The Microbiome and Human Biology

Annual Review of Genomics and Human Genetics

Volumn 18, Issue , 2017, Pages 65-86

  Knight, Rob ^a,b,c   Callewaert, Chris ^a,d   Marotz, Clarisse ^a   Hyde, Embriette R ^a   Debelius, Justine W ^a   McDonald, Daniel ^a   Sogin, Mitchell L ^e  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^d GHENT UNIVERSITY   (Belgium)

^e MARINE BIOLOGICAL LABORATORY   (United States)

Author keywords

DNA sequencing; Gut brain axis; Immunology; Metabolism; Metagenomics; Microbiome; Neuroscience

Indexed keywords

ANIMAL MODEL; ARTICLE; DNA SEQUENCE; HUMAN; HUMAN DEVELOPMENT; IMMUNE SYSTEM; METABOLOME; MICROBIAL COMMUNITY; MICROBIOME; NEXT GENERATION SEQUENCING; NONHUMAN; ANIMAL; GENETICS; METAGENOME; MICROFLORA;

ANIMALS; HUMANS; IMMUNE SYSTEM; METABOLOME; METAGENOME; MICROBIOTA; SEQUENCE ANALYSIS, DNA;

EID: 85028768566     PISSN: 15278204     EISSN: 1545293X     Source Type: Book Series    
DOI: 10.1146/annurev-genom-083115-022438     Document Type: Article

References (173)

1. Aagaard KM. 2014. Author response to comment on "The placenta harbors a unique microbiome. " Sci. Transl. Med. 6: 254lr3
2. Aagaard KM, Riehle K, Ma J, Segata N, Mistretta T-A, et al. 2012. A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy. PLOS ONE 7: e36466
3. Alekseyenko AV, Perez-Perez GI, De Souza A, Strober B, Gao Z, et al. 2013. Community differentiation of the cutaneous microbiota in psoriasis. Microbiome 1: 31
4. Altschul SF, GishW, MillerW, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403-10
5. Aminov RI. 2010. A brief history of the antibiotic era: lessons learned and challenges for the future. Front. Microbiol. 1: 134
6. Amir A, McDonald D, Navas-Molina JA, Kopylova E, Morton JT, et al. 2017. Deblur rapidly resolves single-nucleotide community sequence patterns. mSystems 2: e00191-16
7. Anderson MJ. 2001. A new method for non-parametric multivariate analysis of variance. Aust. Ecol. 26: 32-46
8. ArrietaM-C, Stiemsma LT, Dimitriu PA, Thorson L, Russell S, et al. 2015. Early infancy microbial and metabolic alterations affect risk of childhood asthma. Sci. Transl. Med. 7: 307ra152
9. Atarashi K, Tanoue T, Shima T, Imaoka A, Kuwahara T, et al. 2011. Induction of colonic regulatory T cells by indigenous Clostridium species. Science 331: 337-41
10. Azad MB, Bridgman SL, Becker AB, Kozyrskyj AL. 2014. Infant antibiotic exposure and the development of childhood overweight and central adiposity. Int. J. Obes. 38: 1290-98
11. Bäckhed F, Roswall J, Peng Y, Feng Q, Jia H, et al. 2015. Dynamics and stabilization of the human gut microbiome during the first year of life. Cell Host Microbe 17: 690-703
12. Bartlett JG, Gerding DN. 2008. Clinical recognition and diagnosis of Clostridium difficile infection. Clin. Infect. Dis. 46(Suppl. 1): S12-18
13. Baum BR. 1989. PHYLIP: Phylogeny Inference Package. Version 3. 2. Q. Rev. Biol. 64: 539-41
14. Benedict C, Vogel H, Jonas W, Woting A, Blaut M, et al. 2016. Gut microbiota and glucometabolic alterations in response to recurrent partial sleep deprivation in normal-weight young individuals. Mol. Metab. 5: 1175-86
15. Bergey DH, Brown CP, Etris S. 1939. Immunization against tetanus with alum-precipitated tetanus toxoid. Am. J. Public Health Nations Health 29: 334-36
16. Bessa LJ, Fazii P, Di Giulio M, Cellini L. 2015. Bacterial isolates from infected wounds and their antibiotic susceptibility pattern: some remarks about wound infection. Int. Wound J. 12: 47-52
