Viewport Size Code:
Login | Create New Account


About | Classical Genetics | Timelines | What's New | What's Hot

About | Classical Genetics | Timelines | What's New | What's Hot


Bibliography Options Menu

Hide Abstracts   |   Hide Additional Links
Long bibliographies are displayed in blocks of 100 citations at a time. At the end of each block there is an option to load the next block.

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 12 Aug 2022 at 01:49 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: 2022-08-11

Kong C, Liang L, Liu G, et al (2022)

Integrated metagenomic and metabolomic analysis reveals distinct gut-microbiome-derived phenotypes in early-onset colorectal cancer.

Gut pii:gutjnl-2022-327156 [Epub ahead of print].

OBJECTIVE: The incidence of early-onset colorectal cancer (EO-CRC) is steadily increasing. Here, we aimed to characterise the interactions between gut microbiome, metabolites and microbial enzymes in EO-CRC patients and evaluate their potential as non-invasive biomarkers for EO-CRC.

DESIGN: We performed metagenomic and metabolomic analyses, identified multiomics markers and constructed CRC classifiers for the discovery cohort with 130 late-onset CRC (LO-CRC), 114 EO-CRC subjects and age-matched healthy controls (97 LO-Control and 100 EO-Control). An independent cohort of 38 LO-CRC, 24 EO-CRC, 22 LO-Controls and 24 EO-Controls was analysed to validate the results.

RESULTS: Compared with controls, reduced alpha-diversity was apparent in both, LO-CRC and EO-CRC subjects. Although common variations existed, integrative analyses identified distinct microbiome-metabolome associations in LO-CRC and EO-CRC. Fusobacterium nucleatum enrichment and short-chain fatty acid depletion, including reduced microbial GABA biosynthesis and a shift in acetate/acetaldehyde metabolism towards acetyl-CoA production characterises LO-CRC. In comparison, multiomics signatures of EO-CRC tended to be associated with enriched Flavonifractor plauti and increased tryptophan, bile acid and choline metabolism. Notably, elevated red meat intake-related species, choline metabolites and KEGG orthology (KO) pldB and cbh gene axis may be potential tumour stimulators in EO-CRC. The predictive model based on metagenomic, metabolomic and KO gene markers achieved a powerful classification performance for distinguishing EO-CRC from controls.

CONCLUSION: Our large-sample multiomics data suggest that altered microbiome-metabolome interplay helps explain the pathogenesis of EO-CRC and LO-CRC. The potential of microbiome-derived biomarkers as promising non-invasive tools could be used for the accurate detection and distinction of individuals with EO-CRC.

RevDate: 2022-08-11

Al Naggar Y, Singavarapu B, Paxton RJ, et al (2022)

Bees under interactive stressors: The novel insecticides flupyradifurone and sulfoxaflor along with the fungicide azoxystrobin disrupt the gut microbiota of honey bees and increase opportunistic bacterial pathogens.

The Science of the total environment pii:S0048-9697(22)05040-9 [Epub ahead of print].

The gut microbiome plays an important role in bee health and disease. But it can be disrupted by pesticides and in-hive chemicals, putting honey bee health in danger. We used a controlled and fully crossed laboratory experimental design to test the effects of a 10-day period of chronic exposure to field-realistic sublethal concentrations of two nicotinic acetylcholine receptor agonist insecticides (nACHRs), namely flupyradifurone (FPF) and sulfoxaflor (Sulf), and a fungicide, azoxystrobin (Azoxy), individually and in combination, on the survival of individual honey bee workers and the composition of their gut microbiota (fungal and bacterial diversity). Metabarcoding was used to examine the gut microbiota on days 0, 5, and 10 of pesticide exposure to determine how the microbial response varies over time; to do so, the fungal ITS2 fragment and the V4 region of the bacterial 16S rRNA were targeted. We found that FPF has a negative impact on honey bee survival, but interactive (additive or synergistic) effects between either insecticide and the fungicide on honey bee survival were not statistically significant. Pesticide treatments significantly impacted the microbial community composition. The fungicide Azoxy substantially reduced the Shannon diversity of fungi after chronic exposure for 10 days. The relative abundance of the top 10 genera of the bee gut microbiota was also differentially affected by the fungicide, insecticides, and fungicide-insecticide combinations. Gut microbiota dysbiosis was associated with an increase in the relative abundance of opportunistic pathogens such as Serratia spp. (e.g. S. marcescens), which can have devastating consequences for host health such as increased susceptibility to infection and reduced lifespan. Our findings raise concerns about the long-term impact of novel nACHR insecticides, particularly FPF, on pollinator health and recommend a novel methodology for a refined risk assessment that includes the potential effects of agrochemicals on the gut microbiome of bees.

RevDate: 2022-08-11

Mori T (2022)

Possibly underestimated microbial carbon limitation determined by enzymatic stoichiometry approach: Comments on "Crop rotation stage has a greater effect than fertilisation on soil microbiome assembly and enzymatic stoichiometry".

RevDate: 2022-08-11

Hodkovicova N, Hollerova A, Blahova J, et al (2022)

Non-steroidal anti-inflammatory drugs caused an outbreak of inflammation and oxidative stress with changes in the gut microbiota in rainbow trout (Oncorhynchus mykiss).

The Science of the total environment pii:S0048-9697(22)05020-3 [Epub ahead of print].

One of the main contributors to pharmaceutical pollution of surface waters are non-steroidal anti-inflammatory drugs (NSAIDs) that contaminate the food chain and affect non-target water species. As there are not many studies focusing on toxic effects of NSAIDs on freshwater fish species and specially effects after dietary exposure, we selected rainbow trout (Oncorhynchus mykiss) as the ideal model to examine the impact of two NSAIDs - diclofenac (DCF) and ibuprofen (IBP). The aim of our study was to test toxicity of environmentally relevant concentrations of these drugs together with exposure doses of 100× higher, including their mixture; and to deepen knowledge about the mechanism of toxicity of these drugs. This study revealed kidneys as the most affected organ with hyalinosis, an increase in oxidative stress markers, and changes in gene expression of heat shock protein 70 to be signs of renal toxicity. Furthermore, hepatotoxicity was confirmed by histopathological analysis (i.e. dystrophy, congestion, and inflammatory cell increase), change in biochemical markers, increase in heat shock protein 70 mRNA, and by oxidative stress analysis. The gills were locally deformed and showed signs of inflammatory processes and necrotic areas. Given the increase in oxidative stress markers and heat shock protein 70 mRNA, severe impairment of oxygen transport may be one of the toxic pathways of NSAIDs. Regarding the microbiota, an overgrowth of Gram-positive species was detected; in particular, significant dysbiosis in the Fusobacteria/Firmicutes ratio was observed. In conclusion, the changes observed after dietary exposure to NSAIDs can influence the organism homeostasis, induce ROS production, potentiate inflammations, and cause gut dysbiosis. Even the environmentally relevant concentration of NSAIDs pose a risk to the aquatic ecosystem as it changed O. mykiss health parameters and we assume that the toxicity of NSAIDs manifests itself at the level of mitochondria and proteins.

RevDate: 2022-08-11

Santos D, Frota EG, Vargas BK, et al (2022)

What is the role of phenolic compounds of yerba mate (Ilex paraguariensis) in gut microbiota?.

Phytochemistry pii:S0031-9422(22)00257-6 [Epub ahead of print].

Diet actively influences gut microbiota and body homeostasis. The predominance of beneficial species results in symbiosis, while dysbiosis is characterized by an imbalance between microbial communities. Food plays a key role in this dynamic and in promoting the health of individuals. Ilex paraguariensis, also known as yerba mate, is a traditional plant from Latin America that has a complex matrix of bioactive substances, including methylxanthines, triterpenes, saponins, and phenolics. The consumption of yerba mate is associated with antioxidant, cardioprotective, anti-inflammatory, and anti-obesity effects. However, to the best of our knowledge, there have been no studies on yerba mate as a modulating agent of intestinal microbiota. Phenolics are the major compounds in yerba mate and have been reported to act in modulating the microbiome. In this review, we explore the activity of yerba mate as a possible stimulant of gut microbiota and present its main phenolics and their biological effects. We also propose different mechanisms of action of these phenolics and possible doses for their effectiveness.

RevDate: 2022-08-11

Salazar AM, Neugent ML, De Nisco NJ, et al (2022)

Gut-bladder axis enters the stage: Implication for recurrent urinary tract infections.

Cell host & microbe, 30(8):1066-1069.

The gut microbiome is a critical modulator of systemic physiology, including infectious disease susceptibility. Although this niche is a reservoir for uropathogenic Escherichia coli, knowledge of its role in urinary tract infections (UTIs) is limited. We discuss two recent studies, Thänert et al. (2022) and Worby et al. (2022), that interrogate the roles of the gut-bladder axis in UTIs.

RevDate: 2022-08-11

Sztandarski P, Marchewka J, Konieczka P, et al (2022)

Gut microbiota activity in chickens from two genetic lines and with outdoor-preferring, moderate-preferring, and indoor-preferring ranging profiles.

Poultry science, 101(10):102039 pii:S0032-5791(22)00330-3 [Epub ahead of print].

Despite the existing research into the gut microbiome of meat chickens, the associations between gut microbiome composition, its activity and chicken outdoor ranging frequency remain unexplored. The aim of this study was to determine the gut microbiota composition, activity and metabolic products in chickens of 2 different lines and 3 ranging profiles. Sixty non-beak trimmed birds, either Sasso or Green-legged Partridge were housed with access to outdoor ranges from wk. 5 to 10 of age. Outdoor ranges were video recorded to obtain frequencies of the birds' range use. The information about relative abundance of selected bacterial groups in the ceca including Lactobacillus spp., E. coli, Bifidobacterium spp., and Clostridium spp. was obtained with the PCR method. Gut microbiota activity was assessed based on the glycolytic activity of bacterial enzymes including, α-glucosidase, β-glucosidase, α-galactosidase, β-galactosidase, and β-glucuronidase as well as based on the concentration of short-chain fatty acids (SCFA) in the caecal digesta. Statistical analysis was conducted by generalized linear mixed models, applying the breed and ranging profile as fixed effects and pen as a random factor. The lowest relative abundance of Bifidobacterium spp. was found in the cecal content of indoor-preferring Sasso birds (0.01 ± 0.001), as compared to all other birds in the experiment (ranging from 0.03 ± 0.01 to 0.11 ± 0.07; P = 0.0002). The lowest relative abundance of E. coli was identified for all outdoor-preferring birds and indoor- preferring Sasso birds (0.01 ± 0.001; P = 0.0087). Cecal activity of: α-glucosidase, β-glucuronidase and β-galactosidase was higher in Green-legged Partridges, as compared to Sasso (P = 0.013; P = 0.008; P = 0.004). Valeric acid concentrations were higher in moderate Green-legged Partridges than in Sasso of the same ranging profile (2.03 ± 0.16 vs. 1.5 ± 0.17; 0.016). The majority of the current results confirmed an effect of genotype and ranging profile on the various analyzed parameters. In outdoor-preferring birds, the consumption of pasture originating feed sources as a supplement to the indoor accessible cereal-based diet likely caused the positive effects on the birds' microbial profile.

RevDate: 2022-08-11

Brunt VE, Greenberg NT, Sapinsley ZJ, et al (2022)

Suppression of trimethylamine N-oxide with DMB mitigates vascular dysfunction, exercise intolerance, and frailty associated with a Western-style diet in mice.

Journal of applied physiology (Bethesda, Md. : 1985) [Epub ahead of print].

Consumption of a Western-style diet (WD; high fat, high sugar, low fiber) is associated with impaired vascular function and increased risk of cardiovascular diseases (CVD), which could be mediated partly by increased circulating concentrations of the gut microbiome-derived metabolite trimethylamine N-oxide (TMAO). We investigated if suppression of TMAO with 3,3-dimethyl-1-butanol (DMB; inhibitor of microbial TMA lyase) in mice could prevent: 1) WD-induced vascular endothelial dysfunction and aortic stiffening; and 2) WD-induced reductions in endurance exercise tolerance and increases in frailty, as both are linked to WD, vascular dysfunction, and increased CVD risk. C57BL/6N mice were fed standard chow or WD (41% fat, ~25% sugar, 4% fiber) for 5 months beginning at ~2 months of age. Within each diet, mice randomly received (n=11-13/group) normal drinking water (control) or 1% DMB in drinking water for the last 8 weeks (from 5-7 months of age). Plasma TMAO was increased in WD-fed mice but suppressed by DMB. WD induced endothelial dysfunction, assessed as carotid artery endothelium-dependent dilation to acetylcholine, and progressive increases in aortic stiffness (measured serially in vivo as pulse wave velocity), both of which were fully prevented by supplementation with DMB. Endurance exercise tolerance, assessed as time to fatigue on a rotarod test, was impaired in WD-fed mice but partially recovered by DMB. Lastly, WD-induced increases in frailty (31-point index) were prevented by DMB. Our findings indicate DMB or other TMAO-lowering therapies may be promising for mitigating the adverse effects of WD on physiological function, and thereby reducing risk of chronic diseases.

RevDate: 2022-08-11

Lee SK, Jhun J, Lee SY, et al (2022)

A decrease in functional microbiomes represented as Faecalibacterium affects immune homeostasis in long-term stable liver transplant patients.

Gut microbes, 14(1):2102885.

ABBREVIATIONS: LT, liver transplantation; HCC, hepatocellular carcinoma; IS, immunosuppressants; DC, dendritic cells; Treg, regulatory T; Th17, T helper 17; AST, aspartate transaminase; ALT, alanine transaminase; OUT, operational taxonomic unit; LEfSe, linear discriminant analysis effect size; LDA, linear discriminant analysis; IL, interleukin; TGF, transforming growth factor; GM-CSF, granulocyte-macrophage colony-stimulating factor; IFN, interferon; TNF-α, tumor necrosis factor-α; MIP-1α, macrophage inflammatory protein-1α; IP-10, interferon γ-induced protein; MCP-1, monocyte chemoattractant protein-1; ACR, acute cellular rejection; NF-κB, nuclear factor κB; PT INR, prothrombin time; QC, quality check; PBMC, peripheral blood mononuclear cells; PBS, phosphate-buffered saline; ELISA, enzyme-linked immunosorbent assay.

RevDate: 2022-08-11

VanWallendael A, Benucci GMN, da Costa PB, et al (2022)

Host genotype controls ecological change in the leaf fungal microbiome.

PLoS biology, 20(8):e3001681 pii:PBIOLOGY-D-21-02944.

Leaf fungal microbiomes can be fundamental drivers of host plant success, as they contain pathogens that devastate crop plants and taxa that enhance nutrient uptake, discourage herbivory, and antagonize pathogens. We measured leaf fungal diversity with amplicon sequencing across an entire growing season in a diversity panel of switchgrass (Panicum virgatum). We also sampled a replicated subset of genotypes across 3 additional sites to compare the importance of time, space, ecology, and genetics. We found a strong successional pattern in the microbiome shaped both by host genetics and environmental factors. Further, we used genome-wide association (GWA) mapping and RNA sequencing to show that 3 cysteine-rich receptor-like kinases (crRLKs) were linked to a genetic locus associated with microbiome structure. We confirmed GWAS results in an independent set of genotypes for both the internal transcribed spacer (ITS) and large subunit (LSU) ribosomal DNA markers. Fungal pathogens were central to microbial covariance networks, and genotypes susceptible to pathogens differed in their expression of the 3 crRLKs, suggesting that host immune genes are a principal means of controlling the entire leaf microbiome.

RevDate: 2022-08-11

Parker KD, Mueller JL, Westfal M, et al (2022)

A pilot study characterizing longitudinal changes in fecal microbiota of patients with Hirschsprung-associated enterocolitis.

Pediatric surgery international [Epub ahead of print].

PURPOSE: Hirschsprung disease is a neurointestinal disease that occurs due to failure of enteric neural crest-derived cells to complete their rostrocaudal migration along the gut mesenchyme, resulting in aganglionosis along variable lengths of the distal bowel. Despite the effective surgery that removes the aganglionic segment, children with Hirschsprung disease remain at high risk for developing a potentially life-threatening enterocolitis (Hirschsprung-associated enterocolitis). Although the etiology of this enterocolitis remains poorly understood, several recent studies in both mouse models and in human subjects suggest potential involvement of gastrointestinal microbiota in the underlying pathogenesis of Hirschsprung-associated enterocolitis.

METHODS: We present the first study to exploit the Illumina MiSeq next-generation sequencing platform within a longitudinal framework focused on microbiomes of Hirschsprung-associated enterocolitis in five patients. We analyzed bacterial communities from fecal samples collected at different timepoints starting from active enterocolitis and progressing into remission.

RESULTS: We observed compositional differences between patients largely attributable to variability in age at the time of sample collection. Remission samples across patients exhibited compositional similarity, including enrichment of Blautia, while active enterocolitis samples showed substantial variability in composition.

CONCLUSIONS: Overall, our findings provide continued support for the role of GI microbiota in the pathogenesis of Hirschsprung-associated enterocolitis.

RevDate: 2022-08-11

Hotkani ZG, Ghaedmohammadi S, N Mozdoori (2022)

Meta-analysis of race and age influence on the vaginal microbiome in pregnant and nonpregnant healthy women.

Future microbiology [Epub ahead of print].

Aim: The presence of microbial species in reproductive tubes plays an essential protective role against the proliferation of harmful organisms and is an important factor in reproductive health. High-throughput culture-independent technologies allow the study of the vaginal microbiome on a large scale. This study aimed to compare the vaginal microbiota between pregnant and nonpregnant women of different ages and races using the meta-analysis method. Materials & methods: Seven articles with 16S rRNA gene sequences were studied and analyzed using CLC Genomics Workbench 20.1.1. Results & conclusion: This study revealed new insights into the effects of age and ethnicity on the pregnant and nonpregnant vaginal microbiome and found that the microbiome of Chinese women is more distinct than that of other ethnicities.

RevDate: 2022-08-11

Ponomarova O (2022)

Teaming up to make kombucha.

eLife, 11: pii:81670.

Reducing the microbial diversity in a type of fermented tea reveals the core metabolic interactions responsible for the drink's signature taste and characteristics.

RevDate: 2022-08-11

Huang X, Xin Y, T Lu (2022)

A systematic, complexity-reduction approach to dissect the kombucha tea microbiome.

eLife, 11: pii:76401.

One defining goal of microbiome research is to uncover mechanistic causation that dictates the emergence of structural and functional traits of microbiomes. However, the extraordinary degree of ecosystem complexity has hampered the realization of the goal. Here, we developed a systematic, complexity-reducing strategy to mechanistically elucidate the compositional and metabolic characteristics of microbiome by using the kombucha tea microbiome as an example. The strategy centered around a two-species core that was abstracted from but recapitulated the native counterpart. The core was convergent in its composition, coordinated on temporal metabolic patterns, and capable for pellicle formation. Controlled fermentations uncovered the drivers of these characteristics, which were also demonstrated translatable to provide insights into the properties of communities with increased complexity and altered conditions. This work unravels the pattern and process underlying the kombucha tea microbiome, providing a potential conceptual framework for mechanistic investigation of microbiome behaviors.

RevDate: 2022-08-11

Wang Y, Sun Q, Liu J, et al (2022)

Suaeda salsa Root-Associated Microorganisms Could Effectively Improve Maize Growth and Resistance under Salt Stress.

Microbiology spectrum [Epub ahead of print].

Root-associated microorganisms are widely recognized as playing an important role in mitigating stress-induced damage to plants, but the responses of rhizosphere microbial communities after inoculation and their relationship with plant responses remain unclear. In this study, the bacterium Providencia vermicola BR68 and the fungus Sarocladium kiliense FS18 were selected from among 91 strains isolated from the halophyte Suaeda salsa to interact with maize seedlings under salt stress. The results showed that compared with NaCl-only treatment, inoculation with strains BR68 and FS18 significantly improved the growth, net photosynthetic rate, and antioxidant enzyme activities of maize; significantly reduced proline content and generation rate of reactive oxygen species (ROS); and alleviated oxidative stress and osmotic stress. Moreover, inoculation with these two strains increased the activities of soil microbiome enzymes such as sucrase, catalase, and fluorescein diacetate hydrolase, which improved maize physiologies and promoted maize growth under salt stress. In addition, these inoculated strains significantly affected the abundance of certain genera, and the correlation trends for these genera with soil properties and maize physiologies were similar to those of these inoculated strains. Strain BR68 was indirectly associated with bacterial communities through BR-specific biomarkers, and bacterial communities and soil properties explained most of the variation in maize physiologies and growth. Inoculation of strain FS18 was directly associated with variations in soil properties and maize physiologies. The two strains improved maize growth under salt stress and alleviated stress damage in maize in different ways. The links among salt-tolerant microorganisms, soil, and plants established in this study can inform strategies for improving crop cultivation in salinized lands. IMPORTANCE This study demonstrates that halophyte root-associated microorganisms can promote crop tolerance to salt stress and clarify the mechanism by which the strains work in rhizosphere soil. The links among salt-tolerant microorganisms, soil, and plants established in this study can inform strategies for improving crop cultivation in salinized lands.

