TY - STD TI - Hadhazy A. Think twice: how the gut’s “second brain” influences mood and well-being. In: Scientific American. New York: Nature America, Inc.; 2010. ID - ref1 ER - TY - STD TI - Brown H. The other brain also deals with many woes. In: The New York times. New York: The New York Times Company; 2005. ID - ref2 ER - TY - JOUR AU - Berasategui, A. AU - Shukla, S. AU - Salem, H. AU - Kaltenpoth, M. PY - 2016 DA - 2016// TI - Potential applications of insect symbionts in biotechnology JO - Appl Microbiol Biotechnol VL - 100 UR - https://doi.org/10.1007/s00253-015-7186-9 DO - 10.1007/s00253-015-7186-9 ID - Berasategui2016 ER - TY - JOUR AU - O'Hara, A. M. AU - Shanahan, F. PY - 2006 DA - 2006// TI - The gut flora as a forgotten organ JO - EMBO Rep VL - 7 UR - https://doi.org/10.1038/sj.embor.7400731 DO - 10.1038/sj.embor.7400731 ID - O'Hara2006 ER - TY - JOUR AU - Marteau, P. AU - Pochart, P. AU - Dore, J. AU - Bera-Maillet, C. AU - Bernalier, A. PY - 2001 DA - 2001// TI - Comparative study of bacterial groups within the human cecal and fecal microbiota JO - Appl Environ Microbiol VL - 67 UR - https://doi.org/10.1128/AEM.67.10.4939-4942.2001 DO - 10.1128/AEM.67.10.4939-4942.2001 ID - Marteau2001 ER - TY - JOUR AU - Zoetendal, E. G. AU - Raes, J. AU - van den Bogert, B. AU - Arumugam, M. AU - Booijink, C. C. PY - 2012 DA - 2012// TI - The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates JO - ISME J VL - 6 UR - https://doi.org/10.1038/ismej.2011.212 DO - 10.1038/ismej.2011.212 ID - Zoetendal2012 ER - TY - JOUR AU - Flint, H. J. AU - Scott, K. P. AU - Duncan, S. H. AU - Louis, P. AU - Forano, E. PY - 2012 DA - 2012// TI - Microbial degradation of complex carbohydrates in the gut JO - Gut Microbes VL - 3 UR - https://doi.org/10.4161/gmic.19897 DO - 10.4161/gmic.19897 ID - Flint2012 ER - TY - JOUR AU - Gerritsen, J. AU - Smidt, H. AU - Rijkers, G. T. AU - de Vos, W. M. PY - 2011 DA - 2011// TI - Intestinal microbiota in human health and disease: the impact of probiotics JO - Genes Nutr VL - 6 UR - https://doi.org/10.1007/s12263-011-0229-7 DO - 10.1007/s12263-011-0229-7 ID - Gerritsen2011 ER - TY - JOUR AU - Fofanova, T. Y. AU - Petrosino, J. F. AU - Kellermayer, R. PY - 2016 DA - 2016// TI - Microbiome-epigenome interactions and the environmental origins of inflammatory bowel diseases JO - J Pediatr Gastroenterol Nutr VL - 62 UR - https://doi.org/10.1097/MPG.0000000000000950 DO - 10.1097/MPG.0000000000000950 ID - Fofanova2016 ER - TY - JOUR AU - Lopez, J. AU - Grinspan, A. PY - 2016 DA - 2016// TI - Fecal microbiota transplantation for inflammatory bowel disease JO - Gastroenterol Heaptology VL - 12 ID - Lopez2016 ER - TY - JOUR AU - Qin, J. AU - Li, R. AU - Raes, J. AU - Arumugam, M. AU - Burgdorf, K. S. PY - 2010 DA - 2010// TI - A human gut microbial gene catalogue established by metagenomic sequencing JO - Nature VL - 464 UR - https://doi.org/10.1038/nature08821 DO - 10.1038/nature08821 ID - Qin2010 ER - TY - JOUR AU - Sender, R. AU - Fuchs, S. AU - Milo, R. PY - 2016 DA - 2016// TI - Revised estimates for the number of human and bacteria cells in the body JO - PLoS Biol VL - 14 UR - https://doi.org/10.1371/journal.pbio.1002533 DO - 10.1371/journal.pbio.1002533 ID - Sender2016 ER - TY - JOUR AU - Ravel, J. AU - Gajer, P. AU - Abdo, Z. AU - Schneider, G. M. AU - Koenig, S. S. PY - 2011 DA - 2011// TI - Vaginal microbiome of reproductive-age women JO - Proc Natl Acad Sci U S A VL - 108 UR - https://doi.org/10.1073/pnas.1002611107 DO - 10.1073/pnas.1002611107 ID - Ravel2011 ER - TY - JOUR AU - van Passel, M. W. AU - Kant, R. AU - Zoetendal, E. G. AU - Plugge, C. M. AU - Derrien, M. PY - 2011 DA - 2011// TI - The genome of Akkermansia muciniphila, a dedicated intestinal mucin degrader, and its use in exploring intestinal metagenomes JO - PLoS One VL - 6 UR - https://doi.org/10.1371/journal.pone.0016876 DO - 10.1371/journal.pone.0016876 ID - van Passel2011 ER - TY - JOUR AU - den Besten, G. AU - van Eunen, K. AU - Groen, A. K. AU - Venema, K. AU - Reijngoud, D. J. PY - 2013 DA - 2013// TI - The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism JO - J Lipid Res VL - 54 UR - https://doi.org/10.1194/jlr.R036012 DO - 10.1194/jlr.R036012 ID - den Besten2013 ER - TY - JOUR AU - WEW, R. PY - 1980 DA - 1980// TI - Role of anaerobic bacteria in the metabolic welfare of the colonic mucosa in man JO - Gut Microbes VL - 21 ID - WEW1980 ER - TY - JOUR AU - den Besten, G. AU - Lange, K. AU - Havinga, R. AU - van Dijk, T. H. AU - Gerding, A. PY - 2013 DA - 2013// TI - Gut-derived short-chain fatty acids are vividly assimilated into host carbohydrates and lipids JO - Am J Physiol Gastrointest Liver Physiol VL - 305 UR - https://doi.org/10.1152/ajpgi.00265.2013 DO - 10.1152/ajpgi.00265.2013 ID - den Besten2013 ER - TY - JOUR AU - Turroni, F. AU - Milani, C. AU - Duranti, S. AU - Mancabelli, L. AU - Mangifesta, M. PY - 2016 DA - 2016// TI - Deciphering bifidobacterial-mediated metabolic interactions and their impact on gut microbiota by a multi-omics approach JO - ISME J VL - 10 UR - https://doi.org/10.1038/ismej.2015.236 DO - 10.1038/ismej.2015.236 ID - Turroni2016 ER - TY - JOUR AU - Riviere, A. AU - Gagnon, M. AU - Weckx, S. AU - Roy, D. AU - De Vuyst, L. PY - 2015 DA - 2015// TI - Mutual cross-feeding interactions between Bifidobacterium longum subsp. longum NCC2705 and Eubacterium rectale ATCC 33656 explain the bifidogenic and butyrogenic effects of arabinoxylan oligosaccharides JO - Appl Environ Microbiol VL - 81 UR - https://doi.org/10.1128/AEM.02089-15 DO - 10.1128/AEM.02089-15 ID - Riviere2015 ER - TY - JOUR AU - He, X. AU - McLean, J. S. AU - Edlund, A. AU - Yooseph, S. AU - Hall, A. P. PY - 2015 DA - 2015// TI - Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle JO - Proc Natl Acad Sci U S A VL - 112 UR - https://doi.org/10.1073/pnas.1419038112 DO - 10.1073/pnas.1419038112 ID - He2015 