17. Binladen J, Gilbert MTP, Bollback JP, Panitz F, Bendixen C, et al. 2007. The use of coded PCR primers enables high-throughput sequencing ofmultiple homolog amplification products by 454 parallel sequencing. PLOS ONE 2: e197
18. Bond PL, Hugenholtz P, Keller J, Blackall LL. 1995. Bacterial community structures of phosphateremoving and non-phosphate-removing activated sludges from sequencing batch reactors. Appl. Environ. Microbiol. 61: 1910-16
19. Bouslimani A, Porto C, Rath CM, Wang M, Guo Y, et al. 2015. Molecular cartography of the human skin surface in 3D. PNAS 112: E2120-19
20. Bray JR, Curtis JT. 1957. An ordination of the upland forest communities of southern Wisconsin. Ecol. Monogr. 27: 325-49
21. Brosius J, Palmer ML, Kennedy PJ, NollerHF. 1978. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. PNAS 75: 4801-5
22. Cabrera-Rubio R, Collado MC, Laitinen K, Salminen S, Isolauri E, Mira A. 2012. The human milk microbiome changes over lactation and is shaped by maternal weight and mode of delivery. Am. J. Clin. Nutr. 96: 544-51
23. Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. 2016. DADA2: highresolution sample inference from Illumina amplicon data. Nat. Methods 13: 581-83
24. Cambies. 1949. Parodontose et cure thermale. Rev. Odontol. 71: 447-52
25. Campbell SC, Wisniewski PJ. 2017. Exercise is a novel promoter of intestinal health and microbial diversity. Exerc. Sport Sci. Rev. 45: 41-47
26. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, et al. 2010. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7: 335-36
27. Charbonneau MR, O'Donnell D, Blanton LV, Totten SM, Davis JCC, et al. 2016. Sialylated milk oligosaccharides promote microbiota-dependent growth in models of infant undernutrition. Cell 164: 859-71
28. Chassaing B, Koren O, Goodrich JK, Poole AC, Srinivasan S, et al. 2015. Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome. Nature 519: 92-96
29. Clayton TA, Baker D, Lindon JC, Everett JR, Nicholson JK. 2009. Pharmacometabonomic identification of a significant host-microbiome metabolic interaction affecting human drug metabolism. PNAS 106: 14728-33
30. Coppa GV, Gabrielli O, Pierani P, Catassi C, Carlucci A, Giorgi PL. 1993. Changes in carbohydrate composition in human milk over 4 months of lactation. Pediatrics 91: 637-41
31. Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R. 2009. Bacterial community variation in human body habitats across space and time. Science 326: 1694-97
32. David LA, Materna AC, Friedman J, Campos-Baptista MI, Blackburn MC, et al. 2014. Host lifestyle affects human microbiota on daily timescales. Genome Biol. 15: R89
33. David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, et al. 2014. Diet rapidly and reproducibly alters the human gut microbiome. Nature 505: 559-63
34. Debelius J, Song SJ, Vazquez-Baeza Y, Xu ZZ, Gonzalez A, Knight R. 2016. Tiny microbes, enormous impacts: What matters in gut microbiome studies? Genome Biol. 17: 217
35. Dethlefsen L, Relman DA. 2011. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. PNAS 108(Suppl. ): 4554-61
36. Diaz Heijtz R, Wang S, Anuar F, Qian Y, Björkholm B, et al. 2011. Normal gut microbiota modulates brain development and behavior. PNAS 108: 3047-52
37. Ding HT, Taur Y, Walkup JT. 2017. Gut microbiota and autism: key concepts and findings. J. Autism Dev. Disord. 47: 480-89
38. Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, et al. 2010. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. PNAS 107: 11971-75
39. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, et al. 2005. Diversity of the human intestinal microbial flora. Science 308: 1635-38
40. Elwood HJ, Olsen GJ, Sogin ML. 1985. The small-subunit ribosomal RNA gene sequences from the hypotrichous ciliates Oxytricha nova and Stylonychia pustulata. Mol. Biol. Evol. 2: 399-410
41. Eren AM, Maignien L, SulWJ, Murphy LG, Grim SL, et al. 2013. Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data. Methods Ecol. Evol. 4: 1111-19
42. Eren AM, Morrison HG, Lescault PJ, Reveillaud J, Vineis JH, Sogin ML. 2015. Minimum entropy decomposition: unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences. ISME J. 9: 968-79
43. Fierer N, Lauber CL, Zhou N, McDonald D, Costello EK, Knight R. 2010. Forensic identification using skin bacterial communities. PNAS 107: 6477-81
44. Fitz-Gibbon S, Tomida S, Chiu B-H, Nguyen L, Du C, et al. 2013. Propionibacterium acnes strain populations in the human skin microbiome associated with acne. J. Investig. Dermatol. 133: 2152-60
45. Forslund K, Hildebrand F, Nielsen T, Falony G, Le Chatelier E, et al. 2015. Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nature 528: 262-66
46. Fouhy F, Guinane CM, Hussey S, Wall R, Ryan CA, et al. 2012. High-throughput sequencing reveals the incomplete, short-term recovery of infant gut microbiota following parenteral antibiotic treatment with ampicillin and gentamicin. Antimicrob. Agents Chemother. 56: 5811-20
47. Francino MP. 2015. Antibiotics and the human gut microbiome: dysbioses and accumulation of resistances. Front. Microbiol. 6: 1543
48. Franzosa EA, HuangK, Meadow JF, GeversD, Lemon KP, et al. 2015. Identifying personalmicrobiomes using metagenomic codes. PNAS 112: E2930-38
49. Fredricks DN, Fiedler TL, Marrazzo JM. 2005. Molecular identification of bacteria associated with bacterial vaginosis. N. Engl. J. Med. 353: 1899-911
50. Gao R, Gao Z, Huang L, Qin H. 2017. Gut microbiota and colorectal cancer. Eur. J. Clin. Microbiol. Infect. Dis. 36: 757-69
51. Gevers D, Kugathasan S, Denson LA, Vazquez-Baeza Y, Van Treuren W, et al. 2014. The treatmentnaive microbiome in new-onset Crohn's disease. Cell Host Microbe 15: 382-92
52. Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, et al. 2006. Metagenomic analysis of the human distal gut microbiome. Science 312: 1355-59
53. Girard C, Tromas N, Amyot M, Shapiro BJ. 2017. Gutmicrobiome of the Canadian Arctic Inuit. mSphere 2: e00297-16
54. Gonzalez A, Stombaugh J, Lauber CL, Fierer N, Knight R. 2012. SitePainter: a tool for exploring biogeographical patterns. Bioinformatics 28: 436-38
55. Goodrich JK, Waters JL, Poole AC, Sutter JL, Koren O, et al. 2014. Human genetics shape the gut microbiome. Cell 159: 789-99
56. Hamady M, Walker JJ, Harris JK, Gold NJ, Knight R. 2008. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat. Methods 5: 235-37
57. Harris RA, Shah R, Hollister EB, Tronstad RR, Hovdenak N, et al. 2016. Colonic mucosal epigenome and microbiome development in children and adolescents. J. Immunol. Res. 2016: 9170162
58. Hartmann P, Seebauer CT, Schnabl B. 2015. Alcoholic liver disease: the gut microbiome and liver cross talk. Alcohol. Clin. Exp. Res. 39: 763-75
59. Hernandez CJ, Guss JD, Luna M, Goldring SR. 2016. Links between the microbiome and bone. J. Bone Miner. Res. 31: 1638-46
60. Hillier SL, Nugent RP, Eschenbach DA, Krohn MA, Gibbs RS, et al. (Bact. Vaginosis Prematur. Study Group). 1995. Association between bacterial vaginosis and preterm delivery of a low-birth-weight infant. N. Engl. J. Med. 333: 1737-42
