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MBio Apr 2024Inflammatory bowel disease (IBD) is a group of inflammatory conditions of the gastrointestinal tract. The etiology of IBD remains elusive, but the disease is suggested...
UNLABELLED
Inflammatory bowel disease (IBD) is a group of inflammatory conditions of the gastrointestinal tract. The etiology of IBD remains elusive, but the disease is suggested to arise from the interaction of environmental and genetic factors that trigger inadequate immune responses and inflammation in the intestine. The gut microbiome majorly contributes to disease as an environmental variable, and although some causative bacteria are identified, little is known about which specific members of the microbiome aid in the intestinal epithelial barrier function to protect from disease. While chemically inducing colitis in mice from two distinct animal facilities, we serendipitously found that mice in one facility showed remarkable resistance to disease development, which was associated with increased markers of epithelial barrier integrity. Importantly, we show that and were significantly increased in the microbiota of resistant mice. To causally connect these microbes to protection against disease, we colonized susceptible mice with the two bacterial species. Our results demonstrate that and . synergistically drive a protective effect in both acute and chronic models of colitis by boosting the frequency of type 3 innate lymphoid cells in the colon and by improving gut epithelial integrity. Altogether, our work reveals a combined effort of commensal microbes in offering protection against severe intestinal inflammation by shaping gut immunity and by enhancing intestinal epithelial barrier stability. Our study highlights the beneficial role of gut bacteria in dictating intestinal homeostasis, which is an important step toward employing microbiome-driven therapeutic approaches for IBD clinical management.
IMPORTANCE
The contribution of the gut microbiome to the balance between homeostasis and inflammation is widely known. Nevertheless, the etiology of inflammatory bowel disease, which is known to be influenced by genetics, immune response, and environmental cues, remains unclear. Unlocking novel players involved in the dictation of a protective gut, namely, in the microbiota component, is therefore crucial to develop novel strategies to tackle IBD. Herein, we revealed a synergistic interaction between two commensal bacterial strains, and , which induce protection against both acute and chronic models of colitis induction, by enhancing epithelial barrier integrity and promoting group 3 innate lymphoid cells in the colonic mucosa. This study provides a novel insight on how commensal bacteria can beneficially act to promote intestinal homeostasis, which may open new avenues toward the use of microbiome-derived strategies to tackle IBD.
Topics: Animals; Mice; Immunity, Innate; Lymphocytes; Colitis; Inflammatory Bowel Diseases; Inflammation; Verrucomicrobia; Akkermansia; Bacteroidetes
PubMed: 38470269
DOI: 10.1128/mbio.00078-24 -
Journal of Global Antimicrobial... Jun 2018The aims of this study were (i) to analyse strains of the genera Bacteroides and Parabacteroides isolated from clinical specimens for phenotypic resistance to... (Review)
Review
OBJECTIVES
The aims of this study were (i) to analyse strains of the genera Bacteroides and Parabacteroides isolated from clinical specimens for phenotypic resistance to clindamycin, (ii) to detect erm genes in the isolates and (iii) to determine any correlation between in vitro resistance and the presence of erm genes.
METHODS
The Bacteroides and Parabacteroides isolates analysed were obtained from patients hospitalised at teaching hospitals in Poland. Antimicrobial susceptibility testing was performed by Etest and the results were interpreted according to European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines. All isolates were analysed by PCR for the presence of the resistance genes ermF, ermB and ermG.
RESULTS
Resistance to clindamycin was detected in 31.0% (62/200) of all evaluated isolates, with the ermF and ermB genes detected in 31.0% (62/200) and 0.5% (1/200) of isolates, respectively. No isolates with ermG were detected among the evaluated strains. Pearson's test showed an almost perfect correlation between clindamycin minimum inhibitory concentrations (MICs) and the presence of ermF in Bacteroides spp. and Parabacteroides distasonis isolates, although the ermF gene was also present in 10 clindamycin-susceptible isolates of Bacteroides spp.