RevDate: 2022-08-11

Ortiz Sanjuán JM, Manzanilla EG, Cabrera-Rubio R, et al (2022)

Using Shotgun Sequencing to Describe the Changes Induced by In-Feed Zinc Oxide and Apramycin in the Microbiomes of Pigs One Week Postweaning.

Microbiology spectrum [Epub ahead of print].

Postweaning diarrhea (PWD) is a relevant problem associated with early weaning on pig farms. For decades, in-feed antibiotics and therapeutic zinc oxide (ZnO) have been widely used to prevent PWD in piglets. The European Union is banning both strategies in 2022 due to antimicrobial resistance and environmental contamination concerns, respectively. Understanding the effects of these products on the pig microbiome is crucial for correcting potential microbial disbalances that would prompt PWD. Using shotgun sequencing, three trials were carried out to explore the impact of in-feed apramycin and ZnO, combined with different farm hygiene protocols, on the fecal microbiomes of piglets 7 days postweaning. In trial 1, 28-day-old piglets were allocated to one of three groups: control diet (Ct), Ct + ZnO (Zn), and Ct + apramycin (Ab). In trials 2 and 3, piglets were allocated to the same treatments, but the trials also included different cleaning protocols, achieving different hygiene levels. In-feed treatments impacted the richness, diversity, and relative abundance of the piglets' microbiome more than hygiene. Pigs in the Ct group showed higher species richness than pigs in the Ab and Zn groups. A clustering analysis evidenced a link between Enterobacteriaceae in the Ct group; Lactobacillaceae and Veillonellaceae mainly in the Ct group; and Bacteroidaceae, Ruminococcaceae, Oscillospiraceae, Acidaminococcaceae, and Lactobacillaceae in the Ab and Zn groups. Functional data analysis revealed a higher abundance of virulence genes in the Ct group microbiomes and heavy metal and antimicrobial resistance-related functions in the Zn treatment group. The results demonstrate that alternatives to Ab and ZnO should balance the microbial abundance and stimulate the growth of commensals to outcompete potential pathogens. IMPORTANCE Weaning is a critical period for piglets, during which potentially harmful bacteria such as Escherichia coli can increase in abundance in the intestine, creating digestive problems and diarrhea. In-feed antibiotics, the most frequent administration route for antibiotics in livestock, and therapeutic doses of zinc oxide (ZnO) help to control diarrhea but prompt secondary problems such as antimicrobial resistance and soil pollution from heavy metals. Understanding how these strategies impact the gut microbiota is crucial for establishing health biomarkers and designing successful replacement strategies. Using shotgun sequencing, this study compares the microbiota of pigs after early weaning when treated with in-feed antibiotics, ZnO, or treatment-free diets to describe differences that could define the susceptibility to infections, providing the basis for future research on improving intestinal resilience through microbiota-based strategies.

RevDate: 2022-08-11

Hu X, Wei Y, Zhang T, et al (2022)

Gastrointestinal Biogeography of Luminal Microbiota and Short-Chain Fatty Acids in Sika Deer (Cervus nippon).

Applied and environmental microbiology [Epub ahead of print].

The gut microbiota of sika deer has been widely investigated, but the spatial distribution of symbiotic microbes among physical niches in the gastrointestinal tract remains to be established. While feces are the most commonly used biological samples in these studies, the accuracy of fecal matter as a proxy of the microbiome at other gastrointestinal sites is as yet unknown. In the present study, luminal contents obtained along the longitudinal axis of deer gastrointestinal tract (rumen, reticulum, omasum, abomasum, small intestine, cecum, colon, and rectum) were subjected to 16S rRNA gene sequencing for profiling of the microbial composition, and samples from the rumen, small intestine, and cecum were subjected to metabolomic analysis to evaluate short-chain fatty acid (SCFA) profiles. Prevotella bacteria were the dominant gastric core microbes, while Christensenellaceae_R-7_group was predominantly observed in the intestine. While the eight gastrointestinal sites displayed variations in microbial diversity, abundance, and function, they could be clustered into stomach, small intestine, and large intestine segments, and the results further highlighted a specific microbial niche of the small intestine. SCFA levels in the rumen, small intestine, and cecum were significantly different, with Bacteroidetes and Spirochaetes were shown to play a critical role in SCFA production. Finally, the rectal microbial composition was significantly correlated with colonic and cecum communities but not those of the small intestine and four gastric sites. Quantification of the compositions and biogeographic relationships between gut microbes and SCFAs in sika deer should provide valuable insights into the interactions contributing to microbial functions and metabolites. IMPORTANCE Feces or specific segments of the gastrointestinal tract (in particular, the rumen) were sampled to explore the gut microbiome. The gastrointestinal biogeography of the luminal microbiota in ruminants, which is critical to guide accurate sampling for different purposes, is poorly understood at present. The microbial community of the rectal sample (as a proxy of fecal sample) showed higher correlation with those of other large intestinal sites relative to the small intestine or stomach, suggesting that the microbial composition is specifically shaped by the unique physiological characteristics of different gastrointestinal niches. In addition, significant differences in microbiomes and SCFAs were observed among the different gastrointestinal sites.

RevDate: 2022-08-11

Simopoulos CMA, Ning Z, Li L, et al (2022)

MetaProClust-MS1: an MS1 Profiling Approach for Large-Scale Microbiome Screening.

mSystems [Epub ahead of print].

Metaproteomics is used to explore the functional dynamics of microbial communities. However, acquiring metaproteomic data by tandem mass spectrometry (MS/MS) is time-consuming and resource-intensive, and there is a demand for computational methods that can be used to reduce these resource requirements. We present MetaProClust-MS1, a computational framework for microbiome feature screening developed to prioritize samples for follow-up MS/MS. In this proof-of-concept study, we tested and compared MetaProClust-MS1 results on gut microbiome data, from fecal samples, acquired using short 15-min MS1-only chromatographic gradients and MS1 spectra from longer 60-min gradients to MS/MS-acquired data. We found that MetaProClust-MS1 identified robust gut microbiome responses caused by xenobiotics with significantly correlated cluster topologies of comparable data sets. We also used MetaProClust-MS1 to reanalyze data from both a clinical MS/MS diagnostic study of pediatric patients with inflammatory bowel disease and an experiment evaluating the therapeutic effects of a small molecule on the brain tissue of Alzheimer's disease mouse models. MetaProClust-MS1 clusters could distinguish between inflammatory bowel disease diagnoses (ulcerative colitis and Crohn's disease) using samples from mucosal luminal interface samples and identified hippocampal proteome shifts of Alzheimer's disease mouse models after small-molecule treatment. Therefore, we demonstrate that MetaProClust-MS1 can screen both microbiomes and single-species proteomes using only MS1 profiles, and our results suggest that this approach may be generalizable to any proteomics experiment. MetaProClust-MS1 may be especially useful for large-scale metaproteomic screening for the prioritization of samples for further metaproteomic characterization, using MS/MS, for instance, in addition to being a promising novel approach for clinical diagnostic screening. IMPORTANCE Growing evidence suggests that human gut microbiome composition and function are highly associated with health and disease. As such, high-throughput metaproteomic studies are becoming more common in gut microbiome research. However, using a conventional long liquid chromatography (LC)-MS/MS gradient metaproteomics approach as an initial screen in large-scale microbiome experiments can be slow and expensive. To combat this challenge, we introduce MetaProClust-MS1, a computational framework for microbiome screening using MS1-only profiles. In this proof-of-concept study, we show that MetaProClust-MS1 identifies clusters of gut microbiome treatments using MS1-only profiles similar to those identified using MS/MS. Our approach allows researchers to prioritize samples and treatments of interest for further metaproteomic analyses and may be generally applicable to any proteomic analysis. In particular, this approach may be especially useful for large-scale metaproteomic screening or in clinical settings where rapid diagnostic evidence is required.

RevDate: 2022-08-11

Fu KL, Chiu MJ, Wara-Aswapati N, et al (2022)

Oral microbiome and serological analyses on association of Alzheimer's disease and periodontitis.

Oral diseases [Epub ahead of print].

OBJECTIVE: To investigate the association between Alzheimer's disease (AD) and periodontitis in the aspects of periodontal status, serological markers and oral microbiome.

MATERIALS AND METHODS: Twenty AD and 20 healthy subjects were enrolled in this age- and gender-matched case-control study. Clinical periodontal parameters and serum biomarkers, including amyloid β42 (Aβ42), Tau, phosphorylated Tau (pTau), triglyceride, pro-inflammatory cytokines and anti-P. gingivalis lipopolysaccharide (LPS) antibody were examined. The saliva samples were analyzed for oral microbiome composition.

RESULTS: AD patients with Clinical Dementia Rating (CDR) >1 exhibited significantly more clinical attachment loss (CAL) than those with lower CDR. The levels of serum Tau protein, hsCRP and anti-P. gingivalis LPS antibody were markedly elevated in the AD group compared to the control group. Serum pTau protein level was positively correlated with anti-P. gingivalis LPS antibody titer. Moreover, the increased abundances of Capnocytophaga sp ora clone DZ074, Eubacterium infirmum, Prevotella buccae and Selenomonas artemidis were detected in the AD group. Interestingly, serum levels of Aβ42, pTau, and anti-P. gingivalis LPS antibody were strongly related to the gene upregulation in human pathogen septicemia.

CONCLUSIONS: Our study suggested the association of periodontal infection and oral microbiome with AD. Further large-scale studies with longitudinal follow-up are warranted.

RevDate: 2022-08-11

Duan H, Li J, Yu L, et al (2022)

The road ahead of dietary restriction on anti-aging: focusing on personalized nutrition.

Critical reviews in food science and nutrition [Epub ahead of print].

Dietary restriction (DR), including caloric restriction (CR), intermittent fasting (IF), and restriction of specific food compositions, can delay aging, and the main mechanisms include regulation of nutrient-sensing pathways and gut microbiota. However, the effects of DR regimens on longevity remain controversial, as some studies have demonstrated that IF, rather than CR or diet composition, influences longevity, while other studies have shown that the restricted-carbohydrate or -protein diets, rather than CR, determine health and longevity. Many factors, including DR-related factors (carbohydrate or protein composition, degree and duration of DR), and individual differences (health status, sex, genotype, and age of starting DR), would be used to explain the controversial anti-aging effects of DR, thus highlighting the necessity of precise DR intervention for anti-aging. Personalized DR intervention in humans is challenging because of the lack of accurate aging molecular biomarkers and vast individual variability. Using machine learning to build a predictive model based on the data set of clinical features, gut microbiome and metabolome, may be a good method to achieve precise DR intervention. Therefore, this review analyzed the anti-aging effects of various DR regimens, summarized their mechanisms and influencing factors, and proposed a future research direction for achieving personalized DR regimens for slowing aging.

RevDate: 2022-08-11

Mj O, Turner GA, A S, et al (2022)

Distinct changes in the colonic microbiome associated with acute diverticulitis.

Colorectal disease : the official journal of the Association of Coloproctology of Great Britain and Ireland [Epub ahead of print].

AIM: The pathogenesis of acute diverticulitis (AD) remains incompletely understood, despite it being one of the most common gastrointestinal conditions worldwide. The aim of this study was to investigate the role of the colonic microbiome in the pathogenesis of AD.

METHOD: A prospective case-control study was performed, comparing the microbiome of AD patients with that of controls, using 16S rRNA sequencing of rectal swab samples.

RESULTS: The microbiome of individuals with AD showed lower diversity than that of controls. There were significant compositional differences observed, with a lower abundance of commensal bacterial families and genera such as Lachnospiraceae, Ruminococcus and Faecalibacterium in AD patients compared with controls, and there was an increase in several genera with known pathogenic roles including Fusobacteria, Prevotella and Paraprevotella.

CONCLUSION: This is the largest study to date to examine the microbiota of AD patients, and adds evidence to the proposed hypothesis that alterations in the colonic microbiome play a role in the pathogenesis of AD.

RevDate: 2022-08-11

Xie C, Teng J, Wang X, et al (2022)

Multi-omics analysis reveals gut microbiota-induced intramuscular fat deposition via regulating expression of lipogenesis-associated genes.

Animal nutrition (Zhongguo xu mu shou yi xue hui), 9:84-99 pii:S2405-6545(21)00211-0.

The gut microbiome has great effects on the digestion, absorption, and metabolism of lipids. However, the microbiota composition that can alter the fat deposition and the meat quality of pigs remains unclear. Here, we used Laiwu (LW) pigs (a native Chinese breed with higher intramuscular fat) compared with commercial crossbreed Duroc × (Landrace × Yorkshire) (DLY) pigs to investigate the effects of microbiota on meat quality, especially in intramuscular fat content. A total of 32 DLY piglets were randomly allotted to 4 groups and transplanted with fecal microbiota from healthy LW pigs. The results indicated that the high dose of fecal microbiota transplantation (HFMT) selectively enhanced fat deposition in longissimus dorsi (P < 0.05) but decreased backfat thickness (P < 0.05) compared with control group. HFMT significantly altered meat color and increased feed conversation ratio (P < 0.05). Furthermore, the multi-omics analysis revealed that Bacteroides uniformis, Sphaerochaeta globosa, Hydrogenoanaerobacterium saccharovorans, and Pyramidobacter piscolens are the core species which can regulate lipid deposition. A total of 140 male SPF C57BL/6j mice were randomly allotted into 7 groups and administrated with these 4 microbes alone or consortium to validate the relationships between microbiota and lipid deposition. Inoculating the bacterial consortium into mice increased intramuscular fat content (P < 0.05) compared with control mice. Increased expressions of lipogenesis-associated genes including cluster of differentiation 36 (Cd36), diacylglycerol O-acyltransferase 2 (Dgat2), and fatty acid synthase (FASN) were observed in skeletal muscle in the mice with mixed bacteria compared with control mice. Together, our results suggest that the gut microbiota may play an important role in regulating the lipid deposition in the muscle of pigs and mice.

RevDate: 2022-08-11

Deng L, Luo YZ, Liu F, et al (2022)

Subcutaneous infection caused by Mycobacterium abscessus following cosmetic injections of botulinum toxin: A case report.

World journal of clinical cases, 10(18):6141-6147.

BACKGROUND: In recent years, the cosmetic intervention related infections caused by nontuberculous mycobacteria (NTM) are increasing as the informal cosmetic treatments are performed. However, many dermatologists are inexperienced in the diagnosis and management of similar cases. Here we report a case of subcutaneous infection caused by Mycobacterium abscessus (M. abscessus) following cosmetic injections of botulinum toxin.

CASE SUMMARY: A 53-year-old woman presented with multiple abscesses and nodules on her forehead and both temporal sites for half a month after cosmetic injections of botulinum toxin. Her lesions did not show any alleviation after 2-wk prescription of antibiotics. Laboratory examinations indicated that she had no sign of immunodeficiency and the whole body of computed tomography did not find any systemic infection or diseases. The pathology of skin tissue showed inflammatory cell infiltration with the negative results of Periodic acid Schiff (PAS) and Acid-fast staining and the culture yielded no microbiome. Afterwards, the puncture on abscess was performed and M. abscessus was successfully isolated. The pathogen was identified by acid-fast staining and DNA sequencing. The patient was treated with the strategy of clarithromycin, ofloxacin, and amikacin according to the result of drug sensitivity test and got complete remission of the lesions.

CONCLUSION: The case presents the whole process of diagnosis and management of NTM infection after cosmetic intervention and highlights the diagnostic thoughts. In a word, the mycobacterium infection should be aware in patients after cosmetic performance.

RevDate: 2022-08-11

Tong KPS, Green SJ, Ortiz J, et al (2022)

Association between hemoglobin A1c, Vitamin C, and microbiome in diabetic foot ulcers and intact skin: A cross-sectional study.

Health science reports, 5(5):e718 pii:HSR2718.

Background and Aims: Diabetic foot ulcers (DFUs) add billions of dollars to the direct annual costs associated with diabetes. Despite various treatments, many DFUs do not heal and become infected. Both skin-associated microbial communities and glycemic control are believed to be important in nonhealing DFUs. Recent studies have linked serum Vitamin C levels with glycemic control and DFUs. This cross-sectional study assessed skin microbiome in DFUs, intact diabetic skin, and nondiabetic skin to identify correlations between hemoglobin A1c (HbA1c), Vitamin C, and microbial community structure. Correlations between Vitamin C, HbA1c, wound size, and ulcer duration were also determined.

Methods: Participants had their DFUs or intact skin culture swabbed. HbA1c was obtained via point-of-care fingerstick testing and serum Vitamin C was obtained via venipuncture. All participants completed a dietary questionnaire. Participants with ulcers were stratified into the controlled (≤8.0%) or uncontrolled (>8.0%) HbA1c group. Analysis of microbial communities was performed via 16S ribosomal RNA (rRNA) gene amplicon sequencing and bacterial load was measured by the domain-level quantitative polymerase chain reaction of the 16S rRNA gene.

Results: Forty-two patients were recruited over 6 months. Bacteria from the genera Staphylococcus and Stenotrophomonas were present in all samples and often dominant, but a shift towards anaerobic pathogenic taxa was observed in ulcers. No global significant differences were observed for HbA1c and Vitamin C levels in the microbial community structure (R < 0.013/p > 0.375). Bacterial loads were 4-5 orders of magnitude higher in ulcers than in intact skin samples. Bacterial load was not significantly higher in the uncontrolled HbA1c group (p = 0.67). Larger wound sizes (p = 0.46) were observed in the uncontrolled HbA1c group compared to the control. Lower Vitamin C levels (p = 0.002) were observed in the uncontrolled HbA1c group compared to nondiabetic controls.

Conclusion: Understanding the link between Vitamin C and HbA1c and DFU microbiome may aid in new therapies.

RevDate: 2022-08-11

Sakabe Y, Nishizawa H, Kato A, et al (2022)

Longitudinal study of the vaginal microbiome in pregnancies involving preterm labor.

Fujita medical journal, 8(3):96-101.

Objectives: Alterations in the vaginal bacterial flora reflect the status of various obstetric conditions and are associated with mechanisms that underlie certain pregnancy-associated complications. These changes are also a predictive biomarker for clinical outcomes of these adverse events.

Methods: We examined the vaginal microbiome in samples from pregnant Japanese women with preterm labor.

Results: The microbiota composition in preterm delivery (PD) samples differed from those of control or threatened preterm delivery (TPD) samples in principal component analysis. An increase in Firmicutes and a decrease in Actinobacteria were significantly associated with PD only (both P<0.01). In the Firmicutes phylum, Lactobacillus tended to be abundant, and the abundance of L. iners and L. crispatus was especially high, whereas the L. gasseri population was low in PD samples. Longitudinal analysis showed that the abundance of L. iners decreased after commencing tocolytic treatment in TPD samples compared with before treatment, but it remained high in PD samples.

Conclusions: The vaginal microbiome may be a useful prognostic indicator of preterm labor and a monitoring tool for tocolytic treatment to prevent preterm birth.

RevDate: 2022-08-11

Zheng L, Ji YY, Wen XL, et al (2022)

Fecal microbiota transplantation in the metabolic diseases: Current status and perspectives.

World journal of gastroenterology, 28(23):2546-2560.

With the development of microbiology and metabolomics, the relationship between the intestinal microbiome and intestinal diseases has been revealed. Fecal microbiota transplantation (FMT), as a new treatment method, can affect the course of many chronic diseases such as metabolic syndrome, malignant tumor, autoimmune disease and nervous system disease. Although the mechanism of action of FMT is now well understood, there is some controversy in metabolic diseases, so its clinical application may be limited. Microflora transplantation is recommended by clinical medical guidelines and consensus for the treatment of recurrent or refractory Clostridium difficile infection, and has been gradually promoted for the treatment of other intestinal and extraintestinal diseases. However, the initial results are varied, suggesting that the heterogeneity of the donor stools may affect the efficacy of FMT. The success of FMT depends on the microbial diversity and composition of donor feces. Therefore, clinical trials may fail due to the selection of ineffective donors, and not to faulty indication selection for FMT. A new understanding is that FMT not only improves insulin sensitivity, but may also alter the natural course of type 1 diabetes by modulating autoimmunity. In this review, we focus on the main mechanisms and deficiencies of FMT, and explore the optimal design of FMT research, especially in the field of cardiometabolic diseases.

RevDate: 2022-08-11

Xiong J, Chen X, Zhao Z, et al (2022)

A potential link between plasma short-chain fatty acids, TNF-α level and disease progression in non-alcoholic fatty liver disease: A retrospective study.

