The Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486:207–14.
Article
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;326:1694–7.
Article
PubMed Central
CAS
PubMed
Google Scholar
Faust K, Sathirapongsasuti JF, Izard J, Segata N, Gevers D, Raes J, et al. Microbial co-occurrence relationships in the human microbiome. PLoS Comput Biol. 2012;8:e1002606.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ding T, Schloss PD. Dynamics and associations of microbial community types across the human body. Nature. 2014;509:357–60.
Article
PubMed Central
CAS
PubMed
Google Scholar
David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014;505:559–63.
Article
PubMed Central
CAS
PubMed
Google Scholar
Faith JJ, Guruge JL, Charbonneau M, Subramanian S, Seedorf H, Goodman AL, et al. The long-term stability of the human gut microbiota. Science. 2013;341:1237439.
Article
PubMed Central
PubMed
Google Scholar
Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, et al. A core gut microbiome in obese and lean twins. Nature. 2009;457:480–4.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wen L, Ley RE, Volchkov PY, Stranges PB, Avanesyan L, Stonebraker AC, et al. Innate immunity and intestinal microbiota in the development of Type 1 diabetes. Nature. 2008;455:1109–13.
Article
PubMed Central
CAS
PubMed
Google Scholar
Marchesi JR, Holmes E, Khan F, Kochhar S, Scanlan P, Shanahan F, et al. Rapid and noninvasive metabonomic characterization of inflammatory bowel disease. J Proteome Res. 2007;6:546–51.
Article
CAS
PubMed
Google Scholar
Kinross JM, Darzi AW, Nicholson JK. Gut microbiome-host interactions in health and disease. Genome Med. 2011;3:14.
Article
PubMed Central
PubMed
Google Scholar
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. Nature. 2012;490:55–60.
Article
CAS
PubMed
Google Scholar
Koren O, Goodrich Julia K, Cullender Tyler C, Spor A, Laitinen K, Kling Bäckhed H, et al. Host remodeling of the gut microbiome and metabolic changes during pregnancy. Cell. 2012;150:470–80.
Article
PubMed Central
CAS
PubMed
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;444:1027–31.
Article
PubMed
Google Scholar
Goodrich JK, Waters JL, Poole AC, Sutter JL, Koren O, Blekhman R, et al. Human genetics shape the gut microbiome. Cell. 2014;159:789–99.
Article
CAS
PubMed
Google Scholar
Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, Gordon JI. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med. 2009;1:6ra14.
Article
PubMed Central
PubMed
Google Scholar
Vangay P, Ward T, Gerber JS, Knights D. Antibiotics, pediatric dysbiosis, and disease. Cell Host Microbe. 2015;17:553–64.
Article
CAS
PubMed
Google Scholar
Maurice CF, Haiser HJ, Turnbaugh PJ. Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell. 2013;152:39–50.
Article
PubMed Central
CAS
PubMed
Google Scholar
Morton ER, Lynch J, Froment A, Lafosse S, Heyer E, Przeworski M, et al. Variation in rural African gut microbiomes is strongly shaped by parasitism and diet. bioRxiv 2015. DOI: 10.1101/016949
Hoffmann C, Hill DA, Minkah N, Kirn T, Troy A, Artis D, et al. Community-wide response of the gut microbiota to enteropathogenic Citrobacter rodentium infection revealed by deep sequencing. Infect Immun. 2009;77:4668–78.
Article
PubMed Central
CAS
PubMed
Google Scholar
Tung J, Barreiro LB, Burns MB, Grenier JC, Lynch J, Grieneisen LE, et al. Social networks predict gut microbiome composition in wild baboons. Elife. 2015;4
Meadow JF, Bateman AC, Herkert KM, O’Connor TK, Green JL. Significant changes in the skin microbiome mediated by the sport of roller derby. Peer J. 2013;1:e53.
Article
PubMed Central
PubMed
Google Scholar
Lax S, Smith DP, Hampton-Marcell J, Owens SM, Handley KM, Scott NM, et al. Longitudinal analysis of microbial interaction between humans and the indoor environment. Science. 2014;345:1048–52.