61. Hsiao EY, McBride SW, Hsien S, Sharon G, Hyde ER, et al. 2013. Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders. Cell 155: 1451-63
62. Huber JA, Mark Welch DB, Morrison HG, Huse SM, Neal PR, et al. 2007. Microbial population structures in the deep marine biosphere. Science 318: 97-100
63. Hum. Microbiome Proj. Consort. 2012. A framework for human microbiome research. Nature 486: 215-21
64. Hum. Microbiome Proj. Consort. 2012. Structure, function and diversity of the healthy human microbiome. Nature 486: 207-14
65. Huse SM, Huber JA, MorrisonHG, SoginML, Mark Welch DB. 2007. Accuracy and quality ofmassively parallel DNA pyrosequencing. Genome Biol. 8: R143
66. Huse SM, Mark Welch DB, Voorhis A, Shipunova A, Morrison HG, et al. 2014. VAMPS: a website for visualization and analysis of microbial population structures. BMC Bioinform. 15: 41
67. Hviid A, Svanstrom H, Frisch M. 2011. Antibiotic use and inflammatory bowel diseases in childhood. Gut 60: 49-54
68. Inan MS, Rasoulpour RJ, Yin L, Hubbard AK, Rosenberg DW, Giardina C. 2000. The luminal shortchain fatty acid butyratemodulates NF-activity in a human colonic epithelial cell line. Gastroenterology 118: 724-34
69. Jakobsson HE, Jernberg C, Andersson AF, Sjölund-KarlssonM, Jansson JK, Engstrand L. 2010. Shortterm antibiotic treatment has differing long-term impacts on the human throat and gut microbiome. PLOS ONE 5: e9836
70. Jangi S, Gandhi R, Cox LM, Li N, von Glehn F, et al. 2016. Alterations of the human gut microbiome in multiple sclerosis. Nat. Commun. 7: 12015
71. Jonsson AL, Bäckhed F. 2017. Role of gut microbiota in atherosclerosis. Nat. Rev. Cardiol. 14: 79-87
72. Kane AV, Dinh DM, Ward HD. 2015. Childhood malnutrition and the intestinal microbiome. Pediatr. Res. 77: 256-62
73. Kilkkinen A, Virtanen SM, Klaukka T, Kenward MG, Salkinoja-Salonen M, et al. 2006. Use of antimicrobials and risk of type 1 diabetes in a population-based mother-child cohort. Diabetologia 49: 66-70
74. Kiraly DD, Walker DM, Calipari ES, Labonte B, Issler O, et al. 2016. Alterations of the host microbiome affect behavioral responses to cocaine. Sci. Rep. 6: 35455
75. Kleiman SC, Watson HJ, Bulik-Sullivan EC, Huh EY, Tarantino LM, et al. 2015. The intestinal microbiota in acute anorexia nervosa and during renourishment: relationship to depression, anxiety, and eating disorder psychopathology. Psychosom. Med. 77: 969-81
76. Kliman HJ. 2014. Comment on "The placenta harbors a unique microbiome. " Sci. Transl. Med. 6: 254le4
77. Knights D, Lassen KG, Xavier RJ. 2013. Advances in inflammatory bowel disease pathogenesis: linking host genetics and the microbiome. Gut 62: 1505-10
78. Kobayashi T, Glatz M, Horiuchi K, Kawasaki H, Akiyama H, et al. 2015. Dysbiosis and Staphylococcus aureus colonization drives inflammation in atopic dermatitis. Immunity 42: 756-66
79. Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J, et al. 2011. Succession of microbial consortia in the developing infant gut microbiome. PNAS 108(Suppl. ): 4578-85
80. Koren O, Goodrich JK, Cullender TC, Spor A, Laitinen K, et al. 2012. Host remodeling of the gut microbiome and metabolic changes during pregnancy. Cell 150: 470-80
81. Kostic AD, Gevers D, Siljander H, Vatanen T, Hyötyläinen T, et al. 2015. The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes. Cell Host Microbe 17: 260-73
82. Kostic AD, Xavier RJ, Gevers D. 2014. The microbiome in inflammatory bowel disease: current status and the future ahead. Gastroenterology 146: 1489-99