Experimental and therapeutic medicine, 24(3):598 pii:ETM-24-3-11536.

The onset and progression of non-alcoholic fatty liver disease (NAFLD) remains unclear, but short-chain fatty acids (SCFAs) in circulation may participate in its pathogenesis by acting as inflammation inhibitors. The aim of this retrospective study was to investigate plasma concentrations of general SCFAs in healthy individuals and in patients with distinct stages of NAFLD. Three main SCFAs (including acetate, propionate and butyrate) were analyzed by gas chromatography. The plasma TNF-α concentration was measured by ELISA. One-way ANOVA, Spearman's correlation and Pearson's correlation analysis were performed to estimate the associations between SCFAs, TNF-α and disease progression. Multiple linear stepwise regression was computed to explore the predictor variables of TNF-α in circulation. A total of 71 patients with NAFLD [including 27 patients with NAFL, 20 patients with non-alcoholic steatohepatitis (NASH) and 24 patients with NAFLD-related cirrhosis (NAFLD-cirrhosis)] and 9 healthy control (HC) subjects were enrolled for analysis. Although not statistically significant, plasma SCFAs were elevated in patients with NAFL compared with HC subjects, whereas the vast majority of SCFAs were statistically reduced in patients with NASH or NAFLD-cirrhosis compared with patients with NAFL. Plasma SCFAs had no significant differences in NASH or NAFLD-cirrhosis patients compared with HC subjects. In addition, significant negative correlations were observed between TNF-α and SCFAs. The progression of NAFLD (β=0.849; P<0.001) and the decline of the total three SCFA concentrations (β=-0.189; P<0.001) were recognized as independent risk variables related to the elevated peripheral TNF-α in the multiple linear stepwise regression model. Plasma SCFA concentrations may alter with the development of NAFLD and may have a potential link to TNF-α and the progression of NAFLD, which may serve a protective role toward disease advancement. Further mechanistic studies, such as analysis of gastrointestinal microecology, signaling pathways and functions involved in TNF-α, need to be performed. Also, therapeutic supplementation of SCFAs for NASH and NAFLD-cirrhosis needs further research and verification.

RevDate: 2022-08-10

Ali A, Elrys AS, Liu L, et al (2022)

Deciphering the Synergies of Reductive Soil Disinfestation Combined with Biochar and Antagonistic Microbial Inoculation in Cucumber Fusarium Wilt Suppression Through Rhizosphere Microbiota Structure.

Microbial ecology [Epub ahead of print].

Application of reductive soil disinfestation (RSD), biochar, and antagonistic microbes have become increasingly popular strategies in a microbiome-based approach to control soil-borne diseases. The combined effect of these remediation methods on the suppression of cucumber Fusarium wilt associated with microbiota reconstruction, however, is still unknown. In this study, we applied RSD treatment together with biochar and microbial application of Trichoderma and Bacillus spp. in Fusarium-diseased cucumbers to investigate their effects on wilt suppression, soil chemical changes, microbial abundances, and the rhizosphere communities. The results showed that initial RSD treatment followed by biochar amendment (RSD-BC) and combined applications of microbial inoculation and biochar (RSD-SQR-T37-BC) decreased nitrate concentration and raised soil pH, soil organic carbon (SOC), and ammonium in the treated soils. Under RSD, the applications of Bacillus (RSD-SQR), Trichoderma (RSD-T37), and biochar (RSD-BC) suppressed wilt incidence by 26.8%, 37.5%, and 32.5%, respectively, compared to non-RSD treatments. Moreover, RSD-SQR-T37-BC and RSD-T37 caused greater suppressiveness of Fusarium wilt and F. oxysporum by 57.0 and 33.5%, respectively. Rhizosphere beta diversity and alpha diversity revealed a difference between RSD-treated and non-RSD microbial groups. The significant increase in the abundance, richness, and diversity of bacteria, and the decrease in the abundance and diversity of fungi under RSD-induced treatments attributed to the general suppression. Identified bacterial (Bacillus, Pseudoxanthomonas, Flavobacterium, Flavisolibacter, and Arthrobacter) and fungal (Trichoderma, Chaetomium, Cladosporium, Psathyrella, and Westerdykella) genera were likely the potential antagonists of specific disease suppression for their significant increase of abundances under RSD-treated soils and high relative importance in linear models. This study infers that the RSD treatment induces potential synergies with biochar amendment and microbial applications, resulting in enhanced general-to-specific suppression mechanisms by changing the microbial community composition in the cucumber rhizosphere.

RevDate: 2022-08-10

Xie L, L Hu (2022)

Research progress in the early diagnosis of Parkinson's disease.

Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology [Epub ahead of print].

Parkinson's disease is the second major neurodegenerative disease with increasing incidence and population in the world year by year. The pathogenesis of Parkinson's disease is still not completely clear, and the identification of Parkinson's disease prodromal manifestations and accurate diagnosis is still facing great challenges. This review summarizes the interaction of environmental toxicants, mitochondrial dysfunction, α-synuclein, gut microbiome dysbiosis, neuroinflammation, and other pathophysiological factors in Parkinson's disease. It also discusses the prodromal manifestations of Parkinson's disease, such as olfactory dysfunction, sleep dysfunction and other non-motor symptoms, the current diagnostic challenges, and the application status of emerging neuroimaging technologies such as magnetic resonance imaging (MRI), positron emission tomography (PET), and single-photon emission tomography (SPECT).

RevDate: 2022-08-10

Lu B, Yan Y, Dong L, et al (2022)

Author Correction: Integrated characterization of SARS-CoV-2 genome, microbiome, antibiotic resistance and host response from single throat swabs.

Cell discovery, 8(1):78 pii:10.1038/s41421-022-00448-5.

RevDate: 2022-08-10

Coleman JL, Hatch-McChesney A, Small SD, et al (2022)

Orally Ingested Probiotics, Prebiotics, and Synbiotics as Countermeasures for Respiratory Tract Infections in Non-elderly Adults: A Systematic Review and Meta-analysis.

Advances in nutrition (Bethesda, Md.) pii:6660647 [Epub ahead of print].

BACKGROUND: The impact of gut microbiota-targeted interventions on the incidence, duration, and severity of respiratory tract infections (RTI) in non-elderly adults, and factors moderating any such effects, are unclear.

OBJECTIVES: This systematic review and meta-analysis aimed to determine the effects of orally ingested probiotics, prebiotics, and synbiotics versus placebo on RTI incidence, duration, and severity in non-elderly adults, and to identify potential sources of heterogeneity.

METHODS: Studies were identified by searching CENTRAL, PubMed, Scopus, and Web of Science up to December 2021. English-language peer-reviewed publications of randomized, placebo-controlled studies that tested an orally ingested probiotic, prebiotic or synbiotic intervention of any dose for ≥ 1 week in adults 18-65 yr were included. Results were synthesized using intention-to-treat and per protocol random effects meta-analysis. Heterogeneity was explored by sub-group meta-analysis and meta-regression. Risk of bias (RoB) was assessed using the Cochrane RoBv.2 tool for randomized trials.

RESULTS: Forty-two manuscripts reporting effects of probiotics (n = 38), prebiotics (n = 2), synbiotics (n = 1) or multiple -biotic types (n = 1) were identified (n = 9,179 subjects). Probiotics reduced the risk of experiencing ≥ 1 RTI (relative risk = 0.91 [95%CI: 0.84, 0.98] P = 0.01), and total days (rate ratio = 0.77 [0.71, 0.83] P < 0.001), duration (Hedges's g = -0.23 [-0.39, -0.08] P = 0.004) and severity (Hedges's g = -0.16 [-0.29, -0.03] P = 0.02) of RTI. Effects were relatively consistent across different strain combinations, doses and durations, though reductions in RTI duration were larger with fermented dairy as the delivery matrix, and beneficial effects of probiotics were not observed in physically active populations. Overall RoB was rated as "some concerns" for most studies.

CONCLUSIONS: Orally ingested probiotics, relative to placebo, modestly reduce the incidence, duration and severity of RTI in non-elderly adults. Physical activity and delivery matrix may moderate some of these effects. Whether prebiotic and synbiotic interventions confer similar protection remains unclear due to few relevant studies. PROSPERO registration: CRD42020220213.

RevDate: 2022-08-10

Easson DD, Murphy VA, Ballok AE, et al (2022)

Food safety assessment and toxicity study of the synbiotic consortium SBD111.

Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association pii:S0278-6915(22)00527-0 [Epub ahead of print].

The human gut microbiome plays a crucial role in skeletal homeostasis. The synbiotic consortium or Defined Microbial Assemblage™ (DMA™) food product, SBD111, consisting of probiotic microbes and prebiotic fibers was designed to promote bone health based on its capacity to produce short chain fatty acid (SCFA) in vitro, possess genes for vitamin K2 production and degrade plant fibers leading to improved skeletal health in mice. A 28-day repeated administration study was performed to evaluate the oral toxicity of SBD111 in female rats (age/weight at study start: 5-7 weeks/120-180 g) administered levels of 0, 2.0 x 1010, 9.8 x 1010, or 2.0 x 1011 colony forming units (CFU)/kg-bw. No mortality or morbidity occurred during the study. There were no significant differences in body weights, hematology, serum chemistry, coagulation, organ weights, or food consumption in the test groups compared to the controls. Liver weight to body weight ratios were signficantly decreased at 9.8 x 1010 CFU/kg-bw when compared to controls. No treatment related changes in motor activity, sensory stimuli, or grip strength were observed. Based on these findings, SBD111 administered to female rats has a no-observable adverse effect level (NOAEL) at the highest level tested of 2.0 x 1011 CFU/kg-bw.

RevDate: 2022-08-10

Dawud LM, Holbrook EM, CA Lowry (2022)

Evolutionary Aspects of Diverse Microbial Exposures and Mental Health: Focus on "Old Friends" and Stress Resilience.

Current topics in behavioral neurosciences [Epub ahead of print].

The prevalence of inflammatory disease conditions, including allergies, asthma, and autoimmune disorders, increased during the latter half of the twentieth century, as societies transitioned from rural to urban lifestyles. A number of hypotheses have been put forward to explain the increasing prevalence of inflammatory disease in modern urban societies, including the hygiene hypothesis and the "Old Friends" hypothesis. In 2008, Rook and Lowry proposed, based on the evidence that increased inflammation was a risk factor for stress-related psychiatric disorders, that the hygiene hypothesis or "Old Friends" hypothesis may be relevant to psychiatric disorders. Since then, it has become more clear that chronic low-grade inflammation is a risk factor for stress-related psychiatric disorders, including anxiety disorders, mood disorders, and trauma- and stressor-related disorders, such as posttraumatic stress disorder (PTSD). Evidence now indicates that persons raised in modern urban environments without daily contact with pets, relative to persons raised in rural environments in proximity to farm animals, respond with greater systemic inflammation to psychosocial stress. Here we consider the possibility that increased inflammation in persons living in modern urban environments is due to a failure of immunoregulation, i.e., a balanced expression of regulatory and effector T cells, which is known to be dependent on microbial signals. We highlight evidence that microbial signals that can drive immunoregulation arise from phylogenetically diverse taxa but are strain specific. Finally, we highlight Mycobacterium vaccae NCTC 11659, a soil-derived bacterium with anti-inflammatory and immunoregulatory properties, as a case study of how single strains of bacteria might be used in a psychoneuroimmunologic approach for prevention and treatment of stress-related psychiatric disorders.

RevDate: 2022-08-10

Dickerson F, Dilmore AH, Godoy-Vitorino F, et al (2022)

The Microbiome and Mental Health Across the Lifespan.

Current topics in behavioral neurosciences [Epub ahead of print].

INTRODUCTION: The combined genetic material of the microorganisms in the human body, known as the microbiome, is being increasingly recognized as a major determinant of human health and disease. Although located predominantly on mucosal surfaces, these microorganisms have profound effects on brain functioning through the gut-brain axis.

METHOD: The content of the chapter is based on a study group session at the annual meeting of the American College of Neuropsychopharmacology (ACNP). The objective was to discuss the emerging relationship between the human microbiome and mental health as relevant to ACNP's interests in developing and evaluating novel neuropsychiatric treatment strategies. The focus is on specific brain disorders, such as schizophrenia, substance use, and Alzheimer's disease, as well as on broader clinical issues such as suicidality, loneliness and wisdom in old age, and longevity.

RESULTS: Studies of schizophrenia indicate that the microbiome of individuals with this disorder differs from that of non-psychiatric comparison groups in terms of diversity and composition. Differences are also found in microbial metabolic pathways. An early study in substance use disorders found that individuals with this disorder have lower levels of beta diversity in their oral microbiome than a comparison group. This measure, along with others, was used to distinguish individuals with substance use disorders from controls. In terms of suicidality, there is preliminary evidence that persons who have made a suicide attempt differ from psychiatric and non-psychiatric comparison groups in measures of beta diversity. Exploratory studies in Alzheimer's disease indicate that gut microbes may contribute to disease pathogenesis by regulating innate immunity and neuroinflammation and thus influencing brain function. In another study looking at the microbiome in older adults, positive associations were found between wisdom and alpha diversity and negative associations with subjective loneliness. In other studies of older adults, here with a focus on longevity, individuals with healthy aging and unusually long lives had an abundance of specific microorganisms which distinguished them from other individuals.

DISCUSSION: Future studies would benefit from standardizing methods of sample collection, processing, and analysis. There is also a need for the standardized collection of relevant demographic and clinical data, including diet, medications, cigarette smoking, and other potentially confounding factors. While still in its infancy, research to date indicates a role for the microbiome in mental health disorders and conditions. Interventions are available which can modulate the microbiome and lead to clinical improvements. These include microbiome-altering medications as well as probiotic microorganisms capable of modulating the inflammation in the brain through the gut-brain axis. This research holds great promise in terms of developing new methods for the prevention and treatment of a range of human brain disorders.

RevDate: 2022-08-10

Serpas Higbie V, Rogers J, Hwang H, et al (2022)

Antibiotic Exposure Does Not Impact Immune Checkpoint Blockade Response in MSI-H/dMMR Metastatic Colorectal Cancer: A Single-Center Experience.

The oncologist pii:6659732 [Epub ahead of print].

BACKGROUND: Immune checkpoint blockade (ICB) has improved outcomes for patients with microsatellite instability high (MSI-H)/deficient mismatch repair (dMMR) tumors. However, not all MSI-H/dMMR patients will exhibit the same ICB efficacy. Previous studies suggest that concomitant antibiotic use while receiving ICB may result in poorer outcomes. We aimed to evaluate this association in patients with MSI-H/dMMR metastatic colorectal cancer (mCRC).

MATERIALS AND METHODS: A single-site, retrospective review of 57 patients with MSI-H/dMMR mCRC that received ICB was completed. Data collected included patient demographics, ICB information, and antibiotic use. Antibiotic exposure was considered from 90 days prior to ICB through 6 weeks after initiation. Primary endpoint was overall response rate (ORR).

RESULTS: The majority of patients received pembrolizumab (27 [47%]) or nivolumab (17 [30%]) monotherapy as their ICB agent. Of the 57 patients, 19 (33.3%) had antibiotic exposure from 90 days prior to ICB initiation through 6 weeks after initiation with most (13 [68%]) having antibiotic use in the 30 days preceding ICB initiation. Similar ORRs were seen in both groups (P-value > .99). No difference was observed in OS (P-value .29) or PFS (P-value .36) between groups.

CONCLUSION: Our data show no association of lower response rates or survival in those MSI-H/dMMR patients with mCRC who receive antibiotics around the initiation of ICB. This information needs to be confirmed in a larger prospective cohort.

RevDate: 2022-08-10

Qiao J, Zhang SX, Chang MJ, et al (2022)

Specific enterotype of gut microbiota predicted clinical effect of methotrexate in patients with rheumatoid arthritis.

Rheumatology (Oxford, England) pii:6659539 [Epub ahead of print].

OBJECTIVE: The most used drug in rheumatoid arthritis (RA) remains methotrexate (MTX). Unfortunately, up to 50% of patients do not achieve a clinically adequate outcome. Here we study whether the gut microbiota patterns can aid in the prediction of MTX efficacy in RA.

METHOD: To dissect gut microbiome profiles of RA patients (n = 145), 16S rRNA gene sequencing was performed. Dirichlet multinomial mixture (DMM) clustering was used to identify enterotypes at genus level. The relationships between enterotypes and clinical measures (such as lymphocyte subsets and cytokines detected by flow cytometry) were explored. Then, enterotype stability was evaluated by the stratification of the RA patients cohort in Shanghai, China (n = 66) using the same method. Finally, the enterotype-based gut microbial human index (EGMI) classifier was applied to another independent RA patients cohort (n = 27) to identify the factors associated with MTX clinical response.

RESULTS: Our analysis revealed that the RA patients always displayed two different dysbiotic microbiota patterns: RA E1 comprised predominantly Prevotella and RA E2 comprised predominantly Bacteroides. Among all of the lymphocyte subsets and cytokines, only the number of CD8+ T cells showed a significant difference between RA E1 and RA E2. These results were validated in the RA patients cohort in Shanghai, China. Significant associations of RA E1 with clinical response to subsequent MTX treatment were confirmed by another independent RA patients cohort.

CONCLUSION: Together, EGMI classifier was useful to identify precisely and effectively enterotypes of individual RA patients, which could effectively evaluate MTX clinical responses.

RevDate: 2022-08-10

Castro Lima Silva do Amaral G, Hassan MA, Sloniak MC, et al (2022)

Effects of antimicrobial mouthwashes on the human oral microbiome: Systematic review of controlled clinical trials.

International journal of dental hygiene [Epub ahead of print].

OBJECTIVES: This review aimed to assess the impact of mouthwashes on the composition of the human oral microbiome.

METHOD: An electronic search algorithm was adapted to MEDLINE- PubMed, Scopus, Embase, and ISI Web of Science, and reference lists of relevant sources were manually searched. Inclusion criteria were controlled clinical trials published in English whose population were adult individuals who rinse with antimicrobial mouthwashes and that analyzed changes in the oral microbiome by metataxonomy, metagenomics, or phylogenetic microarray. Identified studies were screened and assessed following the PRISMA guidelines and results were compiled into qualitative synthesis of the evidence.

RESULTS: Five controlled-clinical studies were included. These studies found associations between the daily use of mouthwashes and changes in the oral microbiome, but the nature of the effect varied according to the mouthwash. Chlorhexidine (CHX) rinses lowered microbial diversity. While 7-day use of CHX led to increases in the abundance of Neisseria, Streptococcus and Granulicatella and a decrease in the abundance of Actinomyces, its prolonged use led to widespread reductions in several genera and species. Cetylpyridinium chloride-containing mouthwashes specifically lowered the abundance of gingivitis-associated genera. In contrast, N-acetyl cysteine-based mouthwashes did not promote changes in the oral microbiome.

CONCLUSIONS: Despite substantial heterogeneity, we found evidence to support the hypothesis that CHX and CPC mouthwashes promote changes in oral microbial structure and/or reductions in community diversity that favor resolution of dysbiosis. However, future large population-based studies of adequate duration are needed to fully understand the extent to which antimicrobial mouthwashes modulate the microbiome.

RevDate: 2022-08-10

Angarita-Díaz MDP, Fong C, Bedoya-Correa CM, et al (2022)

Does high sugar intake really alter the oral microbiota?: A systematic review.

Clinical and experimental dental research [Epub ahead of print].

OBJECTIVES: Diet is one of the main factors influencing the diversity and interactions of the oral microbiota. The purpose of this study is to determine the impact of sugar intake on the microbial diversity and bacteria that predominate under these conditions.

MATERIAL AND METHODS: A systematic review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guide, using the PubMed, Scopus, and Science Direct databases and combinations of the words "microbiota," "microbiology," "bacteria," "sugars," "dysbiosis," "caries," "microbiome," "oral microbial," and "oral microbiota profile pattern." The selection criteria included year, language, type of publication, comparison of microbiota during low and high sugar intake, and bacterial identification by molecular sequencing of the 16S subunit of ribosomal RNA.

RESULTS: Out of a total of 374 papers that came up after the initial search, 8 met the criteria for this review. The papers included research on populations comprising children, young adults, and adults, with most of the studies reporting selection criteria for the participants and using validated instruments to determine sugar intake. Apart from one study, all others reported for high sugar intake conditions a significant decrease in microbial diversity of the oral microbiome and the predominance of several bacterial genera or species, including Streptococcus, Scardovia, Veillonella, Rothia, Actinomyces, and Lactobacillus.

CONCLUSIONS: Sugar-rich diets have a significantly unfavorable effect on the diversity and balance of oral microbiota; however, further studies are required to determine the exact role of sugar in microbial interactions.

