Enlightening the taxonomy darkness of human gut microbiomes with a cultured biobank

Microbiome, Год журнала: 2021, Номер 9(1)

Опубликована: Май 21, 2021

Abstract Background In gut microbiome studies, the cultured microbial resource plays essential roles, such as helping to unravel functions and host-microbe interactions. Although several major studies have been performed elucidate human microbiota, up 70% of Unified Human Gastrointestinal Genome species not date. Large-scale isolation identification well availability public are imperative for further characterizing functions. Results this study, we constructed a Gut Microbial Biobank (hGMB; homepage: hgmb.nmdc.cn ) through cultivation 10,558 isolates from 31 sample mixtures 239 fresh fecal samples healthy Chinese volunteers, deposited 1170 strains representing 400 different in culture collections International Depository Authority long-term preservation access worldwide. Following rules Code Nomenclature Prokaryotes, 102 new were characterized denominated, while 28 genera 3 families proposed. hGMB represented over 80% common dominant global 16S rRNA gene amplicon data ( n = 11,647) 24 “most-wanted” “medium priority” taxa proposed by Microbiome Project. We total sequenced 115 genomes novel 13 previously known species. Further silico analysis revealed that newly 22 uncultured (UHGG) contributed representatives potentially “dark taxa” had discovered UHGG. The nonredundant catalogs generated covered 50% functionally genes (KEGG orthologs) largest approximately 10% “most wanted” unknown proteins FUnkFams database. Conclusions A publicly accessible (hGMB) was established contained represents expands resources genomic repository adding species, genera, families, microbes.

Язык: Английский

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Understanding the glucoregulatory mechanisms of metformin in type 2 diabetes mellitus

Nature Reviews Endocrinology, Год журнала: 2019, Номер 15(10), С. 569 - 589

Опубликована: Авг. 22, 2019

Язык: Английский

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The Short-Chain Fatty Acid Acetate in Body Weight Control and Insulin Sensitivity

Nutrients, Год журнала: 2019, Номер 11(8), С. 1943 - 1943

Опубликована: Авг. 18, 2019

The interplay of gut microbiota, host metabolism, and metabolic health has gained increased attention. Gut microbiota may play a regulatory role in gastrointestinal health, substrate peripheral tissues including adipose tissue, skeletal muscle, liver, pancreas via its metabolites short-chain fatty acids (SCFA). Animal human data demonstrated that, particular, acetate beneficially affects energy metabolism secretion the hormones like glucagon-like peptide-1 peptide YY, which, thereby, appetite, reduction whole-body lipolysis, systemic pro-inflammatory cytokine levels, an increase expenditure fat oxidation. Thus, potential therapies to microbial fermentation production have been under vigorous scientific scrutiny. In this review, relevance colonically systemically most abundant SCFA effects on previously mentioned will be discussed relation body weight control glucose homeostasis. We discuss detail differential oral administration (vinegar intake), colonic infusions, acetogenic fiber, probiotic administrations as approaches combat obesity comorbidities. Notably, are scarce, which highlights necessity for further research investigate acetate’s physiology, metabolic, cardiovascular health.

Язык: Английский

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Gut Microbiota as a Trigger for Metabolic Inflammation in Obesity and Type 2 Diabetes

Frontiers in Immunology, Год журнала: 2020, Номер 11

Опубликована: Окт. 16, 2020

The gut microbiota has been linked to the development of obesity and type 2 diabetes (T2D). underlying mechanisms as how intestinal may contribute T2D are only partly understood. It becomes progressively clear that is characterized by a chronic state low-grade inflammation, which insulin resistance. Here, we review current evidence microbiota, metabolites they produce, could drive resistance in T2D, possibly initiating an inflammatory response. First, will summarize major findings about immunological microbial changes these metabolic diseases. Next, give detailed view on have implicated inflammation. Lastly, critically discuss clinical studies focus interaction between immune system disease. Overall, there strong tripartite host metabolism critical partaker pathophysiology T2D.