ER - TY - JOUR AU - Dwidar, M. AU - Monnappa, A. K. AU - Mitchell, R. J. PY - 2012 DA - 2012// TI - The dual probiotic and antibiotic nature of Bdellovibrio bacteriovorus JO - BMB Rep VL - 45 UR - https://doi.org/10.5483/BMBRep.2012.45.2.71 DO - 10.5483/BMBRep.2012.45.2.71 ID - Dwidar2012 ER - TY - JOUR AU - Atterbury, R. J. AU - Hobley, L. AU - Till, R. AU - Lambert, C. AU - Capeness, M. J. PY - 2011 DA - 2011// TI - Effects of orally administered Bdellovibrio bacteriovorus on the well-being and Salmonella colonization of young chicks JO - Appl Environ Microbiol VL - 77 UR - https://doi.org/10.1128/AEM.00426-11 DO - 10.1128/AEM.00426-11 ID - Atterbury2011 ER - TY - JOUR AU - Lozupone, C. A. AU - Stombaugh, J. I. AU - Gordon, J. I. AU - Jansson, J. K. AU - Knight, R. PY - 2012 DA - 2012// TI - Diversity, stability and resilience of the human gut microbiota JO - Nature VL - 489 UR - https://doi.org/10.1038/nature11550 DO - 10.1038/nature11550 ID - Lozupone2012 ER - TY - JOUR AU - Lessa, F. C. AU - Mu, Y. AU - Bamberg, W. M. AU - Beldavs, Z. G. AU - Dumyati, G. K. PY - 2015 DA - 2015// TI - Burden of Clostridium difficile infection in the United States JO - N Engl J Med VL - 372 UR - https://doi.org/10.1056/NEJMoa1408913 DO - 10.1056/NEJMoa1408913 ID - Lessa2015 ER - TY - JOUR AU - Stein, R. R. AU - Bucci, V. AU - Toussaint, N. C. AU - Buffie, C. G. AU - Ratsch, G. PY - 2013 DA - 2013// TI - Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota JO - PLoS Comput Biol VL - 9 UR - https://doi.org/10.1371/journal.pcbi.1003388 DO - 10.1371/journal.pcbi.1003388 ID - Stein2013 ER - TY - JOUR AU - Voth, D. E. AU - Ballard, J. D. PY - 2005 DA - 2005// TI - Clostridium difficile toxins: mechanism of action and role in disease JO - Clin Microbiol Rev VL - 18 UR - https://doi.org/10.1128/CMR.18.2.247-263.2005 DO - 10.1128/CMR.18.2.247-263.2005 ID - Voth2005 ER - TY - JOUR AU - Grundy, S. M. PY - 2005 DA - 2005// TI - A constellation of complicatons: the metabolic syndrome JO - Clin Cornerstone VL - 7 UR - https://doi.org/10.1016/S1098-3597(05)80066-3 DO - 10.1016/S1098-3597(05)80066-3 ID - Grundy2005 ER - TY - JOUR AU - O'Neill, S. AU - O'Driscoll, L. PY - 2015 DA - 2015// TI - Metabolic syndrome: a closer look at the growing epidemic and its associated pathologies JO - Obes Rev VL - 16 UR - https://doi.org/10.1111/obr.12229 DO - 10.1111/obr.12229 ID - O'Neill2015 ER - TY - STD TI - Xia Q, Grant SF. The genetics of human obesity. Ann N Y Acad Sci. 2013;1281:178–190 ID - ref29 ER - TY - JOUR AU - Swinburn, B. A. AU - Caterson, I. AU - Seidell, J. C. AU - James, W. P. PY - 2007 DA - 2007// TI - Diet, nutrition and the prevention of excess weight gain and obesity JO - Public Health Nutr VL - 7 ID - Swinburn2007 ER - TY - JOUR AU - Le Chatelier, E. AU - Nielsen, T. AU - Qin, J. AU - Prifti, E. AU - Hildebrand, F. PY - 2013 DA - 2013// TI - Richness of human gut microbiome correlates with metabolic markers JO - Nature VL - 500 UR - https://doi.org/10.1038/nature12506 DO - 10.1038/nature12506 ID - Le Chatelier2013 ER - TY - JOUR AU - McNeil, N. I. PY - 1984 DA - 1984// TI - The contribution of the large intestine to energy supplies in man JO - Am J Clin Nutr VL - 39 UR - https://doi.org/10.1093/ajcn/39.2.338 DO - 10.1093/ajcn/39.2.338 ID - McNeil1984 ER - TY - JOUR AU - Turnbaugh, P. J. AU - Ley, R. E. AU - Mahowald, M. A. AU - Magrini, V. AU - Mardis, E. R. PY - 2006 DA - 2006// TI - An obesity-associated gut microbiome with increased capacity for energy harvest JO - Nature VL - 444 UR - https://doi.org/10.1038/nature05414 DO - 10.1038/nature05414 ID - Turnbaugh2006 ER - TY - JOUR AU - Bergman, E. N. PY - 1990 DA - 1990// TI - Energy contributions of volatile fatty acids from the gastrointestinal tract in various species JO - Physiol Rev VL - 70 UR - https://doi.org/10.1152/physrev.1990.70.2.567 DO - 10.1152/physrev.1990.70.2.567 ID - Bergman1990 ER - TY - STD TI - Xu J, Bjursell MK, Himrod J, Deng S, Carmichael LK, et al. A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science. 2003;299(5615):2074–6 ID - ref35 ER - TY - STD TI - Lammerts van Bueren A, Saraf A, Martens EC, Dijkhuizen L. Differential metabolism of exopolysaccharides from probiotic lactobacilli by the human gut symbiont Bacteroides thetaiotaomicron. Appl Environ Microbiol. 2015;81(12):3973–83 ID - ref36 ER - TY - STD TI - Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, et al. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Genet Diet. 2009;1(6):6ra14 ID - ref37 ER - TY - STD TI - Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science. 2013;341(6150):1241214-1 - 1241214-10 ID - ref38 ER - TY - STD TI - Minihane AM, Vinoy S, Russell WR, Baka A, Roche HM, et al. Low-grade inflammation, diet composition and health: current research evidence and its translation. Br J Nutr. 2015;114(7):999–1012 ID - ref39 ER - TY - STD TI - Chassaing B, Gewirtz AT. Has provoking microbiota aggression driven the obesity epidemic? BioEssays. 2016;38(2):122–8 ID - ref40 ER - TY - STD TI - Chassaing B, Gewirtz AT. Gut microbiota, low-grade inflammation, and metabolic syndrome. Toxicol Pathol. 2014;42(1):49–53 ID - ref41 ER - TY - STD TI - MacIver NJ, Jacobs SR, Wieman HL, Wofford JA, Coloff JL, et al. Glucose metabolism in lymphocytes is a regulated process with significant effects on immune cell function and survivial. J Leukoc Biol. 2008;84(4):949–57 ID - ref42 ER - TY - STD TI - Grundy SM, Brewer HB Jr, Cleeman JI, Smith SC Jr, Lenfant C, et al. Definition of metabolic syndrome: report of the National Heart, Lung, and Blood Institute/American Heart Association conference on scientific issues related to definition. Circulation. 2004;109(3):e13–8 ID - ref43 ER - TY - STD TI - Al Khodor S, Reichert B, Shatat IF. The microbiome and blood pressure: can microbes regulate our blood pressure? Front Pediatr. 