1 Sender, R., Fuchs, S. & Milo, R. Are we really vastly outnumbered? Revisiting the ratio of bacterial to host cells in humans. Cell 164, 337–340 (2016).

2 Turnbaugh, P.J. et al. The human microbiome project. Nature 449, 804–810 (2007).

3 Locey, K.J. & Lennon, J.T. Scaling laws predict global microbial diversity. Proc. Natl. Acad. Sci. USA 113, 5970–5975 (2016).

4 Frank, D.N. et al. Molecular–phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc. Natl. Acad. Sci. USA 104, 13780–13785 (2007).

5 Gevers, D. et al. The treatment-naive microbiome in new-onset Crohn's disease. Cell Host Microbe 15, 382–392 (2014).

6 Ni, J. et al. A role for bacterial urease in gut dysbiosis and Crohn's disease. Sci. Transl. Med. 9, eaah6888 (2017).

7 Kostic, A.D. et al. Fusobacterium nucleatum potentiates intestinal tumorigenesis and modulates the tumor-immune microenvironment. Cell Host Microbe 14, 207–215 (2013).

8 Jiang, H. et al. Altered fecal microbiota composition in patients with major depressive disorder. Brain Behav. Immun. 48, 186–194 (2015).

9 Zheng, P. et al. Gut microbiome remodeling induces depressive-like behaviors through a pathway mediated by the host's metabolism. Mol. Psychiatry 21, 786–796 (2016).

10 Gilbert, J.A. et al. Microbiome-wide association studies link dynamic microbial consortia to disease. Nature 535, 94–103 (2016).

11 Punt, C.J.A., Koopman, M. & Vermeulen, L. From tumour heterogeneity to advances in precision treatment of colorectal cancer. Nat. Rev. Clin. Oncol. 14, 235–246 (2017).

12 Debelius, J. et al. Tiny microbes, enormous impacts: what matters in gut microbiome studies? Genome Biol. 17, 217 (2016).

13 Integrative HMP (iHMP) Research Network Consortium. The Integrative Human Microbiome Project: dynamic analysis of microbiome-host omics profiles during periods of human health and disease. Cell Host Microbe 16, 276–289 (2014).

14 Lax, S. et al. Longitudinal analysis of microbial interaction between humans and the indoor environment. Science 345, 1048–1052 (2014).

15 Goodrich, J.K. et al. Human genetics shape the gut microbiome. Cell 159, 789–799 (2014).

16 Ridaura, V.K. et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science 341, 1241214 (2013).

17 Turnbaugh, P.J. et al. Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. Proc. Natl. Acad. Sci. USA 107, 7503–7508 (2010).

18 Turnbaugh, P.J. et al. A core gut microbiome in obese and lean twins. Nature 457, 480–484 (2009).

19 Seedorf, H. et al. Bacteria from diverse habitats colonize and compete in the mouse gut. Cell 159, 253–266 (2014).

20 Karczewski, J., Poniedziałek, B., Adamski, Z. & Rzymski, P. The effects of the microbiota on the host immune system. Autoimmunity 47, 494–504 (2014).

21 Schirmer, M. et al. Linking the human gut microbiome to inflammatory cytokine production capacity. Cell 167, 1897 (2016).

22 Lozupone, C.A., Stombaugh, J.I., Gordon, J.I., Jansson, J.K. & Knight, R. Diversity, stability and resilience of the human gut microbiota. Nature 489, 220–230 (2012).

23 O'Toole, P.W. Changes in the intestinal microbiota from adulthood through to old age. Clin. Microbiol. Infect. 18 (Suppl. 4), 44–46 (2012).

24 Koenig, J.E. et al. Succession of microbial consortia in the developing infant gut microbiome. Proc. Natl. Acad. Sci. USA 108 (Suppl. 1), 4578–4585 (2011).

25 Weng, M. & Walker, W.A. The role of gut microbiota in programming the immune phenotype. J. Dev. Orig. Health Dis. 4, 203–214 (2013).

