A system biology perspective on environment–host–microbe interactions

Sonnenburg, 2016, Diet-induced extinctions in the gut microbiota compound over generations, Nature, 529, 212, 10.1038/nature16504

Holmes, 2011, Understanding the role of gut microbiome-host metabolic signal disruption in health and disease, Trends Microbiol, 19, 349, 10.1016/j.tim.2011.05.006

Sender, 2016, Revised estimates for the number of human and bacteria cells in the body, PLoS Biol, 14, e1002533., 10.1371/journal.pbio.1002533

Qin, 2010, A human gut microbial gene catalogue established by metagenomic sequencing, Nature, 464, 59, 10.1038/nature08821

Imhann, 2016, Proton pump inhibitors affect the gut microbiome, Gut, 65, 740, 10.1136/gutjnl-2015-310376

Zhernakova, 2016, Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity, Science, 352, 565, 10.1126/science.aad3369

Mirzaei, 2017, Ménage à trois in the human gut: interactions between host, bacteria and phages, Nat. Rev. Microbiol, 15, 397., 10.1038/nrmicro.2017.30

Schirmer, 2016, Linking the human gut microbiome to inflammatory cytokine production capacity, Cell, 167, 10.1016/j.cell.2016.10.020

Li, 2017, Intermittent fasting promotes white adipose browning and decreases obesity by shaping the gut microbiota, Cell Metab, 26, 672, 10.1016/j.cmet.2017.08.019

Wu, 2017, Metformin alters the gut microbiome of individuals with treatment-naive type 2 diabetes, contributing to the therapeutic effects of the drug, Nat. Med, 23, 850, 10.1038/nm.4345

Atanasovska, 2015, GWAS as a driver of gene discovery in cardiometabolic diseases, Trends Endocrinol. Metab, 26, 722, 10.1016/j.tem.2015.10.004

Vazquez-Baeza, 2017

Gopalakrishnan, 2017, Gut microbiome modulates response to anti–PD-1 immunotherapy in melanoma patients, Science, 359, 97, 10.1126/science.aan4236

Routy, 2017, Gut microbiome influences efficacy of PD-1–based immunotherapy against epithelial tumors, Science, 359, 91, 10.1126/science.aan3706

Stevens, 2017

Tremlett, 2017, The gut microbiome in human neurological disease: a review, Ann. Neurol, 81, 369, 10.1002/ana.24901

Bauer, 2017, Metformin alters upper small intestinal microbiota that impact a glucose-SGLT1-sensing glucoregulatory pathway, Cell Metab, 27, 101, 10.1016/j.cmet.2017.09.019

Rothschild, 2018, Environment dominates over host genetics in shaping human gut microbiota, Nature, 555, 210, 10.1038/nature25973

Faith, 2013, The long-term stability of the human gut microbiota, Science, 341, 1237439., 10.1126/science.1237439

Falony, 2016, Population-level analysis of gut microbiome variation, Science, 352, 560, 10.1126/science.aad3503

Xie, 2016, Shotgun metagenomics of 250 adult twins reveals genetic and environmental impacts on the gut microbiome, Cell Syst, 3, 572, 10.1016/j.cels.2016.10.004

Carmody, 2015, Diet dominates host genotype in shaping the murine gut microbiota, Cell Host Microbe, 17, 72, 10.1016/j.chom.2014.11.010

Fujisaka, 2018, Diet, genetics, and the gut microbiome drive dynamic changes in plasma metabolites, Cell Rep, 22, 3072, 10.1016/j.celrep.2018.02.060

Zhao, 2018, Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes, Science, 359, 1151, 10.1126/science.aao5774

Forslund, 2015, Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota, Nature, 528, 262, 10.1038/nature15766

Luca, 2018, Functional genomics of host-microbiome interactions in humans, Trends Genet, 34, 30, 10.1016/j.tig.2017.10.001

Maier, 2018, Extensive impact of non-antibiotic drugs on human gut bacteria, Nature, 623

Zeissig, 2014, Life at the beginning: perturbation of the microbiota by antibiotics in early life and its role in health and disease, Nat. Immunol, 15, 307, 10.1038/ni.2847

Gensollen, 2016, How colonization by microbiota in early life shapes the immune system, Science, 352, 539, 10.1126/science.aad9378

Knutie, 2017, Early-life disruption of amphibian microbiota decreases later-life resistance to parasites, Nat. Commun, 8, 86., 10.1038/s41467-017-00119-0

Maruvada, 2017, The human microbiome and obesity: moving beyond associations, Cell Host Microbe, 22, 589, 10.1016/j.chom.2017.10.005

Goodrich, 2014, Human genetics shape the gut microbiome, Cell, 159, 789, 10.1016/j.cell.2014.09.053