CONCLUSIONS
This study demonstrated a substantial proportion of Bacteroides (22.5-100% depending on the species) and 50.0% of Parabacteroides strains exhibiting resistance to clindamycin. The clindamycin MIC for resistant strains in each case was ≥256mg/L. Resistance to clindamycin in Bacteroides and Parabacteroides species is correlated mainly with the presence of the ermF gene.
Topics: Anti-Bacterial Agents; Bacteroides Infections; Bacteroidetes; Clindamycin; Disk Diffusion Antimicrobial Tests; Drug Resistance, Bacterial; Hospitals, Teaching; Humans; Poland; Polymerase Chain Reaction; tRNA Methyltransferases
PubMed: 29129778
DOI: 10.1016/j.jgar.2017.11.001 -
Science (New York, N.Y.) Aug 2022A gut microbiota-derived antigen elicits distinct subsets of regulatory T cells to suppress inflammation in mice.
A gut microbiota-derived antigen elicits distinct subsets of regulatory T cells to suppress inflammation in mice.
Topics: Animals; Antigens, Bacterial; Bacteroidetes; Colitis; Gastrointestinal Microbiome; Immune Tolerance; Mice; T-Lymphocytes, Regulatory; beta-N-Acetylhexosaminidases
PubMed: 35926048
DOI: 10.1126/science.add7145 -
Voprosy Pitaniia 2021The intestinal microbiota, due to new data on its functions obtained in the last decade, has become a new target point of influence on the organism. However, nowadays... (Review)
Review
The intestinal microbiota, due to new data on its functions obtained in the last decade, has become a new target point of influence on the organism. However, nowadays knowledge about the possible impact of physical activity and sports on the composition of the gut microbiota and, as a result, on the organism is limited. of this review was to summarize current knowledge about the gut microbiota of healthy people with different levels of physical activity (from athletes to physically inactive people), and to identify patterns in the composition of the microbiota of various surveyed groups. . A systematic search was carried out in electronic databases including EMBASE, MEDLINE, Web of Science, Google Scholar and eLIBRARY. The search process was carried out using keywords and logical operators. We included the following studies in our review: a) crossover studies comparing the gut microbiome of subjects with different physical activity; b) studies involving healthy adult women and men (18-45 years old); c) studies written in English and Russian. We excluded studies containing dietary changes, consumption of probiotics or prebiotics, and studies of physical activity in sick people. . Total 743 articles were received, of which 14 articles fully met the search criteria, and 101 articles partially corresponded. An analysis of the data from these studies indicated noticeable differences in the microbiota between athletes and people leading an sedentary lifestyle: the athletes had a greater α-diversity of the microbiota, while the level of microorganisms of the phylum Bacteroidetes was reduced; Akkermansiaceae and Faecalibacterium bacteria are elevated in athletes and people with active lifestyles. Different levels of physical activity in physically active people according to the levels of cardiorespiratory endurance did not affect the level of α- and β-diversity. When analyzing the effect of loads on the microbiota in various sports disciplines and skill levels, a connection was found with an increase in α-diversity in professionals and highly qualified athletes, with the relative content of series of bacteria (Methanobrevibacter smithii in professional cyclists; Parabacteroides, Phascolarctobacterium, Oscillibacter, Bilophila, Megasphaera in athletes of high martial arts qualifications of wushu; Eubacterium rectale, Polynucleobacter needarius, Faecalibacterium prausnitzii, Bacteroides vulgatus, Gordonibacter massiliensis in athletes of international level of various sports), and certain genera of bacteria have been identified (Parabacteroides, Phascolarctobacterium, Besilibacterium). . The data obtained indicate a higher relative proportion of microbiota effective members, which are involved in the fermentation of complex polysaccharides and the production of short-chain fatty acids such as Faecalibacterium prausnitzii, Eubacterium hallii, Phascolarctobacterium, Eubacterium rectale, and Methanobrevibacter smithii, which increases the fermentation efficiency of many bacterial taxa in the gut by using hydrogen gas (H) and formate to reduce carbon dioxide (CO) to methane. There is a need to study other members of the microecological community, leading to a better understanding of the adaptation of the gut microbiota to levels of physical activity and its potentially positive effects on metabolism and endurance.
