Human Gut Microbiome: Function Matters

Trends in Microbiology - Tập 26 Số 7 - Trang 563-574 - 2018
Anna Heintz‐Buschart1,2,3, Paul Wilmes3
1Current addresses: Helmholtz-Centre for Environmental Research GmbH – UFZ, Department of Soil Ecology, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
2German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
3Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg

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Karasov, 2011, Ecological physiology of diet and digestive systems, Annu. Rev. Physiol., 73, 69, 10.1146/annurev-physiol-012110-142152

LeBlanc, 2013, Bacteria as vitamin suppliers to their host: a gut microbiota perspective, Curr. Opin. Biotechnol., 24, 160, 10.1016/j.copbio.2012.08.005

Claus, 2016, The gut microbiota: a major player in the toxicity of environmental pollutants?, NPJ Biofilms Microbiomes, 2, 10.1038/npjbiofilms.2016.3

Kamada, 2013, Role of the gut microbiota in immunity and inflammatory disease, Nat. Rev. Immunol., 13, 321, 10.1038/nri3430

Abreu, 2010, Toll-like receptor signalling in the intestinal epithelium: how bacterial recognition shapes intestinal function, Nat. Rev. Immunol., 10, 131, 10.1038/nri2707

Sommer, 2013, The gut microbiota – masters of host development and physiology, Nat. Rev. Microbiol., 11, 227, 10.1038/nrmicro2974

Hooper, 2012, Interactions between the microbiota and the immune system, Science, 336, 1268, 10.1126/science.1223490

Gilbert, 2016, Microbiome-wide association studies link dynamic microbial consortia to disease, Nature, 535, 94, 10.1038/nature18850

Verberkmoes, 2008, Shotgun metaproteomics of the human distal gut microbiota, ISME J., 3, 179, 10.1038/ismej.2008.108

Turnbaugh, 2010, Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins, Proc. Natl. Acad. Sci. U. S. A., 107, 7503, 10.1073/pnas.1002355107

Gosalbes, 2011, Metatranscriptomic approach to analyze the functional human gut microbiota, PLoS One, 6, 10.1371/journal.pone.0017447

Erickson, 2012, Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn’s disease, PLoS One, 7, 10.1371/journal.pone.0049138

Ferrer, 2012, Microbiota from the distal guts of lean and obese adolescents exhibit partial functional redundancy besides clear differences in community structure, Environ. Microbiol., 15, 211, 10.1111/j.1462-2920.2012.02845.x

Maurice, 2013, Xenobiotics shape the physiology and gene expression of the active human gut microbiome, Cell, 152, 39, 10.1016/j.cell.2012.10.052

Pérez-Cobas, 2013, Gut microbiota disturbance during antibiotic therapy: a multi-omic approach, Gut, 62, 1591, 10.1136/gutjnl-2012-303184

Franzosa, 2014, Relating the metatranscriptome and metagenome of the human gut, Proc. Natl. Acad. Sci. U. S. A., 111, E2329, 10.1073/pnas.1319284111

Xiong, 2015, Development of an enhanced metaproteomic approach for deepening the microbiome characterization of the human infant gut, J. Proteome Res., 14, 133, 10.1021/pr500936p

Heintz-Buschart, 2016, Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes, Nat. Microbiol., 2

McNulty, 2011, The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins, Sci. Transl. Med., 3, 106ra106, 10.1126/scitranslmed.3002701

Proctor, 2016, The National Institutes of Health Human Microbiome Project, Seminars in Fetal & Neonatal Medicine, Semin. Fetal Neonatal. Med., 21, 368, 10.1016/j.siny.2016.05.002

Börnigen, 2013, Functional profiling of the gut microbiome in disease-associated inflammation, Genome Med., 5, 65, 10.1186/gm469

Cho, 2012, The human microbiome: at the interface of health and disease, Nat. Rev. Genet., 13, 260, 10.1038/nrg3182