Article
PubMed Central
CAS
PubMed
Google Scholar
Spor A, Koren O, Ley R. Unravelling the effects of the environment and host genotype on the gut microbiome. Nat Rev Micro. 2011;9:279–90.
Article
CAS
Google Scholar
Khachatryan ZA, Ktsoyan ZA, Manukyan GP, Kelly D, Ghazaryan KA, Aminov RI. Predominant role of host genetics in controlling the composition of gut microbiota. PLoS One. 2008;3:e3064.
Article
PubMed Central
PubMed
Google Scholar
Li E, Hamm CM, Gulati AS, Sartor RB, Chen H, Wu X, et al. Inflammatory bowel diseases phenotype, c. difficile and NOD2 genotype are associated with shifts in human ileum associated microbial composition. PLoS One. 2012;7:e26284.
Article
PubMed Central
CAS
PubMed
Google Scholar
Tong M, McHardy I, Ruegger P, Goudarzi M, Kashyap PC, Haritunians T, et al. Reprograming of gut microbiome energy metabolism by the FUT2 Crohn’s disease risk polymorphism. Isme J. 2014;8:2193–206.
Article
CAS
PubMed
Google Scholar
Knights D, Silverberg MS, Weersma RK, Gevers D, Dijkstra G, Huang H, et al. Complex host genetics influence the microbiome in inflammatory bowel disease. Genome Med. 2014;6:107.
Article
PubMed Central
PubMed
Google Scholar
Benson AK, Kelly SA, Legge R, Ma F, Low SJ, Kim J, et al. Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors. Proc Natl Acad Sci U S A. 2010;107:18933–8.
Article
PubMed Central
CAS
PubMed
Google Scholar
McKnite AM, Perez-Munoz ME, Lu L, Williams EG, Brewer S, Andreux PA, et al. Murine gut microbiota is defined by host genetics and modulates variation of metabolic traits. PLoS One. 2012;7:e39191.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ma J, Coarfa C, Qin X, Bonnen PE, Milosavljevic A, Versalovic J, et al. mtDNA haplogroup and single nucleotide polymorphisms structure human microbiome communities. BMC Genomics. 2014;15:257.
Article
PubMed Central
PubMed
Google Scholar
Khor B, Gardet A, Xavier RJ. Genetics and pathogenesis of inflammatory bowel disease. Nature. 2011;474:307–17.
Article
PubMed Central
CAS
PubMed
Google Scholar
Virgin HW, Todd JA. Metagenomics and personalized medicine. Cell. 2011;147:44–56.
Article
CAS
PubMed
Google Scholar
The Human Microbiome Project Consortium. A framework for human microbiome research. Nature. 2012;486:215–21.
Article
Google Scholar
Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, et al. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012;491:56–65.
Article
PubMed
Google Scholar
Le Chatelier E, Nielsen T, Qin J, Prifti E, Hildebrand F, Falony G, et al. Richness of human gut microbiome correlates with metabolic markers. Nature. 2013;500:541–6.
Article
PubMed
Google Scholar
De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci. 2010;107:14691–6.
Article
PubMed Central
PubMed
Google Scholar
Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, et al. Human gut microbiome viewed across age and geography. Nature. 2012;486:222–7.
PubMed Central
CAS
PubMed
Google Scholar
Ravussin Y, Koren O, Spor A, LeDuc C, Gutman R, Stombaugh J, et al. Responses of gut microbiota to diet composition and weight loss in lean and obese mice. Obesity (Silver Spring). 2012;20:738–47.
Article
CAS
Google Scholar
La Cava A, Matarese G. The weight of leptin in immunity. Nat Rev Immunol. 2004;4:371–9.
Article
PubMed
Google Scholar
Groschl M, Topf HG, Kratzsch J, Dotsch J, Rascher W, Rauh M. Salivary leptin induces increased expression of growth factors in oral keratinocytes. J Mol Endocrinol. 2005;34:353–66.
