Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Nature Biotechnology, Год журнала: 2019, Номер 37(8), С. 852 - 857

Опубликована: Июль 24, 2019

Язык: Английский

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Bile acid metabolites control TH17 and Treg cell differentiation

Nature, Год журнала: 2019, Номер 576(7785), С. 143 - 148

Опубликована: Ноя. 27, 2019

Язык: Английский

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Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice

Cell, Год журнала: 2019, Номер 177(6), С. 1600 - 1618.e17

Опубликована: Май 1, 2019

Язык: Английский

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Long-term benefit of Microbiota Transfer Therapy on autism symptoms and gut microbiota

Scientific Reports, Год журнала: 2019, Номер 9(1)

Опубликована: Апрель 9, 2019

Abstract Many studies have reported abnormal gut microbiota in individuals with Autism Spectrum Disorders (ASD), suggesting a link between microbiome and autism-like behaviors. Modifying the is potential route to improve gastrointestinal (GI) behavioral symptoms children ASD, fecal transplant could transform dysbiotic toward healthy one by delivering large number of commensal microbes from donor. We previously performed an open-label trial Microbiota Transfer Therapy (MTT) that combined antibiotics, bowel cleanse, stomach-acid suppressant, transplant, observed significant improvements GI symptoms, autism-related microbiota. Here, we report on follow-up same 18 participants two years after treatment was completed. Notably, most were maintained, improved even more end treatment. Important changes at remained follow-up, including increases bacterial diversity relative abundances Bifidobacteria Prevotella . Our observations demonstrate long-term safety efficacy MTT as therapy treat ASD who problems, warrant double-blind, placebo-controlled future.

Язык: Английский

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RESCRIPt: Reproducible sequence taxonomy reference database management

PLoS Computational Biology, Год журнала: 2021, Номер 17(11), С. e1009581 - e1009581

Опубликована: Ноя. 8, 2021

Nucleotide sequence and taxonomy reference databases are critical resources for widespread applications including marker-gene metagenome sequencing microbiome analysis, diet metabarcoding, environmental DNA (eDNA) surveys. Reproducibly generating, managing, using, evaluating nucleotide creates a significant bottleneck researchers aiming to generate custom databases. Furthermore, database composition drastically influences results, lack of standardization limits cross-study comparisons. To address these challenges, we developed RESCRIPt, Python 3 software package QIIME 2 plugin reproducible generation management databases, dedicated functions that streamline creating from popular sources, evaluating, comparing, interactively exploring qualitative quantitative characteristics across highlight the breadth capabilities provide several examples working with profiling (SILVA, Greengenes, NCBI-RefSeq, GTDB), eDNA metabarcoding surveys (BOLD, GenBank), as well genome comparison. We show bigger is not always better, standardized taxonomies those focus on type strains have advantages, though may be appropriate all use cases. Most appear benefit some curation (quality filtering), clustering appears detrimental quality. Finally, demonstrate extensibility RESCRIPt workflows comparison global hepatitis genomes. provides tools democratize process acquisition management, enabling reproducibly transparently create materials diverse research applications. released under permissive BSD-3 license at https://github.com/bokulich-lab/RESCRIPt .

Язык: Английский

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IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences

Microbiome, Год журнала: 2018, Номер 6(1)

Опубликована: Авг. 9, 2018

Microbiome studies often involve sequencing a marker gene to identify the microorganisms in samples of interest. Sequence classification is critical component this process, whereby sequences are assigned reference taxonomy containing known sequence representatives many microbial groups. Previous have shown that existing programs assign groups even if they belong novel taxonomic absent from taxonomy. This high rate "over classification" particularly detrimental microbiome because taxonomies far comprehensive.Here, we introduce IDTAXA, approach employs principles machine learning reduce over errors. Using multiple taxonomies, demonstrate IDTAXA has higher accuracy than popular classifiers such as BLAST, MAPSeq, QIIME, SINTAX, SPINGO, and RDP Classifier. Similarly, yields fewer classifications on Illumina mock community data when expected taxa training set. Furthermore, offers practical advantages other classifiers, maintaining low error rates across varying input lengths withholding composed random nucleotides or repeats.IDTAXA's may lead different conclusions substantially reduced number incorrectly identified through classification. Although misclassification relatively minor, believe remaining misclassifications likely caused by errors We describe how able putative mislabeling enabling sets be automatically corrected eliminating spurious sequences. part DECIPHER package for R programming language, available Bioconductor repository accessible online ( http://DECIPHER.codes ).

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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Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades

Nature Communications, Год журнала: 2019, Номер 10(1)

Опубликована: Май 16, 2019

Abstract Multiple factors modulate microbial community assembly in the vertebrate gut, though studies disagree as to their relative contribution. One cause may be a reliance on captive animals, which can have very different gut microbiomes compared wild counterparts. To resolve this disagreement, we analyze new, large, and highly diverse animal distal 16 S rRNA microbiome dataset, comprises 80% animals includes members of Mammalia, Aves, Reptilia, Amphibia, Actinopterygii. We decouple effects host evolutionary history diet diversity show that each factor modulates aspects diversity. Moreover, particular taxa associated with phylogeny or Mammalia stronger signal cophylogeny. Finally, find environmental filtering microbe-microbe interactions differ among clades. These findings provide robust assessment processes driving intestine.

Язык: Английский

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A longitudinal big data approach for precision health

Nature Medicine, Год журнала: 2019, Номер 25(5), С. 792 - 804

Опубликована: Май 1, 2019

Язык: Английский

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Microplastics change soil properties, heavy metal availability and bacterial community in a Pb-Zn-contaminated soil

Journal of Hazardous Materials, Год журнала: 2021, Номер 424, С. 127364 - 127364

Опубликована: Сен. 30, 2021

Язык: Английский

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