RevDate: 2022-08-10

Liao LB, Chen XX, Xiang J, et al (2022)

Zanthoxylum bungeanum root-rot associated shifts in microbiomes of root endosphere, rhizosphere, and soil.

PeerJ, 10:e13808 pii:13808.

Root-rot disease has lead to serious reduction in yields and jeopardized the survival of the economically and ecologically important Zanthoxylum bungeanum trees cultured in Sichuan Province. In order to investigate the interaction between the microbiome and the root-rot disease, a metagenomic analysis was performed to characterize the microbial communities and functions in Z. bungeanum root endosphere, rhizosphere and bulk soil with/without root-rot disease. Soil physicochemical properties, microbial population size and enzyme activities were also analyzed for finding their interactions with the root-rot disease. As results, lower total nitrogen (TN) and available phosphorus (AP) contents but higher pH in rhizosphere and bulk soil, as well as lower substrate-induced respiration (SIR) and higher protease activity in bulk soil of diseased trees were found, in comparison with that of healthy trees. Microbial diversity and community composition were changed by root-rot disease in the endosphere, but not in rhizosphere and bulk soils. The endophytic microbiome of diseased trees presented higher Proteobacteria abundance and lower abundances of Bacteroidetes, Firmicutes and dominant fungal phyla. The relative abundances of nitrogen cycle- and carbon cycle-related genes in endophytic microbiomes were different between the diseased and healthy trees. Based on ANOSIM and PCoA, functional profiles (KEGG and CAZy) of microbiomes in rhizosphere and bulk soil shifted significantly between the diseased and healthy trees. In addition, soil pH, TN, AP, SIR, invertase and protease were estimated as the main factors influencing the shifts of taxonomic and functional groups in microbiomes of rhizosphere and bulk soil. Conclusively, the imbalance of root and soil microbial function groups might lead to shifts in the root endosphere-rhizosphere microenvironment, which in turn resulted in Z. bungeanum root-rot.

RevDate: 2022-08-09

Sergaki C, Anwar S, Fritzsche M, et al (2022)

Developing whole cell standards for the microbiome field.

Microbiome, 10(1):123.

BACKGROUND: Effective standardisation of the microbiome field is essential to facilitate global translational research and increase the reproducibility of microbiome studies. In this study, we describe the development and validation of a whole cell reference reagent specific to the gut microbiome by the UK National Institute for Biological Standards and Control. We also provide and test a two-step reporting framework to allow microbiome researchers to quickly and accurately validate choices of DNA extraction, sequencing, and bioinformatic pipelines.

RESULTS: Using 20 strains that are commonly found in the gut, we developed a whole cell reference reagent (WC-Gut RR) for the evaluation of the DNA extraction protocols commonly used in microbiome pipelines. DNA was first analysed using the physicochemical measures of yield, integrity, and purity, which demonstrated kits widely differed in the quality of the DNA they produced. Importantly, the combination of the WC-Gut RR and the three physicochemical measures allowed us to differentiate clearly between kit performance. We next assessed the ability of WC-Gut RR to evaluate kit performance in the reconstitution of accurate taxonomic profiles. We applied a four-measure framework consisting of Sensitivity, false-positive relative abundance (FPRA), Diversity, and Similarity as previously described for DNA reagents. Using the WC-Gut RR and these four measures, we could reliably identify the DNA extraction kits' biases when using with both 16S rRNA sequencing and shotgun sequencing. Moreover, when combining this with complementary DNA standards, we could estimate the relative bias contributions of DNA extraction kits vs bioinformatic analysis. Finally, we assessed WC-Gut RR alongside other commercially available reagents. The analysis here clearly demonstrates that reagents of lower complexity, not composed of anaerobic and hard-to-lyse strains from the gut, can artificially inflate the performance of microbiome DNA extraction kits and bioinformatic pipelines.

CONCLUSIONS: We produced a complex whole cell reagent that is specific for the gut microbiome and can be used to evaluate and benchmark DNA extractions in microbiome studies. Used alongside a DNA standard, the NIBSC DNA-Gut-Mix RR helps estimating where biases occur in microbiome pipelines. In the future, we aim to establish minimum thresholds for data quality through an interlaboratory collaborative study. Video Abstract.

RevDate: 2022-08-09

Schmid DW, Fackelmann G, Wasimuddin , et al (2022)

A framework for testing the impact of co-infections on host gut microbiomes.

Animal microbiome, 4(1):48.

Parasitic infections disturb gut microbial communities beyond their natural range of variation, possibly leading to dysbiosis. Yet it remains underappreciated that most infections are accompanied by one or more co-infections and their collective impact is largely unexplored. Here we developed a framework illustrating changes to the host gut microbiome following single infections, and build on it by describing the neutral, synergistic or antagonistic impacts on microbial α- and ß-diversity expected from co-infections. We tested the framework on microbiome data from a non-human primate population co-infected with helminths and Adenovirus, and matched patterns reported in published studies to the introduced framework. In this case study, α-diversity of co-infected Malagasy mouse lemurs (Microcebus griseorufus) did not differ in comparison with that of singly infected or uninfected individuals, even though community composition captured with ß-diversity metrices changed significantly. Explicitly, we record stochastic changes in dispersion, a sign of dysbiosis, following the Anna-Karenina principle rather than deterministic shifts in the microbial gut community. From the literature review and our case study, neutral and synergistic impacts emerged as common outcomes from co-infections, wherein both shifts and dispersion of microbial communities following co-infections were often more severe than after a single infection alone, but microbial α-diversity was not universally altered. Important functions of the microbiome may also suffer from such heavily altered, though no less species-rich microbial community. Lastly, we pose the hypothesis that the reshuffling of host-associated microbial communities due to the impact of various, often coinciding parasitic infections may become a source of novel or zoonotic diseases.

RevDate: 2022-08-09

Gómez M, Martinez D, Muñoz M, et al (2022)

Aedes aegypti and Ae. albopictus microbiome/virome: new strategies for controlling arboviral transmission?.

Parasites & vectors, 15(1):287.

Aedes aegypti and Aedes albopictus are the main vectors of highly pathogenic viruses for humans, such as dengue (DENV), chikungunya (CHIKV), and Zika (ZIKV), which cause febrile, hemorrhagic, and neurological diseases and remain a major threat to global public health. The high ecological plasticity, opportunistic feeding patterns, and versatility in the use of urban and natural breeding sites of these vectors have favored their dispersal and adaptation in tropical, subtropical, and even temperate zones. Due to the lack of available treatments and vaccines, mosquito population control is the most effective way to prevent arboviral diseases. Resident microorganisms play a crucial role in host fitness by preventing or enhancing its vectorial ability to transmit viral pathogens. High-throughput sequencing and metagenomic analyses have advanced our understanding of the composition and functionality of the microbiota of Aedes spp. Interestingly, shotgun metagenomics studies have established that mosquito vectors harbor a highly conserved virome composed of insect-specific viruses (ISV). Although ISVs are not infectious to vertebrates, they can alter different phases of the arboviral cycle, interfering with transmission to the human host. Therefore, this review focuses on the description of Ae. aegypti and Ae. albopictus as vectors susceptible to infection by viral pathogens, highlighting the role of the microbiota-virome in vectorial competence and its potential in control strategies for new emerging and re-emerging arboviruses.

RevDate: 2022-08-09

Ziomber-Lisiak A, Talaga-Ćwiertnia K, Sroka-Oleksiak A, et al (2022)

Repetitive transcranial direct current stimulation modulates the brain-gut-microbiome axis in obese rodents.

Pharmacological reports : PR [Epub ahead of print].

BACKGROUND: Complex interactions between the brain, gut and adipose tissue allow to recognize obesity as a neurometabolic disorder. The recent data have shown that gut microbiota can play a potential role in obesity development. Transcranial direct current stimulation (tDCS) is a safe and non-invasive technique to modulate the activity of cerebral cortex and other connected brain areas also in context of appetite control. The objective of this study was to evaluate the effects of repetitive anodal tDCS (AtDCS) of prefrontal cortex on feeding behavior, metabolic status and selected phyla of gut microbiota in rats with obesity induced by high-calorie diet (HCD).

METHODS: 32 female Wistar rats were equally divided into 4 subgroups depending on diet effect (lean versus obese) and type of stimulation (active versus sham tDCS versus no stimulation). Feed intake, body weight, blood lipoproteins and leptin levels as well as Firmicutes and Bacteroidetes in intestines and stool were examined.

RESULTS: HCD changed feeding behavior and metabolic parameters typically for obesity-related ranges and resulted in an abundance of Firmicutes at the expanse of Bacteroidetes in the large intestine and stool. AtDCS decreased appetite, body weight, and cholesterol levels. In addition, AtDCS reduced ratio of the average number of Firmicutes to average number of Bacteroidetes in all examined tissues.

CONCLUSIONS: Repetitive AtDCS is not only effective for appetite restriction but can also modulate gut microbiome composition which demonstrates the existence of the brain-gut-microbiome axis and points at this technique as a promising complementary treatment for obesity. However, the effects should be further replicated in human studies.

RevDate: 2022-08-09

Turunen J, Tejesvi MV, Suokas M, et al (2022)

Bacterial extracellular vesicles in the microbiome of first-pass meconium in newborn infants.

Pediatric research [Epub ahead of print].

BACKGROUND: Bacterial extracellular vesicles (EVs) are more likely to cross biological barriers than whole-cell bacteria. We previously observed EV-sized particles by electron microscopy in the first-pass meconium of newborn infants. We hypothesized that EVs may be of bacterial origin and represent a novel entity in the human microbiome during fetal and perinatal periods.

METHODS: We extracted EVs from first-pass meconium samples of 17 newborn infants and performed bacterial 16S rRNA gene sequencing of the vesicles. We compared the EV content from the meconium samples of infants based on the delivery mode, and in vaginal delivery samples, based on the usage of intrapartum antibiotics.

RESULTS: We found bacterial EVs in all first-pass meconium samples. All EV samples had bacterial RNA. Most of the phyla present in the samples were Firmicutes (62%), Actinobacteriota (18%), Proteobacteria (10%), and Bacteroidota (7.3%). The most abundant genera were Streptococcus (21%) and Staphylococcus (17%). The differences between the delivery mode and exposure to antibiotics were not statistically significant.

CONCLUSIONS: Bacterial EVs were present in the first-pass meconium of newborn infants. Bacterial EVs may represent an important novel feature of the gut microbiome during fetal and perinatal periods.

IMPACT: We show that bacterial extracellular vesicles are present in the microbiome of first-pass meconium in newborn infants. This is a novel finding. To our knowledge, this is the first study to report the presence of bacterial extracellular vesicles in the gut microbiome during fetal and perinatal periods. This finding is important because bacterial extracellular vesicles are more likely to cross biological barriers than whole-cell bacteria. Thus, the early gut microbiome may potentially interact with the host through bacterial EVs.

RevDate: 2022-08-09

Widmer D, Widmer AF, Jeger R, et al (2022)

Prevalence of enterococcal groin colonization in patients undergoing cardiac interventions: Challenging antimicrobial prophylaxis with cephalosporins in TAVR patients.

The Journal of hospital infection pii:S0195-6701(22)00242-0 [Epub ahead of print].

BACKGROUND: Cephalosporins are recommended for prophylaxis before transcatheter aortic valve replacement (TAVR). Infective endocarditis (IE) after TAVR is caused by enterococci in up to 30%, especially early after TAVR. Enterococcal colonization in the groin has been postulated as a source of infection, not only because prophylaxis is not covering enterococci but also because most TAVR are performed by transfemoral access. There are few data analysing the groin microbiome to demonstrate the presence of enterococci.

AIM: To assess prevalence of enterococci in groins of cardiological patients receiving transfemoral interventions.

METHODS: Prospective cohort study at the University Hospital Basel, Switzerland, between February and August 2020. From consecutive patients with transfemoral cardiac interventions two skin swabs from the groin were taken before antibiotic prophylaxis was administered: each one before/after groin disinfection. Swabs were analysed in the local microbiological laboratory following validated culture methods.

FINDINGS: Of 290 included patients, 245 (84.5%) received coronary angiography, 31 (10.7%) TAVR, eight (2.8%) right heart catheterization, five (1.7%) closure of patent foramen ovale, one (0.3%) MitraClip®. In 48 patients, enterococci were detected before disinfection, in three, enterococci were still cultured after disinfection, and in one enterococci were only detected after disinfection. Enterococcal prevalence was 16.6% before and 1.4% after disinfection. Patients colonized with enterococci had a significantly higher body mass index and more often were diabetic.

CONCLUSION: Common enterococcal colonization of the groin coupled with frequently isolated enterococci from patients with TAVR-associated IE provide strong evidence to replace currently recommended antimicrobial prophylaxis with cephalosporins before TAVR with a compound that is active against enterococci.

RevDate: 2022-08-09

URycki DR, Bassiouni M, Good SP, et al (2022)

The streamwater microbiome encodes hydrologic data across scales.

The Science of the total environment pii:S0048-9697(22)05010-0 [Epub ahead of print].

Many fundamental questions in hydrology remain unanswered due to the limited information that can be extracted from existing data sources. Microbial communities constitute a novel type of environmental data, as they are comprised of many thousands of taxonomically and functionally diverse groups known to respond to both biotic and abiotic environmental factors. As such, these microscale communities reflect a range of macroscale conditions and characteristics, some of which also drive hydrologic regimes. Here, we assess the extent to which streamwater microbial communities (as characterized by 16S gene amplicon sequence abundance) encode information about catchment hydrology across scales. We analyzed 64 summer streamwater DNA samples collected from subcatchments within the Willamette, Deschutes, and John Day river basins in Oregon, USA, which range 0.03-29,000 km2 in area and 343-2334 mm/year of precipitation. We applied information theory to quantify the breadth and depth of information about common hydrologic metrics encoded within microbial taxa. Of the 256 microbial taxa that spanned all three watersheds, we found 9.6 % (24.5/256) of taxa, on average, shared information with a given hydrologic metric, with a median 15.6 % (range = 12.4-49.2 %) reduction in uncertainty of that metric based on knowledge of the microbial biogeography. All of the hydrologic metrics we assessed, including daily discharge at different time lags, mean monthly discharge, and seasonal high and low flow durations were encoded within the microbial community. Summer microbial taxa shared the most information with winter mean flows. Our study demonstrates quantifiable relationships between streamwater microbial taxa and hydrologic metrics at different scales, likely resulting from the integration of multiple overlapping drivers of each. Streamwater microbial communities are rich sources of information that may contribute fresh insight to unresolved hydrologic questions.

RevDate: 2022-08-09

Jørgensen C (2022)

Untangling the tumorigenic role of homotrimeric collagen I.

Cancer cell, 40(8):802-804.

Pancreatic ductal adenocarcinoma is characterized by a complex microenvironment. In this issue of Cancer Cell, Chen and colleagues define an oncogenic role of tumor-cell-produced collagen I homotrimers, wherein tumor development is promoted by integrin α3/β1-dependent activation of tumor cell signaling and modulation of tumor microbiome and immunity.

RevDate: 2022-08-09

Lei X, Liu Y, Guo Y, et al (2022)

Debaryomyces nepalensis reduces fungal decay by affecting the postharvest microbiome during jujube storage.

International journal of food microbiology, 379:109866 pii:S0168-1605(22)00338-5 [Epub ahead of print].

Microbial antagonists are effective and environmentally friendly in controlling postharvest diseases of fruit. The present study investigated the influence of D. nepalensis on epiphytic microbiome and postharvest decay of jujube. Results showed that D. nepalensis notably reduced fungal decay, maintained the fruit firmness and delayed discoloration. The epiphytic microbiome revealed that D. nepalensis changed the fungal communities, but few influence on bacterial communities were observed. D. nepalensis, as the dominant population in the treatment group, decreased the abundance of pathogenic fungi of Alternaria, Penicillium, Fusarium and Botrytis, while increased the beneficial bacteria of Pantoea. The canonical correspondence analysis revealed that Debaryomyces was negatively correlated with the decay rate, whereas Penicillium, Acremonium, Rhodosporidiobolus and Hansfordia were positively correlated. In conclusion, D. nepalensis altered the successional process of fungal and bacterial communities to reduce the decay rate of jujube during storage.

RevDate: 2022-08-09

Dhondge HV, Barvkar VT, Paul D, et al (2022)

Exploring the core microbiota in scented rice (Oryza sativa L.) rhizosphere through metagenomics approach.

Microbiological research, 263:127157 pii:S0944-5013(22)00197-5 [Epub ahead of print].

Rice is a major food crop cultivated around the globe. Specially scented rice varieties are of commercial importance but they are low-yielding. The rhizospheric microflora plays a significant role in improving yield and aroma. However, the core microbiome of the scented rice rhizosphere is comparatively less explored. Here, we analyzed the core microbiome associated with the rhizosphere of the scented (Ambemohar-157 and Dehradun basmati) in comparison with non-scented rice (Kolam and Arize 6444 Gold) cultivated at two different geoclimatic zones of India (Maharashtra and Uttarakhand) using the metagenomics approach. The alpha and beta diversity analysis showed that the microbial communities associated with scented and non-scented varieties significantly changes with respect to richness, diversity, and evenness. The taxonomic profiling revealed the variation in composition, diversity, and abundance of the microbiome in terms of phyla and genera associated with scented rice varieties over non-scented. The cluster analysis distinguishes the microbial communities based on their geographical positions. The core microbiome analysis revealed that scented rice rhizosphere shelters distinct and unique microbiota. 28.6 % of genera were exclusively present only in the scented rice rhizosphere. The putative functional gene annotation revealed the high abundance of genes related to the biosynthesis of 2-acetyl-1-pyrroline (2AP) precursors in scented rice. The precursor feeding analysis revealed proline as a preferred substrate by 2AP synthesizing bacteria. The 2AP precursor proline and proline metabolism genes showed a positive correlation. The scented rice-specific rhizobacteria pointed out in this study can be used as bio-inoculants for enhancing aroma, yield, and sustainable rice cultivation.

RevDate: 2022-08-09

Ambalavanan N, KA Willis (2022)

Reply to Pantaleón García et al.

American journal of physiology. Lung cellular and molecular physiology, 323(2):L221-L222.

RevDate: 2022-08-09

Pantaleón García J, Dickson RP, SE Evans (2022)

Minimizing caging effects in murine lung microbiome studies.

American journal of physiology. Lung cellular and molecular physiology, 323(2):L219-L220.

RevDate: 2022-08-09

Yang Z, Zhang Y, Stubbe-Espejel A, et al (2022)

Vaginal microbiota and personal risk factors associated with HPV status conversion-A new approach to reduce the risk of cervical cancer?.

PloS one, 17(8):e0270521 pii:PONE-D-21-39382.

Vaginal microbiota (VMB) is associated with changes in Human papilloma virus (HPV) status, which consequently influences the risk of cervical cancer. This association was often confounded by personal risk factors. This pilot research aimed to explore the relationship between vaginal microbiota, personal risk factors and their interactions with HPV status conversion to identify the vaginal microbiota that was associated with HPV clearance under heterogeneous personal risk factors. A total of 38 women participated by self-collecting a cervicovaginal mucus (CVM) sample that was sent for metagenomics sequencing. Most of the participants also filled in personal risk factors questionnaire through an eHealth platform and authorized the use of their previous HPV genotyping results stored in this eHealth platform. Based on the two HPV results, the participants were grouped into three cohorts, namely HPV negative, HPV persistent infection, and HPV status conversion. The relative abundance of VMB and personal factors were compared among these three cohorts. A correlation investigation was performed between VMB and the significant personal factors to characterize a robustness of the panel for HPV status change using R programming. At baseline, 12 participants were HPV-negative, and 22 were HPV-positive. Within one year, 18 women remained HPV-positive, 12 were HPV-negative and 4 participants showed HPV clearance. The factors in the eHealth questionnaire were systematically evaluated which identified several factors significantly associated with persistent HPV infection, including age, salary, history of reproductive tract infection, and the total number of sexual partners. Concurrent vaginal microbiome samples suggest that a candidate biomarker panel consisting of Lactobacillus gasseri, Streptococcus agalactiae, and Timona prevotella bacteria, which may be associated with HPV clearance. This pilot study indicates a stable HPV status-related vaginal microbe environment. To establish a robust biomarker panel for clinical use, larger cohorts will be recruited into follow-up studies.

RevDate: 2022-08-09

Yu Z, Huang Y, Gan Z, et al (2022)

State-Space-Based Framework for Predicting Microbial Interaction Variability in Wastewater Treatment Plants.

Environmental science & technology [Epub ahead of print].