26 Maynard, C.L., Elson, C.O., Hatton, R.D. & Weaver, C.T. Reciprocal interactions of the intestinal microbiota and immune system. Nature 489, 231–241 (2012).

27 Knights, D. et al. Rethinking “enterotypes”. Cell Host Microbe 16, 433–437 (2014).

28 Jeffery, I.B., Claesson, M.J., O'Toole, P.W. & Shanahan, F. Categorization of the gut microbiota: enterotypes or gradients? Nat. Rev. Microbiol. 10, 591–592 (2012).

29 Grice, E.A. & Segre, J.A. The skin microbiome. Nat. Rev. Microbiol. 9, 244–253 (2011).

30 Grice, E.A. et al. Topographical and temporal diversity of the human skin microbiome. Science 324, 1190–1192 (2009).

31 Caporaso, J.G. et al. Moving pictures of the human microbiome. Genome Biol. 12, R50 (2011).

32 Kort, R. et al. Shaping the oral microbiota through intimate kissing. Microbiome 2, 41 (2014).

33 Lazarevic, V., Whiteson, K., Hernandez, D., François, P. & Schrenzel, J. Study of inter- and intra-individual variations in the salivary microbiota. BMC Genomics 11, 523 (2010).

34 David, L.A. et al. Host lifestyle affects human microbiota on daily timescales. Genome Biol. 15, R89 (2014).

35 David, L.A. et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 505, 559–563 (2014).

36 Maier, T.V. et al. Impact of dietary resistant starch on the human gut microbiome, metaproteome, and metabolome. MBio. 8, e01343–e17 (2017).

37 Hannigan, G.D. et al. The human skin double-stranded DNA virome: topographical and temporal diversity, genetic enrichment, and dynamic associations with the host microbiome. MBio 6, e01578–e15 (2015).

38 Vandeputte, D. et al. Quantitative microbiome profiling links gut community variation to microbial load. Nature 551, 507–511 (2017).

39 Vandeputte, D. et al. Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates. Gut 65, 57–62 (2016).

40 Ma, B., Forney, L.J. & Ravel, J. Vaginal microbiome: rethinking health and disease. Annu. Rev. Microbiol. 66, 371–389 (2012).

41 Ravel, J. et al. Daily temporal dynamics of vaginal microbiota before, during and after episodes of bacterial vaginosis. Microbiome 1, 29 (2013).

42 Romero, R. et al. The composition and stability of the vaginal microbiota of normal pregnant women is different from that of non-pregnant women. Microbiome 2, 4 (2014).

43 Xiao, B. et al. Predictive value of the composition of the vaginal microbiota in bacterial vaginosis, a dynamic study to identify recurrence-related flora. Sci. Rep. 6, 26674 (2016).

44 Albenberg, L.G. & Wu, G.D. Diet and the intestinal microbiome: associations, functions, and implications for health and disease. Gastroenterology 146, 1564–1572 (2014).

45 Wu, G.D. et al. Linking long-term dietary patterns with gut microbial enterotypes. Science 334, 105–108 (2011).

46 Zeevi, D. et al. Personalized nutrition by prediction of glycemic responses. Cell 163, 1079–1094 (2015).

47 Zhang, C. et al. Dietary Modulation of gut microbiota contributes to alleviation of both genetic and simple obesity in children. EBioMedicine 2, 968–984 (2015).

48 Modi, S.R., Collins, J.J. & Relman, D.A. Antibiotics and the gut microbiota. J. Clin. Invest. 124, 4212–4218 (2014).

49 Dethlefsen, L. & Relman, D.A. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc. Natl. Acad. Sci. USA 108 (Suppl. 1), 4554–4561 (2011).

50 Maurice, C.F., Haiser, H.J. & Turnbaugh, P.J. Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell 152, 39–50 (2013).

51 Trasande, L. et al. Infant antibiotic exposures and early-life body mass. Int. J. Obes. (Lond). 37, 16–23 (2013).

52 Song, S.J. et al. Cohabiting family members share microbiota with one another and with their dogs. eLife 2, e00458 (2013).