Huttenhower, 2012, Structure, function and diversity of the healthy human microbiome, Nature, 486, 207, 10.1038/nature11234

Manor, 2017, Revised computational metagenomic processing uncovers hidden and biologically meaningful functional variation in the human microbiome, Microbiome, 5, 19, 10.1186/s40168-017-0231-4

Li, 2014, An integrated catalog of reference genes in the human gut microbiome, Nat. Biotechnol., 32, 834, 10.1038/nbt.2942

Schloissnig, 2013, Genomic variation landscape of the human gut microbiome, Nature, 493, 45, 10.1038/nature11711

Franzosa, 2015, Identifying personal microbiomes using metagenomic codes, Proc. Natl. Acad. Sci. U. S. A., 112, E2930, 10.1073/pnas.1423854112

van Iterson, 2013, General power and sample size calculations for high-dimensional genomic data, Stat. Appl. Genet. Mol. Biol., 12, 449, 10.1515/sagmb-2012-0046

Bi, 2016, Sample size calculation while controlling false discovery rate for differential expression analysis with RNA-sequencing experiments, BMC Bioinformatics, 17, 146, 10.1186/s12859-016-0994-9

Browne, 2016, Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation, Nature, 533, 543, 10.1038/nature17645

Zhang, 2017, Sampling strategies for three-dimensional spatial community structures in IBD microbiota research, Front. Cell. Infect. Microbiol., 7, 51, 10.3389/fcimb.2017.00051

Prestat, 2014, FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus, Nucleic Acids Res., 42, 10.1093/nar/gku702

Powell, 2012, eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges, Nucleic Acids Res., 40, D284, 10.1093/nar/gkr1060

Narayanasamy, 2016, IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses, Genome Biol., 17, 260, 10.1186/s13059-016-1116-8

Timmons, 2015, Multiple sources of bias confound functional enrichment analysis of global -omics data, Genome Biol., 16, 186, 10.1186/s13059-015-0761-7

Brito, 2016, Mobile genes in the human microbiome are structured from global to individual scales, Nature, 535, 435, 10.1038/nature18927

Zhang, 2016, Strain-level dissection of the contribution of the gut microbiome to human metabolic disease, Genome Med., 8, 41, 10.1186/s13073-016-0304-1

Antony-Babu, 2017, Multiple Streptomyces species with distinct secondary metabolomes have identical 16S rRNA gene sequences, Sci. Rep., 7, 10.1038/s41598-017-11363-1

McClean, 2015, Single gene locus changes perturb complex microbial communities as much as apex predator loss, Nat. Commun., 6, 10.1038/ncomms9235

Sommer, 2014, The human microbiome harbors a diverse reservoir of antibiotic resistance genes, Virulence, 1, 299, 10.4161/viru.1.4.12010

Dutilh, 2013, Screening metatranscriptomes for toxin genes as functional drivers of human colorectal cancer, Best Pract. Res. Clin. Gastroenterol., 27, 85, 10.1016/j.bpg.2013.03.008

Langille, 2013, Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences, Nat. Biotechnol., 31, 814, 10.1038/nbt.2676

Jun, 2015, PanFP: pangenome-based functional profiles for microbial communities, BMC Res. Notes, 8, 479, 10.1186/s13104-015-1462-8

Magnúsdóttir, 2017, Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota, Nat. Biotechnol., 35, 81, 10.1038/nbt.3703

Sunagawa, 2013, Metagenomic species profiling using universal phylogenetic marker genes, Nat. Methods, 10, 1196, 10.1038/nmeth.2693

Nielsen, 2014, Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes, Nat. Biotechnol., 32, 822, 10.1038/nbt.2939

Huerta-Cepas, 2016, eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences, Nucleic Acids Res., 44, D286, 10.1093/nar/gkv1248

Mende, 2017, proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes, Nucleic Acids Res., 45, D529, 10.1093/nar/gkw989

