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Microbiology Resource Announcements Apr 2020We report a complete genome sequence of JCM 1471 The genome consists of a single circular chromosome of 6,197,116 bp with a G+C content of 45.7%. The genome was...
We report a complete genome sequence of JCM 1471 The genome consists of a single circular chromosome of 6,197,116 bp with a G+C content of 45.7%. The genome was annotated as containing 5 complete sets of rRNA genes, 70 tRNA genes, and 5,516 protein-coding sequences.
PubMed: 32327523
DOI: 10.1128/MRA.00141-20 -
Cancer Research Communications Jan 2023Although short-term feeding studies demonstrated effects of grains, fiber, and gluten on gut microbiome composition, the impact of habitual intake of these dietary...
UNLABELLED
Although short-term feeding studies demonstrated effects of grains, fiber, and gluten on gut microbiome composition, the impact of habitual intake of these dietary factors is poorly understood. We examined whether habitual intakes of whole and refined grains, fiber, and gluten are associated with gut microbiota in a cross-sectional study. This study included 779 participants from the multi-ethnic Food and Microbiome Longitudinal Investigation study. Bacterial 16SV4 rRNA gene from baseline stool was amplified and sequenced using Illumina MiSeq. Read clustering and taxonomic assignment was performed using QIIME2. Usual dietary intake was assessed by a 137-item food frequency questionnaire. Association of diet with gut microbiota was assessed with respect to overall composition and specific taxon abundances. Whole grain intake was associated with overall composition, as measured by the Jensen-Shannon divergence (multivariable-adjusted for quartiles = 0.03). The highest intake quartile was associated with higher abundance of , , , and Erysipelotrichaceae and lower abundance of . These bacteria also varied by dietary fiber intake. Higher refined grain and gluten intake was associated with lower Shannon diversity ( < 0.05). These findings suggest that whole grain and dietary fiber are associated with overall gut microbiome structure, largely fiber-fermenting microbiota. Higher refined grain and gluten intakes may be associated with lower microbial diversity.
SIGNIFICANCE
Regular consumption of whole grains and dietary fiber was associated with greater abundance of gut bacteria that may lower risk of colorectal cancer. Further research on the association of refined grains and gluten with gut microbial composition is needed to understand their roles in health and disease.
Topics: Humans; Gastrointestinal Microbiome; Glutens; Cross-Sectional Studies; Diet; Bacteria; Dietary Fiber
PubMed: 36968219
DOI: 10.1158/2767-9764.CRC-22-0154 -
BMC Microbiology Jan 2021Berberine (BBR) is a plant-based nutraceutical that has been used for millennia to treat diarrheal infections and in contemporary medicine to improve patient lipid...
BACKGROUND
Berberine (BBR) is a plant-based nutraceutical that has been used for millennia to treat diarrheal infections and in contemporary medicine to improve patient lipid profiles. Reduction in lipids, particularly cholesterol, is achieved partly through up-regulation of bile acid synthesis and excretion into the gastrointestinal tract (GI). The efficacy of BBR is also thought to be dependent on structural and functional alterations of the gut microbiome. However, knowledge of the effects of BBR on gut microbiome communities is currently lacking. Distinguishing indirect effects of BBR on bacteria through altered bile acid profiles is particularly important in understanding how dietary nutraceuticals alter the microbiome.
RESULTS
Germfree mice were colonized with a defined minimal gut bacterial consortium capable of functional bile acid metabolism (Bacteroides vulgatus, Bacteroides uniformis, Parabacteroides distasonis, Bilophila wadsworthia, Clostridium hylemonae, Clostridium hiranonis, Blautia producta; B4PC2). Multi-omics (bile acid metabolomics, 16S rDNA sequencing, cecal metatranscriptomics) were performed in order to provide a simple in vivo model from which to identify network-based correlations between bile acids and bacterial transcripts in the presence and absence of dietary BBR. Significant alterations in network topology and connectivity in function were observed, despite similarity in gut microbial alpha diversity (P = 0.30) and beta-diversity (P = 0.123) between control and BBR treatment. BBR increased cecal bile acid concentrations, (P < 0.05), most notably deoxycholic acid (DCA) (P < 0.001). Overall, analysis of transcriptomes and correlation networks indicates both bacterial species-specific responses to BBR, as well as functional commonalities among species, such as up-regulation of Na/H antiporter, cell wall synthesis/repair, carbohydrate metabolism and amino acid metabolism. Bile acid concentrations in the GI tract increased significantly during BBR treatment and developed extensive correlation networks with expressed genes in the B4PC2 community.
