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Volumn 5, Issue 1, 2017, Pages

Revised computational metagenomic processing uncovers hidden and biologically meaningful functional variation in the human microbiome

Author keywords

Functional metagenomics; Functional variation; Gut microbiome

Indexed keywords

AMINO ACID METABOLISM; ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BIOFILM; CARBOHYDRATE METABOLISM; COPY NUMBER VARIATION; DISEASE ASSOCIATION; ENERGY METABOLISM; GENE DOSAGE; GENE MAPPING; GENETIC VARIATION; GENOME SIZE; HUMAN; INTESTINE FLORA; METAGENOMICS; MICROBIOME; MULTIGENE FAMILY; NONHUMAN; PRIORITY JOURNAL; TAXONOMY; BACTERIUM; BIOLOGY; GASTROINTESTINAL TRACT; GENETICS; MICROBIOLOGY; PROCEDURES;

EID: 85015820719     PISSN: None     EISSN: 20492618     Source Type: Journal    
DOI: 10.1186/s40168-017-0231-4     Document Type: Article
Times cited : (19)

References (37)
  • 1
    • 84858439578 scopus 로고    scopus 로고
    • The human microbiome: at the interface of health and disease
    • Cho I, Blaser MJ. The human microbiome: at the interface of health and disease. Nat Rev Genet. 2012;13:260-70.
    • (2012) Nat Rev Genet , vol.13 , pp. 260-270
    • Cho, I.1    Blaser, M.J.2
  • 3
    • 84922735613 scopus 로고    scopus 로고
    • Extensive strain-level copy-number variation across human gut microbiome species
    • Greenblum S, Carr R, Borenstein E. Extensive strain-level copy-number variation across human gut microbiome species. Cell. 2015;160:583-94.
    • (2015) Cell , vol.160 , pp. 583-594
    • Greenblum, S.1    Carr, R.2    Borenstein, E.3
  • 6
    • 84864718456 scopus 로고    scopus 로고
    • Structure, function and diversity of the healthy human microbiome
    • Consortium HMP. Structure, function and diversity of the healthy human microbiome. Nat Nat Publ Group. 2013;486:207-14.
    • (2013) Nat Nat Publ Group , vol.486 , pp. 207-214
    • Consortium, H.M.P.1
  • 8
    • 84961291157 scopus 로고    scopus 로고
    • Which is more important for classifying microbial communities: who's there or what they can do?
    • Xu Z, Malmer D, Langille MGI, Way SF, Knight R. Which is more important for classifying microbial communities: who's there or what they can do? ISME J. 2014;8:2357-9.
    • (2014) ISME J , vol.8 , pp. 2357-2359
    • Xu, Z.1    Malmer, D.2    Langille, M.G.I.3    Way, S.F.4    Knight, R.5
  • 9
    • 84951815312 scopus 로고    scopus 로고
    • The players may change but the game remains: network analyses of ruminal microbiomes suggest taxonomic differences mask functional similarity
    • Taxis TM, WolffS, Gregg SJ, Minton NO, Zhang C, Dai J, et al. The players may change but the game remains: network analyses of ruminal microbiomes suggest taxonomic differences mask functional similarity. Nucleic Acids Res. 2015;29:gkv973.
    • (2015) Nucleic Acids Res , vol.29
    • Taxis, T.M.1    Wolff, S.2    Gregg, S.J.3    Minton, N.O.4    Zhang, C.5    Dai, J.6
  • 11
    • 84867074831 scopus 로고    scopus 로고
    • A metagenome-wide association study of gut microbiota in type 2 diabetes
    • Qin J, Li Y, Cai Z, Li S, Zhu J, Zhang F, et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nat Nat Publ Group. 2013;490:55-60.
    • (2013) Nat Nat Publ Group , vol.490 , pp. 55-60
    • Qin, J.1    Li, Y.2    Cai, Z.3    Li, S.4    Zhu, J.5    Zhang, F.6
  • 13
    • 84893859801 scopus 로고    scopus 로고
    • The microbial metabolite butyrate regulates intestinal macrophage function via histone deacetylase inhibition
    • Chang PV, Hao L, Offermanns S, Medzhitov R. The microbial metabolite butyrate regulates intestinal macrophage function via histone deacetylase inhibition. Proc Natl Acad Sci U S A. 2014;111:2247-52.
    • (2014) Proc Natl Acad Sci U S A , vol.111 , pp. 2247-2252