Substantial attempts have been made to control microbial communities for environmental integrity, biosystem performance, and human health. However, it is difficult to manipulate microbial communities in practice due to the varying and nonlinear nature of interspecific interaction networks. Here, we develop a manifold-based framework to investigate the patterns of microbial interaction variability in wastewater treatment plants using manifold geometric properties and design a simple control strategy to manipulate the microbes in nonlinear communities. We validate our framework using the readily available and nonsequential microbiome profiles of wastewater treatment plants. Our results show that some microbes in the activated sludge and anammox communities display deterministic rival or cooperative relationships and constitute a stable subnetwork within the whole nonlinear community network. We further use a simulation to demonstrate that these microbes can be used to drive a microbe in a target direction regardless of the community dynamics. Overall, our framework can provide a time-efficient solution to select effective control inputs for reliable manipulation in varying microbial networks, opening up new possibilities across a range of biological fields, including wastewater treatment plants.

RevDate: 2022-08-09

Wang J, J Wang (2022)

Blood group-gut microbiome-health axis gains further support from landmark multi-omics study in swines.

Science China. Life sciences [Epub ahead of print].

RevDate: 2022-08-09

Ma W, Drew DA, K Staller (2022)

The Gut Microbiome and Colonic Motility Disorders: A Practical Framework for the Gastroenterologist.

Current gastroenterology reports [Epub ahead of print].

PURPOSE OF REVIEW: Colonic motility disorders may be influenced by the gut microbiota, which plays a role in modulating sensory and motor function. However, existing data are inconsistent, possibly due to complex disease pathophysiology, fluctuation in symptoms, and difficulty characterizing high-resolution taxonomic composition and function of the gut microbiome.

RECENT FINDINGS: Increasingly, human studies have reported associations between gut microbiome features and colonic motility disorders, such as irritable bowel syndrome and constipation. Several microbial metabolites have been identified as regulators of colonic motility in animal models. Modulation of the gut microbiota via dietary intervention, probiotics, and fecal microbiota transplant is a promising avenue for treatment for these diseases. An integration of longitudinal multi-omics data will facilitate further understanding of the causal effects of dysbiosis on disease. Further understanding of the microbiome-driven mechanisms underlying colonic motility disorders may be leveraged to develop personalized, microbiota-based approaches for disease prevention and treatment.

RevDate: 2022-08-09

Zhang XF, Li QY, Wang M, et al (2022)

2E,4E-Decadienoic Acid, a Novel Anti-Oomycete Agent from Coculture of Bacillus subtilis and Trichoderma asperellum.

Microbiology spectrum [Epub ahead of print].

Phytophthora nicotianae is an oomycete pathogen of global significance threatening many important crops. It is mainly controlled by chemosynthetic fungicides, which endangers ecosystem and human health; thus, there is an urgent need to explore alternatives for these fungicides. In this study, a new anti-oomycete aliphatic compound, 2E,4E-decadienoic acid (DDA), was obtained through coculture of Bacillus subtilis Tpb55 and Trichoderma asperellum HG1. Both in vitro and in vivo tests showed that DDA had a strong inhibitory effect against P. nicotianae. In addition, rhizosphere microbiome analysis showed that DDA reduced the relative abundance of Oomycota in rhizosphere soil. Transcriptome sequencing (RNA-Seq) analysis revealed that treatment of P. nicotianae with DDA resulted in significant downregulation of antioxidant activity and energy metabolism, including antioxidant enzymes and ATP generation, and upregulation of membrane-destabilizing activity, such as phospholipid synthesis and degradation. The metabolomic analysis results implied that the pathways influenced by DDA were mainly related to carbohydrate metabolism, energy metabolism, and the cell membrane. The biophysical tests further indicated that DDA produced oxidative stress on P. nicotianae, inhibited antioxidant enzyme and ATPase activity, and increased cell membrane permeability. Overall, DDA exerts inhibitory activity by acting on multiple targets in P. nicotianae, especially on the cell membrane and mitochondria, and can therefore serve as a novel environment-friendly agent for controlling crop oomycete disease. IMPORTANCE P. nicotianae is an oomycete pathogen that is destructive to crops. Although some oomycete inhibitors have been used during crop production, most are harmful to the ecology and lead to pathogen resistance. Alternatively, medium-chain fatty acids have been reported to exhibit antimicrobial activity in the medical field in previous studies; however, their potential as biocontrol agents has rarely been evaluated. Our in vivo and in vitro analyses revealed that the medium-chain fatty acid 2E,4E-decadienoic acid (DDA) displayed specific inhibitory activity against oomycetes. Further analysis indicated that DDA may acted on multiple targets in P. nicotianae, especially on the cell membrane and mitochondria. Our findings highlight the potential of DDA in controlling oomycete diseases. In conclusion, these results provide insights regarding the future use of green and environment-friendly anti-oomycete natural products for the prevention and control of crop oomycete diseases.

RevDate: 2022-08-09

Laanbroek HJ, Cassman NA, Keijzer RM, et al (2022)

The Stochastic Assembly of Nitrobacter winogradskyi-Selected Microbiomes with Heterotrophs from Sewage Sludge or Grassland Soil.

Applied and environmental microbiology [Epub ahead of print].

Chemolitho-autotrophic microorganisms like the nitrite-oxidizing Nitrobacter winogradskyi create an environment for heterotrophic microorganisms that profit from the production of organic compounds. It was hypothesized that the assembly of a community of heterotrophic microorganisms around N. winogradskyi depends on the ecosystem from which the heterotrophs are picked. To test this hypothesis, pure cultures of N. winogradskyi were grown in continuously nitrite-fed bioreactors in a mineral medium free of added organic carbon that had been inoculated with diluted sewage sludge or with a suspension from a grassland soil. Samples for chemical and 16S rRNA gene amplicon analyses were taken after each volume change in the bioreactor. At the end of the enrichment runs, samples for shotgun metagenomics were also collected. Already after two volume changes, the transformations in community structure became less dynamic. The enrichment of heterotrophs from both sewage and soil was highly stochastic and yielded different dominant genera in most of the enrichment runs that were independent of the origin of the inoculum. Hence, the hypothesis had to be refuted. Notwithstanding the large variation in taxonomic community structure among the enrichments, the functional compositions of the communities were statistically not different between soil- and sludge-based enrichments. IMPORTANCE In the process of aerobic nitrification, nitrite-oxidizing bacteria together with ammonia-oxidizing microorganisms convert mineral nitrogen from its most reduced appearance, i.e., ammonium, into its most oxidized form, i.e., nitrate. Because the form of mineral nitrogen has large environmental implications, nitrite-oxidizing bacteria such as Nitrobacter winogradskyi play a central role in the global biogeochemical nitrogen cycle. In addition to this central role, the autotrophic nitrite-oxidizing bacteria also play a fundamental role in the global carbon cycle. They form the basis of heterotrophic food webs, in which the assimilated carbon is recycled. Little is known about the heterotrophic microorganisms that participate in these food webs, let alone their assembly in different ecosystems. This study showed that the assembly of microbial food webs by N. winogradskyi was a highly stochastic process and independent of the origin of the heterotrophic microorganisms, but the functional characteristics of the different food webs were similar.

RevDate: 2022-08-09

Valeris-Chacin R, Weber B, Johnson TJ, et al (2022)

Longitudinal Changes in Campylobacter and the Litter Microbiome throughout the Broiler Production Cycle.

Applied and environmental microbiology [Epub ahead of print].

Broiler chickens are an important source of Campylobacter to humans and become colonized on the farm, but the role of the litter in the ecology of Campylobacter is still not clear. The aim of this study was to examine the relationship between Campylobacter and the changes in the litter microbiome throughout the broiler production cycle. Twenty-six commercial broiler flocks representing two production types (small and big broilers) were followed from 1 to 2 weeks after placement to the end of the production cycle. Composite litter samples from the broiler chicken house were collected weekly. Litter DNA was extracted and used for Campylobacter jejuni and Campylobacter coli qPCR as well as for 16S rRNA gene V4 region sequencing. Campylobacter jejuni concentration in litter significantly differed by production type and flock age. Campylobacter jejuni concentration in litter from big broilers was 2.4 log10 units higher, on average, than that of small broilers at 3 weeks of age. Sixteen amplicon sequence variants (ASVs) differentially abundant over time were detected in both production types. A negative correlation of Campylobacter with Bogoriella and Pseudogracilibacillus was observed in the litter microbiome network at 6 weeks of flock age. Dynamic Bayesian networks provided evidence of negative associations between Campylobacter and two bacterial genera, Ornithinibacillus and Oceanobacillus, at 2 and 4 weeks of flock age, respectively. In conclusion, dynamic associations between Campylobacter and the litter microbiome were observed during grow-out, suggesting a potential role of the litter microbiome in the ecology of Campylobacter colonization and persistence on farm. IMPORTANCE This study interrogated the longitudinal association between Campylobacter and broiler litter microbiome in commercial broiler flocks. The results of this investigation highlighted differences in Campylobacter dynamics in the litter throughout the broiler production cycle and between small and big broilers. Besides documenting the changing nature of the microbial networks in broiler litter during grow-out, we detected bacterial genera (Oceanobacillus and Ornithinibacillus) negatively associated with Campylobacter abundance and concentration in litter via the Bayesian network framework. These bacteria should be investigated as possible antagonists to Campylobacter colonization of the broiler environment.

RevDate: 2022-08-09

Li F, Jin Z, Wang Z, et al (2022)

Host Plant Selection Imprints Structure and Assembly of Fungal Community along the Soil-Root Continuum.

mSystems [Epub ahead of print].

The soil fungal community plays pivotal roles in soil nutrient cycling and plant health and productivity in agricultural ecosystems. However, the differential adaptability of soil fungi to different microenvironments (niches) is a bottleneck limiting their application in agriculture. Hence, the understanding of ecological processes that drive fungal microbiome assembly along the soil-root continuum is fundamental to harnessing the plant-associated microbiome for sustainable agriculture. Here, we investigated the factors that shape fungal community structure and assembly in three compartment niches (the bulk soil, rhizosphere, and rhizoplane) associated with tobacco (Nicotiana tabacum L.), with four soil types tested under controlled greenhouse conditions. Our results demonstrate that fungal community assembly along the soil-root continuum is governed by host plant rather than soil type and that soil chemical properties exert a negligible effect on the fungal community assembly in the rhizoplane. Fungal diversity and network complexity decreased in the order bulk soil > rhizosphere > rhizoplane, with a dramatic decrease in Ascomycota species number and abundance along the soil-root continuum. However, facilitations (positive interactions) were enhanced among fungal taxa in the rhizoplane niche. The rhizoplane supported species specialization with enrichment of some rare species, contributing to assimilative community assembly in the rhizoplane in all soil types. Mortierella and Pyrenochaetopsis were identified as important indicator genera of the soil-root microbiome continuum and good predictors of plant agronomic traits. The findings provide empirical evidence for host plant selection and enrichment/depletion processes of fungal microbiome assembly along the soil-root continuum. IMPORTANCE Fungal community assembly along the soil-root continuum is shaped largely by the host plant rather than the soil type. This finding facilitates the implementations of fungi-associated biocontrol and growth-promoting for specific plants in agriculture practice, regardless of the impacts from variations in geographical environments. Furthermore, the depletion of complex ecological associations in the fungal community along the soil-root continuum and the enhancement of facilitations among rhizoplane-associated fungal taxa provide empirical evidence for the potential of community simplification as an approach to target the plant rhizoplane for specific applications. The identified indicators Mortierella and Pyrenochaetopsis along the soil-root microbiome continuum are good predictors of tobacco plant agronomic traits, which should be given attention when manipulating the root-associated microbiome.

RevDate: 2022-08-09

Burcham LR, Burcham ZM, Akbari MS, et al (2022)

Interrelated Effects of Zinc Deficiency and the Microbiome on Group B Streptococcal Vaginal Colonization.

mSphere [Epub ahead of print].

Group B Streptococcus (GBS) in the vaginal tract is a risk factor for preterm birth and adverse pregnancy outcomes. GBS colonization is also transient in nature, which likely reflects the contributions of pathogen determinants, interactions with commensal flora, and host factors, making this environment particularly challenging to understand. Additionally, dietary zinc deficiency is a health concern on the global scale that is known to be associated with recurrent bacterial infection and increased rate of preterm birth or stillbirth. However, the impact of zinc deficiency on vaginal health has not yet been studied. Here we use a murine model to assess the role of dietary zinc on GBS burden and the impact of GBS colonization on the vaginal microbiome. We show that GBS vaginal colonization is increased in a zinc-deficient host and that the presence of GBS significantly alters the microbial community structure of the vagina. Using machine learning approaches, we show that vaginal community turnover during GBS colonization is driven by computationally predictable changes in key taxa, including several organisms not previously described in the context of the vaginal microbiota, such as Akkermansia muciniphila. We observed that A. muciniphila increases GBS vaginal persistence and, in a cohort of human vaginal microbiome samples collected throughout pregnancy, we observed an increased prevalence of codetection of GBS and A. muciniphila in patients who delivered preterm compared to those who delivered at full term. These findings reveal the importance and complexity of both host zinc availability and native microbiome to GBS vaginal persistence. IMPORTANCE The presence of group B Streptococcus (GBS) in the vaginal tract, perturbations in the vaginal microbiota, and dietary zinc deficiency are three factors that are independently known to be associated with increased risk of adverse pregnancy outcomes. Here, we developed an experimental mouse model to assess the impact of dietary zinc deficiency on GBS vaginal burden and persistence and to determine how changes in GBS colonization impact vaginal microbial structure. We have employed unique animal, in silica metabolic, and machine learning models, paired with analyses of human cohort data, to identify taxonomic biomarkers that contribute to host susceptibility to GBS vaginal persistence. Collectively, the data reported here identify that both dietary zinc deficiency and the presence of A. muciniphila could perpetuate an increased GBS burden and prolonged exposure in the vaginal tract, which potentiate the risk of invasive infection in utero and in the newborn.

RevDate: 2022-08-09

Moya-Gonzálvez EM, Peña-Gil N, Rubio-Del-Campo A, et al (2022)

Infant Gut Microbial Metagenome Mining of α-l-Fucosidases with Activity on Fucosylated Human Milk Oligosaccharides and Glycoconjugates.

Microbiology spectrum [Epub ahead of print].

The gastrointestinal microbiota members produce α-l-fucosidases that play key roles in mucosal, human milk, and dietary oligosaccharide assimilation. Here, 36 open reading frames (ORFs) coding for putative α-l-fucosidases belonging to glycosyl hydrolase family 29 (GH29) were identified through metagenome analysis of breast-fed infant fecal microbiome. Twenty-two of those ORFs showed a complete coding sequence with deduced amino acid sequences displaying the highest degree of identity with α-l-fucosidases from Bacteroides thetaiotaomicron, Bacteroides caccae, Phocaeicola vulgatus, Phocaeicola dorei, Ruminococcus gnavus, and Streptococcus parasanguinis. Based on sequence homology, 10 α-l-fucosidase genes were selected for substrate specificity characterization. The α-l-fucosidases Fuc18, Fuc19A, Fuc35B, Fuc39, and Fuc1584 showed hydrolytic activity on α1,3/4-linked fucose present in Lewis blood antigens and the human milk oligosaccharide (HMO) 3-fucosyllactose. In addition, Fuc1584 also hydrolyzed fucosyl-α-1,6-N-acetylglucosamine (6FN), a component of the core fucosylation of N-glycans. Fuc35A and Fuc193 showed activity on α1,2/3/4/6 linkages from H type-2, Lewis blood antigens, HMOs and 6FN. Fuc30 displayed activity only on α1,6-linked l-fucose, and Fuc5372 showed a preference for α1,2 linkages. Fuc2358 exhibited a broad substrate specificity releasing l-fucose from all the tested free histo-blood group antigens, HMOs, and 6FN. This latest enzyme also displayed activity in glycoconjugates carrying lacto-N-fucopentaose II (Lea) and lacto-N-fucopentaose III (Lex) and in the glycoprotein mucin. Fuc18, Fuc19A, and Fuc39 also removed l-fucose from neoglycoproteins and human α-1 acid glycoprotein. These results give insight into the great diversity of α-l-fucosidases from the infant gut microbiota, thus supporting the hypothesis that fucosylated glycans are crucial for shaping the newborn microbiota composition. IMPORTANCE α-l-Fucosyl residues are frequently present in many relevant glycans, such as human milk oligosaccharides (HMOs), histo-blood group antigens (HBGAs), and epitopes on cell surface glycoconjugate receptors. These fucosylated glycans are involved in a number of mammalian physiological processes, including adhesion of pathogens and immune responses. The modulation of l-fucose content in such processes may provide new insights and knowledge regarding molecular interactions and may help to devise new therapeutic strategies. Microbial α-l-fucosidases are exoglycosidases that remove α-l-fucosyl residues from free oligosaccharides and glycoconjugates and can be also used in transglycosylation reactions to synthesize oligosaccharides. In this work, α-l-fucosidases from the GH29 family were identified and characterized from the metagenome of fecal samples of breastfed infants. These enzymes showed different substrate specificities toward HMOs, HBGAs, naturally occurring glycoproteins, and neoglycoproteins. These novel glycosidase enzymes from the breast-fed infant gut microbiota, which resulted in a good source of α-l-fucosidases, have great biotechnological potential.

RevDate: 2022-08-09

Shannon OM, Gregory S, M Siervo (2022)

Dietary nitrate, aging and brain health: the latest evidence.

Current opinion in clinical nutrition and metabolic care [Epub ahead of print].

PURPOSE OF REVIEW: With an increasing population age, cognitive decline and age-associated neurodegenerative diseases are becoming increasingly prevalent and burdensome in society. Dietary supplementation with inorganic nitrate, which serves as a nitric oxide precursor, has been suggested as a potential nutritional strategy to improve brain health in older adults. In this review, we discuss recent findings in this area.

RECENT FINDINGS: A number of studies have emerged in the past 12-18 months exploring the effects of dietary nitrate supplementation on cognitive function, with typically (although not exclusively) null findings emerging. This research is characterized by small, acute/short-term studies, although observational studies and longer-duration randomised controlled trials are beginning to emerge. From the limited research reporting benefits of nitrate supplementation on cognitive function, one important discovery has been the identification of a potential pathway through which nitrate could impact cognitive health, involving modulation of the oral microbiome, which warrants further investigation.

SUMMARY: Despite some promising early findings, there is currently insufficient evidence to recommend increased dietary nitrate intake for the purpose of improving brain health. However, longer-term, larger-scale trials in potentially responsive groups are warranted to provide definitive evidence in this area.

RevDate: 2022-08-09

Verma KK, Song XP, Li DM, et al (2022)

Silicon and soil microorganisms improve rhizospheric soil health with bacterial community, plant growth, performance and yield.

Plant signaling & behavior, 17(1):2104004.

The interaction of silicon and soil microorganisms stimulates crop enhancement to ensure sustainable agriculture. Silicon may potentially increase nutrient availability in rhizosphere with improved plants' growth, development as it does not produce phytotoxicity. The rhizospheric microbiome accommodates a variety of microbial species that live in a small area of soil directly associated with the hidden half plants' system. Plant growth-promoting rhizobacteria (PGPR) play a major role in plant development in response to adverse climatic conditions. PGPRs may enhance the growth, quality, productivity in variety of crops, and mitigate abiotic stresses by reprogramming stress-induced physiological variations in plants via different mechanisms, such as synthesis of indole-3-acetic acid, 1-aminocyclopropane-1-carboxylate deaminase, exopolysaccharides, volatile organic compounds, atmospheric nitrogen fixation, and phosphate solubilization. Our article eye upon interactions of silicon and plant microbes which seems to be an opportunity for sustainable agriculture for series of crops and cropping systems in years to come, essential to safeguard the food security for masses.

RevDate: 2022-08-09

Mohammadi Z, Bishehsari F, Masoudi S, et al (2022)

Association between Sleeping Patterns and Mealtime with Gut Microbiome: A Pilot Study.

Archives of Iranian medicine, 25(5):279-284.

BACKGROUND: Disruptions in sleep related to mealtime may contribute to gut microbial imbalances, and put individuals at higher risk for metabolic diseases. The aim of this pilot study was to investigate the relationships between late-night eating habits and sleep quality and duration, with gut microbiota (GM) profiles.

METHODS: In this cross-sectional study, 36 men referred to a clinic were enrolled. In addition to demographic information, each participant completed questionnaires regarding medical history, physical activity, late-night eating habits, sleep quality and sleep duration. The scores from these questionnaires were used to categorize study participants into the following groups: sleep quality (good or poor), late-night eating (yes or no) and sleep duration (<7 or ≥7 hours). Five grams of stool was also obtained from each participant for GM profiling analysis by sequencing.