83. Kuczynski J, Liu Z, Lozupone CA, McDonald D, Fierer N, Knight R. 2010. Microbial community resemblance methods differ in their ability to detect biologically relevant patterns. Nat. Methods 7: 813-19
84. Kutty N. 2011. Treating children without antibiotics in primary healthcare. Oman Med. J. 26: 303-5
85. Kwak M-J, Kwon S-K, Yoon J-K, Song JY, Seo J-G, et al. 2016. Evolutionary architecture of the infantadapted group of Bifidobacterium species associated with the probiotic function. Syst. Appl. Microbiol. 39: 429-39
86. Lane DJ, Pace B, Olsen GJ, Stahl DA, SoginML, Pace NR. 1985. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. PNAS 82: 6955-59
87. Lauder AP, Roche AM, Sherrill-Mix S, Bailey A, Laughlin AL, et al. 2016. Comparison of placenta samples with contamination controls does not provide evidence for a distinct placentamicrobiota. Microbiome 4: 29
88. Lax S, Smith DP, Hampton-Marcell J, Owens SM, Handley KM, et al. 2014. Longitudinal analysis of microbial interaction between humans and the indoor environment. Science 345: 1048-52
89. Ley RE, Hamady M, Lozupone CA, Turnbaugh PJ, Ramey RR, et al. 2008. Evolution of mammals and their gut microbes. Science 320: 1647-51
90. Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI. 2008. Worlds within worlds: evolution of the vertebrate gut microbiota. Nat. Rev. Microbiol. 6: 776-88
91. Li J, Jia H, Cai X, Zhong H, Feng Q, et al. 2014. An integrated catalog of reference genes in the human gut microbiome. Nat. Biotechnol. 32: 834-41
92. Liu Z, DeSantis TZ, Andersen GL, Knight R. 2008. Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers. Nucleic Acids Res. 36: e120
93. Liu Z, Lozupone CA, Hamady M, Bushman FD, Knight R. 2007. Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Res. 35: e120
94. Lowry CA, Smith DG, Siebler PH, Schmidt D, Stamper CE, et al. 2016. The microbiota, immunoregulation, and mental health: implications for public health. Curr. Environ. Heal. Rep. 3: 270-86
95. Lozupone CA, Knight R. 2005. UniFrac: a new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 71: 8228-35
96. Lozupone CA, Knight R. 2007. Global patterns in bacterial diversity. PNAS 104: 11436-40
97. Ludwig W, Strunk O, Westram R, Richter L, Meier H, et al. 2004. ARB: a software environment for sequence data. Nucleic Acids Res. 32: 1363-71
98. Lynch SV, Bruce KD. 2013. The cystic fibrosis airway microbiome. Cold Spring Harb. Perspect. Med. 3: a009738
99. MacIntyre DA, Chandiramani M, Lee YS, Kindinger L, Smith A, et al. 2015. The vaginal microbiome during pregnancy and the postpartum period in a European population. Sci. Rep. 5: 8988
100. Makrides M, Simmer K, Neumann M, Gibson R. 1995. Changes in the polyunsaturated fatty acids of breast milk from mothers of full-term infants over 30 wk of lactation. Am. J. Clin. Nutr. 61: 1231-33
101. MarguliesM, EgholmM, AltmanWE, Attiya S, Bader JS, et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-80
102. Maurice CF, Haiser HJ, Turnbaugh PJ. 2013. Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell 152: 39-50
103. Maxam AM, GilbertW. 1977. A new method for sequencing DNA. PNAS 74: 560-64
104. Mazmanian SK, Liu CH, Tzianabos AO, Kasper DL. 2005. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell 122: 107-18
105. McCaig AE, Glover LA, Prosser JI. 1999. Molecular analysis of bacterial community structure and diversity in unimproved and improved upland grass pastures. Appl. Environ. Microbiol. 65: 1721-30