Язык: Английский

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Prevotella diversity, niches and interactions with the human host

Nature Reviews Microbiology, Год журнала: 2021, Номер 19(9), С. 585 - 599

Опубликована: Май 28, 2021

Язык: Английский

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Shaping the Future of Probiotics and Prebiotics

Trends in Microbiology, Год журнала: 2021, Номер 29(8), С. 667 - 685

Опубликована: Фев. 5, 2021

An expanding range of candidate probiotic species and prebiotic substrates is emerging to address newly elucidated data-driven microbial niches host targets.Overlapping with, adjacent to, the fields, new variants microbiome-modulating interventions are developing, including synbiotics, postbiotics, consortia, live biotherapeutic products, genetically modified organisms, with renewed interest in polyphenols, fibres, fermented foods.Personalised nutrition precision medicine beginning influence application probiotics prebiotics, growing modulation signatures health disease.Demand for prebiotics across divergent product formats driving innovation quality assurance techniques measure dose, viability, structural functional integrity. Recent ongoing developments microbiome science enabling frontiers research prebiotics. Novel types, mechanisms, applications currently under study have potential change scientific understanding as well nutritional healthcare these interventions. The expansion related fields microbiome-targeted interventions, an evolving landscape implementation regulatory, policy, prescriber, consumer spheres, portends era significant change. In this review we examine recent, emerging, anticipated trends science, create a vision broad areas developing field. Probiotics (see Glossary) received escalating attention recent years scientific, healthcare, public arenas. Publicity around has also broadened perception microorganisms, beyond disease-causing agents that should be avoided, more rational view integrating beneficial roles microorganisms human health. line advances, awareness acceptance continues expand [1.Chin-Lee B. et al.Patient experience use community-based care settings.Patient Prefer. Adhere. 2014; 8: 1513-1520PubMed Google Scholar], industry growth estimated at 7% annually [2.Jackson S.A. al.Improving end-user trust commercial products.Front. Microbiol. 2019; 10: 739Crossref PubMed Scopus (19) forecast 12.7% over next 8 [3.Mano M.C.R. al.Oligosaccharide biotechnology: approach revolution on industry.Appl. Biotechnol. 2018; 102: 17-37Crossref (40) Scholar]. While there general beneficial, still gap definitions terms 'probiotics' 'prebiotics', their benefits health, how they function, where find best sources food products Scholar,4.Viana J.V. al.Probiotic foods: attitudes.Int. J. Food Sci. Technol. 2008; 43: 1577-1580Crossref (30) Both increasingly incorporated into wide foods, beverages, topical (even toilet paper), some cases questionable or no validation any benefit host, requirement existing consensus definitions. field, both clearly established, International Scientific Association Prebiotics (ISAPP) having convened panels whereby experts reviewed published behind [5.Hill C. al.Expert document. statement scope appropriate term probiotic.Nat. Rev. Gastroenterol. Hepatol. 11: 506-514Crossref (2566) Scholar] [6.Gibson G.R. document: definition prebiotics.Nat. 2017; 14: 491-502Crossref (1252) conclusions highlighted play integral role status. Some key mechanisms been (Box 1) used variety states, prophylactically therapeutically.Box 1Mechanisms Action PrebioticsMechanisms action complex, diverse, heterogeneous, often strain- compound-specific. many described, remain calls increased understanding, especially structure–function explanations observed effects long-term influences [134.Kleerebezem M. al.Understanding mode can drive translational pipeline towards reliable probiotics.Curr. Opin. 56: 55-60Crossref (26) Scholar,152.Plaza-Diaz