Topics: Adolescent; Adult; Athletes; Bacteria; Exercise; Female; Gastrointestinal Microbiome; Humans; Male; Middle Aged; Prebiotics; Young Adult
PubMed: 34538034
DOI: 10.33029/0042-8833-2021-90-4-36-52 -
Ecotoxicology and Environmental Safety Nov 2023As the concerned emerging pollutants, several lines of evidence have indicated that nanoplastics (NPs) lead to reproductive toxicity. However, the biological mechanism... (Review)
Review
As the concerned emerging pollutants, several lines of evidence have indicated that nanoplastics (NPs) lead to reproductive toxicity. However, the biological mechanism underlying NPs disturbed spermatogenesis remains largely unknown. Therefore, we aimed to reveal the potential mechanism of impaired spermatogenesis caused by long-term NPs exposure from the perspective of integrated metabolome and microbiome analysis. After 12 weeks of gavage of polystyrene nanoplastics (PS-NPs) and animo-modified polystyrene nanoplastics (Amino-NPs), a well-designed two-exposure stages experimental condition. We found that NPs exposure induced apparent abnormal spermatogenesis, which appeared more severe in the Amino-NPs group. Mechanistically, 14 floras associated with glucose and lipid metabolism were significantly altered, as evidenced by 16 S rRNA sequencing. Testicular metabolome revealed that the Top 50 changed metabolites were also enriched in lipid metabolism. Subsequently, the combined gut microbiome and metabolome analysis uncovered the strong correlations between Klebsiella, Blautia, Parabacteroides, and lipid metabolites (e.g., PC, LysoPC and GPCho). We speculate that the dysbiosis of gut microbiota-related disturbed lipid metabolism may be responsible for long-term NPs-induced damaged spermatogenesis, which provides new insights into NPs-induced dysregulated spermatogenesis.
Topics: Male; Humans; Gastrointestinal Microbiome; Microplastics; Polystyrenes; Spermatogenesis; Metabolome
PubMed: 37890247
DOI: 10.1016/j.ecoenv.2023.115626 -
New Microbes and New Infections Mar 2020Strains Marseille-P4001 and Marseille-P3668 are new species from the order isolated from healthy French volunteers. They are anaerobic Gram-negative rod-shaped...
Strains Marseille-P4001 and Marseille-P3668 are new species from the order isolated from healthy French volunteers. They are anaerobic Gram-negative rod-shaped bacteria. They exhibited 92.68% and 96.68% 16S rRNA sequence identities with strain MS-1 and JCM 17104, respectively, the phylogenetically closest species. Their respective draft genomes measured 5.23 Mb and 3.73 Mb with 39.2 mol% and 40.8 mol% of G + C content. Using a taxonogenomics method, we propose here a brief description of sp. nov., strain Marseille-P4001 and sp. nov., strain Marseille-P3668 as new bacterial species.
PubMed: 32071723
DOI: 10.1016/j.nmni.2019.100642 -
Clinical Immunology (Orlando, Fla.) Oct 2023The clinical relevance and pathogenic role of gut microbiome in both myositis and its associated interstitial lung disease (ILD) are still unclear. The purpose of this...
PURPOSE
The clinical relevance and pathogenic role of gut microbiome in both myositis and its associated interstitial lung disease (ILD) are still unclear. The purpose of this study was to investigate the role of gut microbiome in myositis through comprehensive metagenomic-wide association studies (MWAS).
METHODS
We conducted MWAS of the myositis gut microbiome in a Chinese cohort by using whole-genome shotgun sequencing of high depth, including 30 myositis patients and 31 healthy controls (HC). Among the myositis patients, 11 developed rapidly progressive interstitial lung disease (RP-ILD) and 10 had chronic ILD (C-ILD).
