1932

Abstract

Although antibiotics have significantly improved human health and life expectancy, their disruption of the existing microbiota has been linked to significant side effects such as antibiotic-associated diarrhea, pseudomembranous colitis, and increased susceptibility to subsequent disease. By using antibiotics to break colonization resistance against , , and species, researchers are now exploring mechanisms for microbiota-mediated modulation against pathogenic infection, revealing potential roles for different phyla and family members as well as microbiota-liberated sugars, hormones, and short-chain fatty acids in regulating pathogenicity. Furthermore, connections are now being made between microbiota dysbiosis and a variety of different diseases such as rheumatoid arthritis, inflammatory bowel disease, type 1 diabetes, atopy, and obesity. Future advances in the rapidly developing field of microbial bioinformatics will enable researchers to further characterize the mechanisms of microbiota modulation of disease and potentially identify novel therapeutics against disease.

Loading

Article metrics loading...

/content/journals/10.1146/annurev-micro-091313-103456
2014-09-08
2024-04-12
Loading full text...

Full text loading...

/deliver/fulltext/micro/68/1/annurev-micro-091313-103456.html?itemId=/content/journals/10.1146/annurev-micro-091313-103456&mimeType=html&fmt=ahah

Literature Cited

  1. Adler JL, Anderson RL, Boring JR, Nahmias AJ. 1.  1970. A protracted hospital-associated outbreak of salmonellosis due to a multiple-antibiotic-resistant strain of Salmonella indiana. J. Pediatr. 77:6970–75 [Google Scholar]
  2. Angelakis E, Armougom F, Million M, Raoult D. 2.  2012. The relationship between gut microbiota and weight gain in humans. Future Microbiol. 7:191–109 [Google Scholar]
  3. Antunes LCM, Finlay BB. 3.  2011. A comparative analysis of the effect of antibiotic treatment and enteric infection on intestinal homeostasis. Gut Microbes 2:2105–8 [Google Scholar]
  4. Armougom F, Henry M, Vialettes B, Raccah D, Raoult D. 4.  2009. Monitoring bacterial community of human gut microbiota reveals an increase in Lactobacillus in obese patients and methanogens in anorexic patients. PLoS ONE 4:9e7125 [Google Scholar]
  5. Arnold IC, Dehzad N, Reuter S, Martin H, Becher B. 5.  et al. 2011. Helicobacter pylori infection prevents allergic asthma in mouse models through the induction of regulatory T cells. J. Clin. Investig. 121:83088–93 [Google Scholar]
  6. Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T. 6.  et al. 2011. Enterotypes of the human gut microbiome. Nature 473:7346174–80 [Google Scholar]
  7. Atarashi K, Tanoue T, Shima T, Imaoka A, Kuwahara T. 7.  et al. 2011. Induction of colonic regulatory T cells by indigenous Clostridium species. Science 331:6015337–41 [Google Scholar]
  8. Balamurugan R, George G, Kabeerdoss J, Hepsiba J. 8.  Chandragunasekaran AMS, Ramakrishna BS. 2010. Quantitative differences in intestinal Faecalibacterium prausnitzii in obese Indian children. Br. J. Nutr. 103:3335–38 [Google Scholar]
  9. Beaugerie L, Flahault A, Barbut F, Atlan P, Lalande V. 9.  et al. 2003. Antibiotic-associated diarrhoea and Clostridium difficile in the community. Aliment. Pharmacol. Ther. 17:7905–12 [Google Scholar]
  10. Bergstrom KSB, Kissoon-Singh V, Gibson DL, Ma C, Montero M. 10.  et al. 2010. Muc2 protects against lethal infectious colitis by disassociating pathogenic and commensal bacteria from the colonic mucosa. PLoS Pathog. 6:5e1000902 [Google Scholar]