CONCLUSIONS
This work has important implications for interpreting the effects of BBR on structure and function of the complex gut microbiome, which may lead to targeted pharmaceutical interventions aimed to achieve the positive physiological effects previously observed with BBR supplementation.
Topics: Animals; Bacteria; Bacterial Proteins; Berberine; Bile Acids and Salts; DNA, Bacterial; DNA, Ribosomal; Female; Gastrointestinal Microbiome; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Male; Metabolomics; Mice; RNA, Ribosomal, 16S; Sequence Analysis, RNA; Species Specificity
PubMed: 33430766
DOI: 10.1186/s12866-020-02020-1 -
Molecules (Basel, Switzerland) Sep 2022Recent studies have demonstrated that changes in the abundance of the intestinal bacterium , a potential probiotic, are closely associated with the development of...
Recent studies have demonstrated that changes in the abundance of the intestinal bacterium , a potential probiotic, are closely associated with the development of various diseases such as obesity, diabetes, some neurodegenerative diseases, and certain cancers. However, there is still a lack of an effective method to detect the abundance of in the gut rapidly. Especially, DNA aptamers are now widely used as biometric components for medical testing due to their unique characteristics, including high chemical stability, low production cost, ease of chemical modification, low immunogenicity, and fast reproducibility. We successfully obtained a high-affinity nucleic acid aptamer library (B.p-R14) after 14 SELEX rounds, which efficiently discriminates in different analysis techniques including fluorometric suspension assays or fluorescence microscopy from other major gut bacteria in complex mixtures and even in human stool samples. These preliminary findings will be the basis towards aptamer-based biosensing applications for the fast and reliable monitoring of in the human gut microbiome.
Topics: Aptamers, Nucleotide; Bacteria; Clostridiales; Humans; Reproducibility of Results; SELEX Aptamer Technique
PubMed: 36080459
DOI: 10.3390/molecules27175693 -
Microbiome Sep 2021Non-alcoholic liver disease (NAFLD) is the hepatic manifestation of metabolic syndrome, and it can progress to non-alcoholic steatohepatitis (NASH). Alterations in the...
BACKGROUND
Non-alcoholic liver disease (NAFLD) is the hepatic manifestation of metabolic syndrome, and it can progress to non-alcoholic steatohepatitis (NASH). Alterations in the gut microbiome have been implicated in the development of NAFLD/NASH, although the underlying mechanisms remain unclear.
RESULTS
We found that the consumption of the prebiotic inulin markedly ameliorated the phenotype of NAFLD/NASH, including hepatic steatosis and fibrosis, in mice. Inulin consumption resulted in global changes in the gut microbiome, including concomitant enrichment of the genera Bacteroides and Blautia, and increased concentrations of short-chain fatty acids, particularly acetate, in the gut lumen and portal blood. The consumption of acetate-releasing resistant starch protected against NAFLD development. Colonisation by Bacteroides acidifaciens and Blautia producta in germ-free mice resulted in synergetic effects on acetate production from inulin. Furthermore, the absence of free fatty acid receptor 2 (FFAR2), an acetate receptor, abolished the protective effect of inulin, as indicated by the more severe liver hypertrophy, hypercholesterolaemia and inflammation. These effects can be attributed to an exacerbation of insulin resistance in the liver, but not in muscle or adipose tissue.
CONCLUSION
These findings demonstrated that the commensal microbiome-acetate-FFAR2 molecular circuit improves insulin sensitivity in the liver and prevents the development of NAFLD/NASH. Video abstract.