106. McNulty NP, Yatsunenko T, Hsiao A, Faith JJ, Muegge BD, et al. 2011. The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins. Sci. Transl. Med. 3: 106ra106
107. Medlin L, Elwood HJ, Stickel S, Sogin ML. 1988. The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene 71: 491-99
108. Metcalf JL, Xu ZZ, Weiss S, Lax S, Van Treuren W, et al. 2016. Microbial community assembly and metabolic function during mammalian corpse decomposition. Science 351: 158-62
109. Metsälä J, Lundqvist A, Virta LJ, Kaila M, Gissler M, Virtanen SM. 2013. Mother's and offspring's use of antibiotics and infant allergy to cow's milk. Epidemiology 24: 303-9
110. Miller JB, Bull S, Miller J, McVeagh P. 1994. The oligosaccharide composition of human milk: temporal and individual variations in monosaccharide components. J. Pediatr. Gastroenterol. Nutr. 19: 371-76
111. Mimouna S, Gonçalvès D, Barnich N, Darfeuille-Michaud A, Hofman P, Vouret-Craviari V. 2011. Crohn disease-associated Escherichia coli promote gastrointestinal inflammatory disorders by activation of HIF-dependent responses. Gut Microbes 2: 335-46
112. Moeller AH, Caro-Quintero A, Mjungu D, Georgiev AV, Lonsdorf EV, et al. 2016. Cospeciation of gut microbiota with hominids. Science 353: 380-82
113. Moeller AH, Peeters M, Ndjango J-B, Li Y, Hahn BH, Ochman H. 2013. Sympatric chimpanzees and gorillas harbor convergent gut microbial communities. Genome Res. 23: 1715-20
114. Mohr JL. 1952. Protozoa as indicators of pollution. Sci. Mon. 74: 7-9
115. Morgan XC, Tickle TL, Sokol H, Gevers D, Devaney KL, et al. 2012. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol. 13: R79
116. Muegge BD, Kuczynski J, Knights D, Clemente JC, Gonzalez A, et al. 2011. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science 332: 970-74
117. Niehues H, Schalkwijk J, van Vlijmen-Willems IMJJ, Rodijk-Olthuis D, van Rossum MM, et al. 2017. Epidermal equivalents of filaggrin null keratinocytes do not show impaired skin barrier function. J. Allergy Clin. Immunol. 139: 1979-81. e13
118. Nobel YR, Cox LM, Kirigin FF, Bokulich NA, Yamanishi S, et al. 2015. Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment. Nat. Commun. 6: 7486
119. Ochman H, Worobey M, Kuo C-H, Ndjango J-BN, Peeters M, et al. 2010. Evolutionary relationships of wild hominids recapitulated by gut microbial communities. PLOS BIOL. 8: e1000546
120. Oliver A, Cantón R, CampoP, Baquero F, Blázquez J. 2000. High frequency of hypermutable Pseudomonas aeruginosa in cystic fibrosis lung infection. Science 288: 1251-54
121. Olm MR, Brown CT, Brooks B, Firek B, Baker R, et al. 2017. Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates. Genome Res. 27: 601-12
122. Olsen GJ, Overbeek R, Larsen N, Marsh TL, McCaughey MJ, et al. 1992. The ribosomal database project. Nucleic Acids Res. 20(Suppl. ): 2199-200
123. Pace B, Campbell LL. 1971. Homology of ribosomal ribonucleic acid diverse bacterial species with Escherichia coli and Bacillus stearothermophilus. J. Bacteriol. 107: 543-47
124. Pace NR. 1997. A molecular view of microbial diversity and the biosphere. Science 276: 734-40
125. Paun A, Yau C, Danska JS. 2017. The influence of the microbiome on type 1 diabetes. J. Immunol. 198: 590-95
126. Peterson SN, Snesrud E, Liu J, Ong AC, Kilian M, et al. 2013. The dental plaque microbiome in health and disease. PLOS ONE 8: e58487
127. Prince AL, Ma J, Kannan PS, Alvarez M, Gisslen T, et al. 2016. The placental membrane microbiome is altered among subjects with spontaneous preterm birth with and without chorioamnionitis. Am. J. Obstet. Gynecol. 214: 627. e1-16
128. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, et al. 2010. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464: 59-65
129. Quince C, Lanzen A, Curtis TP, Davenport RJ, Hall N, et al. 2009. Accurate determination ofmicrobial diversity from 454 pyrosequencing data. Nat. Methods 6: 639-41
130. Quinn RA, Lim YW, Maughan H, Conrad D, Rohwer F, Whiteson KL. 2014. Biogeochemical forces shape the composition and physiology of polymicrobial communities in the cystic fibrosis lung. mBio 5: e00956-13
131. Ravel J, Gajer P, Abdo Z, SchneiderGM, Koenig SS, et al. 2011. Vaginal microbiome of reproductive-age women. PNAS 108(Suppl. ): 4680-87
132. Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, et al. 2013. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science 341: 1241214
133. Romero R, Hassan SS, Gajer P, Tarca AL, Fadrosh DW, et al. 2014. The composition and stability of the vaginal microbiota of normal pregnant women is different from that of non-pregnant women. Microbiome 2: 4
134. Round JL, Mazmanian SK. 2009. The gut microbiota shapes intestinal immune responses during health and disease. Nat. Rev. Immunol. 9: 313-23
135. Sampson TR, Debelius JW, Thron T, Janssen S, Shastri GG, et al. 2016. Gutmicrobiota regulatemotor deficits and neuroinflammation in a model of Parkinson's disease. Cell 167: 1469-80. e12
136. Sanger F, Nicklen S, Coulson AR. 1977. DNA sequencing with chain-terminating inhibitors. PNAS 74: 5463-67
137. Schloss PD, Handelsman J. 2005. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl. Environ. Microbiol. 71: 1501-6
138. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, et al. 2009. Introducing mothur: opensource, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75: 7537-41
139. Seedorf H, Griffin NW, Ridaura VK, Reyes A, Cheng J, et al. 2014. Bacteria from diverse habitats colonize and compete in the mouse gut. Cell 159: 253-66
140. Sender R, Fuchs S, Milo R. 2016. Are we really vastly outnumbered? Revisiting the ratio of bacterial to host cells in humans. Cell 164: 337-40
141. Shulman JM, De Jager PL, Feany MB. 2011. Parkinson's disease: genetics and pathogenesis. Annu. Rev. Pathol. Mech. Dis. 6: 193-222
142. Simrén M, BarbaraG, FlintHJ, Spiegel BMR, Spiller RC, et al. 2013. Intestinal microbiota in functional bowel disorders: a Rome Foundation report. Gut 62: 159-76
143. Smith LM, Sanders JZ, Kaiser RJ, Hughes P, Dodd C, et al. 1986. Fluorescence detection in automated DNA sequence analysis. Nature 321: 674-79
144. SmithMI, Yatsunenko T, Manary MJ, Trehan I, Mkakosya R, et al. 2013. Gutmicrobiomes of Malawian twin pairs discordant for kwashiorkor. Science 339: 548-54
145. Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM, et al. 2006. Microbial diversity in the deep sea and the underexplored "rare biosphere. " PNAS 103: 12115-20
146. Sogin SJ, SoginML, Woese CR. 1971. Phylogenetic measurement in procaryotes by primary structural characterization. J. Mol. Evol. 1: 173-84
147. Song SJ, Lauber C, Costello EK, Lozupone CA, Humphrey G, et al. 2013. Cohabiting family members share microbiota with one another and with their dogs. eLife 2: e00458
148. Stanier RY, Van Niel CB. 1941. The main outlines of bacterial classification. J. Bacteriol. 42: 437-66
149. Steele JA, Countway PD, Xia L, Vigil PD, Beman JM, et al. 2011. Marine bacterial, archaeal and protistan association networks reveal ecological linkages. ISME J. 5: 1414-25