2017;5(138) ID - ref44 ER - TY - STD TI - Durgan DJ, Ganesh BP, Cope JL, Ajami NJ, Phillips SC, et al. Role of the gut microbiome in obstructive sleep apnea-induced hypertension. Hypertension. 2016;67(2):469–74 ID - ref45 ER - TY - STD TI - Schiffrin EL. Immune mechanisms in hypertension and vascular injury. Clin Sci (Lond). 2014;126(4):267–74 ID - ref46 ER - TY - STD TI - Pluznick JL, Protzko RJ, Gevorgyan H, Peterlin Z, Sipos A, et al. Olfactory receptor responding to gut microbiota-derived signals plays a role in renin secretion and blood pressure regulation. Proc Natl Acad Sci U S A. 2013;110(11):4410–5 ID - ref47 ER - TY - STD TI - Ghazalpour A, Cespedes I, Bennett BJ, Allayee H. Expanding role of gut microbiota in lipid metabolism. Curr Opin Lipidol. 2016;27(2):141–7 ID - ref48 ER - TY - STD TI - Joyce SA, MacSharry J, Casey PG, Kinsella M, Murphy EF, et al. Regulation of host weight gain and lipid metabolism by bacterial bile acid modification in the gut. Proc Natl Acad Sci U S A. 2014;111(20):7421–6 ID - ref49 ER - TY - STD TI - Fu J, Bonder MJ, Cenit MC, Tigchelaar EF, Maatman A, et al. The gut microbiome contributes to a substantial proportion of the variation in blood lipids. Circ Res. 2015;117(9):817–24 ID - ref50 ER - TY - STD TI - Raza GS, Putaala H, Hibberd AA, Alhoniemi E, Tiihonen K, et al. Polydextrose changes the gut microbiome and attenuates fasting triglyceride and cholesterol levels in western diet fed mice. Sci Rep. 2017;7(1) ID - ref51 ER - TY - STD TI - Staley JT, Konopka A. Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu Rev Microbiol. 1985;39:321–46 ID - ref52 ER - TY - STD TI - Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature. 2013;499(7459):431–7 ID - ref53 ER - TY - STD TI - Lagier JC, Armougom F, Million M, Hugon P, Pagnier I, et al. Microbial culturomics: paradigm shift in the human gut microbiome study. Clin Microbiol Infect. 2012;18(12):1185–93 ID - ref54 ER - TY - STD TI - Moissl-Eichinger C, Huber H. Archaeal symbionts and parasites. Curr Opin Microbiol. 2011;14(3):364–70 ID - ref55 ER - TY - STD TI - Reyes A, Haynes M, Hanson N, Angly FE, Heath AC, et al. Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature. 2010;466(7304):334–338 ID - ref56 ER - TY - STD TI - Parfrey LW, Walters WA, Knight R. Microbial eukaryotes in the human microbiome: ecology, evolution, and future directions. Front Microbiol. 2011;2 ID - ref57 ER - TY - STD TI - Samuel BS, Gordon JI. A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism. Proc Natl Acad Sci U S A. 2006;103(26):10011–6 ID - ref58 ER - TY - STD TI - Turroni F, Ozcan E, Milani C, Mancabelli L, Viappiani A, et al. Glycan cross-feeding activities between bifidobacteria under in vitro conditions. Front Microbiol. 2015;6 ID - ref59 ER - TY - STD TI - Mahowald MA, Rey FE, Seedorf H, Turnbaugh PJ, Fulton RS, et al. Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla. Proc Natl Acad Sci U S A. 2009;106(14):5859–64 ID - ref60 ER - TY - STD TI - de Vos WM. Microbial biofilms and the human intestinal microbiome. NPJ Biofilms Microbiomes. 2015;1 ID - ref61 ER - TY - STD TI - Elias S, Banin E. Multi-species biofilms: living with friendly neighbors. FEMS Microbiol Rev. 2012;36(5):990–1004 ID - ref62 ER - TY - STD TI - Parsek MR, Greenberg EP. Sociomicrobiology: the connections between quorum sensing and biofilms. Trends Microbiol. 2005;13(1):27–33 ID - ref63 ER - TY - STD TI - Marchesi JR, Ravel J. The vocabulary of microbiome research: a proposal. Microbiome. 2015;3 ID - ref64 ER - TY - STD TI - Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol. 2013;31(9):814–21 ID - ref65 ER - TY - STD TI - Asshauer KP, Wemheuer B, Daniel R, Meinicke P. Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data. Bioinformatics. 2015;31(17):2882–2884 ID - ref66 ER - TY - STD TI - Iwai S, Weinmaier T, Schmidt BL, Albertson DG, Poloso NJ, et al. Piphillin: improved prediction of metagenomic content by direct inference from human microbiomes. PLoS One. 2016;11(11) ID - ref67 ER - TY - STD TI - Rooijers K, Kolmeder C, Juste C, Dore J, de Been M, et al. In iterative workflow for mining the human intestinal metaproteome. BMC Genomics. 2011;12(6) ID - ref68 ER - TY - STD TI - Walker A, Pfitzner B, Neschen S, Kahle M, Harir M, et al. Distinct signatures of host-microbial meta-metabolome and gut microbiome in two C57BL/6 strains under high-fat diet. ISME J. 2014;8(12):2380–96 ID - ref69 ER - TY - STD TI - El Aidy S, Derrien M, Merrifield CA, Levenez F, Dore J, et al. Gut bacteria-host metabolic interplay during conventionalisation of the mouse germfree colon. ISME J. 2013;7(4):743–55 ID - ref70 ER - TY - STD TI - Wilmes P, Heintz-Buschart A, Bond PL. A decade of metaproteomics: where we stand and what the future holds. Proteomics. 2015;15(20):3409–17 ID - ref71 ER - TY - STD TI - Nicholson JK, Lindon JC. Metabonomics. Nature. 2008;455:1054–6 ID - ref72 ER - TY - STD TI - Goodwin S, McPherson JD, McCombie WR. Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet. 2016;17(6):333–51 ID - ref73 ER - TY - STD TI - Eid J, Fehr A, Gray J, Luong K, Lyle J, et al. Real-time DNA sequencing from single polymerase molecules. Science. 2009;323:133–8 ID - ref74 ER - TY - STD TI - Deamer D, Akeson M, Branton D. Three decades of nanopore sequencing. Nat Biotechnol. 2016;34(5):518–24 ID - ref75 ER - TY - STD TI - Frank JA, Pan Y, Tooming-Klunderud A, Eijsink VG, McHardy AC, et al. Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data. Sci Rep. 2016;6 ID - ref76 ER - TY - STD TI - Marshall CW, Ross DE, Fichot EB, Norman RS, May HD. Electrosynthesis of commodity chemicals by an autotrophic microbial community. Appl Environ Microbiol. 2012;78(23):8412–20 ID - ref77 ER - TY - STD TI - Singer E, Bushnell B, Coleman-Derr D, Bowman B, Bowers RM, et al. High-resolution phylogenetic microbial community profiling. ISME J. 2016;10(8):2020–32 ID - ref78 ER - TY - STD TI - Schloss PD, Jenior ML, Koumpouras CC, Westcott SL, Highlander SK. Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system. PeerJ. 2016;4 ID - ref79 ER - TY - STD TI - Wagner J, Coupland P, Browne HP, Lawley TD, Francis SC, et al. Evaluation of PacBio sequencing for full-length bacterial 16S rRNA gene classification. BMC Microbiol. 2016;16(1) ID - ref80 ER - TY - STD TI - Mosher JJ, Bowman B, Bernberg EL, Shevchenko O, Kan J, et al. Improved performance of the PacBio SMRT technology for 16S rDNA sequencing. J Microbiol Methods. 2014;104:59–60 ID - ref81 ER - TY - STD TI - Greninger AL, Naccache SN, Federman S, Yu G, Mbala P, et al. Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis. Genome Med. 2015;7 ID - ref82 ER - TY - STD TI - Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 2013;41(1) ID - ref83 ER - TY - STD TI - Stackebrandt E. Goebel BM: taxonomic note: a place for DNA-DNA reassociation and 16s rRNA sequence analysis in the prsent species definition in bacteriology. Int J Syst Evol Microbiol. 1994;44:846–849 ID - ref84 ER - TY - STD TI - Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol. 1987;37(4):463–4 ID - ref85 ER - TY - STD TI - van de Peer Y, Chapelle S. De Wachter R: a quantitative map of nucleotide substitution rates in bacterial rRNA. Nucleic Acids Res. 1996;24(17):3381–91 ID - ref86 ER - TY - STD TI - Hermes GD, Zoetendal EG, Smidt H. Molecular ecological tools to decipher the role of our microbial mass in obesity. Benef Microbes. 2015;6(1):61–81 ID - ref87 ER - TY - STD TI - Claesson MJ, Wang Q, O'Sullivan O, Greene-Diniz R, Cole JR, et al. Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions. Nucleic Acids Res. 2010;38(22) ID - ref88 ER - TY - STD TI - Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, et al. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for fungi. Proc Natl Acad Sci U S A. 2012;109(16):6241–6 ID - ref89 ER - TY - STD TI - McMurdie PJ. Holmes S: waste not, want not: why rarefying microbiome data is inadmissable. PLoS Comput Biol. 2014;10(4) ID - ref90 ER - TY - STD TI - Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41 Database issue:D590–596 ID - ref91 ER - TY - STD TI - Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, et al. Ribosomal database project: data and tools for high throughput rRNA analysis. Nucleic Acids Res. 2014;42 Database issue:D633–42 ID - ref92 ER - TY - STD TI - DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006;72(7):5069–72 ID - ref93 ER - TY - STD TI - Nakamura K, Oshima T, Morimoto T, Ikeda S, Yoshikawa H, et al. Sequence-specific error profile of Illumina sequencers. Nucleic Acids Res. 2011;39(13) ID - ref94 ER - TY - STD TI - Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335–6 ID - ref95 ER - TY - STD TI - Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75(23):7537–41 ID - ref96 ER - TY - STD TI - McMurdie PJ, Holmes S. Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One. 2013;8(4) ID - ref97 ER - TY - STD TI - Albanese D, Fontana P, De Filippo C, Cavalieri D, Donati C. MICCA: a complete and accurate software for taxonomic profiling of metagenomic data. Sci Rep. 2015;5 ID - ref98 ER - TY - STD TI - Ramiro-Garcia J, Hermes GDA, Giatsis C, Sipkema D, Zoetendal EG, et al. NG-Tax, a highly accurate and validated pipeline for analysis of 16S rRNA amplicons from complex biomes. F1000Res. 2016;5 ID - ref99 ER - TY - STD TI - Faith D. Conservation evaluation and phylogenetic diversity. Biol Conserv. 1992;61:1–10 ID - ref100 ER - TY - STD TI - Shannon CE. A mathematical theory of communication. Bell Syst Tech J. 1948;27:523–656 ID - ref101 ER - TY - STD TI - Simpson EH. Measurement of diversity. Nature. 1949;163:688 ID - ref102 ER - TY - STD TI - Chiarucci A, Bacaro G, Scheiner SM. Old and new challenges in using species diversity for assessing biodiversity. Philos Trans R Soc Lond Ser B Biol Sci. 2011;366(1576):2426–2437 ID - ref103 ER - TY - STD TI - Heip CHR, Herman PMJ, Soetart K. Indices of diversity and evenness. Oceanis. 1998;24(4):61–87 ID - ref104 ER - TY - STD TI - Chao A. Nonparametric estimation of the number of classes in a population. Scand J Stat. 1984;11(4):265–70 ID - ref105 ER - TY - STD TI - Chao A, Lee S-M. Estimating the number of classes via sample coverage. J Am Stat Assoc. 1992;84(417):210–217 ID - ref106 ER - TY - STD TI - Hughes JB, Hellmann JJ, Ricketts TH, Bohannan BJM. Counting the uncountable: statistical approaches to estimating microbial diversity. Appl Environ Microbiol. 2001;67(10):4399–406 ID - ref107 ER - TY - STD TI - Jaccard P. The distribution of the flora in the alpine zone. New Phytol. 1912;XI(2):37–50 ID - ref108 ER - TY - STD TI - Bray JR, Curtis JT. An ordination of the upland Forest communities of southern Wisconsin. Ecol Monogr. 1957;27(4):326–49 ID - ref109 ER - TY - STD TI - Lozupone C, Knight R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol. 2005;71(12):8228–35 ID - ref110 ER - TY - STD TI - Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, et al. A core gut microbiome in obese and lean twins. Nature. 2009;457(7228):480–4 ID - ref111 ER - TY - STD TI - Ley RE, Backhed F, Turnbaugh P, Lozupone CA, Knight RD, et al. Obesity alters gut microbial ecology. Proc Natl Acad Sci U S A. 2005;102(31) ID - ref112 ER - TY - STD TI - Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, et al. Human gut microbiome viewed across age and geography. Nature. 2012;486(7402):222–7 ID - ref113 ER - TY - STD TI - Walker AW, Ince J, Duncan SH, Webster LM, Holtrop G, et al. Dominant and diet-responsive groups of bacteria within the human colonic microbiota. ISME J. 2011;5(2):220–30 ID - ref114 ER - TY - STD TI - Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, et al. Linking long-term dietary patterns with gut microbial enterotypes. Science. 