Lakhdari, 2010, Functional metagenomics: a high throughput screening method to decipher microbiota-driven NF-κB modulation in the human gut, PLoS One, 5, 10.1371/annotation/9f1b7f00-bcc0-4442-9775-491ebdafc7bc

Dobrijevic, 2013, High-throughput system for the presentation of secreted and surface-exposed proteins from Gram-positive bacteria in functional metagenomics studies, PLoS One, 8, 10.1371/journal.pone.0065956

Lam, 2015, Current and future resources for functional metagenomics, Front. Microbiol., 6, 149, 10.3389/fmicb.2015.01196

Colin, 2015, Ultrahigh-throughput discovery of promiscuous enzymes by picodroplet functional metagenomics, Nat. Commun., 6, 10.1038/ncomms10008

Lagier, 2016, Culture of previously uncultured members of the human gut microbiota by culturomics, Nat. Microbiol., 1, 10.1038/nmicrobiol.2016.203

Berdy, 2017, In situ cultivation of previously uncultivable microorganisms using the ichip, Nat. Protoc., 12, 2232, 10.1038/nprot.2017.074

Cadotte, 2011, Beyond species: functional diversity and the maintenance of ecological processes and services, J. Appl. Ecol., 48, 1079, 10.1111/j.1365-2664.2011.02048.x

Walker, 1995, Conserving biological diversity through ecosystem resilience, Conserv. Biol., 9, 747, 10.1046/j.1523-1739.1995.09040747.x

Naeem, 1998, Species redundancy and ecosystem reliability, Conserv. Biol., 12, 39, 10.1046/j.1523-1739.1998.96379.x

Lozupone, 2012, Diversity, stability and resilience of the human gut microbiota, Nature, 489, 220, 10.1038/nature11550

Allison, 2008, Colloquium paper: resistance, resilience, and redundancy in microbial communities, Proc. Natl. Acad. Sci. U. S. A., 105, 11512, 10.1073/pnas.0801925105

Delgado-Baquerizo, 2016, Microbial diversity drives multifunctionality in terrestrial ecosystems, Nat. Commun., 7, 10541, 10.1038/ncomms10541

Blount, 2012, Genomic analysis of a key innovation in an experimental Escherichia coli population, Nature, 488, 513, 10.1038/nature11514

Louwen, 2012, A novel link between Campylobacter jejuni bacteriophage defence, virulence and Guillain–Barré syndrome, Eur. J. Clin. Microbiol. Infect. Dis., 32, 207, 10.1007/s10096-012-1733-4

Sahl, 2015, Genomic characterization of Burkholderia pseudomallei isolates selected for medical countermeasures testing: comparative genomics associated with differential virulence, PLoS One, 10, 10.1371/journal.pone.0121052

Flores, 2014, Temporal variability is a personalized feature of the human microbiome, Genome Biol., 15, 531, 10.1186/s13059-014-0531-y

de Meij, 2016, Composition and stability of intestinal microbiota of healthy children within a Dutch population, FASEB J., 30, 1512, 10.1096/fj.15-278622

Coyte, 2015, The ecology of the microbiome: Networks, competition, and stability, Science, 350, 663, 10.1126/science.aad2602

McCann, 2000, The diversity–stability debate, Nature, 405, 228, 10.1038/35012234

Erkus, O. et al. (2013) Multifactorial diversity sustains microbial community stability. 7, 2126–2136

Carrara, 2015, Experimental evidence for strong stabilizing forces at high functional diversity of aquatic microbial communities, Ecology, 96, 1340, 10.1890/14-1324.1

Le Chatelier, 2013, Richness of human gut microbiome correlates with metabolic markers, Nature, 500, 541, 10.1038/nature12506

Roager, 2016, Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut, Nat. Microbiol., 1, 10.1038/nmicrobiol.2016.93

Tap, 2015, Gut microbiota richness promotes its stability upon increased dietary fibre intake in healthy adults, Environ. Microbiol., 17, 4954, 10.1111/1462-2920.13006

Matsen, 2014, Phylogenetics and the Human Microbiome, Syst. Biol., 64, e26, 10.1093/sysbio/syu053

