Diet Dominates Host Genotype in Shaping the Murine Gut Microbiota

Cell Host & Microbe - Tập 17 - Trang 72-84 - 2015
Rachel N. Carmody1,2, Georg K. Gerber3, Jesus M. Luevano1, Daniel M. Gatti4, Lisa Somes4, Karen L. Svenson4, Peter J. Turnbaugh1,2
1FAS Center for Systems Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
2Department of Microbiology and Immunology, Hooper Foundation, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
3Center for Clinical and Translational Metagenomics, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Avenue, Boston, MA 02115, USA
4The Jackson Laboratory, 610 Main Street, Bar Harbor, ME 04609, USA

Tài liệu tham khảo

Atkinson, 1994, Weight cycling, JAMA, 272, 1196, 10.1001/jama.1994.03520150064038 Benjamini, 1995, Controlling the false discovery rate: a practical and powerful approach to multiple testing, J. R. Stat. Soc. Series B Stat. Methodol., 57, 289 Benson, 2010, Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors, Proc. Natl. Acad. Sci. USA, 107, 18933, 10.1073/pnas.1007028107 Blanchard, O.J., and Summers, L.H. (1986). Hysteresis and the European Unemployment Problem. Working Paper No. 1950 (Cambridge, MA: National Bureau of Economic Research). Caporaso, 2010, QIIME allows analysis of high-throughput community sequencing data, Nat. Methods, 7, 335, 10.1038/nmeth.f.303 Churchill, 2012, The Diversity Outbred mouse population, Mamm. Genome, 23, 713, 10.1007/s00335-012-9414-2 Costello, 2012, The application of ecological theory toward an understanding of the human microbiome, Science, 336, 1255, 10.1126/science.1224203 Couturier-Maillard, 2013, NOD2-mediated dysbiosis predisposes mice to transmissible colitis and colorectal cancer, J. Clin. Invest., 123, 700 Das, 2009, Digital signaling and hysteresis characterize ras activation in lymphoid cells, Cell, 136, 337, 10.1016/j.cell.2008.11.051 David, 2014, Diet rapidly and reproducibly alters the human gut microbiome, Nature, 505, 559, 10.1038/nature12820 Faith, 2011, Predicting a human gut microbiota’s response to diet in gnotobiotic mice, Science, 333, 101, 10.1126/science.1206025 Faith, 2013, The long-term stability of the human gut microbiota, Science, 341, 1237439, 10.1126/science.1237439 Gerber, 2012, Inferring dynamic signatures of microbes in complex host ecosystems, PLoS Comput. Biol., 8, e1002624, 10.1371/journal.pcbi.1002624 Haiser, 2013, Predicting and manipulating cardiac drug inactivation by the human gut bacterium Eggerthella lenta, Science, 341, 295, 10.1126/science.1235872 Hashimoto, 2012, ACE2 links amino acid malnutrition to microbial ecology and intestinal inflammation, Nature, 487, 477, 10.1038/nature11228 Hatori, 2012, Time-restricted feeding without reducing caloric intake prevents metabolic diseases in mice fed a high-fat diet, Cell Metab., 15, 848, 10.1016/j.cmet.2012.04.019 Hawkes, 1991, Hunting income patterns among the Hadza: big game, common goods, foraging goals and the evolution of the human diet, Philos. Trans. R. Soc. Lond. B Biol. Sci., 334, 243, 10.1098/rstb.1991.0113 Hildebrand, 2013, Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice, Genome Biol., 14, R4, 10.1186/gb-2013-14-1-r4 Ivanov, 2009, Induction of intestinal Th17 cells by segmented filamentous bacteria, Cell, 139, 485, 10.1016/j.cell.2009.09.033 Jiles, 1986, Theory of ferromagnetic hysteresis, J. Magn. Magn. Mater., 61, 48, 10.1016/0304-8853(86)90066-1 Jumpertz, 2011, Energy-balance studies reveal associations between gut microbes, caloric load, and nutrient absorption in humans, Am. J. Clin. Nutr., 94, 58, 10.3945/ajcn.110.010132 Kashyap, 2013, Genetically dictated change in host mucus carbohydrate landscape exerts a diet-dependent effect on the gut microbiota, Proc. Natl. Acad. Sci. USA, 110, 17059, 10.1073/pnas.1306070110 Langille, 2013, Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences, Nat. Biotechnol., 31, 814, 10.1038/nbt.2676 Levy, 2013, Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules, Proc. Natl. Acad. Sci. USA, 110, 12804, 10.1073/pnas.1300926110 Ley, 2005, Obesity alters gut microbial ecology, Proc. Natl. Acad. Sci. USA, 102, 11070, 10.1073/pnas.0504978102 Li, 2012, Inflammatory bowel diseases phenotype, C. difficile and NOD2 genotype are associated with shifts in human ileum associated microbial composition, PLoS ONE, 7, e26284, 10.1371/journal.pone.0026284 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 McKnite, 2012, Murine gut microbiota is defined by host genetics and modulates variation of metabolic traits, PLoS ONE, 7, e39191, 10.1371/journal.pone.0039191 Meyer, 2008, The metagenomics RAST server—a public resource for the automatic phylogenetic and functional analysis of metagenomes, BMC Bioinformatics, 9, 386, 10.1186/1471-2105-9-386 Muegge, 2011, Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans, Science, 332, 970, 10.1126/science.1198719 Parks, 2013, Genetic control of obesity and gut microbiota composition in response to high-fat, high-sucrose diet in mice, Cell Metab., 17, 141, 10.1016/j.cmet.2012.12.007 Ravussin, 2012, Responses of gut microbiota to diet composition and weight loss in lean and obese mice, Obesity (Silver Spring), 20, 738, 10.1038/oby.2011.111 Scheffer, 2001, Catastrophic shifts in ecosystems, Nature, 413, 591, 10.1038/35098000 Scholz, 2014, Immune mediated shaping of microflora community composition depends on barrier site, PLoS ONE, 9, e84019, 10.1371/journal.pone.0084019 Segata, 2011, Metagenomic biomarker discovery and explanation, Genome Biol., 12, R60, 10.1186/gb-2011-12-6-r60 Sha, 2003, Hysteresis drives cell-cycle transitions in Xenopus laevis egg extracts, Proc. Natl. Acad. Sci. USA, 100, 975, 10.1073/pnas.0235349100 Smeekens, 2014, Skin microbiome imbalance in patients with STAT1/STAT3 defects impairs innate host defense responses, J. Innate Immun., 6, 253, 10.1159/000351912 Spor, 2011, Unravelling the effects of the environment and host genotype on the gut microbiome, Nat. Rev. Microbiol., 9, 279, 10.1038/nrmicro2540 Svenson, 2012, High-resolution genetic mapping using the Mouse Diversity outbred population, Genetics, 190, 437, 10.1534/genetics.111.132597 Threadgill, 2012, Ten years of the Collaborative Cross, Genetics, 190, 291, 10.1534/genetics.111.138032 Turnbaugh, 2009, A core gut microbiome in obese and lean twins, Nature, 457, 480, 10.1038/nature07540 Turnbaugh, 2009, The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice, Sci. Transl. Med., 1, 10.1126/scitranslmed.3000322 Wen, 2008, Innate immunity and intestinal microbiota in the development of Type 1 diabetes, Nature, 455, 1109, 10.1038/nature07336 Yatsunenko, 2012, Human gut microbiome viewed across age and geography, Nature, 486, 222, 10.1038/nature11053 Zhang, 2012, Structural resilience of the gut microbiota in adult mice under high-fat dietary perturbations, ISME J., 6, 1848, 10.1038/ismej.2012.27