  11. Bik EM, Long CD, Armitage GC, Loomer P, Emerson J. 11.  et al. 2010. Bacterial diversity in the oral cavity of 10 healthy individuals. ISME J. 4:8962–74 [Google Scholar]
  12. Bjorksten B, Sepp E, Julge K, Voor T, Mikelsaar M. 12.  2001. Allergy development and the intestinal microflora during the first year of life. J. Allergy Clin. Immunol. 108:4516–20 [Google Scholar]
  13. Bohnhoff M, Miller CP, Martin WR. 13.  1964. Resistance of the mouse's intestinal tract to experimental salmonella infection. I. Factors which interfere with the initiation of infection by oral inoculation. J. Exp. Med. 120:805–16 [Google Scholar]
  14. Booijink CCGM, El-Aidy S, Rajilić-Stojanović M, Heilig HGHJ, Troost FJ. 14.  et al. 2010. High temporal and inter-individual variation detected in the human ileal microbiota. Environ. Microbiol. 12:123213–27 [Google Scholar]
  15. Bornside GH, Cohn I. 15.  1965. The normal microbial flora: comparative bacterial flora of animals and man. Am. J. Dig. Dis. 10:10844–52 [Google Scholar]
  16. Brinig MM, Lepp PW, Ouverney CC, Armitage GC, Relman DA. 16.  2003. Prevalence of bacteria of division TM7 in human subgingival plaque and their association with disease. Appl. Environ. Microbiol. 69:31687–94 [Google Scholar]
  17. Brugman S, Klatter FA, Visser JTJ, Wildeboer-Veloo ACM, Harmsen HJM. 17.  et al. 2006. Antibiotic treatment partially protects against type 1 diabetes in the Bio-Breeding diabetes-prone rat: Is the gut flora involved in the development of type 1 diabetes?. Diabetologia 49:92105–8 [Google Scholar]
  18. Burger-van Paassen N, Vincent A, Puiman PJ, van der Sluis M, Bouma J. 18.  et al. 2009. The regulation of intestinal mucin MUC2 expression by short-chain fatty acids: implications for epithelial protection. Biochem. J. 420:2211–19 [Google Scholar]
  19. Chen T, Yu W-H, Izard J, Baranova OV, Lakshmanan A, Dewhirst FE. 19.  2010. The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information. Database: J. Biol. Databases Curation. 2010:baq013 [Google Scholar]
  20. Chen X, Katchar K, Goldsmith JD, Nanthakumar N, Cheknis A. 20.  et al. 2008. A mouse model of Clostridium difficile–associated disease. Gastroenterology 135:61984–92 [Google Scholar]
  21. Chung H, Pamp SJ, Hill JA, Surana NK, Edelman SM. 21.  et al. 2012. Gut immune maturation depends on colonization with a host-specific microbiota. Cell 149:71578–93 [Google Scholar]
  22. Corthier G, Muller MC, Elmer GW, Lucas F, Dubos-Ramare F. 22.  1989. Interrelationships between digestive proteolytic activities and production and quantitation of toxins in pseudomembranous colitis induced by Clostridium difficile in gnotobiotic mice. Infect. Immun. 57:123922–27 [Google Scholar]
  23. Dabbagh K, Dahl ME, Stepick-Biek P, Lewis DB. 23.  2002. Toll-like receptor 4 is required for optimal development of Th2 immune responses: role of dendritic cells. J. Immunol. 168:94524–30 [Google Scholar]
  24. Danilowicz D, Posnock E, Chase R, Spencer FC. 24.  1974. Salmonella septicemia after open heart surgery in an asymptomatic carrier. Am. J. Cardiol. 34:7864–67 [Google Scholar]
  25. De La Cochetière MF, Durand T, Lepage P, Bourreille A, Galmiche JP, Doré J. 25.  2005. Resilience of the dominant human fecal microbiota upon short-course antibiotic challenge. J. Clin. Microbiol. 43:115588–92 [Google Scholar]