2011;334(6052):105–8 ID - ref115 ER - TY - STD TI - Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486(7402):207–14 ID - ref116 ER - TY - STD TI - Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, et al. A survey of best practices for RNA-seq data analysis. Genome Biol. 2016;17 ID - ref117 ER - TY - STD TI - Del Fabbro C, Scalabrin S, Morgante M, Giorgi FM. An extensive evaluation of read trimming effects on Illumina NGS data analysis. PLoS One. 2013;8(12) ID - ref118 ER - TY - STD TI - Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403–10 ID - ref119 ER - TY - STD TI - Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12:59–60 ID - ref120 ER - TY - STD TI - Leimena MM, Ramiro-Garcia J, Davids M, Van den Bogert B, Smidt H, et al. A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets. BMC Genomics. 2013;14 ID - ref121 ER - TY - STD TI - Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, et al. Metagenomic microbial community profiling using unique clade-specific marker genes. Nat Methods. 2012;9(8):811–4 ID - ref122 ER - TY - STD TI - Sharon I, Banfield JF. Genomes from metagenomics. Science. 2013;342(1057):1057–8 ID - ref123 ER - TY - STD TI - Pop M. Genome assembly reborn: recent computational challenges. Brief Bioinform. 2009;10(4):354–66 ID - ref124 ER - TY - STD TI - Davids M, Hugenholtz F, Martins Dos Santos V, Smidt H, Kleerebezem M, et al. Functional profiling of unfamiliar microbial communities using a validated de novo assembly metatranscriptome pipeline. PLoS One. 2016;11(1) ID - ref125 ER - TY - STD TI - Namiki T, Hachiya T, Tanaka H, Sakakibara Y. MetaVelvet: an extension of velvet assembler to de novo metagenome assembly from short sequence reads. Nucleic Acids Res. 2012;40(20) ID - ref126 ER - TY - STD TI - Wu Y-W, Tsang Y-H, Tringe SG, Simmons BA, Singer SW. Maxbin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm. Microbiome. 2014;2(26) ID - ref127 ER - TY - STD TI - Yang B, Peng Y, Leung HC-M, Yiu S-M, Chen J-C, et al. Unsupervised binning of environmental genomic fragments based on an error robust selection of l-mers. BMC Bioinformatics. 2010;(11) ID - ref128 ER - TY - STD TI - Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25(7):1043–55 ID - ref129 ER - TY - STD TI - Huson DH, Auch AF, Qi J, Schuster SC. MEGAN analysis of metagenomic data. Genome Res. 2007;17(3):377–86 ID - ref130 ER - TY - STD TI - Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 2014;15(46) ID - ref131 ER - TY - STD TI - McHardy AC, Martin HG, Tsirigos A, Hugenholtz P, Rigoutsos I. Accurate phylogenetic classification of variable-length DNA fragments. Nat Methods. 2007;4(1):63–72 ID - ref132 ER - TY - STD TI - Lindgreen S, Adair KL, Gardner PP. An evaluation of the accuracy and speed of metagenome analysis tools. Sci Rep. 2016;6 ID - ref133 ER - TY - STD TI - Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11 ID - ref134 ER - TY - STD TI - Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 2000;28(1):33–36 ID - ref135 ER - TY - STD TI - Claudel-Renard C, Chevalet C, Faraut T. Khan D: enzyme-specific profiles for genome annotation - PRIAM. Nucleic Acids Res. 2003;31(22):6633–9 ID - ref136 ER - TY - CHAP AU - Karp, P. D. AU - Paley, S. AU - Altman, T. PY - 2013 DA - 2013// TI - Data mining in the MetaCyc family of pathway databases BT - Data mining for systems biology: methods and protocols. Vol. 939 PB - Springer Science+Business Media CY - New York UR - https://doi.org/10.1007/978-1-62703-107-3_12 DO - 10.1007/978-1-62703-107-3_12 ID - Karp2013 ER - TY - STD TI - Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 2014;42 Database issue:D490–5 ID - ref138 ER - TY - STD TI - Yin Y, Mao X, Yang J, Chen X, Mao F, et al. dbCAN: a web resource for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 2012;40 Web Server issue:w445–51 ID - ref139 ER - TY - STD TI - The Gene Ontology Consortium. Gene ontology: tool for the unification of biology. Nat Genet. 2000;(25):25–9 ID - ref140 ER - TY - STD TI - Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, et al. InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res. 2012;40 Database issue:D306–12 ID - ref141 ER - TY - STD TI - Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, et al. A large-scale evaluation of computational protein function prediction. Nat Methods. 2013;10(3):221–7 ID - ref142 ER - TY - STD TI - Kantor RS, Wrighton KC, Handley KM, Sharon I, Hug LA, et al. Small genomes and sparse metabolisms of sediment-associated bacteria from four candidate phyla. MBio. 2013;4(5) ID - ref143 ER - TY - STD TI - Probst AJ, Weinmaier T, Raymann K, Perras A, Emerson JB, et al. Biology of a widespread uncultivated archaeon that contributes to carbon fixation in the subsurface. Nat Commun. 2014;5 ID - ref144 ER - TY - STD TI - Wrighton KC, Thomas BC, Sharon I, Miller CS, Castelle CJ, et al. Fermentation, hydrogen, and sulfur metabolism in mulitple uncultivated bacterial phyla. Science. 2012;(337):1661–5 ID - ref145 ER - TY - STD TI - Go Enrichment Analysis [http://geneontology.org/page/go-enrichment-analysis]. Accessed 12 Feb 2017. UR - http://geneontology.org/page/go-enrichment-analysis ID - ref146 ER - TY - STD TI - Prosser JI. Replicate or lie. Environ Microbiol. 2010;12(7):1806–10 ID - ref147 ER - TY - STD TI - Markowitz VM, Ivanova NN, Szeto E, Palaniappan K, Chu K, et al. IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Res. 2008;36 Database issue:D534–8 ID - ref148 ER - TY - STD TI - Mitchell A, Bucchini F, Cochrane G, Denise H, ten Hoopen P, et al. EBI metagenomics in 2016—an expanding and evolving resource for the analysis and archiving of metagenomic data. Nucleic Acids Res. 2016;44(D1):D595–603 ID - ref149 ER - TY - STD TI - Shi Y, Tyson GW, Eppley JM, DeLong EF. Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean. ISME J. 2011;5(6):999–1013 ID - ref150 ER - TY - STD TI - Nocker A, Richter-Heitmann T, Montijn R, Schuren F, Kort R. Discrimination between live and dead cellsin bacterial communities from environmental water samples analyzed by 454 pyrosequencing. Int Microbiol. 