Moya, 2016, Functional redundancy-induced stability of gut microbiota subjected to disturbance, Trends Microbiol., 24, 402, 10.1016/j.tim.2016.02.002

Sommer, 2017, The resilience of the intestinal microbiota influences health and disease, Nat. Rev. Microbiol., 15, 630, 10.1038/nrmicro.2017.58

Jiang, 2016, Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality, Microbiome, 4, 2, 10.1186/s40168-015-0146-x

Plichta, 2016, Transcriptional interactions suggest niche segregation among microorganisms in the human gut, Nat. Microbiol., 1, 10.1038/nmicrobiol.2016.152

Manor, 2017, Systematic characterization and analysis of the taxonomic drivers of functional shifts in the human microbiome, Cell Host Microbe, 21, 254, 10.1016/j.chom.2016.12.014

Luo, 2015, Constrains identifies microbial strains in metagenomic datasets, Nat. Biotechnol., 33, 1045, 10.1038/nbt.3319

Nayfach, 2016, An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography, Genome Res., 26, 1612, 10.1101/gr.201863.115

Scholz, 2016, Strain-level microbial epidemiology and population genomics from shotgun metagenomics, Nat. Methods, 13, 435, 10.1038/nmeth.3802

Truong, 2017, Microbial strain-level population structure and genetic diversity from metagenomes, Genome Res., 27, 626, 10.1101/gr.216242.116

Costea, 2017, metaSNV: A tool for metagenomic strain level analysis, PLoS One, 12, 10.1371/journal.pone.0182392

Quince, 2017, DESMAN: a new tool for de novo extraction of strains from metagenomes, Genome Biol., 18, 181, 10.1186/s13059-017-1309-9

Olesen, 2016, Dysbiosis is not an answer, Nat. Microbiol., 1, 10.1038/nmicrobiol.2016.228

Fodor, 2012, The ‘most wanted’ taxa from the human microbiome for whole genome sequencing, PLoS One, 7, 10.1371/journal.pone.0041294

Almeida, 2016, Capturing the most wanted taxa through cross-sample correlations, ISME J., 10, 2459, 10.1038/ismej.2016.35

Mayers, 2017, Quantitative metaproteomics and activity-based probe enrichment reveals significant alterations in protein expression from a mouse model of inflammatory bowel disease, J. Proteome Res., 16, 1014, 10.1021/acs.jproteome.6b00938

Prosser, 2014, Metabolomic strategies for the identification of new enzyme functions and metabolic pathways, EMBO Rep., 15, 657, 10.15252/embr.201338283

Nayfach, 2015, MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome, Bioinformatics, 31, 3368, 10.1093/bioinformatics/btv382

Caspi, 2013, The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases, Nucleic Acids Res., 42, D459, 10.1093/nar/gkt1103

Korem, 2015, Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples, Science, 349, 1101, 10.1126/science.aac4812

Brown, 2016, Measurement of bacterial replication rates in microbial communities, Nat. Biotechnol., 34, 1256, 10.1038/nbt.3704

Nawrocki, 2014, Computational identification of functional RNA homologs in metagenomic data, RNA Biol., 10, 1170, 10.4161/rna.25038

Bao, 2015, Strand-specific community RNA-seq reveals prevalent and dynamic antisense transcription in human gut microbiota, Front. Microbiol., 6, 94, 10.3389/fmicb.2015.00896

Kato, 2014, Multiple omics uncovers host-gut microbial mutualism during prebiotic fructooligosaccharide supplementation, DNA Res., 21, 469, 10.1093/dnares/dsu013

Palm, 2014, Immunoglobulin A coating identifies colitogenic bacteria in inflammatory bowel disease, Cell, 158, 1000, 10.1016/j.cell.2014.08.006

Kolmeder, 2015, Colonic metaproteomic signatures of active bacteria and the host in obesity, Proteomics, 15, 3544, 10.1002/pmic.201500049