RESULTS: The mean age of the study population was 42.1 ± 1.6 years. Firmicutes and Actinobacteria were the two dominant phyla present in all participant samples. Differences in the relative abundance of GM at each taxonomic rank between study groups were insignificant. Only Erysipelotrichales at the order level were found to be significantly different between individuals who had late-night eating habits and those who did not (P & q < 0.05). No other parameter demonstrated a significant difference in GM profiles of participants.

CONCLUSION: In this pilot study, we found Erysipelotrichales to be more abundant in individuals with late-night eating habits. Studies with higher sample sizes are warranted to better delineate the possible effects of time of eating on microbial composition.

RevDate: 2022-08-09

Wehrman A, CK Lee (2022)

The cholestatic infant: updates on diagnosis and genetics.

Current opinion in pediatrics [Epub ahead of print].

PURPOSE OF REVIEW: Cholestasis in infants can indicate a serious hepatobiliary disease and requires timely assessment, diagnosis and intervention to prevent progression to serious liver decompensation. This report aims to highlight recently published studies regarding diagnosis and treatment of cholestasis in infants.

RECENT FINDINGS: The evaluation of neonatal cholestasis can be challenging, requiring the assessment of a broad differential diagnosis in timely fashion. The Italian Society of pediatric gastroenterology, hepatology, and nutrition position paper on the evaluation of neonatal cholestasis is reviewed and compared to other published guidelines. In biliary atresia, the most time-sensitive of these diagnoses, serum matrix metalloproteinase-7 was studied in Japanese infants with biliary atresia with excellent diagnostic performance characteristics. Genetic testing panels are an increasingly used tool to help identify causes of cholestasis. An American experience of genetic testing in large cohort of infants identified a definite or possible genetic diagnosis in 11% of cholestatic infants. In the treatment of prutitus in Alagille syndrome and progressive familial intrahepatic cholestasis the clinical studies of two newly Food and Drug Administration approved ileal bile acid transport inhibitors are discussed. New information on the prevalence of cytomegalovirus and idiopathic cholestasis as other etiologies of infant cholestasis is also reviewed. Lastly, new insight on potential maternal microbiome regulation on biliary disease in neonates on experimental biliary atresia models is discussed.

SUMMARY: Cholestasis in infants requires timely diagnosis and intervention. There are exciting new diagnostic and treatment options now being studied which could help minimize the likelihood of advanced liver disease and development of serious complications.

RevDate: 2022-08-09

Spilsbury F, Foysal MJ, Tay A, et al (2022)

Gut Microbiome as a Potential Biomarker in Fish: Dietary Exposure to Petroleum Hydrocarbons and Metals, Metabolic Functions and Cytokine Expression in Juvenile Lates calcarifer.

Frontiers in microbiology, 13:827371.

The gut microbiome of fish contains core taxa whose relative abundances are modulated in response to diet, environmental factors, and exposure to toxicogenic chemicals, influencing the health of the host fish. Recent advances in genomics and metabolomics have suggested the potential of microbiome analysis as a biomarker for exposure to toxicogenic compounds. In this 35-day laboratory study, 16S RNA sequencing and multivariate analysis were used to explore changes in the gut microbiome of juvenile Lates calcarifer exposed to dietary sub-lethal doses of three metals: vanadium (20 mg/kg), nickel (480 mg/kg), and iron (470 mg/kg), and to two oils: bunker C heavy fuel oil (HFO) (1% w/w) and Montara, a typical Australian medium crude oil (ACO) (1% w/w). Diversity of the gut microbiome was significantly reduced compared to negative controls in fish exposed to metals, but not petroleum hydrocarbons. The core taxa in the microbiome of negative control fish comprised phyla Proteobacteria (62%), Firmicutes (7%), Planctomycetes (3%), Actinobacteria (2%), Bacteroidetes (1%), and others (25%). Differences in the relative abundances of bacterial phyla of metal-exposed fish were pronounced, with the microbiome of Ni-, V-, and Fe-exposed fish dominated by Proteobacteria (81%), Firmicutes (68%), and Bacteroidetes (48%), respectively. The genus Photobacterium was enriched proportionally to the concentration of polycyclic aromatic hydrocarbons (PAHs) in oil-exposed fish. The probiotic lactic acid bacterium Lactobacillus was significantly reduced in the microbiota of fish exposed to metals. Transcription of cytokines IL-1, IL-10, and TNF-a was significantly upregulated in fish exposed to metals but unchanged in oil-exposed fish compared to negative controls. However, IL-7 was significantly downregulated in fish exposed to V, Ni, Fe, and HFOs. Fish gut microbiome exhibits distinctive changes in response to specific toxicants and shows potential for use as biomarkers of exposure to V, Ni, Fe, and to PAHs present in crude oil.

RevDate: 2022-08-09

Zhang M, Bai H, Zhao Y, et al (2022)

Effects of supplementation with lysophospholipids on performance, nutrient digestibility, and bacterial communities of beef cattle.

Frontiers in veterinary science, 9:927369.

An experiment was conducted to investigate the influences of supplemental lysophospholipids (LPL) on the growth performance, nutrient digestibility, and fecal bacterial profile, and short-chain fatty acids (SCFAs) of beef cattle. Thirty-six Angus beef cattle [565 ± 10.25 kg body weight (BW)] were grouped by BW and age, and randomly allocated to 1 of 3 treatment groups: (1) control (CON, basal diet); (2) LLPL [CON supplemented with 0.5 g/kg LPL, dry matter (DM) basis]; and (3) HLPL (CON supplemented with 0.75 g/kg, DM basis). The Angus cattle were fed a total mixed ration that consisted of 25% roughage and 75% concentrate (dry matter [DM] basis). The results reveal that LPL inclusion linearly increased the average daily gain (P = 0.02) and the feed efficiency (ADG/feed intake, P = 0.02), while quadratically increasing the final weight (P = 0.02) of the beef cattle. Compared with CON, the total tract digestibilities of DM (P < 0.01), ether extract (P = 0.04) and crude protein (P < 0.01) were increased with LPL supplementation. At the phylum-level, the relative abundance of Firmicutes (P = 0.05) and ratio of Firmicutes: Bacteroidetes (P = 0.04) were linearly increased, while the relative abundances of Bacteroidetes (P = 0.04) and Proteobacteria (P < 0.01) were linearly decreased with increasing LPL inclusion. At the genus-level, the relative abundances of Clostridium (P < 0.01) and Roseburia (P < 0.01) were quadratically increased, and the relative abundances of Ruminococcus was linearly increased (P < 0.01) with LPL supplementation. Additionally, increasing the dose of LPL in diets linearly increased the molar proportion of butyrate (P < 0.01) and total SCFAs (P = 0.01) concentrations. A conclusion was drawn that, as a promising feed additive, LPL promoted growth performance and nutrient digestibility, which may be associated with the change of fecal microbiome and SCFAs.

RevDate: 2022-08-09

Bunjun R, Ramla TF, Jaumdally SZ, et al (2022)

Initiating Intramuscular Depot Medroxyprogesterone Acetate (DMPA-IM) Increases Frequencies of Th17-like Human Immunodeficiency Virus (HIV) Target Cells in the Genital Tract of Women in South Africa: A Randomized Trial.

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America pii:6658490 [Epub ahead of print].

BACKGROUND: Cervicovaginal CD4+ T cells are preferential targets for human immunodeficiency virus (HIV) infection and have consequently been used as a proxy measure for HIV susceptibility. The ECHO randomized trial offered a unique opportunity to consider the association between contraceptives and Th17-like cells within a trial designed to evaluate HIV risk. In a mucosal substudy of the ECHO trial, we compared the impact of initiating intramuscular depot medroxyprogesterone acetate (DMPA-IM), copper-IUD, and the levonorgestrel (LNG) implant on cervical T cells.

METHODS: Cervical cytobrushes from 58 women enrolled in the ECHO trial were collected at baseline and 1 month after contraceptive initiation. We phenotyped cervical T cells using multiparameter flow cytometry, characterized the vaginal microbiome using 16s sequencing, and determined proteomic signatures associated with Th17-like cells using mass spectrometry.

RESULTS: Unlike the LNG implant or copper-IUD, DMPA-IM was associated with higher frequencies of cervical Th17-like cells within 1 month of initiation (P = .012), including a highly susceptible, activated population co-expressing CD38, CCR5, and α4β7 (P = .003). After 1 month, women using DMPA-IM also had more Th17-like cells than women using the Cu-IUD (P = .0002) or LNG implant (P = .04). Importantly, in women using DMPA-IM, proteomic signatures signifying enhanced mucosal barrier function were associated with the increased abundance of Th17-like cells. We also found that a non-Lactobacillus-dominant microbiome at baseline was associated with more Th17-like cells post-DMPA-IM (P = .03), although this did not influence barrier function.

CONCLUSIONS: Our data suggest that DMPA-IM-driven accumulation of HIV-susceptible Th17-like cells might be counteracted by their role in maintaining mucosal barrier integrity.

RevDate: 2022-08-08

Xue C, Xie Q, Zhang C, et al (2022)

Vertical transmission of the gut microbiota influences glucose metabolism in offspring of mice with hyperglycaemia in pregnancy.

Microbiome, 10(1):122.

BACKGROUND: Hyperglycaemia in pregnancy (HIP) is a common metabolic disorder that not only poses risks to maternal health but also associates with an increased risk of diabetes among offspring. Vertical transmission of microbiota may influence the offspring microbiome and subsequent glucose metabolism. However, the mechanism by which maternal gut microbiota may influence glucose metabolism of the offspring remains unclear and whether intervening microbiota vertical transmission could be used as a strategy to prevent diabetes in the offspring of mothers with HIP has not been investigated. So we blocked vertical transmission to investigate its effect on glucose metabolism in the offspring.

RESULTS: We established a murine HIP model with a high-fat diet (HFD) and investigated the importance of vertical transmission of gut microbiota on the glucose metabolism of offspring via birth and nursing by blocking these events through caesarean section (C-section) and cross-fostering. After weaning, all offspring were fed a normal diet. Based on multi-omics analysis, biochemical and transcriptional assays, we found that the glucometabolic deficits in the mothers were subsequently 'transmitted' to the offspring. Meanwhile, the partial change in mothers' gut microbial community induced by HIP could be transmitted to offspring, supported by the closed clustering of the microbial structure and composition between the offspring and their mothers. Further study showed that the microbiota vertical transmission was blocked by C-section and cross-fostering, which resulted in improved insulin sensitivity and islet function of the offspring of the mothers with HIP. These effects were correlated with changes in the relative abundances of specific bacteria and their metabolites, such as increased relative abundances of Bifidobacterium and short-chain fatty acids. In particular, gut microbial communities of offspring were closely related to those of their foster mothers but not their biological mothers, and the effect of cross-fostering on the offspring's gut microbiota was more profound than that of C-section.

CONCLUSION: Our study demonstrates that the gut microbiota transmitted via birth and nursing are important contributors to the glucose metabolism phenotype in offspring. Video Abstract.

RevDate: 2022-08-08

Sherman HT, Liu K, Kwong K, et al (2022)

Carbon monoxide (CO) correlates with symptom severity, autoimmunity, and responses to probiotics treatment in a cohort of children with autism spectrum disorder (ASD): a post-hoc analysis of a randomized controlled trial.

BMC psychiatry, 22(1):536.

BACKGROUND: Inflammation, autoimmunity, and gut-brain axis have been implicated in the pathogenesis of autism spectrum disorder (ASD). Carboxyhemoglobin (SpCO) as a non-invasive measurement of inflammation has not been studied in individuals with ASD. We conducted this post-hoc study based on our published clinical trial to explore SpCO and its association with ASD severity, autoimmunity, and response to daily Lactobacillus plantarum probiotic supplementation.

METHODS: In this study, we included 35 individuals with ASD aged 3-20 years from a previously published clinical trial of the probiotic Lactobacillus plantarum. Subjects were randomly assigned to receive daily Lactobacillus plantarum probiotic (6 × 1010 CFUs) or a placebo for 16 weeks. The outcomes in this analysis include Social Responsiveness Scale (SRS), Aberrant Behavior Checklist second edition (ABC-2), Clinical Global Impression (CGI) scale, SpCO measured by CO-oximetry, fecal microbiome by 16 s rRNA sequencing, blood serum inflammatory markers, autoantibodies, and oxytocin (OT) by ELISA. We performed Kendall's correlation to examine their interrelationships and used Wilcoxon rank-sum test to compare the means of all outcomes between the two groups at baseline and 16 weeks.

RESULTS: Elevated levels of serum anti-tubulin, CaM kinase II, anti-dopamine receptor D1 (anti-D1), and SpCO were found in the majority of ASD subjects. ASD severity is correlated with SpCO (baseline, R = 0.38, p = 0.029), anti-lysoganglioside GM1 (R = 0.83, p = 0.022), anti-tubulin (R = 0.69, p = 0.042), and anti-D1 (R = 0.71, p = 0.045) in treatment group.

CONCLUSIONS: The findings of the present study suggests that the easily administered and non-invasive SpCO test offers a potentially promising autoimmunity and inflammatory biomarker to screen/subgroup ASD and monitor the treatment response to probiotics. Furthermore, we propose that the associations between autoantibodies, gut microbiome profile, serum OT level, GI symptom severity, and ASD core symptom severity scores are specific to the usage of probiotic treatment in our subject cohort. Taken together, these results warrant further studies to improve ASD early diagnosis and treatment outcomes.

TRIAL REGISTRATION: NCT03337035 , registered November 8, 2017.

RevDate: 2022-08-08

Ishida JK, Bini AP, Creste S, et al (2022)

Towards defining the core Saccharum microbiome: input from five genotypes.

BMC microbiology, 22(1):193.

BACKGROUND: Plant microbiome and its manipulation inaugurate a new era for plant biotechnology with the potential to benefit sustainable crop production. Here, we used the large-scale 16S rDNA sequencing analysis to unravel the dynamic, structure, and composition of exophytic and endophytic microbial communities in two hybrid commercial cultivars of sugarcane (R570 and SP80-3280), two cultivated genotypes (Saccharum officinarum and Saccharum barberi) and one wild species (Saccharum spontaneum).

RESULTS: Our analysis identified 1372 amplicon sequence variants (ASVs). The microbial communities' profiles are grouped by two, root and bulk soils and stem and leave when these four components are compared. However, PCoA-based data supports that endophytes and epiphytes communities form distinct groups, revealing an active host-derived mechanism to select the resident microbiota. A strong genotype-influence on the assembly of microbial communities in Saccharum ssp. is documented. A total of 220 ASVs persisted across plant cultivars and species. The ubiquitous bacteria are two potential beneficial bacteria, Acinetobacter ssp., and Serratia symbiotica.

CONCLUSIONS: The results presented support the existence of common and cultivar-specific ASVs in two commercial hybrids, two cultivated canes and one species of Saccharum across tissues (leaves, stems, and roots). Also, evidence is provided that under the experimental conditions described here, each genotype bears its microbial community with little impact from the soil conditions, except in the root system. It remains to be demonstrated which aspect, genotype, environment or both, has the most significant impact on the microbial selection in sugarcane fields.

RevDate: 2022-08-08

Straub A, Vollmer A, Lâm TT, et al (2022)

Evaluation of advanced platelet-rich fibrin (PRF) as a bio-carrier for ampicillin/sulbactam.

Clinical oral investigations [Epub ahead of print].

OBJECTIVES: Mechanisms of wound healing are often impaired in patients with osteonecrosis of the jaw (ONJ). According to the guidelines for the treatment of this disease, early surgical intervention is indicated. However, surgery often faces complications such as wound healing disorders. The application of platelet-rich fibrin (PRF) after necrosectomy between bone and mucosa may constitute a promising approach to improve surgical results. An aspect that was not investigated until now is that PRF acts as a "bio-carrier" for antibiotics previously applied intravenously.

MATERIALS AND METHODS: We investigated the antimicrobial properties of PRF in 24 patients presenting ONJ undergoing systemic antibiosis with ampicillin/sulbactam. We measured the concentration of ampicillin/sulbactam in plasma and PRF and performed agar diffusion tests. Ampicillin/sulbactam was applied intravenously to the patient 10 minutes for blood sampling for PRF. No further incorporation of patients' blood or PRF product with antibiotic drugs was obtained. Four healthy patients served as controls.

RESULTS: Our results revealed that PRF is highly enriched with ampicillin/sulbactam that is released to the environment. The antibiotic concentration in PRF was comparable to the plasma concentration of ampicillin/sulbactam. The inhibition zone (IZ) of PRF was comparable to the standard ampicillin/sulbactam discs used in sensitivity testing.

CONCLUSIONS: The results of our study demonstrated that PRF is a reliable bio-carrier for systemic applied antibiotics and exhibits a large antimicrobial effect.

CLINICAL RELEVANCE: We describe a clinically useful feature of PRF as a bio-carrier for antibiotics. Especially when applied to poorly perfused tissues and bone such as in ONJ, the local release of antibiotics can reduce wound healing disorders like infections.

RevDate: 2022-08-08

Miyakawa M, Oda H, M Tanaka (2022)

Clinical research review: usefulness of bovine lactoferrin in child health.

Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine [Epub ahead of print].

Lactoferrin (LF) is abundant in human milk and plays an important role in the health of children. Bovine LF (bLF) has high homology with human LF and has been reported to have multiple biological functions. Several clinical studies have been conducted considering these properties, which reported the usefulness of bLF. This review was aimed to provide an overview of the clinical evidence in children. We searched clinical reports investigating the effects of bLF in children and identified 36 studies on the role of bLF in infections, iron metabolism, body growth, cerebral development, and fecal microbiome. Considering the accumulated evidence, bLF may contribute to the child health, particularly by suppressing or alleviating gastrointestinal and respiratory symptoms, and improving the iron status of children with anemia or those at high risk of anemia. The dose of bLF varies depending on the expected effect and target age, but may not necessarily have to be as high as human LF in human milk. Some of the beneficial effects of bLF have not been fully validated due to limited clinical evidence or being observed in the secondary analysis of some studies. Further clinical evidence would add significant value to the use of bLF in child health.

RevDate: 2022-08-08

Rahmeh R, Akbar A, Alomirah H, et al (2022)

Camel milk microbiota: A culture-independent assessment.

Food research international (Ottawa, Ont.), 159:111629.

Camel milk is renowned for its nutritional value and its therapeutic properties. It is considered a promising alternative to bovine milk due to its higher nutritional benefits, hypoallergenic characteristics and greater digestibility in the human gastrointestinal system. This study reports camel milk's bacterial and fungal microbiota, and the effect of geographical location and season on its bacterial community. We sequenced the V3-V4 regions of the16S rRNA gene for bacteria and the internal transcribed spacer (ITS) for fungi. A total of 134 samples of dromedary raw camel milk were collected from south, north and middle Kuwait during two seasons. Raw camel milk showed a diversified bacterial community, with 1196 genera belonging to 33 phyla. The four most predominant phyla of bacteria were Proteobacteria, Firmicutes, Actinobacteria and Bacteroidota. The core microbiota of raw camel milk, represented by the dominant genera shared by the majority of samples, was constituted by the genera Schlegelella, Paenibacillus, Lactobacillus, unclassified Comamonadaceae, Pediococcus, Moraxella, Acinetobacter, Staphylococcus, Enterococcus, Pseudomonas, Streptococcus, unclassified Micrococcaceae, Rothia, unclassified Sphingomonadaceae, unclassified Neisseriaceae and Sphingomonas. The fungal population was assessed in 14 raw camel milk samples, and comprised 87 genera belonging to 3 phyla. The genera Penicillium, Cladosporium, Candida, Aspergillus, Alternaria and Fusarium, dominated the fungal community. These findings shed light on raw camel milk's core bacterial and fungal microbiome. The geographical location and the season had a significant impact on the diversity and composition of camel milk microbiome.

RevDate: 2022-08-08

Berthelot JM, Darrieutort-Laffite C, BL Goff (2022)

Contribution of HLA DRB1, PTPN22, and CTLA4, to RA dysbiosis.

Joint bone spine pii:S1297-319X(22)00106-3 [Epub ahead of print].

This narrative review gathers current evidence for a contribution of rheumatoid arthritis (RA) HLA-DRB1, PTPN22 and CTLA4 polymorphisms to the gut dysbiosis observed in RA, especially at its onset (transient excess of Prevotella). The gut microbiome contains elements which are 30% heritable, including genera like Bacteroides and Veillonella, and to a lesser extent Prevotella. The first months/year seems a critical period for the selection of a core of microbiota, that should be considered as a second self by the immune system, and tolerized by regulatory T and B cells. Imperfect tolerization may increase the risk of RA following further repeated silent translocations of various gut microorganisms, including Prevotella copri, from gut to joints (fostered by a concurrent loss in gut mucosa of protective bacteria like Faecalibacterium prausnitzii). Genetics studies confirmed that Prevotella copri was partly heritable, and strong associations were observed between the overall microbial composition of stools and the HLA-DRB1 RA risk allele, either in a US cohort (P = 0.00001), or the Twins UK cohort (P = 0.033). This finding also stands for persons still free from RA, and was replicated in the Swiss SCREEN-RA cohort. Gene variants of PTPN22 also modify intestinal microbiota composition, compromise granulocyte-mediated antibacterial defence in gut, and reduce the suppressive effect of gut regulatory B cells. CTLA4 variants may similarly contribute to RA dysbiosis, since immunotherapy by CTLA-4 blockade depends on microbiota, and CTLA4 activates T follicular regulatory cells to reduce immune responses to segmented filamentous bacteria. Suggestions for future works are made.

