut-liver axis in an aggressive NASH dietary model. This effect was transferred to GF mice through caecal microbiota transplantation. We suggest that the specific microbiota profile of MCJ-KO, characterised by an increase in the faecal relative abundance of Dorea and Oscillospira genera and a reduction in AF12, Allboaculum and [Ruminococcus], exerted protective actions through enhancing short-chain fatty acids, NAD+ metabolism and sirtuin activity, subsequently increasing fatty acid oxidation in GF mice. Importantly, we identified Dorea genus as one of the main modulators of this microbiota-dependent protective phenotype.

CONCLUSION: Overall, we provide evidence for the relevance of mitochondria-microbiota interplay during NASH, and that targeting it could be a valuable therapeutic approach.

RevDate: 2022-08-03

Pal SC, Eslam M, N Mendez-Sanchez (2022)

Detangling the interrelations between MAFLD, insulin resistance, and key hormones.

Hormones (Athens, Greece) [Epub ahead of print].

Metabolic dysfunction-associated fatty liver disease (MAFLD) has increasingly become a significant and highly prevalent cause of chronic liver disease, displaying a wide array of risk factors and pathophysiologic mechanisms of which only a few have so far been clearly elucidated. A bidirectional interaction between hormonal discrepancies and metabolic-related disorders, including obesity, type 2 diabetes mellitus (T2DM), and polycystic ovarian syndrome (PCOS) has been described. Since the change in nomenclature from non-alcoholic fatty liver disease (NAFLD) to MAFLD is based on the clear impact of metabolic elements on the disease, the reciprocal interactions of hormones such as insulin, adipokines (leptin and adiponectin), and estrogens have strongly pointed to the intrinsic links that lead to the heterogeneous epidemiology, clinical presentations, and risk factors involved in MAFLD in different populations. The objective of this work is twofold. Firstly, there is a brief discussion regarding the change in nomenclature as well as epidemiology, risk factors, and pathophysiologic mechanisms other than hormonal effects, which include nutrition and the gut microbiome, as well as genetic and epigenetic influences. Secondly, we review the basis of the most important hormonal factors involved in the development and progression of MAFLD that act both independently and in an interrelated manner.

RevDate: 2022-08-03

Anonymous (2022)

Lasting Effects of Helicobacter pylori Infection on the Microbial Communities of Patients with and without Small Intestinal Bacterial Overgrowth.

The new microbiologica, 45(3):193-198.

Gastrointestinal (GI) microbial populations are important in maintaining normal functioning of the GI by preventing disorders. Dysbiotic microbiota may increase the likelihood of small intestinal bacterial overgrowth (SIBO), a syndrome associated with significant morbidity. We aimed to inves- tigate the microbiota populations of patients with SIBO. Patients with symptoms of SIBO were consecutively enrolled; they underwent a SIBO hydrogen breath test and stool was collected for microbiome analysis by sequencing of the 16S rRNA. Of the 55 patients recruited, 42 (76.4%) were positive for SIBO. When visualizing the bacterial β-di- versity, a sub-cluster of patients was identified. Further examination of these patients' records re- vealed previous treatment for Helicobacter pylori (HP). Microbiome analysis of these patients demonstrated a significant decrease in β-diversity (p-value<0.001) compared to patients without previous HP therapy. Furthermore, β-diversity was significantly different in this subgroup, and sev- eral bacterial taxa were differentially expressed, including one from the genus Methanobrevibacter, which was reduced in patients that previously underwent HP treatment. Our findings suggest that while symptoms associated with SIBO may cause dysbiosis, there was no differentiation in fecal microbiome composition based on SIBO diagnosis. Furthermore, our results support previous observations regarding antibiotic-altered microbiota with effects extending two and three years post-treatment.

RevDate: 2022-08-03

Vinnik YS, Teplyakova OV, AD Erguleeva (2022)

[Etiology and pathogenesis of infected pancreatic necrosis].


Modern literature data confirm the central role of intestinal barrier complex not only as a target in acute necrotizing pancreatitis, but also as a trigger for septic complications. Intra-abdominal hypertension, endothelial dysfunction and gut microbiome changes following necrotizing pancreatitis might have an independent impact on acute intestinal distress syndrome and bacterial translocation. Monitoring of these conditions and early target therapy can improve the outcomes in patients with severe acute pancreatitis. Adverse outcomes of infected pancreatic necrosis including high mortality and morbidity are largely due to the prevalence of multidrug-resistant bacterial pathogens.

RevDate: 2022-08-03

Li S, Qian Z, Yang J, et al (2022)

Seasonal variation in structure and function of gut microbiota in Pomacea canaliculata.

Ecology and evolution, 12(8):e9162 pii:ECE39162.