Topics: Acetates; Animals; Bacteroides; Clostridiales; Mice; Non-alcoholic Fatty Liver Disease; Receptors, G-Protein-Coupled
PubMed: 34530928
DOI: 10.1186/s40168-021-01125-7 -
Nature Aug 2019Intestinal commensal bacteria can inhibit dense colonization of the gut by vancomycin-resistant Enterococcus faecium (VRE), a leading cause of hospital-acquired...
Intestinal commensal bacteria can inhibit dense colonization of the gut by vancomycin-resistant Enterococcus faecium (VRE), a leading cause of hospital-acquired infections. A four-strained consortium of commensal bacteria that contains Blautia producta BP can reverse antibiotic-induced susceptibility to VRE infection. Here we show that BP reduces growth of VRE by secreting a lantibiotic that is similar to the nisin-A produced by Lactococcus lactis. Although the growth of VRE is inhibited by BP and L. lactis in vitro, only BP colonizes the colon and reduces VRE density in vivo. In comparison to nisin-A, the BP lantibiotic has reduced activity against intestinal commensal bacteria. In patients at high risk of VRE infection, high abundance of the lantibiotic gene is associated with reduced density of E. faecium. In germ-free mice transplanted with patient-derived faeces, resistance to VRE colonization correlates with abundance of the lantibiotic gene. Lantibiotic-producing commensal strains of the gastrointestinal tract reduce colonization by VRE and represent potential probiotic agents to re-establish resistance to VRE.
Topics: Animals; Anti-Bacterial Agents; Bacteriocins; Enterococcus faecium; Feces; Female; Gastrointestinal Tract; Germ-Free Life; Gram-Positive Bacteria; Humans; Lactococcus lactis; Mice; Microbial Sensitivity Tests; Microbiota; Nisin; Probiotics; Symbiosis; Vancomycin; Vancomycin Resistance; Vancomycin-Resistant Enterococci
PubMed: 31435014
DOI: 10.1038/s41586-019-1501-z -
Pathogens (Basel, Switzerland) Feb 2021act as hosts for various microorganisms and pathogens, causing Keratitis (AK). To investigate the association between endosymbionts and AK progression, we performed a...
act as hosts for various microorganisms and pathogens, causing Keratitis (AK). To investigate the association between endosymbionts and AK progression, we performed a metagenomics study to characterize the intracellular microbiome from five lenses associated with AK isolates and standard strains to characterize the role of ocular flora in AK progression. The used clinical isolates were axenic cultured from lenses associated with AK patients. AK isolates and standard controls such as 16S ribosomal RNA sequencing techniques were used for analysis. The microbiome compositions and relative abundance values were compared. The orders of and presented major populations of intracellular microbes belonging to all isolates. Comparison of the different source isolates showed that most of the abundance in keratitis isolates came from (121.0 folds), (54.15 folds), (24.51 folds), and (3.15 folds). Further analysis of the relative abundance data from keratitis isolates showed that was positively correlated with the disease course. In contrast, was found to be abundant in early-stage keratitis isolates. This study reveals the abundant anaerobic Gram-positive rods present in severe keratitis isolate and characterize the association between and ocular flora in AK progression.
PubMed: 33669045
DOI: 10.3390/pathogens10030266 -
Cooperating Commensals Restore Colonization Resistance to Vancomycin-Resistant Enterococcus faecium.Cell Host & Microbe May 2017Antibiotic-mediated microbiota destruction and the consequent loss of colonization resistance can result in intestinal domination with vancomycin-resistant Enterococcus...