RESULTS
Analysis for overall distribution level of the bacteria showed Alistipes onderdonkii, Parabacteroides distasonis and Escherichia coli were upregulated, Lachnospiraceae bacterium GAM79, Roseburia intestinalis, and Akkermansia muciniphila were downregulated in patients with myositis compared to HC. Bacteroides thetaiotaomicron, Parabacteroides distasonis and Escherichia coli were upregulated, Bacteroides A1C1 and Bacteroides xylanisolvens were downregulated in RP-ILD cases compared with C-ILD cases. A variety of biological pathways related to metabolism were enriched in the myositis and HC, RP-ILD and C-ILD comparison. And in the analyses for microbial contribution in metagenomic biological pathways, we have found that E. coli played an important role in the pathway expression in both myositis group and myositis-associated RP-ILD group. Anti-PL-12 antibody, anti-Ro-52 antibody, and anti-EJ antibody were found to have positive correlation with bacterial diversity (Shannon-wiener diversity index and Chao1, richness estimator) between myositis group and control groups. The combination of E. coli and R. intestinalis could distinguish myositis group from HC effectively. R. intestinalis can also be applied in the distinguishment of RP-ILD group vs. C-ILD group in myositis patients.
CONCLUSION
Our MWAS study first revealed the link between gut microbiome and pathgenesis of myositis, which may help us understand the role of gut microbiome in the etiology of myositis and myositis-associated RP-ILD.
Topics: Humans; Gastrointestinal Microbiome; Metagenome; Escherichia coli; Myositis; Lung Diseases, Interstitial; Bacteria; Autoantibodies; Retrospective Studies
PubMed: 37595937
DOI: 10.1016/j.clim.2023.109738 -
International Journal of Systematic and... Nov 2023An obligate anaerobic, Gram-negative, rod-shaped and non-spore-forming bacterium, designated as strain GYB001, was isolated from the blood of a patient with a sigmoid...
An obligate anaerobic, Gram-negative, rod-shaped and non-spore-forming bacterium, designated as strain GYB001, was isolated from the blood of a patient with a sigmoid colon perforation. Taxonomic characterization of the novel isolate was performed using a polyphasic approach. A phylogenetic analysis based on 16S rRNA gene and whole genome sequences revealed that GYB001 represented a member of the genus , in the family . The closest species, based on 16S rRNA sequence, was DSM 23371 with 97.4 % similarity. Average nucleotide identity and digital DNA-DNA hybridization values between strain GYB001 and DSM 23371 were 86.7 and 28.7% and between GYB001 and JCM 18682 were 86.6 and 27.7 %, respectively. The genome was 6.57 Mbp long with 43.3 mol% G+C content. Colonies on Brucella blood agar (BBA) were circular, convex, smooth, grey and small in size. Growth was observed on trypticase soy agar (TSA), TSA +5 % sheep blood and agar. Growth occurred at 18-42 °C on BBA in the presence of 0-3 % NaCl (w/v) and at pH 6.0-8.5. The major polar lipids were phosphatidylethanolamine and phospholipids. The major fatty acids in strain GYB001 were anteiso-C and iso-C 3-OH, and the predominant respiratory quinones were menaquinone-10 (MK-10) and MK-9. The cell wall contained -diaminopimelic acid. Considering these phenotypic features and comparative genome analyses, we propose strain GYB001 as the type strain of sp. nov. (=KCTC 25738=KBN12P06525=LMG 32797).
Topics: Humans; Animals; Sheep; Fatty Acids; Phylogeny; RNA, Ribosomal, 16S; Agar; Base Composition; DNA, Bacterial; Sequence Analysis, DNA; Bacterial Typing Techniques; Phospholipids; Comparative Genomic Hybridization; Vitamin K 2
PubMed: 37999940
DOI: 10.1099/ijsem.0.006187 -
International Journal of Food Sciences... Sep 2023Low-no-calorie sweeteners (LNCS) are used as sugar substitutes as part of strategies to reduce the risk of chronic diseases related to high sugar intake (e.g. type 2...
