Clemente JC, Ursell LK, Parfrey LW, Knight R. The impact of the gut microbiota on human health: an integrative view. Cell. 2012;148(6):1258–70.
Article
CAS
PubMed
Google Scholar
Li M, Wang B, Zhang M, Rantalainen M, Wang S, Zhou H, Zhang Y, Shen J, Pang X, Zhang M, et al. Symbiotic gut microbes modulate human metabolic phenotypes. Proc Natl Acad Sci U S A. 2008;105(6):2117–22.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nicholson JK, Holmes E, Kinross J, Burcelin R, Gibson G, Jia W, Pettersson S. Host-gut microbiota metabolic interactions. Science. 2012;336(6086):1262–7.
Article
CAS
PubMed
Google Scholar
Backhed F, Ding H, Wang T, Hooper LV, Koh GY, Nagy A, Semenkovich CF, Gordon JI. The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci U S A. 2004;101(44):15718–23.
Article
PubMed
PubMed Central
Google Scholar
Fraher MH, O'Toole PW, Quigley EM. Techniques used to characterize the gut microbiota: a guide for the clinician. Nat Rev Gastroenterol Hepatol. 2012;9(6):312–22.
Article
CAS
PubMed
Google Scholar
Franzosa EA, Morgan XC, Segata N, Waldron L, Reyes J, Earl AM, Giannoukos G, Boylan MR, Ciulla D, Gevers D, et al. Relating the metatranscriptome and metagenome of the human gut. Proc Natl Acad Sci U S A. 2014;111(22):E2329–38.
Article
CAS
PubMed
PubMed Central
Google Scholar
Verberkmoes NC, Russell AL, Shah M, Godzik A, Rosenquist M, Halfvarson J, Lefsrud MG, Apajalahti J, Tysk C, Hettich RL, et al. Shotgun metaproteomics of the human distal gut microbiota. ISME J. 2009;3(2):179–89.
Article
CAS
PubMed
Google Scholar
Mayne J, Ning Z, Zhang X, Starr AE, Chen R, Deeke S, Chiang CK, Xu B, Wen M, Cheng K, et al. Bottom-up proteomics (2013-2015): keeping up in the era of systems biology. Anal Chem. 2016;88(1):95–121.
Article
PubMed
Google Scholar
Muth T, Benndorf D, Reichl U, Rapp E, Martens L. Searching for a needle in a stack of needles: challenges in metaproteomics data analysis. Mol Biosyst. 2013;9(4):578–85.
Article
CAS
PubMed
Google Scholar
Muth T, Kolmeder CA, Salojarvi J, Keskitalo S, Varjosalo M, Verdam FJ, Rensen SS, Reichl U, de Vos WM, Rapp E, et al. Navigating through metaproteomics data: a logbook of database searching. Proteomics. 2015;15:3439–53.
Article
CAS
PubMed
Google Scholar
Xiong W, Abraham PE, Li Z, Pan C, Hettich RL. Microbial metaproteomics for characterizing the range of metabolic functions and activities of human gut microbiota. Proteomics. 2015;15(20):3424–38.
Article
CAS
PubMed
Google Scholar
Lichtman JS, Sonnenburg JL, Elias JE. Monitoring host responses to the gut microbiota. ISME J. 2015;9(9):1908–15.
Article
CAS
PubMed
Google Scholar
Jagtap P, Goslinga J, Kooren JA, McGowan T, Wroblewski MS, Seymour SL, Griffin TJ. A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies. Proteomics. 2013;13(8):1352–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Erickson AR, Cantarel BL, Lamendella R, Darzi Y, Mongodin EF, Pan C, Shah M, Halfvarson J, Tysk C, Henrissat B, et al. Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn’s disease. PLoS One. 2012;7(11):e49138.
Article
CAS
PubMed
PubMed Central
Google Scholar
Daniel H, Moghaddas Gholami A, Berry D, Desmarchelier C, Hahne H, Loh G, Mondot S, Lepage P, Rothballer M, Walker A, et al. High-fat diet alters gut microbiota physiology in mice. ISME J. 2014;8(2):295–308.