2010;13(2):59–65 ID - ref151 ER - TY - STD TI - Kopylova E, Noe L, Touzet H. SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics. 2012;28(24):3211–7 ID - ref152 ER - TY - STD TI - Celaj A, Markle J, Danska J, Parkinson J. Comparison of assembly algorithms for improving rate of metatranacriptomic functional annotation. Microbiome. 2014;2(39) ID - ref153 ER - TY - STD TI - Robinson MD, McCarthy DJ, Smyth GK. edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139–40 ID - ref154 ER - TY - STD TI - Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12) ID - ref155 ER - TY - STD TI - David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014;505(7484):7537–41 ID - ref156 ER - TY - STD TI - Turnbaugh PJ, Quince C, Faith JJ, McHardy AC, Yatsunenko T, et al. Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. Proc Natl Acad Sci U S A. 2010;107(16):7503–8 ID - ref157 ER - TY - STD TI - Verberkmoes NC, Russell AL, Shah M, Godzik A, Rosenquist M, et al. Shotgun metaproteomics of the human distal gut microbiota. ISME J. 2009;3(2):179–89 ID - ref158 ER - TY - STD TI - Fisher CK, Mehta P. Identifying keystone species in the human gut microbiome from metagenomic timeseries using sparse linear regression. PLoS One. 2014;9(7) ID - ref159 ER - TY - STD TI - Schubert AM, Rogers MA, Ring C, Mogle J, Petrosino JP, et al. Microbiome data distinguish patients with Clostridium Difficile infection and non-C. Difficile-associated diarrhea from healthy controls. MBio. 2014;5(3) ID - ref160 ER - TY - STD TI - Cui H, Zhang Y. Alignment-free supervised classification of metagenomes by recursive SVM. BMC Genomics. 2013;14(641) ID - ref161 ER - TY - STD TI - Knights D, Costello EK, Knight R. Supervised classification of human microbiota. FEMS Microbiol Rev. 2011;35(2):343–59 ID - ref162 ER - TY - STD TI - Statnikov A, Henaff M, Narendra V, Konganti K, Li Z, et al. A comprehensive evaluation of multicategory classification methods for microbiomic data. Microbiome. 2013;1(11) ID - ref163 ER - TY - STD TI - Parloff R. Why deep learning is suddenly changing your life. In: Fortune. New York: Time Inc.; 2016. ID - ref164 ER - TY - STD TI - Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, et al. Enterotypes of the human gut microbiome. Nature. 2011;473(7346):174–80 ID - ref165 ER - TY - STD TI - Jain AK. Data clustering: 50 years beyond k-means. Pattern Recogn Lett. 2010;(31):651–666 ID - ref166 ER - TY - CHAP AU - Desgraupes, B. PY - 2016 DA - 2016// TI - clusterCrit: clustering indices BT - R package version 1.2.7 edn ID - Desgraupes2016 ER - TY - STD TI - Knights D, Ward TL, McKinlay CE, Miller H, Gonzalez A, et al. Rethinking “enterotypes”. Cell Host Microbe. 2014;16(4):433–7 ID - ref168 ER - TY - STD TI - Schubert E, Koos A, Emrich T, Züfle A, Schmid KA, et al. A framework for clustering uncertain data. Proc VLDB Endowment. 2015;18(12):1976–9 ID - ref169 ER - TY - STD TI - Hall M, Frank E, Holmes G, Pfahringer B, Reutemann P, et al. The WEKA data mining software—an update. SIGKDD Explorations. 2003;11(1):10–18 ID - ref170 ER - TY - STD TI - 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 Database issue:D109–14 ID - ref171 ER - TY - STD TI - May A, Brand BW, El-Kebir M, Klau GW, Zaura E, et al. metaModules identifies key functional subnetworks in microbiome-related disease. Bioinformatics. 2015;32(11):1678–85 ID - ref172 ER - TY - STD TI - Falony G, Joossens M, Vieira-Silva S, Wang J, Darzi Y, et al. Population-level analysis of gut microbiome variation. Science. 2016;352(6285):560–4 ID - ref173 ER - TY - STD TI - Goodrich JK, Waters JL, Poole AC, Sutter JL, Koren O, et al. Human genetics shape the gut microbiome. Cell. 2014;159(4):789–99 ID - ref174 ER - TY - STD TI - Zeevi D, Korem T, Zmora N, Israeli D, Rothschild D, et al. Personalized nutrition by prediction of glycemic responses. Cell. 2015;163(5):1079–94 ID - ref175 ER - TY - STD TI - Ondov BD, Bergman NH. Philippy AM: interactive metagenomic visualization in the web browser. BMC Bioinformatics. 2011;12 ID - ref176 ER - TY - STD TI - Gehlenborg N, O'Donoghue SI, Baliga NS, Goesmann A, Hibbs MA, et al. Visualization of omics data for systems biology. Nat Methods. 2010;7(3 Suppl):S56–68 ID - ref177 ER - TY - STD TI - Heer J, Bostock M, Ogievetsky V. A tour through the visualization zoo. Commun ACM. 2010;53(6):59–67 ID - ref178 ER - TY - STD TI - Kreft JU. Conflicts of interest in biofilms. Biofilms. 2004;1(4):265–276 ID - ref179 ER - TY - STD TI - Shou W, Ram S, Vilar JM. Synthetic cooperation in engineered yeast populations. Proc Natl Acad Sci U S A. 2007;104(6):1877–82 ID - ref180 ER - TY - STD TI - Hansen AK, Moran NA. Aphid genome expression reveals host-symbiont cooperation in the production of amino acids. Proc Natl Acad Sci. 2011;108(7):2849–54 ID - ref181 ER - TY - STD TI - Van Leuven JT, Meister RC, Simon C, McCutcheon JP. Sympatric speciation in a bacterial endosymbiont results in two genomes with the functionality of one. Cell. 2014;158(6):1270–80 ID - ref182 ER - TY - STD TI - Morris JJ, Lenksi RE, Zinser ER. The black queen hypothesis: evolution of dependencies through adaptive gene loss. MBio. 2012;3(2) ID - ref183 ER - TY - STD TI - Shetty SA, Hugenholtz F, Lahti L, Smidt H, de Vos WM. Intestinal microbiome landscaping: insight in community assemblage and implications for microbial modulation strategies. FEMS Microbiol Rev. 2017;41(2):182–99 ID - ref184 ER - TY - STD TI - Borenstein E. Computational systems biology and in silico modeling of the human microbiome. Brief Bioinform. 2012;13(6):769–80 ID - ref185 ER - TY - STD TI - Henry CS, DeJongh M, Best AA, Frybarger PM, Linsay B, et al. High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat Biotechnol. 2010;28(9):977–82 ID - ref186 ER - TY - STD TI - Karp PD, Paley S, Romero P. The pathway tools software. Bioinformatics. 