Qiita: rapid, web-enabled microbiome meta-analysis

Nature Methods, Год журнала: 2018, Номер 15(10), С. 796 - 798

Опубликована: Сен. 20, 2018

Язык: Английский

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Microbiota as Predictor of Mortality in Allogeneic Hematopoietic-Cell Transplantation

New England Journal of Medicine, Год журнала: 2020, Номер 382(9), С. 822 - 834

Опубликована: Фев. 26, 2020

Relationships between microbiota composition and clinical outcomes after allogeneic hematopoietic-cell transplantation have been described in single-center studies. Geographic variations the of human microbial communities differences practices across institutions raise question whether these associations are generalizable.

Язык: Английский

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Environmental factors shaping the gut microbiome in a Dutch population

Nature, Год журнала: 2022, Номер 604(7907), С. 732 - 739

Опубликована: Апрель 13, 2022

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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Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

IMA Fungus, Год журнала: 2020, Номер 11(1)

Опубликована: Июль 10, 2020

True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of based on global richness estimates, with around 3 million predicted species. Compared to plants animals, have simple body plans often morphologically ecologically obscure structures. This poses challenges for accurate precise identifications. Here we provide a conceptual framework identification fungi, encouraging approach integrative (polyphasic) taxonomy species delimitation, i.e. combination genealogy (phylogeny), phenotype (including autecology), reproductive biology (when feasible). allows objective evaluation diagnostic characters, either phenotypic or molecular both. Verification identifications is crucial but neglected. Because clade-specific evolutionary histories, there currently no single tool although DNA barcoding using internal transcribed spacer (ITS) remains first diagnosis, particularly in metabarcoding studies. Secondary barcodes are increasingly implemented groups where ITS does not sufficient precision. Issues pairwise sequence similarity-based OTU clustering discussed, multiple alignment-based phylogenetic approaches subsequent verification recommended as more alternatives. In approaches, trade-off between speed accuracy precision must be carefully considered. Intragenomic variation other markers should properly documented, phylotype diversity necessarily proxy richness. Important strategies improve are: (1) broadly document intraspecific intragenomic markers; (2) substantially expand repositories, focusing undersampled clades missing taxa; (3) curation labels primary repositories increase number sequences verified material; (4) link data digital information voucher specimens including imagery. parallel, technological improvements genome sequencing offer promising alternatives future. Despite prevalence DNA-based fungal taxonomy, phenotype-based remain an important strategy catalog establish initial hypotheses.

Язык: Английский

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Consistent and correctable bias in metagenomic sequencing experiments

eLife, Год журнала: 2019, Номер 8

Опубликована: Сен. 10, 2019

Marker-gene and metagenomic sequencing have profoundly expanded our ability to measure biological communities. But the measurements they provide differ from truth, often dramatically, because these experiments are biased toward detecting some taxa over others. This experimental bias makes taxon or gene abundances measured by different protocols quantitatively incomparable can lead spurious conclusions. We propose a mathematical model for how distorts community based on properties of real experiments. validate this with 16S rRNA shotgun metagenomics data defined bacterial Our better fits despite being simpler than previous models. illustrate be used evaluate protocols, understand effect downstream statistical analyses, correct given suitable calibration controls. These results illuminate new avenues truly quantitative reproducible measurements.

Язык: Английский

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The progress of gut microbiome research related to brain disorders

Journal of Neuroinflammation, Год журнала: 2020, Номер 17(1)

Опубликована: Янв. 17, 2020

Abstract There is increasing evidence showing that the dynamic changes in gut microbiota can alter brain physiology and behavior. Cognition was originally thought to be regulated only by central nervous system. However, it now becoming clear many non-nervous system factors, including gut-resident bacteria of gastrointestinal tract, regulate influence cognitive dysfunction as well process neurodegeneration cerebrovascular diseases. Extrinsic intrinsic factors dietary habits composition microbiota. Microbes release metabolites microbiota-derived molecules further trigger host-derived cytokines inflammation system, which contribute greatly pathogenesis host disorders such pain, depression, anxiety, autism, Alzheimer’s diseases, Parkinson’s disease, stroke. Change blood–brain barrier permeability, vascular physiology, structure are among most critical causes development downstream neurological dysfunction. In this review, we will discuss following parts: Overview technical approaches used microbiome studies Microbiota immunity Gut Microbiota-induced Neuropsychiatric diseases ■ Stress depression Pain migraine Autism spectrum Neurodegenerative disease Amyotrophic lateral sclerosis Multiple Cerebrovascular Atherosclerosis Stroke Arteriovenous malformation Conclusions perspectives

Язык: Английский

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Adapterama I: universal stubs and primers for 384 unique dual-indexed or 147,456 combinatorially-indexed Illumina libraries (iTru & iNext)

PeerJ, Год журнала: 2019, Номер 7, С. e7755 - e7755

Опубликована: Окт. 11, 2019

Massively parallel DNA sequencing offers many benefits, but major inhibitory cost factors include: (1) start-up (i.e., purchasing initial reagents and equipment); (2) buy-in getting the smallest possible amount of data from a run); (3) sample preparation. Reducing preparation costs is commonly addressed, are rarely addressed. We present dual-indexing systems to address all three these issues. By breaking library construction process into universal, re-usable, combinatorial components, we reduce costs, while increasing number samples variety types that can be combined within runs. accomplish this by extending Illumina TruSeq approach 768 (384 + 384) indexed primers produce 384 unique dual-indexes or 147,456 × combinations. maintain eight nucleotide indexes, with compatible index sequences. synthesized indexing primers, purifying them only standard desalting placing small aliquots in replicate plates. In qPCR validation tests, 206 208 tested passed (99% success). then created hundreds libraries various scenarios. Our reduces per-sample requiring one universal adapter works PCR uniquely identify samples. because: relatively few oligonucleotides needed large libraries; allows researchers use primer sets for different projects, which facilitates pooling during sequencing. make sequence length demultiplexed software, thereby minimizing customization headaches. subsequent Adapterama papers, same stubs construct amplicon restriction-site associated libraries, their expanded any type sequenced on platforms.

Язык: Английский

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Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions

Cell, Год журнала: 2022, Номер 185(20), С. 3789 - 3806.e17

Опубликована: Сен. 1, 2022

Cancer-microbe associations have been explored for centuries, but cancer-associated fungi rarely examined. Here, we comprehensively characterize the cancer mycobiome within 17,401 patient tissue, blood, and plasma samples across 35 types in four independent cohorts. We report fungal DNA cells at low abundances many major human cancers, with differences community compositions that differ among types, even when accounting technical background. Fungal histological staining of tissue microarrays supported intratumoral presence frequent spatial association macrophages. Comparing communities matched bacteriomes immunomes revealed co-occurring bi-domain ecologies, often permissive, rather than competitive, microenvironments distinct immune responses. Clinically focused assessments suggested prognostic diagnostic capacities mycobiomes, stage I synergistic predictive performance bacteriomes.

Язык: Английский

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Primer, Pipelines, Parameters: Issues in 16S rRNA Gene Sequencing

mSphere, Год журнала: 2021, Номер 6(1)

Опубликована: Фев. 24, 2021

In 16S rRNA gene sequencing, certain bacterial genera were found to be underrepresented or even missing in taxonomic profiles when using unsuitable primer combinations, outdated reference databases, inadequate pipeline settings. Concerning the last, quality thresholds as well bioinformatic settings (i.e., clustering approach, analysis pipeline, and specific adjustments such truncation) are responsible for a number of observed differences between studies.

Язык: Английский

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