al.Mechanisms probiotics.Adv. Nutr. S49-S66Crossref (96) Scholar,153.Monteagudo-Mera A. al.Adhesion mediated by impact health.Appl. 103: 6463-6472Crossref (91) Scholar].Probiotics interact via molecular effectors present cell structure secreted metabolic products. Probiotic metabolites act microbiota crossfeeding interactions, changes gastrointestinal microenvironment (e.g., pH lowering), competition nutrients binding sites, inhibition production strain-specific antibacterial compounds bacteriocins [133.Lebeer S. al.Identification effector molecules: state future perspectives.Curr. 49: 217-223Crossref (90) Such microbiota-directed contribute ability mediate pathogen overgrowth states such vaginal oral dysbioses [153.Monteagudo-Mera Scholar].With regard cells, molecules directly receptors intestinal epithelial, enteroendocrine, immune cells vagal afferent fibres. These interactions produce local gut effects, enhancement barrier integrity inflammation Toll-like receptors), systemic immune, endocrine, nervous system mediators perform enzymatic metabolism bile salts ingested xenobiotics [152.Plaza-Diaz Specific surface-associated include pili, lipoteichoic acids, exopolysaccharides, various surface-layer proteins, which therefore delivery Scholar].Classical through consumption substrate specific groups within microbiota, promoting activity. Provision select group/s bacteria indirectly other bacterial – inhibitory displacement. Resulting composition metabolite concentrations from administration nervous, endocrine signalling improvements bowel response, glucose lipid metabolism, bone regulation appetite satiety Chief by-products SCFAs acetate, butyrate, propionate, recognised systems facilitate [10.Blaak E.E. al.Short chain fatty acids health.Benefic. Microbes. 2020; 411-455Crossref (3) Scholar].In addition nutritive microbes, receptors, modulating epithelial function [154.Brosseau al.Prebiotics: preventive allergy.Nutrients. 1841Crossref (6) Mechanisms With Classical Currently, multiple spheres acting (Figure 1). Broad technological advances data collection analytical tools exploration providing deeper insights host. Interest grow conditions, body population subgroups, formats. Furthermore, evolution regulatory frameworks, clinical guidelines influencing healthcare. As our knowledge each integrated shaping timely. Traditionally, lactobacilli, bifidobacteria, lactic acid-producing (LAB) probiotics, primarily isolated dairy faecal microbiome. breadth its functions expanded, holds discovery approaches [7.Veiga P. al.Moving probiotics.Nat. 5: 878-880Crossref (5) taxa. Developments affordable complete genome sequencing powerful cultivation methods allowed isolation characterisation microbiomes opportunity developed next-generation [8.O'Toole P.W. al.Next-generation probiotics: spectrum biotherapeutics.Nat. 2: 17057Crossref (213) 2). Various bacteria, Roseburia intestinalis, Faecalibacterium prausnitzii, Eubacterium spp., Bacteroides spp. Akkermansia muciniphila, Scholar,9.Brodmann T. al.Safety novel microbes consumption: practical examples assessment European Union.Front. 1725Crossref (64) candidates represent proportion cultivable offer physiological not always conferred bifidobacteria bioactives Converting industrially viable presents challenges rich media anaerobic conditions adds cost complexity, investment determining optimal fermentation manufacturing processes time. Despite difficulties, muciniphila one promising candidates. Isolated 2004 [11.Derrien al.Akkermansia gen. nov., sp. mucin-degrading bacterium.Int. Syst. Evol. 2004; 54: 1469-1476Crossref (843) it tested preclinical animal models shown prevent development obesity, pasteurisation increasing stability efficacy species. Initial proof-of-concept studies taken place humans pasteurised safe improves several parameters [12.Depommier al.Supplementation overweight obese volunteers: exploratory study.Nat. Med. 25: 1096-1103Crossref (332) Live already market multispecies synbiotic preparation, containing inulin, Bifidobacterium longum subsp. infantis (Clostridium beijerinckii, Clostridium butyricum, Anaerobutyricum hallii) was improve levels type 2 diabetics [13.Perraudeau F. al.Improvements postprandial control subjects diabetes: multicenter, double blind, randomized placebo-controlled trial formulation.BMJ Open Diabetes Res. Care. 8e001319Crossref (1) will only source strains Niches strong species, targets intervention, female urogenital tract, cavity, nasopharyngeal skin [14.Maguire Maguire G. health.Arch. Dermatol. 309: 411-421Crossref (24) Scholar, 15.George V.T. al.The periodontal therapy.J. Int. Oral Heal. 2016; 404-408Google 16.Cribby al.Vaginal probiotics.Interdiscip. Perspect. Infect. Dis. 2008 (art. 256490)Crossref Species genera associated regions being investigated restore populations homeostasis disease states. Examples commensal isolate Staphylococcus hominis eczema atopic dermatitis [17.Nakatsuji al.Antimicrobials protect against aureus deficient dermatitis.Sci. Transl. 9eaah4680Crossref (362) Lactobacillus crispatus dysbiosis [18.Reid health.J. AOAC 2012; 95: 31-34Crossref (29) Fermented foods most common natural potentially LAB, benefits, reduced risk diabetes cardiovascular diseases [19.Marco M.L. al.Health beyond.Curr. 44: 94-102Crossref (363) putatively metabolomic profile [20.Taylor B.C. al.Consumption systematic differences metabolome.mSystems. 5e00901-19Crossref (13) likely major LAB [21.Pasolli E. al.Large-scale genome-wide analysis links acid microbiome.Nat. Commun. 2610Crossref show development. unfermented may fruits, vegetables, grains/cereals, dairy, meat fish honey, environmental soil [22.Zielińska D. Kolożyn-Krajewska Food-origin exhibit properties: Review.Biomed. 2018 5063185)Crossref core heartlands target therapy subfertility [23.García-Velasco J.A. al.What fertility specialists know about microbiome: review.Reprod. BioMed. Online. 35: 103-112Abstract Full Text PDF (28) liver [24.Meroni nonalcoholic disease: insight therapeutic strategies.Nutrients. 2642Crossref mood disorders [25.Dinan T.G. al.Psychobiotics: class psychotropic.Biol. Psychiatry. 2013; 74: 720-726Abstract (510) cognition [26.Dinan Cryan J.F. microbiome–gut–brain axis disease.Gastroenterol. Clin. N. Am. 46: 77-89Abstract [27.Seminario-Amez al.Probiotics health: A review.Med. Patol. Cir. Bucal. 22: e282-e288PubMed asthma [28.Spacova I. airway allergy: factors consider.Dis. Models Mech. 11dmm034314Crossref [29.Koutnikova H. al.Impact non-alcoholic variables: meta-analysis randomised controlled trials.BMJ Open. 9e017995Crossref (65) hypercholesterolaemia [30.Khare Gaur Cholesterol-lowering species.Curr. 77: 638-644Crossref (7) obesity [31.Brusaferro al.Is time treat obesity?.Nutrients. 1613Crossref (39) Significant emphasis placed investigating safety considered Many commonly exploited available generally recognized (GRAS) status USA belong qualified presumption (QPS) Safety Authority (EFSA), yet case history use. Submission GRAS, QPS, frameworks enable path commercialisation, pharmaceutical applications, example, category defined Drug Administration (FDA)i Directorate Quality Medicines [32.European Pharmacopoeia Commission 3053E General monograph products.Eur. Pharmacopoeia. (9.7)Google required [33.Rouanet al.Live road map assessment.Front. 7: 237Crossref comprising retrospective possible linked taxa considered, full sequence, antibiotic resistance genes, toxin transferrable genetic elements, virulence factors, proven models, pharmacokinetics, pharmacodynamics, Phase I–III trials. evidence fall current 2), albeit attracting attention. consortia network synergistic [34.Vázquez-Castellanos al.Design synthetic modulation.Curr. Pharmacol. 52-59Crossref (8) augment single-strain organisms definition, if characterised Adjacent postbiotics 1An updated expert panel ISAPP, press. fragments [35.Aguilar-Toalá al.Postbiotics:

Язык: Английский

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A purified membrane protein from Akkermansia muciniphila or the pasteurised bacterium blunts colitis associated tumourigenesis by modulation of CD8⁺ T cells in mice

Gut, Год журнала: 2020, Номер 69(11), С. 1988 - 1997

Опубликована: Март 13, 2020

Gut microbiota have been linked to inflammatory bowel disease (IBD) and colorectal cancer (CRC). Akkermansia muciniphila (A. muciniphila) is a gram-negative anaerobic bacterium that selectively decreased in the faecal of patients with IBD, but its causative role molecular mechanism blunting colitis-associated (CAC) remain inconclusive. This study investigates how A. engages immune response CAC.Mice were given dextran sulfate sodium induce colitis, followed by azoxymethane establish CAC or without pasteurised specific outer membrane protein (Amuc_1100) treatment. Faeces from mice IBD CRC collected for 16S rRNA sequencing. The effects Amuc_1100 on acute colitis investigated.A. was significantly reduced CAC. could improve reduction infiltrating macrophages CD8+ cytotoxic T lymphocytes (CTLs) colon. Their treatment also CD16/32+ spleen mesenteric lymph nodes (MLN) mice. elevated PD-1+ CTLs spleen. Moreover, blunted tumourigenesis expanding colon MLN. Remarkably, they activated MLN, as indicated TNF-α induction PD-1downregulation. stimulate activate splenocytes CT26 cell conditioned medium.These data indicate can blunt through modulation CTLs.

Язык: Английский

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Administration of Akkermansia muciniphila Ameliorates Dextran Sulfate Sodium-Induced Ulcerative Colitis in Mice

Frontiers in Microbiology, Год журнала: 2019, Номер 10

Опубликована: Окт. 1, 2019

Inflammatory bowel diseases (IBDs) develop as a result of complex interactions among genes, innate immunity and environmental factors, which are related to the gut microbiota. Multiple clinical animal data have shown that Akkermansia muciniphila is associated with healthy mucosa. However, its precise role in colitis currently unknown. Our study aimed determine protective effects underlying mechanisms dextran sulfate sodium (DSS)-induced mouse model. Twenty-four C57BL/6 male mice were administered A. MucT or phosphate-buffered saline (PBS) once daily by oral gavage for 14 days. Colitis was induced drinking 2% DSS from days 0 6, followed 2 normal water. Mice weighed then sacrificed on day 8. We found improved DSS-induced colitis, evidenced reduced weight loss, colon length shortening histopathology scores enhanced barrier function. Serum tissue levels inflammatory cytokines chemokines (TNF-α, IL1α, IL6, IL12A, MIP-1A, G-CSF, KC) decreased administration. Analysis 16S rDNA sequences showed significant microbiota alterations. Furthermore, correlation analysis indicated pro-inflammatory other injury factors negatively Verrucomicrobia, Akkermansia, Ruminococcaceae, Rikenellaceae, prominently abundant muciniphila-treated mice. confirmed treatment could ameliorate mucosal inflammation either via microbe-host interactions, protect function reduce cytokines, improving microbial community. findings suggest may be potential probiotic agent ameliorating colitis.

Язык: Английский

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The gut microbiome as a modulator of healthy ageing

Nature Reviews Gastroenterology & Hepatology, Год журнала: 2022, Номер 19(9), С. 565 - 584

Опубликована: Апрель 25, 2022

Язык: Английский

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How Probiotics Affect the Microbiota

Frontiers in Cellular and Infection Microbiology, Год журнала: 2020, Номер 9

Опубликована: Янв. 15, 2020

Probiotics have been used to treat a variety of diseases for decades: however, what is the rationale under this? Such treatment was first proposed in early 19th century based on observations decreased Bifidobacteria populations children suffering diarrhea, suggesting that oral intake could replete microbiota subpopulation and improve health. Since then, studies shown modifications gut or skin course suggested positive effects certain probiotics. Most failed report any impact microbiota. The probiotics, as well bacteria colonizing food, does not reside their ability graft but rather sharing genes metabolites, supporting challenged microbiota, by direct influence epithelial immune cells. argue probiotics be associated conventional drugs insulin resistance, infectious diseases, inflammatory psychiatric disorders also interfere with drug metabolism. Nevertheless, context plethora probiotic strains associations, produced such conditions do allow comparisons, it remains difficult know whether patient would benefit from taking particular probiotic. In other words, although several mechanisms are observed when studying single strain, all individual expected share same effects. order clarify role clinics, we explore here relation between

Язык: Английский

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