Gut microbiota is associated with host health and its environmental adaption, influenced by seasonal variation. Pomacea canaliculata is one of the world's 100 worst invasive alien species. Here, we used high-throughput sequencing of the 16S rRNA gene to analyze the seasonal variation of gut microbiota of P. canaliculata. The results suggested that the predominant gut microbial phyla of P. canaliculata included Firmicutes and Proteobacteria, which helped digest plant food and accumulate energy. The gut microbiota of P. canaliculata in summer group showed the highest diversity, whereas the winter group possessed the lowest, probably due to the shortage of food resources of P. canaliculata in winter. Principal coordinate analysis analysis based on unweighted unifrac and weighted unifrac indicated that the composition of gut microbiota of P. canaliculata significantly varied across seasons. Bacteroidetes tended to be enriched in summer by linear discriminant analysis effect size analysis. Actinobacteria and Cyanobacteria were extremely abundant in autumn, while Fusobacteria and Cetobacterium enriched in winter. In conclusion, the structure of the gut microbiota of P. canaliculata was significantly different among seasons, which was beneficial to the environment adaptation and the digestion and metabolism of food during different periods.

RevDate: 2022-08-03

Mestre A, Sathiya Narayanan R, Rivas D, et al (2022)

Role of Probiotics in the Management of Helicobacter pylori.

Cureus, 14(6):e26463.

The global prevalence of Helicobacter pylori (H. pylori) is estimated to be around 4.4 billion, with the majority of individuals affected in developing countries. Chronic infection of the gram-negative bacterium results in several gastrointestinal pathologies such as chronic gastritis, peptic ulcer, and cancer. Probiotics compete directly with H. pylori and help restore the gut microbial environment; these living microorganisms are comparatively more effective than the standard triple antibiotic regimen in the management of symptoms related to the pathogenic bacteria. The need for alternative therapy is better explained by the increasing rate of antibiotic resistance and the lowering of patient compliance to the standard treatment. Adjuvant administration of probiotics to H. pylori eradication therapy is associated with a higher H. pylori eradication rate, decreased diarrhea-related treatment, less common self-reported side effects, and higher treatment compliance. Therefore, with the ongoing and future resistance to antibiotics, this systematic review aims to investigate the use and efficacy of probiotics when used alone or in conjunction with the current guideline treatment. A literature search was conducted using Pubmed, MEDLINE, and Cochrane for peer-reviewed articles published between January 1, 2016 and April 2022. MeSH terms used were: "H. pylori," "H. pylori and probiotics," "Probiotics," "H. pylori treatment," "Mechanism of Action" with subheadings as "clinical manifestations," "treatment," and "diagnosis." All literature reviews, original papers, and case reports were included. This search strategy aimed to find literature that could describe the transmission and mechanism of action of H. pylori, the current treatment guidelines, and the efficacy of probiotics in eradicating H. pylori.

RevDate: 2022-08-02

De Bernardini N, Basile A, Zampieri G, et al (2022)

Integrating metagenomic binning with flux balance analysis to unravel syntrophies in anaerobic CO2 methanation.

Microbiome, 10(1):117.

BACKGROUND: Carbon fixation through biological methanation has emerged as a promising technology to produce renewable energy in the context of the circular economy. The anaerobic digestion microbiome is the fundamental biological system operating biogas upgrading and is paramount in power-to-gas conversion. Carbon dioxide (CO2) methanation is frequently performed by microbiota attached to solid supports generating biofilms. Despite the apparent simplicity of the microbial community involved in biogas upgrading, the dynamics behind most of the interspecies interaction remain obscure. To understand the role of the microbial species in CO2 fixation, the biofilm generated during the biogas upgrading process has been selected as a case study. The present work investigates via genome-centric metagenomics, based on a hybrid Nanopore-Illumina approach the biofilm developed on the diffusion devices of four ex situ biogas upgrading reactors. Moreover, genome-guided metabolic reconstruction and flux balance analysis were used to propose a biological role for the dominant microbes.

RESULTS: The combined microbiome was composed of 59 species, with five being dominant (> 70% of total abundance); the metagenome-assembled genomes representing these species were refined to reach a high level of completeness. Genome-guided metabolic analysis appointed Firmicutes sp. GSMM966 as the main responsible for biofilm formation. Additionally, species interactions were investigated considering their co-occurrence in 134 samples, and in terms of metabolic exchanges through flux balance simulation in a simplified medium. Some of the most abundant species (e.g., Limnochordia sp. GSMM975) were widespread (~ 67% of tested experiments), while others (e.g., Methanothermobacter wolfeii GSMM957) had a scattered distribution. Genome-scale metabolic models of the microbial community were built with boundary conditions taken from the biochemical data and showed the presence of a flexible interaction network mainly based on hydrogen and carbon dioxide uptake and formate exchange.

CONCLUSIONS: Our work investigated the interplay between five dominant species within the biofilm and showed their importance in a large spectrum of anaerobic biogas reactor samples. Flux balance analysis provided a deeper insight into the potential syntrophic interaction between species, especially Limnochordia sp. GSMM975 and Methanothermobacter wolfeii GSMM957. Finally, it suggested species interactions to be based on formate and amino acids exchanges. Video Abstract.