Article
CAS
PubMed
Google Scholar
Kolmeder CA, de Been M, Nikkila J, Ritamo I, Matto J, Valmu L, Salojarvi J, Palva A, Salonen A, de Vos WM. Comparative metaproteomics and diversity analysis of human intestinal microbiota testifies for its temporal stability and expression of core functions. PLoS One. 2012;7(1):e29913.
Article
CAS
PubMed
PubMed Central
Google Scholar
Elias JE, Gygi SP. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods. 2007;4(3):207–14.
Article
CAS
PubMed
Google Scholar
Tanca A, Palomba A, Pisanu S, Deligios M, Fraumene C, Manghina V, Pagnozzi D, Addis MF, Uzzau S. A straightforward and efficient analytical pipeline for metaproteome characterization. Microbiome. 2014;2(1):49.
Article
PubMed
PubMed Central
Google Scholar
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464(7285):59–65.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li J, Jia H, Cai X, Zhong H, Feng Q, Sunagawa S, Arumugam M, Kultima JR, Prifti E, Nielsen T, et al. An integrated catalog of reference genes in the human gut microbiome. Nat Biotechnol. 2014;32(8):834–41.
Article
CAS
PubMed
Google Scholar
Human Microbiome Jumpstart Reference Strains C, Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, Rusch DB, Mitreva M, Sodergren E, et al. A catalog of reference genomes from the human microbiome. Science. 2010;328(5981):994–9.
Article
Google Scholar
Cox J, Hein MY, Luber CA, Paron I, Nagaraj N, Mann M. Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ. Mol Cell Proteomics. 2014;13(9):2513–26.
Article
CAS
PubMed
PubMed Central
Google Scholar
Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R. Bacterial community variation in human body habitats across space and time. Science. 2009;326(5960):1694–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xiao L, Feng Q, Liang S, Sonne SB, Xia Z, Qiu X, Li X, Long H, Zhang J, Zhang D, et al. A catalog of the mouse gut metagenome. Nat Biotechnol. 2015;33:1103–8.
Article
CAS
PubMed
Google Scholar
Zhou W, Liotta LA, Petricoin EF. The spectra count label-free quantitation in cancer proteomics. Cancer Genomics Proteomics. 2012;9(3):135–42.
CAS
PubMed
PubMed Central
Google Scholar
Peng J, Elias JE, Thoreen CC, Licklider LJ, Gygi SP. Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. J Proteome Res. 2003;2(1):43–50.
Article
CAS
PubMed
Google Scholar
Kultima JR, Sunagawa S, Li J, Chen W, Chen H, Mende DR, Arumugam M, Pan Q, Liu B, Qin J, et al. MOCAT: a metagenomics assembly and gene prediction toolkit. PLoS One. 2012;7(10):e47656.
Article
PubMed
PubMed Central
Google Scholar
Zhang X, Zhao Y, Zhang M, Pang X, Xu J, Kang C, Li M, Zhang C, Zhang Z, Zhang Y, et al. Structural changes of gut microbiota during berberine-mediated prevention of obesity and insulin resistance in high-fat diet-fed rats. PLoS One. 2012;7(8):e42529.
Article
CAS
PubMed
PubMed Central
Google Scholar
Turnbaugh PJ, Backhed F, Fulton L, Gordon JI. Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe. 2008;3(4):213–23.
Article
CAS
PubMed
PubMed Central
Google Scholar
Song BJ, Akbar M, Abdelmegeed MA, Byun K, Lee B, Yoon SK, Hardwick JP. Mitochondrial dysfunction and tissue injury by alcohol, high fat, nonalcoholic substances and pathological conditions through post-translational protein modifications. Redox Biol. 2014;3:109–23.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mesuere B, Devreese B, Debyser G, Aerts M, Vandamme P, Dawyndt P. Unipept: tryptic peptide-based biodiversity analysis of metaproteome samples. J Proteome Res. 2012;11(12):5773–80.
CAS
PubMed
Google Scholar
Mesuere B, Debyser G, Aerts M, Devreese B, Vandamme P, Dawyndt P. The Unipept metaproteomics analysis pipeline. Proteomics. 2015;15(8):1437–42.