53 von Mutius, E. The microbial environment and its influence on asthma prevention in early life. J. Allergy Clin. Immunol. 137, 680–689 (2016).

54 Stein, M.M. et al. Innate immunity and asthma risk in Amish and hutterite farm children. N. Engl. J. Med. 375, 411–421 (2016).

55 Cook, M.D. et al. Exercise and gut immune function: evidence of alterations in colon immune cell homeostasis and microbiome characteristics with exercise training. Immunol. Cell Biol. 94, 158–163 (2016).

56 Benedict, C. et al. Gut microbiota and glucometabolic alterations in response to recurrent partial sleep deprivation in normal-weight young individuals. Mol. Metab. 5, 1175–1186 (2016).

57 Karl, J.P. et al. Changes in intestinal microbiota composition and metabolism coincide with increased intestinal permeability in young adults under prolonged physiological stress. Am. J. Physiol. Gastrointest. Liver Physiol. 312, G559–G571 (2017).

58 Ying, S. et al. The influence of age and gender on skin-associated microbial communities in urban and rural human populations. PLoS One 10, e0141842 (2015).

59 Zheng, W. et al. Metagenomic sequencing reveals altered metabolic pathways in the oral microbiota of sailors during a long sea voyage. Sci. Rep. 5, 9131 (2015).

60 Zozaya, M. et al. Bacterial communities in penile skin, male urethra, and vaginas of heterosexual couples with and without bacterial vaginosis. Microbiome 4, 16 (2016).

61 Fei, N. & Zhao, L. An opportunistic pathogen isolated from the gut of an obese human causes obesity in germfree mice. ISME J. 7, 880–884 (2013).

62 Leone, V. et al. Effects of diurnal variation of gut microbes and high-fat feeding on host circadian clock function and metabolism. Cell Host Microbe 17, 681–689 (2015).

63 Knight, R. et al. Unlocking the potential of metagenomics through replicated experimental design. Nat. Biotechnol. 30, 513–520 (2012).

64 Fierer, N. et al. Forensic identification using skin bacterial communities. Proc. Natl. Acad. Sci. USA 107, 6477–6481 (2010).

65 Flores, G.E. et al. Temporal variability is a personalized feature of the human microbiome. Genome Biol. 15, 531 (2014).

66 Gajer, P. et al. Temporal dynamics of the human vaginal microbiota. Sci. Transl. Med. 4, 132ra52 (2012).

67 Livanos, A.E. et al. Antibiotic-mediated gut microbiome perturbation accelerates development of type 1 diabetes in mice. Nat. Microbiol. 1, 16140 (2016).

68 Sugihara, G. et al. Detecting causality in complex ecosystems. Science 338, 496–500 (2012).

69 Knights, D. et al. Bayesian community-wide culture-independent microbial source tracking. Nat. Methods 8, 761–763 (2011).

70 Larsen, P.E., Field, D. & Gilbert, J.A. Predicting bacterial community assemblages using an artificial neural network approach. Nat. Methods 9, 621–625 (2012).

71 Larsen, P.E. & Dai, Y. Metabolome of human gut microbiome is predictive of host dysbiosis. Gigascience 4, 42 (2015).

72 Browne, H.P. et al. Culturing of 'unculturable' human microbiota reveals novel taxa and extensive sporulation. Nature 533, 543–546 (2016).

73 Geva-Zatorsky, N. et al. Mining the human gut microbiota for immunomodulatory organisms. Cell 168, 928–943. e11 (2017).

74 Vatanen, T. et al. Variation in microbiome LPS immunogenicity contributes to autoimmunity in humans. Cell 165, 842–853 (2016).

75 Sivan, A. et al. Commensal Bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy. Science 350, 1084–1089 (2015).

76 Dubin, K. et al. Intestinal microbiome analyses identify melanoma patients at risk for checkpoint-blockade-induced colitis. Nat. Commun. 7, 10391 (2016).