RevDate: 2022-08-02

Zhou Y, Zhang F, Mao L, et al (2022)

Bifico relieves irritable bowel syndrome by regulating gut microbiota dysbiosis and inflammatory cytokines.

European journal of nutrition [Epub ahead of print].

PURPOSE: Gut microbiota dysbiosis, a core pathophysiology of irritable bowel syndrome (IBS), is closely related to immunological and metabolic functions. Gut microbiota-based therapeutics have been recently explored in several studies. Bifico is a probiotic cocktail widely used in gastrointestinal disorders which relate to the imbalance of gut microbiota. However, the efficacy and potential mechanisms of Bifico treatment in IBS remains incompletely understood.

METHODS: Adopting a wrap restraint stress (WRS) -induced IBS mice model. Protective effect of Bifico in IBS mice was examined through abdominal withdrawal reflex (AWR) scores. 16S rDNA, 1H nuclear magnetic resonance (1H-NMR) and western blot assays were performed to analyze alterations of gut microbiota, microbiome metabolites and inflammatory cytokines, respectively.

RESULTS: Bifico could decrease intestinal visceral hypersensitivity. Although gut microbiota diversity did not increase, composition of gut microbiota was changed after treatment of Bifico, which were characterized by an increase of Proteobacteria phylum and Actinobacteria phylum, Muribaculum genus, Bifidobacterium genus and a decrease of Parabacteroides genus, Sutterella genus and Lactobacillus genus. Moreover, Bifico elevated the concentration of short-chain fatty acids (SCFAs) and reduced protein levels of interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α). From further Spearman's correlation analysis, Bifidobacterium genus were positively correlated with SCFAs including propionate, butyrate, valerate and negatively correlated with IL-6 and TNF-α.

CONCLUSION: Bifico could alleviate symptoms of IBS mice through regulation of the gut microbiota, elevating production of SCFAs and reducing the colonic inflammatory response.

RevDate: 2022-08-02

Rashidi A, Ebadi M, Rehman TU, et al (2022)

Compilation of longitudinal gut microbiome, serum metabolome, and clinical data in acute myeloid leukemia.

Scientific data, 9(1):468.

Induction chemotherapy for patients with acute myeloid leukemia (AML) is a unique clinical scenario. These patients spend several weeks in the hospital, receiving multiple antibiotics, experiencing gastrointestinal mucosal damage, and suffering severe impairments in their immune system and nutrition. These factors cause major disruptions to the gut microbiota to a level rarely seen in other clinical conditions. Thus, the study of the gut microbiota in these patients can reveal novel aspects of microbiota-host relationships. When combined with the circulating metabolome, such studies could shed light on gut microbiota contribution to circulating metabolites. Collectively, gut microbiota and circulating metabolome are known to regulate host physiology. We have previously deposited amplicon sequences from 566 fecal samples from 68 AML patients. Here, we provide sample-level details and a link, using de-identified patient IDs, to additional data including serum metabolomics (260 samples from 36 patients) and clinical metadata. The detailed information provided enables comprehensive multi-omics analysis. We validate the technical quality of these data through 3 examples and demonstrate a method for integrated analysis.

RevDate: 2022-08-02

Zeuschner P, K Junker (2022)

Optimal Selection of Patients with Genitourinary Cancers for Anti-PD1/PD-L1 Treatment with a Focus on Urothelial and Renal Cell Carcinoma.

European urology focus pii:S2405-4569(22)00163-8 [Epub ahead of print].

Despite the recent approval of numerous immune checkpoint inhibitors (ICIs) for the treatment of genitourinary tumors, predictive biomarkers are still lacking. Different approaches are necessary, as the only approved biomarker for urothelial carcinoma (UC), namely PD-L1 immunostaining, has questionable predictive value. By contrast, tumor-infiltrating cells have been associated with therapy response in both UC and renal cell carcinoma. Tumor-derived gene signatures can further identify patients with pre-existing adaptive immunity. Whereas tumor mutation burden, DNA repair defects, and microsatellite instability are of some predictive value, the utility of single gene mutations has not yet been proved. As ICIs mainly target tumor metastases, analysis of primary tumors appears to be suboptimal. Circulating biomarkers reflecting tumor and systemic alterations in a more complex and dynamic manner are of great potential. The most promising approach is an analysis of complex tumor composition with concomitant consideration of the host immune status, which is also influenced by the gut microbiome. PATIENT SUMMARY: Immunotherapy is one of the treatment options for cancers of the urinary tract and kidney. We review the methods for measuring biomarkers that may predict which patients are most likely to respond to this treatment.

RevDate: 2022-08-02

Said SA, Hossain MS, DeMare A, et al (2022)

Long term assessment of antibiotic prophylaxis and biliary microbiome in pancreaticoduodenectomy.