  26. Dethlefsen L, Huse S, Sogin ML, Relman DA. 26.  2008. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol. 6:e280 [Google Scholar]
  27. Dethlefsen L, Relman DA. 27.  2011. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc. Natl. Acad. Sci. USA 108:Suppl. 14554–61 [Google Scholar]
  28. Dewhirst FE, Chen T, Izard J, Paster BJ, Tanner AC. 28.  et al. 2010. The human oral microbiome. J. Bacteriol. 192:195002–17 [Google Scholar]
  29. Dharmani P, Srivastava V, Kissoon-Singh V, Chadee K. 29.  2009. Role of intestinal mucins in innate host defense mechanisms against pathogens. J. Innate Immun. 1:2123–35 [Google Scholar]
  30. Di Caprio JM, Rantz LA. 30.  1950. Effects of terramycin on the bacterial flora of the bowel in man. AMA Arch. Intern. Med. 86:5649–57 [Google Scholar]
  31. Donskey CJ, Hujer AM, Das SM, Pultz NJ, Bonomo RA, Rice LB. 31.  2003. Use of denaturing gradient gel electrophoresis for analysis of the stool microbiota of hospitalized patients. J. Microbiol. Methods 54:2249–56 [Google Scholar]
  32. Douce G, Goulding D. 32.  2010. Refinement of the hamster model of Clostridium difficile disease. Methods Mol. Biol. 646:Chapter 14215–27 [Google Scholar]
  33. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L. 33.  et al. 2005. Diversity of the human intestinal microbial flora. Science 308:57281635–38 [Google Scholar]
  34. Elli M, Colombo O, Tagliabue A. 34.  2010. A common core microbiota between obese individuals and their lean relatives? Evaluation of the predisposition to obesity on the basis of the fecal microflora profile. Med. Hypotheses 75:4350–52 [Google Scholar]
  35. Evans DF, Pye G, Bramley R, Clark AG, Dyson TJ, Hardcastle JD. 35.  1988. Measurement of gastrointestinal pH profiles in normal ambulant human subjects. Gut 29:81035–41 [Google Scholar]
  36. Fallani M, Young D, Scott J, Norin E, Amarri S. 36.  et al. 2010. Intestinal microbiota of 6-week-old infants across Europe: geographic influence beyond delivery mode, breast-feeding, and antibiotics. J. Pediatr. Gastroenterol. Nutr. 51:177–84 [Google Scholar]
  37. Fanning S, Hall LJ, Cronin M, Zomer A, MacSharry J. 37.  et al. 2012. Bifidobacterial surface-exopolysaccharide facilitates commensal-host interaction through immune modulation and pathogen protection. Proc. Natl. Acad. Sci. USA 109:62108–13 [Google Scholar]
  38. Ferreira RBR, Gill N, Willing BP, Antunes LCM, Russell SL. 38.  et al. 2011. The intestinal microbiota plays a role in Salmonella-induced colitis independent of pathogen colonization. PLoS ONE 6:5e20338 [Google Scholar]
  39. Frank DN, St Amand AL, Feldman RA, Boedeker EC, Harpaz N, Pace NR. 39.  2007. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc. Natl. Acad. Sci. USA 104:3413780–85 [Google Scholar]
  40. Garrett WS, Gallini CA, Yatsunenko T, Michaud M, DuBois A. 40.  et al. 2010. Enterobacteriaceae act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis. Cell Host Microbe 8:3292–300 [Google Scholar]
  41. Ghosh S, Dai C, Brown K, Rajendiran E, Makarenko S. 41.  et al. 2011. Colonic microbiota alters host susceptibility to infectious colitis by modulating inflammation, redox status, and ion transporter gene expression. Am. J. Physiol. Gastrointest. Liver Physiol. 301:1G39–49 [Google Scholar]
  42. Giongo A, Gano KA, Crabb DB, Mukherjee N, Novelo LL. 42.  et al. 2011. Toward defining the autoimmune microbiome for type 1 diabetes. ISME J. 5:182–91 [Google Scholar]