150. Stein MM, Hrusch CL, Gozdz J, Igartua C, Pivniouk V, et al. 2016. Innate immunity and asthma risk in Amish and Hutterite farm children. N. Engl. J. Med. 375: 411-21
151. Subramanian S, Huq S, Yatsunenko T, Haque R, Mahfuz M, et al. 2014. Persistent gut microbiota immaturity in malnourished Bangladeshi children. Nature 510: 417-21
152. Suez J, Korem T, Zeevi D, Zilberman-Schapira G, Thaiss CA, et al. 2014. Artificial sweeteners induce glucose intolerance by altering the gut microbiota. Nature 514: 181-86
153. Tang WHW, Hazen SL. 2014. The contributory role of gut microbiota in cardiovascular disease. J. Clin. Investig. 124: 4204-11
154. Thaiss CA, Zeevi D, Levy M, Zilberman-Schapira G, Suez J, et al. 2014. Transkingdom control of microbiota diurnal oscillations promotes metabolic homeostasis. Cell 159: 514-29
155. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, et al. 2009. A core gut microbiome in obese and lean twins. Nature 457: 480-84
156. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. 2007. The Human Microbiome Project. Nature 449: 804-10
157. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. 2006. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444: 1027-31
158. Wang X, Xu X, Xia Y. 2017. Further analysis reveals new gut microbiome markers of type 2 diabetes mellitus. Antonie van Leeuwenhoek 110: 445-53
159. Weingarden A, González A, Vázquez-Baeza Y, Weiss S, Humphry G, et al. 2015. Dynamic changes in short-and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection. Microbiome 3: 10
160. Woese CR. 1987. Bacterial evolution. Microbiol. Rev. 51: 221-71
161. Woese CR, Fox GE. 1977. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. PNAS 74: 5088-90
162. Woese CR, Kandler O, Wheelis ML. 1990. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. PNAS 87: 4576-79
163. Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, et al. 2011. Linking long-term dietary patterns with gut microbial enterotypes. Science 334: 105-8
164. Yang F, Zeng X, Ning K, Liu KL, Lo CC, et al. 2012. Saliva microbiomes distinguish caries-active from healthy human populations. ISME J. 6: 1-10
165. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W, et al. 2014. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat. Rev. Microbiol. 12: 635-45
166. Yassour M, Vatanen T, Siljander H, Hämäläinen A-M, Härkönen T, et al. 2016. Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability. Sci. Transl. Med. 8: 343ra81
167. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, et al. 2012. Human gut microbiome viewed across age and geography. Nature 486: 222-27
168. Zeevi D, Korem T, Zmora N, Israeli D, Rothschild D, et al. 2015. Personalized nutrition by prediction of glycemic responses. Cell 163: 1079-94
169. Zhang X, Zhang D, Jia H, Feng Q, Wang D, et al. 2015. The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment. Nat. Med. 21: 895-905
170. Zheng J, Xiao X, Zhang Q, Mao L, Yu M, Xu J. 2015. The placental microbiome varies in association with low birth weight in full-term neonates. Nutrients 7: 6924-37
171. Zheng P, Zeng B, Zhou C, Liu M, Fang Z, et al. 2016. Gut microbiome remodeling induces depressivelike behaviors through a pathway mediated by the host's metabolism. Mol. Psychiatry 21: 786-96
172. ZozayaM, FerrisMJ, Siren JD, Lillis R, Myers L, et al. 2016. Bacterial communities in penile skin, male urethra, and vaginas of heterosexual couples with and without bacterial vaginosis. Microbiome 4: 16
173. Zuckerkandl E, Pauling L. 1965. Molecules as documents of evolutionary history. J. Theor. Biol. 8: 357-66