HPB : the official journal of the International Hepato Pancreato Biliary Association pii:S1365-182X(22)01520-9 [Epub ahead of print].

INTRODUCTION: Surgical site infections (SSI) can represent a major complication of pancreaticoduodenectomy (PD). We summarize the outcomes of process improvement efforts to reduce the SSI rates in PD that includes replacing Cefazolin with Ceftriaxone-Metronidazole as antibiotic prophylaxis. Additional efforts included current assessment of biliary microbiome and potential prophylactic failures based on bile cultures and suspected antibiotic allergies.

METHOD: A single-center review of PD patients from January-2012 to March-2021. Study groups were divided into Pre and Post May-2015 (Group 1 and 2, respectively) when Ceftriaxone-Metronidazole prophylaxis and routine intraoperative cultures were standardized. Univariate and multivariable analyses were conducted to assess groups' differences and association with SSI.

RESULTS: Six hundred ninety patients identified [267(38.7%) and 423(61.3%) in Group 1 and Group2, respectively]. After antibiotic change, SSI rates decreased from 28.1% to 16.5% (incisional: 17.6%-7.5%, organ-space or abscess: 17.2%-13.0%), Group 1 and Group 2, respectively, P<0.001. Ceftriaxone-Metronidazole was used in 75.9% of patients Group 2. When adjusting for other covariates, an SSI-decrease was associated only with Ceftriaxone-Metronidazole (OR 0.34, P<0.001).

CONCLUSIONS: Ongoing process improvement has resulted in decreased SSIs with Ceftriaxone-Metronidazole prophylaxis. The benefit of Ceftriaxone-Metronidazole is independent of the biliary microbiome. Improving prophylaxis for those with suspected penicillin allergy is warranted.

RevDate: 2022-08-02

Liu J, Zhang X, Ta X, et al (2022)

Fecal microbiome transplantation attenuates manganese-induced neurotoxicity through regulation of the apelin signaling pathway by inhibition of autophagy in mouse brain.

Ecotoxicology and environmental safety, 242:113925 pii:S0147-6513(22)00765-5 [Epub ahead of print].

Manganese (Mn) is a common environmental pollutant. Mn exposure can lead to neurodegenerative diseases resembling Parkinson's disease, and has become a major public health concern. However, the mechanism of Mn-induced neurotoxicity in the brain is not clear. Fecal microbiome transplantation (FMT) may alleviate the neurotoxicity of Mn exposure by remodeling the gut microbiota. In this study, MnCl2 (manganese chloride) was administered to mice as in drinking water (Mn: 200 mg/L), and fecal matter from donor mice was administered by oral gavage every other day to the recipient mice. The Mn exposure model (Mn group) and FMT model (Mn+FMT group) were established and analyzed 5 weeks post-exposure. The Wipi1 gene exhibited the most significant increase associated with Mn exposure and Mn+FMT treatment groups based on transcriptome analysis. Combined analysis of transcriptomics and proteomics demonstrated that the apelin signaling pathway is the main pathway affected by FMT during Mn exposure. Immunofluorescence and Western blot showed that the expression of key proteins (Beclin-1, LC-3B, and PINK1) associated with autophagy in the hippocampus was robustly activated in the Mn exposure group, but attenuation was observed in Mn+FMT mice, suggesting a critical role of autophagy in neurotoxicity induced by Mn exposure. Our research provides evidence for the neurotoxic effects of Mn exposure through autophagy activation and provides an underlying mechanism of FMT protection against Mn-induced neurotoxicity through regulation of the apelin signaling pathway.

RevDate: 2022-08-02

Burgess EC, RN Schaeffer (2022)

The Floral Microbiome and Its Management in Agroecosystems: A Perspective.

Journal of agricultural and food chemistry [Epub ahead of print].

Disease management is critical to ensuring healthy crop yields and is often targeted at flowers because of their susceptibility to pathogens and direct link to reproduction. Many disease management strategies are unsustainable however because of the potential for pathogens to evolve resistance, or nontarget effects on beneficial insects. Manipulating the floral microbiome holds some promise as a sustainable alternative to chemical means of disease control. In this perspective, we discuss the current state of research concerning floral microbiome assembly and management in agroecosystems as well as future directions aimed at improving the sustainability of disease control and insect-mediated ecosystem services.

RevDate: 2022-08-02

Wu J, Zhu J, Zhang D, et al (2022)

Beneficial effect on the soil microenvironment of Trichoderma applied after fumigation for cucumber production.

PloS one, 17(8):e0266347 pii:PONE-D-22-00468.