Antibiotic-mediated microbiota destruction and the consequent loss of colonization resistance can result in intestinal domination with vancomycin-resistant Enterococcus (VRE), leading to bloodstream infection in hospitalized patients. Clearance of VRE remains a challenging goal that, if achieved, would reduce systemic VRE infections and patient-to-patient transmission. Although obligate anaerobic commensal bacteria have been associated with colonization resistance to VRE, the specific bacterial species involved remain undefined. Herein, we demonstrate that a precisely defined consortium of commensal bacteria containing the Clostridium cluster XIVa species Blautia producta and Clostridium bolteae restores colonization resistance against VRE and clears VRE from the intestines of mice. While C. bolteae did not directly mediate VRE clearance, it enabled intestinal colonization with B. producta, which directly inhibited VRE growth. These findings suggest that therapeutic or prophylactic administration of defined bacterial consortia to individuals with compromised microbiota composition may reduce inter-patient transmission and intra-patient dissemination of highly antibiotic-resistant pathogens.
Topics: Ampicillin; Animals; Anti-Bacterial Agents; Bacteria; Bacterial Physiological Phenomena; Clostridium; Colony Count, Microbial; DNA, Bacterial; Drug Resistance, Bacterial; Enterococcus faecium; Feces; Female; Gram-Positive Bacterial Infections; Intestines; Mice; Mice, Inbred C57BL; Microbiota; RNA, Ribosomal, 16S; Symbiosis; Vancomycin; Vancomycin-Resistant Enterococci
PubMed: 28494240
DOI: 10.1016/j.chom.2017.04.002 -
Journal of Applied Microbiology Sep 2022The gut microbiota modulates dopamine levels in vivo, but the bacteria and biochemical processes responsible remain incompletely characterized. A potential precursor of...
AIMS
The gut microbiota modulates dopamine levels in vivo, but the bacteria and biochemical processes responsible remain incompletely characterized. A potential precursor of bacterial dopamine production is 3-methoxytyramine (3MT); 3MT is produced when dopamine is O-methylated by host catechol O-methyltransferase (COMT), thereby attenuating dopamine levels. This study aimed to identify whether gut bacteria are capable of reverting 3MT to dopamine.
METHODS AND RESULTS
Human faecal bacterial communities O-demethylated 3MT and yielded dopamine. Gut bacteria that mediate this transformation were identified as acetogens Eubacterium limosum and Blautia producta. Upon exposing these acetogens to propyl iodide, a known inhibitor of cobalamin-dependent O-demethylases, 3MT O-demethylation was inhibited. Culturing E. limosum and B. producta with 3MT afforded increased acetate levels as compared with vehicle controls.
CONCLUSIONS
Gut bacterial acetogens E. limosum and B. producta synthesized dopamine from 3MT. This O-demethylation of 3MT was likely performed by cobalamin-dependent O-demethylases implicated in reductive acetogenesis.
SIGNIFICANCE AND IMPACT OF THE STUDY
This is the first report that gut bacteria can synthesize dopamine by O-demethylation of 3MT. Owing to 3MT being the product of host COMT attenuating dopamine levels, gut bacteria that reverse this transformation-converting 3MT to dopamine-may act as a counterbalance for dopamine regulation by COMT.
Topics: Catechol O-Methyltransferase; Dopamine; Gastrointestinal Microbiome; Humans; Oxidoreductases, O-Demethylating; Vitamin B 12
PubMed: 35737746
DOI: 10.1111/jam.15682 -
Microbiology Spectrum Dec 2023The identification of short open reading frame-encoded peptides (SEP) and different proteoforms in single cultures of gut microbes offers new insights into a largely...
The identification of short open reading frame-encoded peptides (SEP) and different proteoforms in single cultures of gut microbes offers new insights into a largely neglected part of the microbial proteome landscape. This is of particular importance as SEP provide various predicted functions, such as acting as antimicrobial peptides, maintaining cell homeostasis under stress conditions, or even contributing to the virulence pattern. They are, thus, taking a poorly understood role in structure and function of microbial networks in the human body. A better understanding of SEP in the context of human health requires a precise understanding of the abundance of SEP both in commensal microbes as well as pathogens. For the gut beneficial , we demonstrate the importance of specific environmental conditions for biosynthesis of SEP expanding previous findings about their role in microbial interactions.
Topics: Humans; Open Reading Frames; Peptides; Antimicrobial Peptides; Proteome
PubMed: 37782090
DOI: 10.1128/spectrum.02528-23