Low-no-calorie sweeteners (LNCS) are used as sugar substitutes as part of strategies to reduce the risk of chronic diseases related to high sugar intake (e.g. type 2 diabetes (T2D)). This study investigated how a range of sweeteners [tagatose (TA)/maltitol (MA)/sorbitol (SO)/stevia (ST)/sucralose (SU)/acesulfame K (ACK)] impact the gut microbiota of T2D subjects and healthy human adults using the SIFR® technology ( = 12). The cohort covered clinically relevant interpersonal and T2D-related differences. ACK/SU remained intact while not impacting microbial composition and metabolite production. In contrast, TA/SO and ST/MA were respectively readily and gradually fermented. ST and particularly TA/SO/MA increased bacterial density and SCFA production product-specifically: SO increased acetate (∼), whilst MA/ST increased propionate (∼). TA exerted low specificity as it increased butyrate for healthy subjects, yet propionate for T2D subjects. Overall, LNCS exerted highly compound-specific effects stressing that results obtained for one LNCS cannot be generalised to other LNCS.
Topics: Adult; Humans; Sweetening Agents; Gastrointestinal Microbiome; Propionates; Diabetes Mellitus, Type 2; Energy Intake; Sorbitol; Stevia
PubMed: 37537786
DOI: 10.1080/09637486.2023.2240037 -
Journal of Translational Medicine Jun 2023The relationship between intestinal microbiome and colorectal cancer (CRC) progression is unclear. This study aims to identify the intestinal microbiome associated with...
OBJECTIVE
The relationship between intestinal microbiome and colorectal cancer (CRC) progression is unclear. This study aims to identify the intestinal microbiome associated with CRC progression and construct predictive labels to support the accurate assessment and treatment of CRC.
METHOD
The 192 patients included in the study were divided into stage I-II and stage III-IV CRC patients according to the pathological stages, and preoperative stools were collected from both groups for 16S rDNA sequencing of the intestinal microbiota. Pearson correlation and Spearman correlation coefficient analysis were used to analyze the differential intestinal microbiome and the correlation with tumor microenvironment and to predict the functional pathway. XGBoost model (XGB) and Random Forest model (RF) were used to construct the microbiome-based signature. The total RNA extraction from 17 CRC tumor simples was used for transcriptome sequencing.
RESULT
The Simpson index of intestinal microbiome in stage III-IV CRC were significantly lower than those in stage I-II CRC. Proteus, Parabacteroides, Alistipes and Ruminococcus etc. are significantly enriched genus in feces of CRC patients with stage III-IV. ko00514: Other types of O - glycan biosynthesis pathway is relevant with CRC progression. Alistipes indistinctus was positively correlated with mast cells, immune activators IL-6 and IL6R, and GOBP_PROTEIN_FOLDING_IN_ENDOPLASMIC_RETICULUM dominantly. The Random Forest (RF) model and eXtreme Gradient Boosting (XGBoost) model constructed with 42 CRC progression-associated differential bacteria were effective in distinguishing CRC patients between stage I-II and stage III-IV.
CONCLUSIONS
The abundance and diversity of intestinal microbiome may increase gradually with the occurrence and progression of CRC. Elevated fetal abundance of Proteus, Parabacteroides, Alistipes and Ruminococcus may contribute to CRC progression. Enhanced synthesis of O - glycans may result in CRC progression. Alistipes indistinctus may play a facilitated role in mast cell maturation by boosting IL-6 production. Alistipes indistinctus may work in the correct folding of endoplasmic reticulum proteins in CRC, reducing ER stress and prompting the survival and deterioration of CRC, which may owe to the enhanced PERK expression and activation of downstream UPR by Alistipes indistinctus. The CRC progression-associated differential intestinal microbiome identified in our study can be served as potential microbial markers for CRC staging prediction.
Topics: Humans; Gastrointestinal Microbiome; Interleukin-6; Colorectal Neoplasms; Bacteroidetes; Feces; RNA, Ribosomal, 16S; Tumor Microenvironment
PubMed: 37291572
DOI: 10.1186/s12967-023-04119-1