Biocontrol agents applied after fumigation play an important role to the soil microenvironment. We studied the effect of Trichoderma applied after dimethyl disulfide (DMDS) plus chloropicrin (PIC) fumigation on the cucumber growth, soil physicochemical properties, enzyme activity, taxonomic diversity, and yield through laboratory and field experiments. The results confirmed that Trichoderma applied after fumigation significantly improved soil physicochemical properties, cucumber growth, soil-borne pathogens, and soil enzyme activity. Genetic analysis indicated that Trichoderma applied after fumigation significantly increased the relative abundance of Pseudomonas, Humicola and Chaetomium, and significantly decreased the relative abundance of the pathogens Fusarium spp. and Gibberella spp., which may help to control pathogens and enhanced the ecological functions of the soil. Moreover, Trichoderma applied after fumigation obviously improved cucumber yield (up to 35.6%), and increased relative efficacy of soil-borne pathogens (up to 99%) and root-knot nematodes (up to 96%). Especially, we found that Trichoderma applied after fumigation increased the relative abundance of some beneficial microorganisms (such as Sodiomyces and Rhizophlyctis) that can optimize soil microbiome. It is worth noting that with the decline in the impact of the fumigant, these beneficial microorganisms still maintain a higher abundance when the cucumber plants were uprooted. Importantly, we found one tested biocontrol agent Trichoderma 267 identified and stored in our laboratory not only improved cucumber growth, reduced soil-borne diseases in late cucumber growth stages but also optimized micro-ecological environment which may have good application prospect and help to keep environmental healthy and sustainable development.

RevDate: 2022-08-02

Dietrich A, Matchado MS, Zwiebel M, et al (2022)

Namco: a microbiome explorer.

Microbial genomics, 8(8):.

16S rRNA gene profiling is currently the most widely used technique in microbiome research and allows the study of microbial diversity, taxonomic profiling, phylogenetics, functional and network analysis. While a plethora of tools have been developed for the analysis of 16S rRNA gene data, only a few platforms offer a user-friendly interface and none comprehensively covers the whole analysis pipeline from raw data processing down to complex analysis. We introduce Namco, an R shiny application that offers a streamlined interface and serves as a one-stop solution for microbiome analysis. We demonstrate Namco's capabilities by studying the association between a rich fibre diet and the gut microbiota composition. Namco helped to prove the hypothesis that butyrate-producing bacteria are prompted by fibre-enriched intervention. Namco provides a broad range of features from raw data processing and basic statistics down to machine learning and network analysis, thus covering complex data analysis tasks that are not comprehensively covered elsewhere. Namco is freely available at

RevDate: 2022-08-02

Banerji R, Iyer P, Bhagwat A, et al (2022)

Spermidine promotes lysozyme tolerance and acid stress resistance in Streptococcus pyogenes M3.

Microbiology (Reading, England), 168(8):.

Streptococcus pyogenes are Gram-positive opportunistic pathogens residing in the human nasopharynx and skin. Changes in environmental conditions, such as pH, temperature and availability of essential ions, can stimulate the expression of S. pyogenes virulence factors. One such factor could be the availability of an extracellular pool of polyamines. Polyamines are synthesized from amino acids, and are universally present in the environment. Polyamines have been implicated in the ecology of pathogenesis by modulating quorum sensing, host adaptation and virulence. Polyamines mediate pathogenesis and help the pathogen resist environmental stress. In this study, we investigated the ability of the polyamine, spermidine, to promote acid stress survival of S. pyogenes. S. pyogenes does not synthesize spermidine, but the extracellular pool of spermidine constituted by the host and microbiome could be utilized as a signalling molecule. We report that spermidine promotes acid stress resistance in S. pyogenes. Moreover, spermidine affects the morphology of S. pyogenes by decreasing the cell size and increasing the dltA gene expression. Along with dltA, spermidine upregulated the gene expression of cell wall-modifying genes such as mur, pgdA, pepO and srtA, which might help the bacteria to resist acidic stress.

RevDate: 2022-08-02

Pellegrinetti TA, Cotta SR, Sarmento H, et al (2022)

Bacterial Communities Along Environmental Gradients in Tropical Soda Lakes.

Microbial ecology [Epub ahead of print].

Soda lake environments are known to be variable and can have distinct differences according to geographical location. In this study, we investigated the effects of different environmental conditions of six adjacent soda lakes in the Pantanal biome (Mato Grosso do Sul state, Brazil) on bacterial communities and their functioning using a metagenomic approach combined with flow cytometry and chemical analyses. Ordination analysis using flow cytometry and water chemistry data from two sampling periods (wet and dry) clustered soda lakes into three different profiles: eutrophic turbid (ET), oligotrophic turbid (OT), and clear vegetated oligotrophic (CVO). Analysis of bacterial community composition and functioning corroborated this ordination; the exception was one ET lake, which was similar to one OT lake during the wet season, indicating drastic shifts between seasons. Microbial abundance and diversity increased during the dry period, along with a considerable number of limnological variables, all indicative of a strong effect of the precipitation-evaporation balance in these systems. Cyanobacteria were associated with high electric conductivity, pH, and nutrient availability, whereas Actinobacteria, Alphaproteobacteria, and Betaproteobacteria were correlated with landscape morphology variability (surface water, surface perimeter, and lake volume) and with lower salinity and pH levels. Stress response metabolism was enhanced in OT and ET lakes and underrepresented in CVO lakes. The microbiome dataset of this study can serve as a baseline for restoring impacted soda lakes. Altogether, the results of this study demonstrate the sensitivity of tropical soda lakes to climate change, as slight changes in hydrological regimes might produce drastic shifts in community diversity.