    • Chang, P.V.1    Hao, L.2    Offermanns, S.3    Medzhitov, R.4
  • 14
    • 79955579989 scopus 로고    scopus 로고
    • The microbiome and butyrate regulate energy metabolism and autophagy in the mammalian colon
    • Donohoe DR, Garge N, Zhang X, Sun W, O'Connell TM, Bunger MK, et al. The microbiome and butyrate regulate energy metabolism and autophagy in the mammalian colon. Cell Metab. 2011;13:517-26.
    • (2011) Cell Metab , vol.13 , pp. 517-526
    • Donohoe, D.R.1    Garge, N.2    Zhang, X.3    Sun, W.4    O'Connell, T.M.5    Bunger, M.K.6
  • 15
    • 84929655318 scopus 로고    scopus 로고
    • Microbiota-dependent metabolite trimethylamine-N-oxide is associated with disease severity and survival of patients with chronic heart failure
    • Trøseid M, Ueland T, Hov JR, Svardal A, Gregersen I, Dahl CP, et al. Microbiota-dependent metabolite trimethylamine-N-oxide is associated with disease severity and survival of patients with chronic heart failure. J Intern Med. 2014;277:717-26.
    • (2014) J Intern Med , vol.277 , pp. 717-726
    • Trøseid, M.1    Ueland, T.2    Hov, J.R.3    Svardal, A.4    Gregersen, I.5    Dahl, C.P.6
  • 16
    • 84958837712 scopus 로고    scopus 로고
    • The gut microbiome, diet, and links to cardiometabolic and chronic disorders
    • Aron-Wisnewsky J, Clément K. The gut microbiome, diet, and links to cardiometabolic and chronic disorders. Nat Rev Nephrol. 2016;12:169-81.
    • (2016) Nat Rev Nephrol , vol.12 , pp. 169-181
    • Aron-Wisnewsky, J.1    Clément, K.2
  • 17
    • 84922717073 scopus 로고    scopus 로고
    • Comparative analysis of functional metagenomic annotation and the mappability of short reads
    • Carr R, Borenstein E. Comparative analysis of functional metagenomic annotation and the mappability of short reads. PLoS One. 2014;9:e105776.
    • (2014) PLoS One , vol.9
    • Carr, R.1    Borenstein, E.2
  • 18
    • 84939202778 scopus 로고    scopus 로고
    • MUSiCC: a marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome
    • Manor O, Borenstein E. MUSiCC: a marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome. Genome Biol. 2015;16:53.
    • (2015) Genome Biol , vol.16 , pp. 53
    • Manor, O.1    Borenstein, E.2
  • 19
    • 79953276286 scopus 로고    scopus 로고
    • Quantitative metagenomic analyses based on average genome size normalization
    • Frank JA, Sørensen SJ. Quantitative metagenomic analyses based on average genome size normalization. Appl Environ Microbiol. 2011;77:2513-21.
    • (2011) Appl Environ Microbiol , vol.77 , pp. 2513-2521
    • Frank, J.A.1    Sørensen, S.J.2
  • 20
    • 84939141968 scopus 로고    scopus 로고
    • Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome
    • Nayfach S, Pollard KS. Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome. Genome Biol BioMed Central Ltd. 2015;16:59.
    • (2015) Genome Biol BioMed Central Ltd , vol.16 , pp. 59
    • Nayfach, S.1    Pollard, K.S.2
  • 21
    • 84866549438 scopus 로고    scopus 로고
    • Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment
    • Morgan XC, Tickle TL, Sokol H, Gevers D, Devaney KL, Ward DV, et al. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol. 2012;13:R79.
    • (2012) Genome Biol , vol.13 , pp. R79
    • Morgan, X.C.1    Tickle, T.L.2    Sokol, H.3    Gevers, D.4    Devaney, K.L.5    Ward, D.V.6
  • 22
    • 66749130197 scopus 로고    scopus 로고
    • Metabolic assessment of gradual development of moderate experimental colitis in IL-10 deficient mice
    • Martin F-PJ, Rezzi S, Philippe D, Tornier L, Messlik A, Hölzlwimmer G, et al. Metabolic assessment of gradual development of moderate experimental colitis in IL-10 deficient mice. J Proteome Res. 2009;8:2376-87.
    • (2009) J Proteome Res , vol.8 , pp. 2376-2387