RevDate: 2022-08-08

McCormick BA, JM Inadomi (2022)

The microbiome modifies the effect of diet on colorectal cancer incidence.

RevDate: 2022-08-08

Fox A, Widmer F, A Lüscher (2022)

Soil microbial community structures are shaped by agricultural systems revealing little temporal variation.

Environmental research pii:S0013-9351(22)01242-7 [Epub ahead of print].

Many studies in soil microbial ecology are undertaken with a single sampling event, with the influence of temporal progression rarely being considered. Under field conditions, soil samples were taken from different agricultural systems; a sown grassland to maize rotation (MC), an intensively managed permanent grassland (INT), as well as extensively managed permanent grasslands with high (EXT_HP), low to sufficient (EXT_LP) and deficient available P (EXT_DP), six times throughout the 2017 growing season. Thus, this study aimed to determine if any differences in soil microbiome structures between both sharply contrasting (MC - INT - EXT), slightly differing (EXT_HP - EXT_DP) and quite similar (EXT_HP - EXT_LP and EXT_LP - EXT_DP) agricultural systems persist through changing growth conditions within the growing season. For both fungal and bacterial community structure, the influence of agricultural system (√CV = 0.256 and 0.145, respectively, both at least P < 0.01) was much greater than that of temporal progression (√CV = 0.065 and 0.042, respectively, both P < 0.001). Importantly, nearly all agricultural systems persistently harbored significantly distinct fungal community structures across each of the six sampling events (all at least P < 0.05). There were not as many pairwise differences in bacterial community structure between the agricultural systems, but some did persist (MC and EXT_HP ∼ EXT_DP, all P < 0.001). Additionally, persistent indicator fungal OTUs (IndVal >0.7, P ≤ 0.05) associated to each agricultural system (except EXT_LP) were found in each of the six sampling events. These results highlight the temporal stability of pairwise differences in soil microbiome structures between established agricultural systems through changing plant growth conditions, even between those with a comparable management regime. This is a highly relevant finding in informing the sampling strategy of studies in soil microbial ecology as well as for designing efficient soil biodiversity monitoring systems.

RevDate: 2022-08-08

Patel BI, Heiss M, Samel-Pommerencke A, et al (2022)

Queuosine salvage in fission yeast by Qng1-mediated hydrolysis to queuine.

Biochemical and biophysical research communications, 624:146-150 pii:S0006-291X(22)01091-9 [Epub ahead of print].

Queuosine (Q) is a hypermodified 7-deaza-guanosine nucleoside that is found at position 34, also known as the wobble position, of tRNAs with a GUN anticodon, and Q ensures faithful translation of the respective C- and U-ending codons. While Q is present in tRNAs in most eukaryotes, only bacteria can synthesize it denovo. In contrast, eukaryotes rely on external sources like their food and the gut microbiome in order to Q-modify their tRNAs, and Q therefore can be regarded as a micronutrient. The eukaryotic tRNA guanine transglycosylase (eTGT) uses the base queuine (q) as a substrate to replace G34 by Q in the tRNAs. Eukaryotic cells can uptake both q and Q, raising the question how the Q nucleoside is converted to q for incorporation into the tRNAs. Here, we identified Qng1 (also termed Duf2419) as a queuosine nucleoside glycosylase in Schizosaccharomyces pombe. S. pombe cells with a deletion of qng1+ contained Q-modified tRNAs only when cultured in the presence of the nucleobase q, but not with the nucleoside Q, indicating that the cells are proficient at q incorporation, but not in Q hydrolysis. Furthermore, purified recombinant Qng1 hydrolyzed Q to q in vitro. Qng1 displays homology to DNA glycosylases and has orthologs across eukaryotes, including flies, mice and humans. Qng1 therefore plays an essential role in allowing eukaryotic cells to salvage Q from bacterial sources and to recycle Q from endogenous tRNAs.

RevDate: 2022-08-08

Pandey SS, Jain R, Bhardwaj P, et al (2022)

Plant probiotics - Endophytes pivotal to plant health.

Microbiological research, 263:127148 pii:S0944-5013(22)00188-4 [Epub ahead of print].

Endophytes as a ubiquitous associate of the plant are considered as a promising candidate for sustainable agriculture. These organisms play a pivotal role in the regulation of the primary and secondary metabolism of their host plant. The direct and long-lasting interaction of endophytes with the host enables them to escape from harsh environmental conditions. Especially, their endophytic nature makes them better candidates over epiphytes and rhizospheric microbes in interaction with plants. Current research findings revealed that the endophytes help plants in making nutrient acquisition from the soil, nitrogen fixation, phosphate availability, phytohormone and antimicrobial production. There is a huge potential for developing novel products like endophytes-based microbial formulations and elicitors to improve plant health, ameliorating stress tolerance in plants and source of therapeutically important secondary metabolites. The present review specifically dealt with attributes such as host-tissue specificity of endophytes, the importance of seed-associated endophytes, endophyte-parasite plant-host plant interaction as well as their applications in plant in-vitro systems and as microbial consortium. In addition, the conserved endophytic microbial communities in different plants are also looked upon possibly to understand the plant-endophytic microbiome on similar lines of the animal-gut microbiome. Primarily, the purpose of this review is to implicate the endophytic flora as probiotics influencing overall plant health and their survival under extreme environmental conditions.

RevDate: 2022-08-08

Abd El-Hack ME, El-Saadony MT, Alqhtani AH, et al (2022)

The relationship among avian influenza, gut microbiota and chicken immunity: an updated overview.

Poultry science, 101(9):102021 pii:S0032-5791(22)00312-1 [Epub ahead of print].

The alimentary tract in chickens plays a crucial role in immune cell formation and immune challenges, which regulate intestinal flora and sustain extra-intestinal immunity. The interaction between pathogenic microorganisms and the host commensal microbiota as well as the variety and integrity of gut microbiota play a vital role in health and disease conditions. Thus, several studies have highlighted the importance of gut microbiota in developing immunity against viral infections in chickens. The gut microbiota (such as different species of Lactobacillus, Blautia Bifidobacterium, Faecalibacterium, Clostridium XlVa, and members of firmicutes) encounters different pathogens through different mechanisms. The digestive tract is a highly reactive environment, and infectious microorganisms can disturb its homeostasis, resulting in dysbiosis and mucosal infections. Avian influenza viruses (AIV) are highly infectious zoonotic viruses that lead to severe economic losses and pose a threat to the poultry industry worldwide. AIV is a challenging virus that affects gut integrity, disrupts microbial homeostasis and induces inflammatory damage in the intestinal mucosa. H9N2 AIV infection elevates the expression of proinflammatory cytokines, such as interferon (IFN-γ and IFNα) and interleukins (IL-17A and IL-22), and increases the proliferation of members of proteobacteria, particularly Escherichia coli. On the contrary, it decreases the proliferation of certain beneficial bacteria, such as Enterococcus, Lactobacillus and other probiotic microorganisms. In addition, H9N2 AIV decreases the expression of primary gel-forming mucin, endogenous trefoil factor family peptides and tight junction proteins (ZO-1, claudin 3, and occludin), resulting in severe intestinal damage. This review highlights the relationship among AIV, gut microbiota and immunity in chicken.

RevDate: 2022-08-08

Cartagena D, Penny F, McGrath JM, et al (2022)

Differences in Neonatal Outcomes Among Premature Infants Exposed to Mother's Own Milk Versus Donor Human Milk.

Advances in neonatal care : official journal of the National Association of Neonatal Nurses pii:00149525-990000000-00024 [Epub ahead of print].

BACKGROUND: Growing evidence supports the superior benefits of exposure to mother's own milk (MOM) in reducing prematurity-related comorbidities. Neonatal exposure to donor human Milk (DHM) is a suitable alternative when MOM is insufficient or unavailable. However, the same protective composition and bioactivity in MOM are not present in DHM. Additional evidence is needed to justify and inform evidence-based practices increasing MOM provision while optimizing adequate use of DHM for premature infants.

PURPOSE: A systematic review of the literature was conducted to determine differences in neonatal outcomes among premature infants exposed to predominately MOM versus DHM.

METHODS/SEARCH STRATEGY: Databases including PubMed, CINAHL and Cochrane were searched (2020-2021) using the PRISMA (Preferred Reporting Items for Systematic reviews and Meta-Analysis) guidelines. Evidence was classified using the John Hopkins evidence-based practice levels and quality of evidence.

RESULTS: Eleven studies met inclusion criteria. Studied neonatal outcomes included (a) growth parameters (n = 8), (b) neonatal morbidities (n = 6), and (c) gut microbiome (n = 4). Overall, evidence suggests DHM exposure is beneficial but not equivalent to MOM feeding. Compared with DHM, greater doses of MOM are ideal to enhance protection primarily related to infant growth, as well as gut microbiome diversity and richness.

IMPLICATIONS FOR PRACTICE: Standardized and evidence-based practices are needed to clearly delineate optimal use of DHM without undermining maternal and neonatal staff efforts to support and promote provision of MOM.

IMPLICATIONS FOR RESEARCH: Additional evidence from high-quality studies should further examine differences in neonatal outcomes among infants exposed to predominately MOM or DHM in settings using standardized and evidence-based feeding practices.

RevDate: 2022-08-08

Basic M, Dardevet D, Abuja PM, et al (2022)

Approaches to discern if microbiome associations reflect causation in metabolic and immune disorders.

Gut microbes, 14(1):2107386.

Our understanding of microorganisms residing within our gut and their roles in the host metabolism and immunity advanced greatly over the past 20 years. Currently, microbiome studies are shifting from association and correlation studies to studies demonstrating causality of identified microbiome signatures and identification of molecular mechanisms underlying these interactions. This transformation is crucial for the efficient translation into clinical application and development of targeted strategies to beneficially modulate the intestinal microbiota. As mechanistic studies are still quite challenging to perform in humans, the causal role of microbiota is frequently evaluated in animal models that need to be appropriately selected. Here, we provide a comprehensive overview on approaches that can be applied in addressing causality of host-microbe interactions in five major animal model organisms (Caenorhabditis elegans, Drosophila melanogaster, zebrafish, rodents, and pigs). We particularly focused on discussing methods available for studying the causality ranging from the usage of gut microbiota transfer, diverse models of metabolic and immune perturbations involving nutritional and chemical factors, gene modifications and surgically induced models, metabolite profiling up to culture-based approached. Furthermore, we addressed the impact of the gut morphology, physiology as well as diet on the microbiota composition in various models and resulting species specificities. Finally, we conclude this review with the discussion on models that can be applied to study the causal role of the gut microbiota in the context of metabolic syndrome and host immunity. We hope this review will facilitate important considerations for appropriate animal model selection.

RevDate: 2022-08-08

Wang J, Qie J, Zhu D, et al (2022)

The landscape in the gut microbiome of long-lived families reveals new insights on longevity and aging - relevant neural and immune function.

Gut microbes, 14(1):2107288.

Human longevity has a strong familial and genetic component. Dynamic characteristics of the gut microbiome during aging associated with longevity, neural, and immune function remained unknown. Here, we aim to reveal the synergistic changes in gut microbiome associated with decline in neural and immune system with aging and further obtain insights into the establishment of microbiome homeostasis that can benefit human longevity. Based on 16S rRNA and metagenomics sequencing data for 32 longevity families including three generations, centenarians, elderly, and young groups, we found centenarians showed increased diversity of gut microbiota, severely damaged connection among bacteria, depleted in microbial-associated essential amino acid function, and increased abundance of anti-inflammatory bacteria in comparison to young and elderly groups. Some potential probiotic species, such as Desulfovibrio piger, Gordonibacter pamelaeae, Odoribacter splanchnicus, and Ruminococcaceae bacterium D5 were enriched with aging, which might possibly support health maintenance. The level of Amyloid-β (Aβ) and brain-derived neurotrophic factor (BDNF) related to neural function showed increased and decreased with aging, respectively. The elevated level of inflammatory factors was observed in centenarians compared with young and elderly groups. The enriched Bacteroides fragilis in centenarians might promote longevity through up-regulating anti-inflammatory factor IL-10 expression to mediate the critical balance between health and disease. Impressively, the associated analysis for gut microbiota with the level of Aβ, BDNF, and inflammatory factors suggests Bifidobacterium pseudocatenulatum could be a particularly beneficial bacteria in the improvement of impaired neural and immune function. Our results provide a rationale for targeting the gut microbiome in future clinical applications of aging-related diseases and extending life span.Abbreviations: 16S rRNA: 16S ribosomal RNA; MAGs: Metagenome-assembled genomes; ASVs: Amplicon sequence variants; DNA: Deoxyribonucleic acid; FDR: False discovery rate: KEGG: Kyoto Encyclopedia of Genes and Genomes; PCoA: Principal coordinates analysis; PCR: Polymerase chain reaction; PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States; Aβ: Amyloid-β (Aβ); BDNF: Brain-derived neurotrophic factor.

RevDate: 2022-08-08

Wang X, Zeng H, Xu J, et al (2022)

Characteristics of ruminal microbiota and metabolome in Holstein cows differing in milk protein concentrations.

Journal of animal science pii:6658282 [Epub ahead of print].

The rumen is a vital organ containing vast amounts of microbes that play a key role in the digestion of nutrients and affect the production performance of ruminants. However, few studies have focused on the characterization of the ruminal microbiota composition and function in cows with long-term difference milk protein concentrations, and the relationship between milk protein concentration and ruminal microbiota remains elusive. In this study, we collected the data of milk protein concentrations of 1,025 Holstein cows for 10 months on a commercial farm. Based on the milk protein concentrations, 30 cows were selected and divided into three groups (n=10 per group): low milk protein group (LMP, milk protein concentration < 3.1 %), medium milk protein group (MMP, 3.1 % ≤ milk protein concentration < 3.4 %), and high milk protein group (HMP, milk protein concentration ≥ 3.4 %). The ruminal microbiome, metabolome, VFA concentrations and proportions, and amino acid profiles of the three groups were analyzed. The data showed that free amino acid (FAA) levels were lower in the rumen and higher in the plasma of HMP cows (P < 0.05). In addition, lower NH3 concentrations were observed in the rumen, plasma, and milk of the HMP cows (P < 0.05). Protease activity and isobutyric acid molar proportion in the rumen were lower in the HMP group (P < 0.05). Microbiome analysis showed that HMP cows had lower microbial diversity (represented as Shannon and Simpson indices) than LMP cows. At the genus level, lower relative abundances of Prevotella_1 and Ruminococcaceae_UCG_005 were observed in the HMP group (P < 0.05). At the operational taxonomic unit (OTU) level, a lower relative abundance of OTU3 (Prevotella ruminicola) was observed in the HMP group (P < 0.05). We found that the relative abundances of ruminal Prevotella_1 and OTU3 (Prevotella ruminicola) were negatively correlated with milk protein concentration (P < 0.05). These findings suggested that the cows with long-term high milk protein concentrations had lower microbial diversity and weaker protein degradation ability in the rumen. Furthermore, our observations identified a correlation between the milk protein concentration and ruminal microbiota.

RevDate: 2022-08-08

Jones ST, Guo K, Cooper EH, et al (2022)

Altered Immunoglobulin Repertoire and Decreased IgA Somatic Hypermutation in the Gut during Chronic HIV-1 Infection.

Journal of virology [Epub ahead of print].

Humoral immune perturbations contribute to pathogenic outcomes in persons with HIV-1 infection (PWH). Gut barrier dysfunction in PWH is associated with microbial translocation and alterations in microbial communities (dysbiosis), and IgA, the most abundant immunoglobulin (Ig) isotype in the gut, is involved in gut homeostasis by interacting with the microbiome. We determined the impact of HIV-1 infection on the antibody repertoire in the gastrointestinal tract by comparing Ig gene utilization and somatic hypermutation (SHM) in colon biopsies from PWH (n = 19) versus age and sex-matched controls (n = 13). We correlated these Ig parameters with clinical, immunological, microbiome and virological data. Gene signatures of enhanced B cell activation were accompanied by skewed frequencies of multiple Ig Variable genes in PWH. PWH showed decreased frequencies of SHM in IgA and possibly IgG, with a substantial loss of highly mutated IgA sequences. The decline in IgA SHM in PWH correlated with gut CD4+ T cell loss and inversely correlated with mucosal inflammation and microbial translocation. Diminished gut IgA SHM in PWH was driven by transversion mutations at A or T deoxynucleotides, suggesting a defect not at the AID/APOBEC3 deamination step but at later stages of IgA SHM. These results expand our understanding of humoral immune perturbations in PWH that could have important implications in understanding mucosal immune defects in individuals with chronic HIV-1 infection. IMPORTANCE The gut is a major site of early HIV-1 replication and pathogenesis. Extensive CD4+ T cell depletion in this compartment results in a compromised epithelial barrier that facilitates the translocation of microbes into the underlying lamina propria and systemic circulation, resulting in chronic immune activation. To date, the consequences of microbial translocation on the mucosal humoral immune response (or vice versa) remains poorly integrated into the panoply of mucosal immune defects in PWH. We utilized next-generation sequencing approaches to profile the Ab repertoire and ascertain frequencies of somatic hypermutation in colon biopsies from antiretroviral therapy-naive PWH versus controls. Our findings identify perturbations in the Ab repertoire of PWH that could contribute to development or maintenance of dysbiosis. Moreover, IgA mutations significantly decreased in PWH and this was associated with adverse clinical outcomes. These data may provide insight into the mechanisms underlying impaired Ab-dependent gut homeostasis during chronic HIV-1 infection.

RevDate: 2022-08-08

Taylor MN, Spandana Boddu S, NM Vega (2022)

Using Single-Worm Data to Quantify Heterogeneity in Caenorhabditis elegans-Bacterial Interactions.

Journal of visualized experiments : JoVE.

The nematode Caenorhabditis elegans is a model system for host-microbe and host-microbiome interactions. Many studies to date use batch digests rather than individual worm samples to quantify bacterial load in this organism. Here it is argued that the large inter-individual variability seen in bacterial colonization of the C. elegans intestine is informative, and that batch digest methods discard information that is important for accurate comparison across conditions. As describing the variation inherent to these samples requires large numbers of individuals, a convenient 96-well plate protocol for disruption and colony plating of individual worms is established.

RevDate: 2022-08-08

Shafeek P, Clegg T, Kawmi N, et al (2022)

The temporal relationship between antibiotic and opioid prescription on the risk of developing an opioid use disorder: A national database study.

Journal of addictive diseases [Epub ahead of print].

Background: Previously, we discovered that subjects co-prescribed both antibiotics and opioids on the same day in a hospital setting displayed an increased risk of developing an opioid use disorder (OUD) 12 months following hospital discharge. The goal of this study was to examine whether prescribing antibiotics in the inpatient or emergency department setting at various time points before or after an opioid prescription impacted the risk OUD.Methods: A propensity score matched cohort study was conducted to identify subjects (18-65 years old) with no previous history of OUD. Two cohorts were defined: subjects who were prescribed antibiotics 0-1, 2-4, 5-7, 8-10, 11-12 months before or after the date of an opioid prescription while in the emergency department or inpatient setting, from the years 2010-2019. The diagnosis of an Opioid Related Disorder (F11.10-F11.20) 12 months following discharge from the emergency department or inpatient unit was then observed.Results: Primary analysis showed that subjects prescribed an antibiotic 0-1 month or 8-10 months before an opioid prescription showed a modest risk of developing an OUD 12 months following an opioid prescription (0.04% and 0.20%, respectively). Similarly, subjects prescribed an antibiotic 0-1 month, 5-7 months, or 8-10 months after an opioid prescription displayed a modest risk of developing OUD 12 months after an opioid prescription (0.02% risk, 0.14% risk, and 0.16% risk, respectively).Conclusions: These findings suggest that there is little to no effect on the risk of developing OUD when antibiotics are prescribed at various time points before or after opioid prescription.

RevDate: 2022-08-08

Du S, Zhang Y, Shen JP, et al (2022)

Alteration of Manure Antibiotic Resistance Genes via Soil Fauna Is Associated with the Intestinal Microbiome.

mSystems [Epub ahead of print].