RevDate: 2022-08-02

FitzGerald J, Patel S, Eckenberger J, et al (2022)

Improved gut microbiome recovery following drug therapy is linked to abundance and replication of probiotic strains.

Gut microbes, 14(1):2094664.

Probiotics have been used for decades to alleviate the negative side-effects of oral antibiotics, but our mechanistic understanding on how they work is so far incomplete. Here, we performed a metagenomic analysis of the fecal microbiota in participants who underwent a 14-d Helicobacter pylori eradication therapy with or without consumption of a multi-strain probiotic intervention (L. paracasei CNCM I-1518, L. paracasei CNCM I-3689, L. rhamnosus CNCM I-3690, and four yogurt strains) in a randomized, double-blinded, controlled clinical trial. Using a strain-level analysis for detection and metagenomic determination of replication rate, ingested strains were detected and replicated transiently in fecal samples and in the gut during and following antibiotic administration. Consumption of the fermented milk product led to a significant, although modest, improvement in the recovery of microbiota composition. Stratification of participants into two groups based on the degree to which their microbiome recovered showed i) a higher fecal abundance of the probiotic L. paracasei and L. rhamnosus strains and ii) an elevated replication rate of one strain (L. paracasei CNCMI-1518) in the recovery group. Collectively, our findings show a small but measurable benefit of a fermented milk product on microbiome recovery after antibiotics, which was linked to the detection and replication of specific probiotic strains. Such functional insight can form the basis for the development of probiotic-based intervention aimed to protect gut microbiome from drug treatments.

RevDate: 2022-08-02

Greenberg JM, Romero R, Winters AD, et al (2022)

Microbiota of the Pregnant Mouse: Characterization of the Bacterial Communities in the Oral Cavity, Lung, Intestine, and Vagina through Culture and DNA Sequencing.

Microbiology spectrum [Epub ahead of print].

Mice are frequently used as animal models for mechanistic studies of infection and obstetrical disease, yet characterization of the murine microbiota during pregnancy is lacking. The objective of this study was to characterize the microbiotas of distinct body sites of the pregnant mouse-vagina, oral cavity, intestine, and lung-that harbor microorganisms that could potentially invade the murine amniotic cavity, thus leading to adverse pregnancy outcomes. The microbiotas of these body sites were characterized through anoxic, hypoxic, and oxic culture as well as through 16S rRNA gene sequencing. With the exception of the vagina, the cultured microbiotas of each body site varied by atmosphere, with the greatest diversity in the cultured microbiota appearing under anoxic conditions. Only cultures of the vagina were comprehensively representative of the microbiota observed through direct DNA sequencing of body site samples, primarily due to the predominance of two Rodentibacter strains. Identified as Rodentibacter pneumotropicus and Rodentibacter heylii, these isolates exhibited predominance patterns similar to those of Lactobacillus crispatus and Lactobacillus iners in the human vagina. Whole-genome sequencing of these Rodentibacter strains revealed shared genomic features, including the ability to degrade glycogen, an abundant polysaccharide in the vagina. In summary, we report body site-specific microbiotas in the pregnant mouse with potential ecological parallels to those of humans. Importantly, our findings indicate that the vaginal microbiotas of pregnant mice can be readily cultured, suggesting that mock vaginal microbiotas can be tractably generated and maintained for experimental manipulation in future mechanistic studies of host vaginal-microbiome interactions. IMPORTANCE Mice are widely utilized as animal models of obstetrical complications; however, the characterization of the murine microbiota during pregnancy has been neglected. Microorganisms from the vagina, oral cavity, intestine, and lung have been found in the intra-amniotic space, where their presence threatens the progression of gestation. Here, we characterized the microbiotas of pregnant mice and established the appropriateness of culture in capturing the microbiota at each site. The high relative abundance of Rodentibacter observed in the vagina is similar to that of Lactobacillus in humans, suggesting potential ecological parallels. Importantly, we report that the vaginal microbiota of the pregnant mouse can be readily cultured under hypoxic conditions, demonstrating that mock microbial communities can be utilized to test the potential ecological parallels between microbiotas in human and murine pregnancy and to evaluate the relevance of the structure of these microbiotas for adverse pregnancy outcomes, especially intra-amniotic infection and preterm birth.

RevDate: 2022-08-02

Wang J, Gou QY, Luo GY, et al (2022)

Total RNA sequencing of Phlebotomus chinensis, a neglected vector in China, simultaneously revealed viral, bacterial, and eukaryotic microbes that are potentially pathogenic to humans.