2002;18 Suppl 1:S225-32 ID - ref187 ER - TY - STD TI - KBase - predictive biology [http://kbase.us]. Accessed 12 Feb 2017. UR - http://kbase.us ID - ref188 ER - TY - STD TI - Thiele I, Palsson BO. A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc. 2010;5(1):93–121 ID - ref189 ER - TY - STD TI - Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, et al. Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc Natl Acad Sci U S A. 2007;104(6):1777–82 ID - ref190 ER - TY - STD TI - Orth JD, Conrad TM, Na J, Lerman JA, Nam H, et al. A comprehensive genome-scale reconstruction of Escherichia coli metabolism—2011. Mol Syst Biol. 2011;7 ID - ref191 ER - TY - STD TI - van Heck RG, Ganter M, Martins Dos Santos VA, Stelling J. Efficient Reconstruction of Predictive Consensus Metabolic Network Models. PLoS Comput Biol. 2016;12(8) ID - ref192 ER - TY - STD TI - Heinken A, Sahoo S, Fleming RM, Thiele I. Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut. Gut Microbes. 2013;4(1):28–40 ID - ref193 ER - TY - STD TI - El-Semman IE, Karlsson FH, Shoaie S, Nookaew I, Soliman TH, et al. Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Facebaclibacterium prausnitzii A2-165 and their interaction. BMC Syst Biol. 2014;8(41) ID - ref194 ER - TY - STD TI - Levy R, Borenstein E. Reverse ecology: from systems to enviornments and back. Adv Exp Med Biol. 2012;751:329–45 ID - ref195 ER - TY - STD TI - Feist AM, Palsson BO. The biomass objective function. Curr Opin Microbiol. 2010;13(3):344–9 ID - ref196 ER - TY - STD TI - Khandelwal RA, Olivier BG, Roling WF, Teusink B, Bruggeman FJ. Community flux balance analysis for microbial consortia at balanced growth. PLoS One. 2013;8(5) ID - ref197 ER - TY - STD TI - Zomorrodi AR, Islam MM. Maranas CD: d-OptCom: dynamic multi-level and multi-objective metabolic modeling of microbial communities. ACS Synth Biol. 2014;3(4):247–57 ID - ref198 ER - TY - STD TI - Harcombe WR, Riehl WJ, Dukovski I, Granger BR, Betts A, et al. Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics. Cell Rep. 2014;7(4):1104–15 ID - ref199 ER - TY - STD TI - Munoz-Tamayo R, Laroche B, Walter E, Dore J, Duncan SH, et al. Kinetic modelling of lactate utilization and butyrate production by key human colonic bacterial species. FEMS Microbiol Ecol. 2011;76(3):615–24 ID - ref200 ER - TY - STD TI - Munoz-Tamayo R, Laroche B, Walter E, Dore J, Leclerc M. Mathematical modelling of carbohydrate degradation by human colonic microbiota. J Theor Biol. 2010;266(1):189–201 ID - ref201 ER - TY - STD TI - Xavier JB, Foster KR. Cooperation and conflict in microbial biofilms. Proc Natl Acad Sci U S A. 2007;104(3):876–881 ID - ref202 ER - TY - STD TI - Bucci V, Bradde S, Biroli G, Xavier JB. Social interaction, noise and antibiotic-mediated switches in the intestinal microbiota. PLoS Comput Biol. 2012;8(4) ID - ref203 ER - TY - STD TI - Marino S, Baxter NT, Huffnagle GB, Petrosino JF, Schloss PD. Mathematical modeling of primary succession of murine intestinal microbiota. Proc Natl Acad Sci U S A. 2014;111(1):439–44 ID - ref204 ER - TY - STD TI - Karr JR, Sanghvi JC, Macklin DN, Gutschow MV, Jacobs JM, et al. A whole-cell computational model predicts phenotype from genotype. Cell. 2012;150(2):389–401 ID - ref205 ER - TY - STD TI - Castiglione F, Pappalardo F, Bianca C, Russo G, Motta S. Modeling biology spanning different scales: an open challenge. Biomed Res Int. 2014;2014 ID - ref206 ER - TY - STD TI - Williams CF, Walton GE, Jiang L, Plummer S, Garaiova I, et al. Comparative analysis of intestinal tract models. Annu Rev Food Sci Technol. 2015;6:329–50 ID - ref207 ER - TY - STD TI - Van den Abbeele P, Belzer C, Goossens M, Kleerebezem M, De Vos WM, et al. Butyrate-producing Clostridium cluster XIVa species specifically colonize mucins in an in vitro gut model. ISME J. 2013;7(5):949–61 ID - ref208 ER - TY - STD TI - Kim HJ, Li H, Collins JJ, Ingber DE. 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. 2016;113(1):E7–15 ID - ref209 ER - TY - STD TI - Williams SC. Gnotobiotics. Proc Natl Acad Sci U S A. 2014;111(5):1661 ID - ref210 ER - TY - STD TI - Lee SM, Donaldson GP, Mikulski Z, Boyajian S, Ley K, et al. Bacterial colonization factors control specificity and stability of the gut microbiota. Nature. 2013;501(7467):426–429 ID - ref211 ER - TY - STD TI - Samuel BS, Hansen EE, Manchester JK, Coutinho PM, Henrissat B, et al. Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut. Proc Natl Acad Sci U S A. 2007;104(25):10643–8 ID - ref212 ER - TY - STD TI - Laycock G, Sait L, Inman C, Lewis M, Smidt H, et al. A defined intestinal colonization microbiota for gnotobiotic pigs. Vet Immunol Immunopathol. 2012;149:216–24. ID - ref213 ER - TY - STD TI - Sonnenburg JL, Chen CT, Gordon JI. Genomic and metabolic studies of the impact of probiotics on a model gut symbiont and host. PLoS Biol. 2006;4(12) ID - ref214 ER - TY - STD TI - Backhed F, Manchester JK, Semenkovich CF, Gordon JI. Mechanisms underlying the resistance to diet-induced obesity in germ-free mice. Proc Natl Acad Sci U S A. 2007;104(3):979–84 ID - ref215 ER - TY - STD TI - Kong LC, Tap J, Aron-Wisnewsky J, Pelloux V, Basdevant A, et al. Gut microbiota after gastric bypass in human obesity: increased richness and associations of bacterial genera with adipose tissue genes. Am J Clin Nutr. 2013;98(1):16–24 ID - ref216 ER - TY - STD TI - Zhang H, DiBaise JK, Zuccolo A, Kudrna D, Braidotti M, et al. Human gut microbiota in obesity and after gastric bypass. Proc Natl Acad Sci U S A. 2009;106(7):2365–70 ID - ref217 ER - TY - STD TI - Tremaroli V, Karlsson F, Werling M, Stahlman M, Kovatcheva-Datchary P, et al. Roux-en-Y gastric bypass and vertical banded Gastroplasty induce long-term changes on the human gut microbiome contributing to fat mass regulation. Cell Metab. 