77 Mueller, N.T. et al. Does vaginal delivery mitigate or strengthen the intergenerational association of overweight and obesity? Findings from the Boston Birth Cohort. Int. J. Obes. (Lond). 41, 497–501 (2017).

78 Raveh-Sadka, T. et al. Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development. eLife 4, 4 (2015).

79 Zhang, X. et al. The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment. Nat. Med. 21, 895–905 (2015).

80 Sinha, R. et al. Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium. Nat. Biotechnol. 35, 1077–1086 (2017).

81 Costea, P.I. et al. Towards standards for human fecal sample processing in metagenomic studies. Nat. Biotechnol. 35, 1069–1076 (2017).

82 Alivisatos, A.P. et al. MICROBIOME. A unified initiative to harness Earth's microbiomes. Science 350, 507–508 (2015).

83 Biteen, J.S. et al. Tools for the microbiome: nano and beyond. ACS Nano 10, 6–37 (2016).

84 Luckey, T.D. Introduction to intestinal microecology. Am. J. Clin. Nutr. 25, 1292–1294 (1972).

85 Rosner, J.L. Ten times more microbial cells than body cells in humans? Microbe 9, 47 (2014).

86 Reyes, A. et al. Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 466, 334–338 (2010).

87 Qin, J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59–65 (2010).

88 Weingarden, A. et al. Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection. Microbiome 3, 10 (2015).

89 Kassam, Z., Lee, C.H., Yuan, Y. & Hunt, R.H. Fecal microbiota transplantation for Clostridium difficile infection: systematic review and meta-analysis. Am. J. Gastroenterol. 108, 500–508 (2013).

90 Knights, D., Parfrey, L.W., Zaneveld, J., Lozupone, C. & Knight, R. Human-associated microbial signatures: examining their predictive value. Cell Host Microbe 10, 292–296 (2011).

91 Walters, W.A., Xu, Z. & Knight, R. Meta-analyses of human gut microbes associated with obesity and IBD. FEBS Lett. 588, 4223–4233 (2014).

92 Sze, M.A. & Schloss, P.D. Looking for a signal in the noise: revisiting obesity and the microbiome. MBio 7 (2016).

93 Sahin, M. & Sur, M. Genes, circuits, and precision therapies for autism and related neurodevelopmental disorders. Science 350, aab3897 (2015).

94 McDonald, D. et al. Towards large-cohort comparative studies to define the factors influencing the gut microbial community structure of ASD patients. Microb. Ecol. Health Dis. 26, 26555 (2015).

95 Kang, D.-W. et al. Reduced incidence of Prevotella and other fermenters in intestinal microflora of autistic children. PLoS One 8, e68322 (2013).

96 Hsiao, E.Y. et al. Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders. Cell 155, 1451–1463 (2013).

97 Kang, D.-W. et al. Microbiota transfer therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study. Microbiome 5, 10 (2017).

98 Snijders, A.M. et al. Influence of early life exposure, host genetics and diet on the mouse gut microbiome and metabolome. Nat. Microbiol. 2, 16221 (2016).

99 Knights, D. et al. Complex host genetics influence the microbiome in inflammatory bowel disease. Genome Med. 6, 107 (2014).

100 Halfvarson, J. et al. Dynamics of the human gut microbiome in inflammatory bowel disease. Nat. Microbiol. 2, 17004 (2017).

101 Uusitalo, U. et al. Association of early exposure of probiotics and islet autoimmunity in the TEDDY study. JAMA Pediatr. 170, 20–28 (2016).

102 Blaser, M.J. The theory of disappearing microbiota and the epidemics of chronic diseases. Nat. Rev. Immunol. 17, 461–463 (2017).

103 Arrieta, M.-C. et al. Early infancy microbial and metabolic alterations affect risk of childhood asthma. Sci. Transl. Med. 7, 307ra152 (2015).

104 Durack, J. et al. Delayed gut microbiota development in high-risk for asthma infants is temporarily modifiable by Lactobacillus supplementation. Nat. Commun. 9, 707 (2018).