Emerging microbes & infections [Epub ahead of print].

Phlebotomus chinensis sandfly is a neglected insect vector in China which is well-known for carrying Leishmania. Recent studies have expanded its pathogen repertoire with two novel arthropod-borne phleboviruses capable of infecting human and animals. Despite these discoveries, our knowledge on the general pathogen diversity and overall microbiome composition of this vector species are still very limited. Here we carried out a meta-transcriptomics analysis which simultaneously revealed the actively replicating/transcribing RNA viruses, DNA viruses, bacteria and eukaryotic microbes, namely, "total microbiome", of several sandfly populations in China. Strikingly, "microbiome" made up 1.8% of total non-ribosomal RNA and were comprised of more than 87 species, among which 70 were novel, including divergent members of the genera Flavivirus and of the family Trypanosomatidae. Importantly, among these microbes we were able to reveal four distinguished types of human and/or mammalian pathogens, including two phleboviruses (hedi and wuxiang viruses), one novel Spotted fever group rickettsia, as well as a member of Leishmania donovani complex, among which hedi virus and Leishmania each had > 50% pool prevalence rate and relatively high abundance levels. Our study also showed the ubiquitous presence of an endosymbiont, namely Wolbachia, although no anti-viral or anti-pathogen effect were detected based on our data. In summary, our results uncovered the much un-explored diversity of microbes harbored by sandflies in China and demonstrated that high pathogen diversity and abundance is currently present in multiple populations, implying disease potential for exposed local human population or domestic animals.

RevDate: 2022-08-02

Isenberg RY, Christensen DG, Visick KL, et al (2022)

High Levels of Cyclic Diguanylate Interfere with Beneficial Bacterial Colonization.

mBio [Epub ahead of print].

During colonization of the Hawaiian bobtail squid (Euprymna scolopes), Vibrio fischeri bacteria undergo a lifestyle transition from a planktonic motile state in the environment to a biofilm state in host mucus. Cyclic diguanylate (c-di-GMP) is a cytoplasmic signaling molecule that is important for regulating motility-biofilm transitions in many bacterial species. V. fischeri encodes 50 proteins predicted to synthesize and/or degrade c-di-GMP, but a role for c-di-GMP regulation during host colonization has not been investigated. We examined strains exhibiting either low or high levels of c-di-GMP during squid colonization and found that while a low-c-di-GMP strain had no colonization defect, a high c-di-GMP strain was severely impaired. Expression of a heterologous c-di-GMP phosphodiesterase restored colonization, demonstrating that the effect is due to high c-di-GMP levels. In the constitutive high-c-di-GMP state, colonizing V. fischeri exhibited reduced motility, altered biofilm aggregate morphology, and a regulatory interaction where transcription of one polysaccharide locus is inhibited by the presence of the other polysaccharide. Our results highlight the importance of proper c-di-GMP regulation during beneficial animal colonization, illustrate multiple pathways regulated by c-di-GMP in the host, and uncover an interplay of multiple exopolysaccharide systems in host-associated aggregates. IMPORTANCE There is substantial interest in studying cyclic diguanylate (c-di-GMP) in pathogenic and environmental bacteria, which has led to an accepted paradigm in which high c-di-GMP levels promote biofilm formation and reduce motility. However, considerably less focus has been placed on understanding how this compound contributes to beneficial colonization. Using the Vibrio fischeri-Hawaiian bobtail squid study system, we took advantage of recent genetic advances in the bacterium to modulate c-di-GMP levels and measure colonization and track c-di-GMP phenotypes in a symbiotic interaction. Studies in the animal host revealed a c-di-GMP-dependent genetic interaction between two distinct biofilm polysaccharides, Syp and cellulose, that was not evident in culture-based studies: elevated c-di-GMP altered the composition and abundance of the in vivo biofilm by decreasing syp transcription due to increased cellulose synthesis. This study reveals important parallels between pathogenic and beneficial colonization and additionally identifies c-di-GMP-dependent regulation that occurs specifically in the squid host.

RevDate: 2022-08-02

Lyu YL, Zhou HF, Yang J, et al (2022)

Biological Activities Underlying the Therapeutic Effect of Quercetin on Inflammatory Bowel Disease.

Mediators of inflammation, 2022:5665778.

Inflammatory bowel disease (IBD) is a chronic autoimmune disorder stemming from unrestrained immune activation and subsequent destruction of colon tissue. Genetic susceptibility, microbiota remodeling, and environmental cues are involved in IBD pathogenesis. Up to now, there are limited treatment options for IBD, so better therapies for IBD are eagerly needed. The therapeutic effects of naturally occurring compounds have been extensively investigated, among which quercetin becomes an attractive candidate owing to its unique biochemical properties. To facilitate the clinical translation of quercetin, we aimed to get a comprehensive understanding of the cellular and molecular mechanisms underlying the anti-IBD role of quercetin. We summarized that quercetin exerts the anti-IBD effect through consolidating the intestinal mucosal barrier, enhancing the diversity of colonic microbiota, restoring local immune homeostasis, and restraining the oxidative stress response. We also delineated the effect of quercetin on gut microbiome and discussed the potential side effects of quercetin administration. Besides, quercetin could serve as a prodrug, and the bioavailability of quercetin is improved through chemical modifications or the utilization of effective drug delivery systems. Altogether, these lines of evidence hint the feasibility of quercetin as a candidate compound for IBD treatment.