    • Martin, F.-P.J.1    Rezzi, S.2    Philippe, D.3    Tornier, L.4    Messlik, A.5    Hölzlwimmer, G.6
  • 23
    • 70149096873 scopus 로고    scopus 로고
    • Pharmacometabonomic identification of a significant host-microbiome metabolic interaction affecting human drug metabolism
    • Clayton TA, Baker D, Lindon JC, Everett JR, Nicholson JK. Pharmacometabonomic identification of a significant host-microbiome metabolic interaction affecting human drug metabolism. Proc Natl Acad Sci U S A. 2009;106:14728-33.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 14728-14733
    • Clayton, T.A.1    Baker, D.2    Lindon, J.C.3    Everett, J.R.4    Nicholson, J.K.5
  • 24
    • 84883478660 scopus 로고    scopus 로고
    • Gut microbiota from twins discordant for obesity modulate metabolism in mice
    • Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL, et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science. 2013;341:1241214-4.
    • (2013) Science , vol.341
    • Ridaura, V.K.1    Faith, J.J.2    Rey, F.E.3    Cheng, J.4    Duncan, A.E.5    Kau, A.L.6
  • 29
    • 27744480818 scopus 로고    scopus 로고
    • Bacterial outer membrane vesicles and the hostpathogen interaction
    • Kuehn MJ, Kesty NC. Bacterial outer membrane vesicles and the hostpathogen interaction. Genes Dev. 2005;19:2645-55.
    • (2005) Genes Dev , vol.19 , pp. 2645-2655
    • Kuehn, M.J.1    Kesty, N.C.2
  • 30
    • 60849116153 scopus 로고    scopus 로고
    • Protein secretion systems in bacterial-host associations, and their description in the Gene Ontology
    • Tseng T-T, Tyler BM, Setubal JC. Protein secretion systems in bacterial-host associations, and their description in the Gene Ontology. BMC Microbiol. 2009;9 Suppl 1:S2.
    • (2009) BMC Microbiol , vol.9 , pp. S2
    • Tseng, T.-T.1    Tyler, B.M.2    Setubal, J.C.3
  • 31
    • 84899787502 scopus 로고    scopus 로고
    • Revealing the bacterial butyrate synthesis pathways by analyzing (meta)genomic data
    • Vital M, Howe AC, Tiedje JM. Revealing the bacterial butyrate synthesis pathways by analyzing (meta)genomic data. MBio. 2014;5:e00889.
    • (2014) MBio , vol.5
    • Vital, M.1    Howe, A.C.2    Tiedje, J.M.3
  • 32
    • 84871627299 scopus 로고    scopus 로고
    • Methanobrevibacter smithii is the predominant methanogen in patients with constipation-predominant IBS and methane on breath
    • Kim G, Deepinder F, Morales W, Hwang L. Methanobrevibacter smithii is the predominant methanogen in patients with constipation-predominant IBS and methane on breath. Digestive diseases and. 2012.
    • (2012) Digestive diseases and
    • Kim, G.1    Deepinder, F.2    Morales, W.3    Hwang, L.4
  • 35
    • 84899459352 scopus 로고    scopus 로고
    • Metagenomic systems biology and metabolic modeling of the human microbiome: from species composition to community assembly rules
    • Levy R, Borenstein E. Metagenomic systems biology and metabolic modeling of the human microbiome: from species composition to community assembly rules. Gut Microbes. 2014;5:265-70.
    • (2014) Gut Microbes , vol.5 , pp. 265-270
    • Levy, R.1    Borenstein, E.2
  • 36
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: kyoto encyclopedia of genes and genomes
    • Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28:27-30.
    • (2000) Nucleic Acids Res , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 37
    • 84858983547 scopus 로고    scopus 로고
    • KEGG for integration and interpretation of large-scale molecular data sets
    • Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 2012;40:D109-14.
    • (2012) Nucleic Acids Res , vol.40 , pp. D109-D114
    • Kanehisa, M.1    Goto, S.2    Sato, Y.3    Furumichi, M.4    Tanabe, M.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.