Livestock wastes contain high levels of antibiotic resistance genes (ARGs) and a variety of human-related pathogens. Bioconversion of livestock manure using larvae of the beetle Protaetia brevitarsis is an effective technique for waste reduction and value creation; however, the fate of manure ARGs during gut passage and interaction with the gut microbiome of P. brevitarsis remains unclear. To investigate this, we fed P. brevitarsis with dry chicken manure for 6 days and measured bacterial community dynamics and ARG abundance and diversity along the P. brevitarsis gut tract using high-throughput quantitative PCR and metagenomics approaches. The diversity of ARGs was significantly lower in larval midgut, hindgut, and frass than in raw chicken manure, and around 80% of pathogenicity-related genes (PRGs) exhibited reduced abundance. Network analysis demonstrated that Bacteroidetes and Firmicutes were the key bacterial phyla associated with ARG reduction. Metagenomic analysis further indicated that ARGs, mobile genetic elements (MGEs), and PRGs were simultaneously attenuated in the hindgut, implicating a decreased likelihood for horizontal gene transfer (HGT) of ARGs among bacteria and pathogens during manure bioconversion. Our findings demonstrated that the attenuation of ARGs is strongly associated with the variation of the gut microbiome of P. brevitarsis, providing insights into mechanisms of risk mitigation of ARG dissemination during manure bioconversion. IMPORTANCE Saprophagous fauna like the oriental edible beetle (P. brevitarsis) plays a fundamental role in converting organic wastes into biofertilizer. Accumulating evidence has shown that soil fauna can reduce the abundance of ARGs, although the underlying mechanism of ARG reduction is still unclear. In our previous research, we found a large reduction of ARGs in vegetable roots and leaves from frass compared with raw manure, providing a promising biofertilizer for soil-vegetable systems. Therefore, in this study, temporal dynamic changes in the microbiomes of the donor (chicken manure) and host (P. brevitarsis) were investigated, and we found a close association between the gut microbiome and the alteration of ARGs. These results shed new light on how the insect gut microbiome can mitigate manure-borne ARGs and provide insights into the bioconversion process via a typical member of the saprophagous fauna, P. brevitarsis.

RevDate: 2022-08-08

Yang D, Li L, Li C, et al (2022)

Formation and inhibition mechanism of novel angiotensin I converting enzyme inhibitory peptides from Chouguiyu.

Frontiers in nutrition, 9:920945.

Angiotensin I converting enzyme (ACE) inhibitory peptides from fermented foods exhibit great potential to alleviate hypertension. In this study, the peptide extract from Chouguiyu exhibited a good inhibition effect on ACE, and the inhibition rate was significantly enhanced after fermentation for 8 days. The ACE inhibitory peptides were further identified, followed by their inhibition and formation mechanisms using microbiome technology and molecular docking. A total of 356 ACE inhibitory peptides were predicted using in silico, and most ACE inhibitory peptides increased after fermentation. These peptides could be hydrolyzed from 94 kinds of precursor proteins, mainly including muscle-type creatine kinase, nebulin, and troponin I. P1 (VEIINARA), P2 (FAVMVKG), P4 (EITWSDDKK), P7 (DFDDIQK), P8 (IGDDPKF), P9 (INDDPKIL), and P10 (GVDNPGHPFI) were selected as the core ACE inhibitory peptides according to their abundance and docking energy. The salt bridge and conventional hydrogen bond connecting unsaturated oxygen atoms in the peptides contributed most to the ACE inhibition. The cleavage proteases from the microbial genera in Chouguiyu for preparing these 7 core ACE inhibitory peptides were further analyzed by hydrolysis prediction and Pearson's correlation. The correlation network showed that P7, P8, and P9 were mainly produced by the proteases from LAB including Lactococcus, Enterococcus, Vagococcus, Peptostreptococcus, and Streptococcus, while P1, P2, P4, and P10 were mainly Produced by Aeromonas, Bacillus, Escherichia, and Psychrobacter. This study is helpful in isolating the proteases and microbial strains to directionally produce the responding ACE inhibitory peptides.

RevDate: 2022-08-08

Bilal M, Ashraf S, X Zhao (2022)

Dietary Component-Induced Inflammation and Its Amelioration by Prebiotics, Probiotics, and Synbiotics.

Frontiers in nutrition, 9:931458.

A balanced diet with many dietary components maintains immune homeostasis directly by interacting with innate and adaptive immune components or indirectly through gut microbiota and their metabolites. Dietary components may inhibit pro-inflammatory mediators and promote anti-inflammatory functions or vice versa. Western diets with imbalanced dietary components skew the immune balance toward pro-inflammation and induce intestinal inflammation, consequently leading to many intestinal and systemic inflammatory diseases like ulcerative colitis, Crohn's disease, irritable bowel syndrome, cardiovascular problems, obesity, and diabetes. The dietary component-induced inflammation is usually chronic in nature and frequently caused or accompanied by alterations in gut microbiota. Therefore, microbiome-targeted therapies such as probiotics, prebiotics and synbiotics hold great potentials to amend immune dysregulation and gut dysbiosis, preventing and treating intestinal and systemic inflammatory diseases. Probiotics, prebiotics and synbioitcs are progressively being added to foods and beverages, with claims of health benefits. However, the underlining mechanisms of these interventions for preventing and treating dietary component-induced inflammation are still not very clear. In addition, possibly ineffective or negative consequences of some probiotics, prebiotics and synbiotics call for stringent testing and regulation. Here, we will first briefly review inflammation, in terms of its types and the relationship between different dietary components and immune responses. Then, we focus on current knowledge about the direct and indirect effects of probiotics, prebiotics and synbiotics on intestinal and systemic inflammation. Understanding how probiotics, prebiotics and synbiotics modulate the immune system and gut microbiota will improve our strategies for preventing and treating dietary component-induced intestinal inflammation and inflammatory diseases.

RevDate: 2022-08-08

Zhang C, Liang D, Li X, et al (2022)

Characteristics of Gut Microbial Profiles of Offshore Workers and Its Associations With Diet.

Frontiers in nutrition, 9:904927.

The composition of gut microbiota is not a static state in humans but fluctuates in response to changes in environments, diet, and lifestyle factors. Here, we explored differences in gut microbiota between populations worked offshore and onshore and further studied microbiota-associated variables in offshore workers (OFWs). We investigated the gut microbiota of 168 healthy subjects (offshore: 145 and onshore: 23) using 16S rRNA sequencing. Our results indicated that the marine environment caused significant changes in intestinal microbial structure, which was mainly reflected in the increase in bacterial diversity, changes in composition, and the emergence of more specific bacteria in OFWs. In addition, characteristics of gut microbiota in OFWs were further explored, and the genus Holdemanella was considered a potential contributor to the stable state of health. Besides, some dietary factors, namely, duck, mutton, dairy products, and algae vegetables were identified as the gut microbial covariates in the OFWs cohort and were positively correlated with the genus Holdemanella. This suggests the positive intervention of diet on Holdemanella. Our data highlight, for the first time to our knowledge, that the marine geographical environment plays an important role in shaping the gut mycobiome composition. And diet could be considered as the targeted intervention that alters the composition of the microbiome to improve host health.

RevDate: 2022-08-08

Kohil A, Chouliaras S, Alabduljabbar S, et al (2022)

Female infertility and diet, is there a role for a personalized nutritional approach in assisted reproductive technologies? A Narrative Review.

Frontiers in nutrition, 9:927972.

Female infertility is a major public health concern and a global challenge. It is a disorder of the reproductive system, defined as the inability to achieve a clinical pregnancy. Nutrition and other environmental factors are found to impact reproductive health in women as well as the outcome of assisted reproductive technologies (ART). Dietary factors, such as polyunsaturated fatty acids (PUFA), fiber as well as the intake of Mediterranean diet appear to exert beneficial effects on female reproductive outcomes. The exact mechanisms associating diet to female fertility are yet to be identified, although genomic, epigenomic, and microbial pathways may be implicated. This review aims to summarize the current knowledge on the impact of dietary components on female reproduction and ART outcomes, and to discuss the relevant interplay of diet with genome, epigenome and microbial composition.

RevDate: 2022-08-08

Kullberg RFJ, Brands X, Klarenbeek AM, et al (2022)

Rectal microbiota are coupled with altered cytokine production capacity following community-acquired pneumonia hospitalization.

iScience, 25(8):104740 pii:S2589-0042(22)01012-4.

Human studies describing the immunomodulatory role of the intestinal microbiota in systemic infections are lacking. Here, we sought to relate microbiota profiles from 115 patients with community-acquired pneumonia (CAP), both on hospital admission and following discharge, to concurrent circulating monocyte and neutrophil function. Rectal microbiota composition did not explain variation in cytokine responses in acute CAP (median 0%, IQR 0.0%-1.9%), but did one month following hospitalization (median 4.1%, IQR 0.0%-6.6%, p = 0.0035). Gene expression analysis of monocytes showed that undisrupted microbiota profiles following hospitalization were associated with upregulated interferon, interleukin-10, and G-protein-coupled-receptor-ligand-binding pathways. While CAP is characterized by profoundly distorted gut microbiota, the effects of these disruptions on cytokine responses and transcriptional profiles during acute infection were absent or modest. However, rectal microbiota were related to altered cytokine responses one month following CAP hospitalization, which may provide insights into potential mechanisms contributing to the high risk of recurrent infections following hospitalization.

RevDate: 2022-08-08

Ross EM, BJ Hayes (2022)

Metagenomic Predictions: A Review 10 years on.

Frontiers in genetics, 13:865765 pii:865765.

Metagenomic predictions use variation in the metagenome (microbiome profile) to predict the unknown phenotype of the associated host. Metagenomic predictions were first developed 10 years ago, where they were used to predict which cattle would produce high or low levels of enteric methane. Since then, the approach has been applied to several traits and species including residual feed intake in cattle, and carcass traits, body mass index and disease state in pigs. Additionally, the method has been extended to include predictions based on other multi-dimensional data such as the metabolome, as well to combine genomic and metagenomic information. While there is still substantial optimisation required, the use of metagenomic predictions is expanding as DNA sequencing costs continue to fall and shows great promise particularly for traits heavily influenced by the microbiome such as feed efficiency and methane emissions.

RevDate: 2022-08-08

Dong Z, Shen X, Hao Y, et al (2022)

Gut microbiome: A potential indicator for predicting treatment outcomes in major depressive disorder.

Frontiers in neuroscience, 16:813075.

The therapeutic outcomes in major depressive disorder (MDD), one of the most common and heterogeneous mental illnesses, are affected by factors that remain unclear and often yield unsatisfactory results. Herein, we characterized the composition and metabolic function of the gut microbiota of patients with MDD during antidepressant treatment, based on 16S rRNA sequencing and metabolomics. The microbial signatures at baseline differed significantly between responder and non-responder groups. The gut microbiota of the non-responder group was mainly characterized by increased relative abundances of the phylum Actinobacteria, families Christensenellaceae and Eggerthellaceae, and genera Adlercreutzia and Christensenellaceae R7 group compared to that of the responder group. Additionally, the gut microbiota composition of the responder and non-responder groups differed significantly before and after treatment, especially at the genus level. Moreover, 20 differential metabolites between the responder and non-responder groups were identified that were mainly involved in lipid metabolism (cholestane steroids and steroid esters). Eggerthellaceae and Adlercreutzia displayed strong co-occurrence relationships with certain metabolites, suggesting alternations in the gut microbiome, and associated metabolites may be potential mediators of successful antidepressant treatment. Overall, our study demonstrates that alterations in gut microbiota composition and metabolic function might be relevant to the response to antidepressants, thereby providing insight into mechanisms responsible for their efficacy.

RevDate: 2022-08-08

MahmoudianDehkordi S, Bhattacharyya S, Brydges CR, et al (2022)

Gut Microbiome-Linked Metabolites in the Pathobiology of Major Depression With or Without Anxiety-A Role for Bile Acids.

Frontiers in neuroscience, 16:937906.

Background: The gut microbiome may play a role in the pathogenesis of neuropsychiatric diseases including major depressive disorder (MDD). Bile acids (BAs) are steroid acids that are synthesized in the liver from cholesterol and further processed by gut-bacterial enzymes, thus requiring both human and gut microbiome enzymatic processes in their metabolism. BAs participate in a range of important host functions such as lipid transport and metabolism, cellular signaling and regulation of energy homeostasis. BAs have recently been implicated in the pathophysiology of Alzheimer's and several other neuropsychiatric diseases, but the biochemical underpinnings of these gut microbiome-linked metabolites in the pathophysiology of depression and anxiety remains largely unknown.

Method: Using targeted metabolomics, we profiled primary and secondary BAs in the baseline serum samples of 208 untreated outpatients with MDD. We assessed the relationship of BA concentrations and the severity of depressive and anxiety symptoms as defined by the 17-item Hamilton Depression Rating Scale (HRSD17) and the 14-item Hamilton Anxiety Rating Scale (HRSA-Total), respectively. We also evaluated whether the baseline metabolic profile of BA informs about treatment outcomes.

Results: The concentration of the primary BA chenodeoxycholic acid (CDCA) was significantly lower at baseline in both severely depressed (log2 fold difference (LFD) = -0.48; p = 0.021) and highly anxious (LFD = -0.43; p = 0.021) participants compared to participants with less severe symptoms. The gut bacteria-derived secondary BAs produced from CDCA such as lithocholic acid (LCA) and several of its metabolites, and their ratios to primary BAs, were significantly higher in the more anxious participants (LFD's range = [0.23, 1.36]; p's range = [6.85E-6, 1.86E-2]). The interaction analysis of HRSD17 and HRSA-Total suggested that the BA concentration differences were more strongly correlated to the symptoms of anxiety than depression. Significant differences in baseline CDCA (LFD = -0.87, p = 0.0009), isoLCA (LFD = -1.08, p = 0.016) and several BA ratios (LFD's range [0.46, 1.66], p's range [0.0003, 0.049]) differentiated treatment failures from remitters.

Conclusion: In patients with MDD, BA profiles representing changes in gut microbiome compositions are associated with higher levels of anxiety and increased probability of first-line treatment failure. If confirmed, these findings suggest the possibility of developing gut microbiome-directed therapies for MDD characterized by gut dysbiosis.

RevDate: 2022-08-08

Yue SR, Tan YY, Zhang L, et al (2022)

Gynostemma pentaphyllum polysaccharides ameliorate non-alcoholic steatohepatitis in mice associated with gut microbiota and the TLR2/NLRP3 pathway.

Frontiers in endocrinology, 13:885039.

Recent studies have revealed the pivotal role of gut microbiota in the progress of liver diseases including non-alcoholic steatohepatitis (NASH). Many natural herbs, such as Gynostemma pentaphyllum (GP), have been extensively applied in the prevention of NASH, while the bioactive components and underlying mechanism remain unclear. The aim of this study was to investigate whether the polysaccharides of GP (GPP) have a protective effect on NASH and to explore the potential mechanism underlying these effects. C57BL/6 male mice were fed with a methionine-choline-deficient (MCD) diet for 4 weeks to induce NASH and administered daily oral gavage of sodium carboxymethylcellulose (CMC-Na), low dose of GPP (LGPP), high dose of GPP (HGPP), and polyene phosphatidylcholine capsules (PPC), compared with the methionine-choline-sufficient (MCS) group. Our results showed that the symptoms of hepatic steatosis, hepatocyte ballooning, liver fibrosis, and oxidative stress could be partially recovered through the intervention of GPP with a dose-dependent effect. Furthermore, gut microbiome sequencing revealed that HGPP altered the composition of gut microbiota, mainly characterized by the enrichment of genera including Akkermansia, Lactobacillus, and A2. Moreover, hepatic transcriptome analysis indicated that the anti-inflammatory effect of HGPP might be associated with toll-like receptor (TLR) and nod-like receptor (NLR) signaling pathways. HGPP could inhibit the expression of TLR2 and downregulate the expression of the NLRP3 inflammasome, as well as the pro-inflammatory cytokine tumor necrosis factor (TNF)-α and interleukin (IL)-1β. In summary, GPP could ameliorate NASH possibly mediated via the modulation of gut microbiota and the TLR2/NLRP3 signaling pathway, indicating that GPP could be tested as a prebiotic agent in the prevention of NASH.

RevDate: 2022-08-08

Fu Y, Wu J, Wang D, et al (2022)

Metagenomic profiling of ocular surface microbiome changes in Demodex blepharitis patients.

Frontiers in cellular and infection microbiology, 12:922753.

Purpose: To compare the ocular surface and meibum microbial communities of humans with Demodex Blepharitis (DB) and healthy controls.

Methods: Conjunctival sac and meibum samples from 25 DB patients and 11 healthy controls were analyzed using metagenomic next-generation sequencing (mNGS).

Results: The alpha-diversity of the conjunctival sac microbiome of the DB group (observed, Chao1, ACE) was lower than that of the control group, whereas all meibum diversity indicators were similar. In conjunctival samples, the relative abundance (RA) of the phylum Proteobacteria was significantly higher (p=0.023), and the RA of both phyla Actinobacteria and Firmicutes was significantly lower (p=0.002, 0.025, respectively) in the DB group than that in the control group. In meibum samples, the RA of the phyla Proteobacteria and Actinobacteria were similar, whereas that of the phylum Firmicutes was significantly lower in the DB group (p=0.019) than that in the control group. Linear discriminant analysis with effect size measurement of the conjunctival and meibum microbiomes showed that Sphingobium sp. YG1 and Acinetobacter guillouiae were enriched in the DB group. Sphingobium sp. YG1, Acinetobacter guillouiae and Pseudomonas putida in the DB group were related to more severe ocular surface clinical parameters. Discriminative genera's principal coordinate analysis separated all control and DB microbiomes into two distinct clusters.

Conclusions: Proteobacteria's increased prevalence may indicate ocular microbial community instability. The species Sphingobium sp. YG1 and Acinetobacter guillouiae are potentially pathogenic bacterial biomarkers in DB. Demodex infection mainly affects the ocular surface microbiome rather than penetrating deeper into the meibomian gland.

RevDate: 2022-08-08

Zhu Y, Tang Y, He H, et al (2022)

Gut Microbiota Correlates With Clinical Responsiveness to Erythropoietin in Hemodialysis Patients With Anemia.

Frontiers in cellular and infection microbiology, 12:919352.

The main treatment for renal anemia in end-stage renal disease (ESRD) patients on hemodialysis is erythropoiesis (EPO). EPO hyporesponsiveness (EH) in dialysis patients is a common clinical problem, which is poorly understood. Recent searches reported that gut microbiota was closely related to the occurrence and development of ESRD. This study aims to explore the changes in gut microbiota between ESRD patients with different responsiveness to EPO treatment. We compared the gut microbiota from 44 poor-response (PR) and 48 good-response (GR) hemodialysis patients treated with EPO using 16S rDNA sequencing analysis. The results showed that PR patients displayed a characteristic composition of the gut microbiome that clearly differed from that of GR patients. Nine genera (Neisseria, Streptococcus, Porphyromonas, Fusobacterium, Prevotella_7, Rothia, Leptotrichia, Prevotella, Actinomyces) we identified by Lasso regression and ROC curves could excellently predict EH. In contrast, five genera (Faecalibacterium, Citrobacter, Bifidobacterium, Escherichia-Shigella, Bacteroides) identified by the same means presented a protective effect against EH. Analyzing the correlation between these biomarkers and clinical indicators, we found that gut microbiota may affect response to EPO through nutritional status and parathyroid function. These findings suggest that gut microbiota is altered in hemodialysis patients with EH, giving new clues to the pathogenesis of renal anemia.

RevDate: 2022-08-08

Taniya MA, Chung HJ, Al Mamun A, et al (2022)

Role of Gut Microbiome in Autism Spectrum Disorder and Its Therapeutic Regulation.

Frontiers in cellular and infection microbiology, 12:915701.

Autism spectrum disorder (ASD) is a neurological disorder that affects normal brain development. The recent finding of the microbiota-gut-brain axis indicates the bidirectional connection between our gut and brain, demonstrating that gut microbiota can influence many neurological disorders such as autism. Most autistic patients suffer from gastrointestinal (GI) symptoms. Many studies have shown that early colonization, mode of delivery, and antibiotic usage significantly affect the gut microbiome and the onset of autism. Microbial fermentation of plant-based fiber can produce different types of short-chain fatty acid (SCFA) that may have a beneficial or detrimental effect on the gut and neurological development of autistic patients. Several comprehensive studies of the gut microbiome and microbiota-gut-brain axis help to understand the mechanism that leads to the onset of neurological disorders and find possible treatments for autism. This review integrates the findings of recent years on the gut microbiota and ASD association, mainly focusing on the characterization of specific microbiota that leads to ASD and addressing potential therapeutic interventions to restore a healthy balance of gut microbiome composition that can treat autism-associated symptoms.


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 )