Article
CAS
PubMed
Google Scholar
Cerman AA, Bozkurt S, Sav A, Tulunay A, Elbasi MO, Ergun T. Serum leptin levels, skin leptin and leptin receptor expression in psoriasis. Br J Dermatol. 2008;159:820–6.
Article
CAS
PubMed
Google Scholar
Tadokoro S, Ide S, Tokuyama R, Umeki H, Tatehara S, Kataoka S, et al. Leptin promotes wound healing in the skin. PLoS One. 2015;10:e0121242.
Article
PubMed Central
PubMed
Google Scholar
Zhu KJ, Zhang C, Li M, Zhu CY, Shi G, Fan YM. Leptin levels in patients with psoriasis: a meta-analysis. Clin Exp Dermatol. 2013;38:478–83.
Article
PubMed
Google Scholar
Song SY, Woo HJ, Bae CH, Kim YW, Kim YD. Expression of leptin receptor in nasal polyps: leptin as a mucosecretagogue. Laryngoscope. 2010;120:1046–50.
CAS
PubMed
Google Scholar
Swann JR, Want EJ, Geier FM, Spagou K, Wilson ID, Sidaway JE, et al. Systemic gut microbial modulation of bile acid metabolism in host tissue compartments. Proc Natl Acad Sci U S A. 2011;108:4523–30.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, et al. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A. 2009;106:9362–7.
Article
PubMed Central
CAS
PubMed
Google Scholar
Michail S, Durbin M, Turner D, Griffiths AM, Mack DR, Hyams J, et al. Alterations in the gut microbiome of children with severe ulcerative colitis. Inflamm Bowel Dis. 2012;18:1799–808.
Article
PubMed Central
PubMed
Google Scholar
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.
Article
PubMed Central
CAS
PubMed
Google Scholar
Consortium G. The Genotype-Tissue Expression (GTEx) project. Nat Genet. 2013;45:580–5.
Article
Google Scholar
Moayyeri A, Hammond CJ, Hart DJ, Spector TD. The UK Adult Twin Registry (TwinsUK Resource). Twin Res Hum Genet. 2013;16:144–9.
Article
PubMed Central
PubMed
Google Scholar
Parche S, Beleut M, Rezzonico E, Jacobs D, Arigoni F, Titgemeyer F, et al. Lactose-over-glucose preference in Bifidobacterium longum NCC2705: glcP, encoding a glucose transporter, is subject to lactose repression. J Bacteriol. 2006;188:1260–5.
Article
PubMed Central
CAS
PubMed
Google Scholar
Tishkoff SA, Reed FA, Ranciaro A, Voight BF, Babbitt CC, Silverman JS, et al. Convergent adaptation of human lactase persistence in Africa and Europe. Nat Genet. 2007;39:31–40.
Article
PubMed Central
CAS
PubMed
Google Scholar
Quintana-Murci L, Clark AG. Population genetic tools for dissecting innate immunity in humans. Nat Rev Immunol. 2013;13:280–93.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ames SK, Gardner SN, Marti JM, Slezak TR, Gokhale MB, Allen JE. Using populations of human and microbial genomes for organism detection in metagenomes. Genome Res. 2015;25:1056–67.
Article
PubMed Central
CAS
PubMed
Google Scholar
Salzman NH, Hung K, Haribhai D, Chu H, Karlsson-Sjoberg J, Amir E, et al. Enteric defensins are essential regulators of intestinal microbial ecology. Nat Immunol. 2010;11:76–83.
Article
PubMed Central
CAS
PubMed
Google Scholar
Lupp C, Robertson M, Wickham M, Sekirov I, Champion O, Gaynor E, et al. Host-mediated inflammation disrupts the intestinal microbiota and promotes the overgrowth of Enterobacteriaceae. Cell Host Microbe. 2007;2:119–29.
Article
CAS
PubMed
Google Scholar
Vijay-Kumar M, Aitken JD, Carvalho FA, Cullender TC, Mwangi S, Srinivasan S, et al. Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science. 2010;328:228–31.