RevDate: 2022-08-02

Brown JA, Sanidad KZ, Lucotti S, et al (2022)

Gut microbiota-derived metabolites confer protection against SARS-CoV-2 infection.

Gut microbes, 14(1):2105609.

The gut microbiome is intricately coupled with immune regulation and metabolism, but its role in Coronavirus Disease 2019 (COVID-19) is not fully understood. Severe and fatal COVID-19 is characterized by poor anti-viral immunity and hypercoagulation, particularly in males. Here, we define multiple pathways by which the gut microbiome protects mammalian hosts from SARS-CoV-2 intranasal infection, both locally and systemically, via production of short-chain fatty acids (SCFAs). SCFAs reduced viral burdens in the airways and intestines by downregulating the SARS-CoV-2 entry receptor, angiotensin-converting enzyme 2 (ACE2), and enhancing adaptive immunity via GPR41 and 43 in male animals. We further identify a novel role for the gut microbiome in regulating systemic coagulation response by limiting megakaryocyte proliferation and platelet turnover via the Sh2b3-Mpl axis. Taken together, our findings have unraveled novel functions of SCFAs and fiber-fermenting gut bacteria to dampen viral entry and hypercoagulation and promote adaptive antiviral immunity.


ESP Quick Facts

ESP Origins

In the early 1990's, Robert Robbins was a faculty member at Johns Hopkins, where he directed the informatics core of GDB — the human gene-mapping database of the international human genome project. To share papers with colleagues around the world, he set up a small paper-sharing section on his personal web page. This small project evolved into The Electronic Scholarly Publishing Project.

ESP Support

In 1995, Robbins became the VP/IT of the Fred Hutchinson Cancer Research Center in Seattle, WA. Soon after arriving in Seattle, Robbins secured funding, through the ELSI component of the US Human Genome Project, to create the original ESP.ORG web site, with the formal goal of providing free, world-wide access to the literature of classical genetics.

ESP Rationale

Although the methods of molecular biology can seem almost magical to the uninitiated, the original techniques of classical genetics are readily appreciated by one and all: cross individuals that differ in some inherited trait, collect all of the progeny, score their attributes, and propose mechanisms to explain the patterns of inheritance observed.

ESP Goal

In reading the early works of classical genetics, one is drawn, almost inexorably, into ever more complex models, until molecular explanations begin to seem both necessary and natural. At that point, the tools for understanding genome research are at hand. Assisting readers reach this point was the original goal of The Electronic Scholarly Publishing Project.

ESP Usage

Usage of the site grew rapidly and has remained high. Faculty began to use the site for their assigned readings. Other on-line publishers, ranging from The New York Times to Nature referenced ESP materials in their own publications. Nobel laureates (e.g., Joshua Lederberg) regularly used the site and even wrote to suggest changes and improvements.

ESP Content

When the site began, no journals were making their early content available in digital format. As a result, ESP was obliged to digitize classic literature before it could be made available. For many important papers — such as Mendel's original paper or the first genetic map — ESP had to produce entirely new typeset versions of the works, if they were to be available in a high-quality format.

ESP Help

Early support from the DOE component of the Human Genome Project was critically important for getting the ESP project on a firm foundation. Since that funding ended (nearly 20 years ago), the project has been operated as a purely volunteer effort. Anyone wishing to assist in these efforts should send an email to Robbins.

ESP Plans

With the development of methods for adding typeset side notes to PDF files, the ESP project now plans to add annotated versions of some classical papers to its holdings. We also plan to add new reference and pedagogical material. We have already started providing regularly updated, comprehensive bibliographies to the ESP.ORG site.

Electronic Scholarly Publishing
961 Red Tail Lane
Bellingham, WA 98226

E-mail: RJR8222 @

Papers in Classical Genetics

The ESP began as an effort to share a handful of key papers from the early days of classical genetics. Now the collection has grown to include hundreds of papers, in full-text format.

Digital Books

Along with papers on classical genetics, ESP offers a collection of full-text digital books, including many works by Darwin (and even a collection of poetry — Chicago Poems by Carl Sandburg).


ESP now offers a much improved and expanded collection of timelines, designed to give the user choice over subject matter and dates.


Biographical information about many key scientists.

Selected Bibliographies

Bibliographies on several topics of potential interest to the ESP community are now being automatically maintained and generated on the ESP site.

ESP Picks from Around the Web (updated 07 JUL 2018 )