Debyser, 2016, Faecal proteomics: A tool to investigate dysbiosis and inflammation in patients with cystic fibrosis, J. Cyst. Fibros., 15, 242, 10.1016/j.jcf.2015.08.003

Liu, 2016, The host shapes the gut microbiota via fecal microRNA, CHOM, 19, 32

Pedersen, 2016, Human gut microbes impact host serum metabolome and insulin sensitivity, Nature, 535, 376, 10.1038/nature18646

Okai, 2016, High-affinity monoclonal IgA regulates gut microbiota and prevents colitis in mice, Nat. Microbiol., 1, 10.1038/nmicrobiol.2016.103

Turpin, 2016, Association of host genome with intestinal microbial composition in a large healthy cohort, Nat. Genet., 48, 1413, 10.1038/ng.3693

Bonder, 2016, The effect of host genetics on the gut microbiome, Nat. Genet., 48, 1407, 10.1038/ng.3663

Wang, 2016, Genome-wide association analysis identifies variation in vitamin D receptor and other host factors influencing the gut microbiota, Nat. Genet., 48, 1396, 10.1038/ng.3695

Kim, 2016, Contributions of microbiome and mechanical deformation to intestinal bacterial overgrowth and inflammation in a human gut-on-a-chip, Proc. Natl. Acad. Sci. U. S. A., 113, E7, 10.1073/pnas.1522193112

Shah, 2016, A microfluidics-based in vitro model of the gastrointestinal human-microbe interface, Nat. Commun., 7, 10.1038/ncomms11535

Fritz, 2013, From meta-omics to causality: experimental models for human microbiome research, Microbiome, 1, 14, 10.1186/2049-2618-1-14

Nguyen, 2015, How informative is the mouse for human gut microbiota research?, Dis. Models Mechan., 8, 1, 10.1242/dmm.017400

Arrieta, 2016, Human microbiota-associated mice: a model with challenges, Cell Host Microbe, 19, 575, 10.1016/j.chom.2016.04.014

Furusawa, 2013, Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells, Nature, 504, 446, 10.1038/nature12721

Atarashi, 2013, Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota, Nature, 500, 232, 10.1038/nature12331

Turroni, 2016, Deciphering bifidobacterial-mediated metabolic interactions and their impact on gut microbiota by a multi-omics approach, ISME J., 10, 1656, 10.1038/ismej.2015.236

David, 2013, Diet rapidly and reproducibly alters the human gut microbiome, Nature, 505, 559, 10.1038/nature12820

O’Keefe, 2015, Fat, fibre and cancer risk in African Americans and rural Africans, Nat. Commun., 6, 10.1038/ncomms7342

van Nood, 2013, Duodenal infusion of donor feces for recurrent Clostridium difficile, N. Engl. J. Med., 368, 407, 10.1056/NEJMoa1205037

Li, 2016, Durable coexistence of donor and recipient strains after fecal microbiota transplantation, Science, 352, 586, 10.1126/science.aad8852

Ott, 2017, Efficacy of sterile fecal filtrate transfer for treating patients with Clostridium difficile infection, Gastroenterology, 152, 10.1053/j.gastro.2016.11.010

Petrof, 2013, Stool substitute transplant therapy for the eradication of Clostridium difficile infection: ‘RePOOPulating’ the gut, Microbiome, 1, 3, 10.1186/2049-2618-1-3

Tanca, 2016, The impact of sequence database choice on metaproteomic results in gut microbiota studies, Microbiome, 4, 51, 10.1186/s40168-016-0196-8

Tang, 2016, A graph-centric approach for metagenome-guided peptide and protein identification in metaproteomics, PLoS Comput. Biol., 12, 10.1371/journal.pcbi.1005224

Gillet, 2012, Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis, Mol. Cell. Proteomics, 11, 10.1074/mcp.O111.016717

Roume, 2013, A biomolecular isolation framework for eco-systems biology, ISME J., 7, 110, 10.1038/ismej.2012.72