Article
CAS
PubMed
Google Scholar
Henao-Mejia J, Elinav E, Jin C, Hao L, Mehal WZ, Strowig T, et al. Inflammasome-mediated dysbiosis regulates progression of NAFLD and obesity. Nature. 2012;482:179–85.
PubMed Central
CAS
PubMed
Google Scholar
Garrett WS, Lord GM, Punit S, Lugo-Villarino G, Mazmanian SK, Ito S, et al. Communicable ulcerative colitis induced by T-bet deficiency in the innate immune system. Cell. 2007;131:33–45.
Article
PubMed Central
CAS
PubMed
Google Scholar
Caricilli AM, Picardi PK, de Abreu LL, Ueno M, Prada PO, Ropelle ER, et al. Gut microbiota is a key modulator of insulin resistance in TLR 2 knockout mice. PLoS Biol. 2011;9:e1001212.
Article
PubMed Central
CAS
PubMed
Google Scholar
Leamy LJ, Kelly SA, Nietfeldt J, Legge RM, Ma F, Hua K, et al. Host genetics and diet, but not immunoglobulin A expression, converge to shape compositional features of the gut microbiome in an advanced intercross population of mice. Genome Biol. 2014;15:552.
Article
PubMed Central
PubMed
Google Scholar
Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754–60.
Article
PubMed Central
CAS
PubMed
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078–9.
Article
PubMed Central
PubMed
Google Scholar
DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011;43:491–8.
Article
PubMed Central
CAS
PubMed
Google Scholar
Consortium TGP. A map of human genome variation from population-scale sequencing. Nature. 2010;467:1061–73.
Article
Google Scholar
Keinan A, Clark AG. Recent explosive human population growth has resulted in an excess of rare genetic variants. Science. 2012;336:740–3.
Article
PubMed Central
CAS
PubMed
Google Scholar
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007;81:559–75.
Article
PubMed Central
CAS
PubMed
Google Scholar
PLINK: Whole genome association analysis toolset. Available at: http://pngu.mgh.harvard.edu/~purcell/plink.
Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38:e164.
Article
PubMed Central
PubMed
Google Scholar
Ingenuity Pathway Analysis. Available at: www.ingenuity.com.
Innate DB. Available at: www.innatedb.com
Consortium TGO. The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res. 2010;38:D331–5.
Article
Google Scholar
Gene Ontology Consortium. Available at: www.geneontology.org.
KEGG: Kyoto Encyclopedia of Genes and Genomes. Available at: www.genome.jp/kegg.
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.
Article
PubMed Central
CAS
PubMed
Google Scholar
Reactome. Available at: www.reactome.org.
National Human Genome Research Institute. Available at: www.genome.gov/26525384.
GTex Portal. Available at: www.broadinstitute.org/gtex/.
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335–6.
Article
PubMed Central
CAS
PubMed
Google Scholar
Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–1.
Article
CAS
PubMed
Google Scholar
Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics. 2010;26:266–7.
Article
PubMed Central
CAS
PubMed
Google Scholar
Price MN, Dehal PS, Arkin AP. FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One. 2010;5:e9490.
Article
PubMed Central
PubMed
Google Scholar
Howie BN, Donnelly P, Marchini J. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet. 2009;5:e1000529.
Article
PubMed Central
PubMed
Google Scholar
Abecasis GR, Cherny SS, Cookson WO, Cardon LR. Merlin--rapid analysis of dense genetic maps using sparse gene flow trees. Nat Genet. 2002;30:97–101.
Article
CAS
PubMed
Google Scholar
Li MJ, Wang LY, Xia Z, Wong MP, Sham PC, Wang J. dbPSHP: a database of recent positive selection across human populations. Nucleic Acids Res. 2014;42:D910–6.
Article
PubMed Central
CAS
PubMed
Google Scholar
dbPSHP: A database of recent positive selection across human populations. Available at: http://jjwanglab.org/dbpshp.
NIH Human Microbiome Project. Available at: http://hmpdacc.org.