2015;22(2):228–38 ID - ref218 ER - TY - STD TI - Graessler J, Qin Y, Zhong H, Zhang J, Licinio J, et al. Metagenomic sequencing of the human gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes: correlation with inflammatory and metabolic parameters. Pharmacogenomics J. 2013;13(6):514–22 ID - ref219 ER - TY - STD TI - van Nood E, Vrieze A, Nieuwdorp M, Fuentes S, Zoetendal EG, et al. Duodenal infusion of donor feces for recurrent Clostridium difficile. N Engl J Med. 2013;368(5):407–15 ID - ref220 ER - TY - STD TI - Jalanka J, Mattila E, Jouhten H, Hartman J, de Vos WM, et al. Long-term effects on luminal and mucosal microbiota and commonly acquired taxa in faecal microbiota transplantation for recurrent Clostridium difficile infection. BMC Med. 2016;14(1) ID - ref221 ER - TY - STD TI - Borody TJ, Warren EF, Leis S, Surace R, Ashman O. Treatment of ulcerative colitis using fecal bacteriotherapy. J Clin Gastroenterol. 2003;37(1):42–7 ID - ref222 ER - TY - STD TI - Bojanova DP, Bordenstein SR. Fecal transplants: what is being transferred? PLoS Biol. 2016;14(7) ID - ref223 ER - TY - STD TI - Ott SJ, Waetzig GH, Rehman A, Moltzau-Anderson J, Bharti R, et al. Efficacy of sterile fecal filtrate transfer for treating patients with Clostridium difficile infection. Gastroenterology. 2017;152(4):799–811 ID - ref224 ER - TY - STD TI - Petrof EO, Khoruts A. From stool transplants to next-generation microbiota therapeutics. Gastroenterology. 2014;146(6):1573–1582 ID - ref225 ER - TY - STD TI - Smith MB, Kelly C, Alm EJ. How to regulate faecal transplants. Nature. 2014;506:290–1 ID - ref226 ER - TY - STD TI - de Vos WM. Fame and future of faecal transplantations--developing next-generation therapies with synthetic microbiomes. Microb Biotechnol. 2013;6(4):316–25 ID - ref227 ER - TY - STD TI - Roberfroid M. Prebiotics: the concept Revisisted. J Nutr. 2007;137(3 Suppl 2): 830S-7S ID - ref228 ER - TY - STD TI - Martin FP, Wang Y, Sprenger N, Yap IK, Lundstedt T, et al. Probiotic modulation of symbiotic gut microbial-host metabolic interactions in a humanized microbiome mouse model. Mol Syst Biol. 2008;4 ID - ref229 ER - TY - STD TI - Ventura M, O'Connell-Motherway M, Leahy S, Moreno-Munoz JA, Fitzgerald GF, et al. From bacterial genome to functionality; case bifidobacteria. Int J Food Microbiol. 2007;120(1-2):2–12 ID - ref230 ER - TY - STD TI - Veiga P, Pons N, Agrawal A, Oozeer R, Guyonnet D, et al. Changes of the human gut microbiome induced by a fermented milk product. Sci Rep. 2014;4 ID - ref231 ER - TY - STD TI - Nami Y, Abdullah N, Haghshenas B, Radiah D, Rosli R, et al. Probiotic assessment of enterococcus durans 6HL and Lactococcus lactis 2HL isolated from vaginal microflora. J Med Microbiol. 2014;63(Pt 8):1044–51 ID - ref232 ER - TY - STD TI - Sakata T, Kojima T, Fujieda M, Takahashi M, Michibata T. Influences of probiotic bacteria on organic acid production by pig caecal bacteria in vitro. Proc Nutr Soc. 2003;62(1):73–80 ID - ref233 ER - TY - STD TI - Hosseini E, Grootaert C, Verstraete W, Van de Wiele T. Propionate as a health-promoting microbial metabolite in the human gut. Nutr Rev. 2011;69(5):245–58 ID - ref234 ER - TY - STD TI - De Keersmaecker SC, Verhoeven TL, Desair J, Marchal K, Vanderleyden J, et al. Strong antimicrobial activity of lactobacillus rhamnosus GG against salmonella typhimurium is due to accumulation of lactic acid. FEMS Microbiol Lett. 2006;259(1):89–96 ID - ref235 ER - TY - STD TI - Gilad O, Jacobsen S, Stuer-Lauridsen B, Pedersen MB, Garrigues C, et al. Combined transcriptome and proteome analysis of Bifidobacterium animalis subsp. lactis BB-12 grown on xylo-oligosaccharides and a model of their utilization. Appl Environ Microbiol. 2010;76(21):7285–91 ID - ref236 ER - TY - STD TI - Everard A, Belzer C, Geurts L, Ouwerkerk J, Druart C, et al. Cross-talk betweeen Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity. Proc Natl Acad Sci U S A. 2013;110(22):9066–71 ID - ref237 ER - TY - STD TI - Etxeberria U, Arias N, Boque N, Macarulla MT, Portillo MP, et al. Reshaping faecal gut microbiota composition by the intake of trans-resveratrol and quercetin in high-fat sucrose diet-fed rats. J Nutr Biochem. 2015;26(6):651–60 ID - ref238 ER - TY - STD TI - Selma MV, Espin JC, Tomas-Barberan FA. Interaction between phenolics and gut microbiota: role in human health. J Agric Food Chem. 2009;57(15):6485–6501 ID - ref239 ER - TY - STD TI - Carrington D. Reading the book of life. In: BBC news. London, UK; 2000. ID - ref240 ER - TY - STD TI - Weiss R, Gillis J. Teams finish mapping human DNA. In: The Washington post. Washington: WP Company LLC; 2000. ID - ref241 ER - TY - STD TI - Drmanac R. The advent of personal genome sequencing. Genet Med. 2011;13(3):188–90 ID - ref242 ER - TY - STD TI - Maher B. Personal genomes: The case of the missing heritability. Nature. 2008;456(6):18–21 ID - ref243 ER - TY - STD TI - Offit K. Personalized medicine: new genomics, old lessons. Hum Genet. 2011;130(1):3–14 ID - ref244 ER - TY - STD TI - Snyder M, Du J, Gerstein M. Personal genome sequencing: current approaches and challenges. Genes Dev. 2010;24(5):423–31 ID - ref245 ER - TY - STD TI - Flores M, Glusman G, Brogaard K, Price ND, Hood L. P4 medicine: how systems medicine will transform the healthcare sector and society. Future Med. 2013;10(6):565–576 ID - ref246 ER - TY - STD TI - Hood L, Balling R, Auffray C. Revolutionizing medicine in the 21st century through systems approaches. Biotechnol J. 2012;7(8):992–1001 ID - ref247 ER - TY - STD TI - Robbins MJ. I got my personal genome mapped and it was bullshit. In: vicecom. New York: VICE Media LLC; 2013. ID - ref248 ER - TY - STD TI - Hanage WP. Microbiology: microbiome science needs a healthy dose of scepticism. Nature. 2014;512(7514):247–8 ID - ref249 ER - TY - STD TI - Carroll AE. Exciting microbe research? Temper that giddy feeling in your gut. In: The New York times. New York: The New York Times Company; 2017. ID - ref250 ER -