Article
CAS
PubMed
Google Scholar
Zhang X, Zhao Y, Xu J, Xue Z, Zhang M, Pang X, Zhang X, Zhao L. Modulation of gut microbiota by berberine and metformin during the treatment of high-fat diet-induced obesity in rats. Sci Rep. 2015;5:14405.
Article
CAS
PubMed
PubMed Central
Google Scholar
Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 2006;444(7122):1027–31.
Article
PubMed
Google Scholar
Wilkins TD, Fulghum R, Wilkins J. Eubacterium plexicaudatum sp. nov., an anaerobic bacterium with a subpolar tuft of flagella, isolated from a mouse cecum. Int J Syst Bacteriol. 1974;24(4):408–11.
Article
Google Scholar
Sokol H, Pigneur B, Watterlot L, Lakhdari O, Bermudez-Humaran LG, Gratadoux JJ, Blugeon S, Bridonneau C, Furet JP, Corthier G, et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc Natl Acad Sci U S A. 2008;105(43):16731–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kanauchi O, Fukuda M, Matsumoto Y, Ishii S, Ozawa T, Shimizu M, Mitsuyama K, Andoh A. Eubacterium limosum ameliorates experimental colitis and metabolite of microbe attenuates colonic inflammatory action with increase of mucosal integrity. World J Gastroenterol. 2006;12(7):1071–7.
Article
PubMed
PubMed Central
Google Scholar
Qin J, Li Y, Cai Z, Li S, Zhu J, Zhang F, Liang S, Zhang W, Guan Y, Shen D, et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature. 2012;490(7418):55–60.
Article
CAS
PubMed
Google Scholar
Wang W, Chen L, Zhou R, Wang X, Song L, Huang S, Wang G, Xia B. Increased proportions of Bifidobacterium and the Lactobacillus group and loss of butyrate-producing bacteria in inflammatory bowel disease. J Clin Microbiol. 2014;52(2):398–406.
Article
PubMed
PubMed Central
Google Scholar
Jimenez-Rivera C, Haas D, Boland M, Barkey JL, Mack DR. Comparison of two common outpatient preparations for colonoscopy in children and youth. Gastroenterol Res Pract. 2009;2009:518932.
Article
PubMed
PubMed Central
Google Scholar
Chen R, Seebun D, Ye M, Zou H, Figeys D. Site-specific characterization of cell membrane N-glycosylation with integrated hydrophilic interaction chromatography solid phase extraction and LC-MS/MS. J Proteomics. 2014;103:194–203.
Article
CAS
PubMed
Google Scholar
Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics. 2009;25(15):1966–7.
Article
CAS
PubMed
Google Scholar
Zhu W, Lomsadze A, Borodovsky M. Ab initio gene identification in metagenomic sequences. Nucleic Acids Res. 2010;38(12):e132.
Article
PubMed
PubMed Central
Google Scholar
Fenyo D, Beavis RC. A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes. Anal Chem. 2003;75(4):768–74.
Article
PubMed
Google Scholar
Craig R, Beavis RC. TANDEM: matching proteins with tandem mass spectra. Bioinformatics. 2004;20(9):1466–7.
Article
CAS
PubMed
Google Scholar
Cox J, Mann M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol. 2008;26(12):1367–72.
Article
CAS
PubMed
Google Scholar
Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12(1):59–60.
Article
CAS
PubMed
Google Scholar
Galperin MY, Makarova KS, Wolf YI, Koonin EV. Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res. 2015;43(Database issue):D261–9.
Article
PubMed
Google Scholar
Webb-Robertson BJ, Wiberg HK, Matzke MM, Brown JN, Wang J, McDermott JE, Smith RD, Rodland KD, Metz TO, Pounds JG, et al. Review, evaluation, and discussion of the challenges of missing value imputation for mass spectrometry-based label-free global proteomics. J Proteome Res. 2015;14(5):1993–2001.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vizcaino JA, Csordas A, Del-Toro N, Dianes JA, Griss J, Lavidas I, Mayer G, Perez-Riverol Y, Reisinger F, Ternent T, et al. 2016 update of the PRIDE database and its related tools. Nucleic Acids Res. 2016;44(D1):D447–56.
Article
PubMed
Google Scholar