Pedersen, 2016, Human gut microbes impact host serum metabolome and insulin sensitivity, Nature, 535, 376, 10.1038/nature18646

Bonder, 2016, The effect of host genetics on the gut microbiome, Nat. Genet, 48, 1407, 10.1038/ng.3663

Wang, 2016, Genome-wide association analysis identifies variation in vitamin D receptor and other host factors influencing the gut microbiota, Nat. Genet, 48, 1396, 10.1038/ng.3695

Goodrich, 2016, Genetic determinants of the gut microbiome in UK Twins, Cell Host Microbe, 19, 731, 10.1016/j.chom.2016.04.017

Wijmenga, 2018, The importance of cohort studies in the post-GWAS era, Nat. Genet, 50, 322, 10.1038/s41588-018-0066-3

Wang, 2014, A shrimp C-type lectin inhibits proliferation of the hemolymph microbiota by maintaining the expression of antimicrobial peptides, J. Biol. Chem, 289, 11779, 10.1074/jbc.M114.552307

Pang, 2016, Mosquito C-type lectins maintain gut microbiome homeostasis, Nat. Microbiol, 1, 16023., 10.1038/nmicrobiol.2016.23

Iliev, 2012, Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis, Science, 336, 1314, 10.1126/science.1221789

Blekhman, 2015, Host genetic variation impacts microbiome composition across human body sites, Genome Biol, 16, 191., 10.1186/s13059-015-0759-1

Fu, 2015, The gut microbiome contributes to a substantial proportion of the variation in blood lipids, Circ. Res, 117, 817, 10.1161/CIRCRESAHA.115.306807

Henao-Mejia, 2012, Inflammasome-mediated dysbiosis regulates progression of NAFLD and obesity, Nature, 482, 179, 10.1038/nature10809

Kang, 2017, Gut microbiota mediates the protective effects of dietary capsaicin against chronic low-grade inflammation and associated obesity induced by high-fat diet, MBio, 8, e00470-17, 10.1128/mBio.00470-17

Chu, 2016, Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease, Science, 352, 1116, 10.1126/science.aad9948

Schirmer, 2018, Dynamics of metatranscription in the inflammatory bowel disease gut microbiome, Nat. Microbiol, 3, 337, 10.1038/s41564-017-0089-z

Abu-Ali, 2018, Metatranscriptome of human faecal microbial communities in a cohort of adult men, Nat. Microbiol, 3, 356, 10.1038/s41564-017-0084-4

Xiong, 2017, Genome-resolved metaproteomic characterization of preterm infant gut microbiota development reveals species-specific metabolic shifts and variabilities during early life, Microbiome, 5, 72., 10.1186/s40168-017-0290-6

Snijders, 2016, Influence of early life exposure, host genetics and diet on the mouse gut microbiome and metabolome, Nat. Microbiol, 2, 16221., 10.1038/nmicrobiol.2016.221

Maier, 2017, Impact of dietary resistant starch on the human gut microbiome, metaproteome, and metabolome, MBio, 8, e01343-17, 10.1128/mBio.01343-17

Zheng, 2017, Honeybee gut microbiota promotes host weight gain via bacterial metabolism and hormonal signaling, Proc. Natl. Acad. Sci. U S A, 114, 4775, 10.1073/pnas.1701819114

Kesnerova, 2017, Disentangling metabolic functions of bacteria in the honey bee gut, PLoS Biol, 15, e2003467., 10.1371/journal.pbio.2003467

Schmidt, 2018, The human gut microbiome: from association to modulation, Cell, 172, 1198, 10.1016/j.cell.2018.02.044

Liu, 2016, A zero-inflated Poisson model for insertion tolerance analysis of genes based on Tn-seq data, Bioinformatics, 32, 1701, 10.1093/bioinformatics/btw061

Chen, 2016, A two-part mixed-effects model for analyzing longitudinal microbiome compositional data, Bioinformatics, 32, 2611, 10.1093/bioinformatics/btw308

Norman, 2015, Disease-specific alterations in the enteric virome in inflammatory bowel disease, Cell, 160, 447, 10.1016/j.cell.2015.01.002

Huh, 2010, Reconstituting organ-level lung functions on a chip, Science, 328, 1662, 10.1126/science.1188302

Zhang, 2016, Biodegradable scaffold with built-in vasculature for organ-on-a-chip engineering and direct surgical anastomosis, Nat. Mater, 15, 669, 10.1038/nmat4570

Lagier, 2016, Culture of previously uncultured members of the human gut microbiota by culturomics, Nat. Microbiol, 1, 16203., 10.1038/nmicrobiol.2016.203