  43. Gronlund MM, Lehtonen OP, Eerola E, Kero P. 43.  1999. Fecal microflora in healthy infants born by different methods of delivery: permanent changes in intestinal flora after cesarean delivery. J. Pediatr. Gastroenterol. Nutr. 28:119–25 [Google Scholar]
  44. Gu S, Chen D, Zhang J-N, Lv X, Wang K. 44.  et al. 2013. Bacterial community mapping of the mouse gastrointestinal tract. PLoS ONE 8:10e74957 [Google Scholar]
  45. Hall IC, O’Toole E. 45.  1935. Intestinal flora in new-born infants: with a description of a new pathogenic anaerobe, Bacillus difficilis. Arch. Pediatr. Adolesc. Med. 49:390–402 [Google Scholar]
  46. Hara N, Alkanani AK, Ir D, Robertson CE, Wagner BD. 46.  et al. 2012. Prevention of virus-induced type 1 diabetes with antibiotic therapy. J. Immunol. 189:83805–14 [Google Scholar]
  47. Hayes GW, Keating CL, Newman JS. 47.  1993. The golden anniversary of the silver bullet. JAMA 270:131610–11 [Google Scholar]
  48. Herbst T, Sichelstiel A, Schär C, Yadava K, Bürki K. 48.  et al. 2011. Dysregulation of allergic airway inflammation in the absence of microbial colonization. Am. J. Respir. Crit. Care Med. 184:2198–205 [Google Scholar]
  49. Hill DA, Siracusa MC, Abt MC, Kim BS, Kobuley D. 49.  et al. 2012. Commensal bacteria-derived signals regulate basophil hematopoiesis and allergic inflammation. Nat. Med. 18:4538–46 [Google Scholar]
  50. Hugenholtz P, Tyson GW, Webb RI, Wagner AM, Blackall LL. 50.  2001. Investigation of candidate division TM7, a recently recognized major lineage of the domain Bacteria with no known pure-culture representatives. Appl. Environ. Microbiol. 67:1411–19 [Google Scholar]
  51. 51. Human Microbiome Project Consortium 2012. A framework for human microbiome research. Nature 486:7402215–21 [Google Scholar]
  52. 52. Human Microbiome Project Consortium 2012. Structure, function and diversity of the healthy human microbiome. Nature 486:7402207–14 [Google Scholar]
  53. Hunt JRF, Martinelli R, Adams VC, Rook GAW, Brunet LR. 53.  2005. Intragastric administration of Mycobacterium vaccae inhibits severe pulmonary allergic inflammation in a mouse model. Clin. Exp. Allergy 35:5685–90 [Google Scholar]
  54. Ivanov II, Atarashi K, Manel N, Brodie EL, Shima T. 54.  et al. 2009. Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell 139:3485–98 [Google Scholar]
  55. Jansson J, Willing B, Lucio M, Fekete A, Dicksved J. 55.  et al. 2009. Metabolomics reveals metabolic biomarkers of Crohn's disease. PLoS ONE 4:7e6386 [Google Scholar]
  56. Jernberg C, Löfmark S, Edlund C, Jansson JK. 56.  2007. Long-term ecological impacts of antibiotic administration on the human intestinal microbiota. ISME J. 1:156–66 [Google Scholar]
  57. Johansson MEV, Larsson JMH, Hansson GC. 57.  2011. The two mucus layers of colon are organized by the MUC2 mucin, whereas the outer layer is a legislator of host-microbial interactions. Proc. Natl. Acad. Sci. USA 108:Suppl. 14659–65 [Google Scholar]
  58. Kalliomäki M, Kirjavainen P, Eerola E, Kero P, Salminen S, Isolauri E. 58.  2001. Distinct patterns of neonatal gut microflora in infants in whom atopy was and was not developing. J. Allergy Clin. Immunol. 107:1129–34 [Google Scholar]
  59. Kamada N, Kim Y-G, Sham HP, Vallance BA, Puente JL. 59.  et al. 2012. Regulated virulence controls the ability of a pathogen to compete with the gut microbiota. Science 336:60861325–29 [Google Scholar]
  60. Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M. 60.  2010. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res. 38:Suppl. 1D355–60 [Google Scholar]
  61. Kang S, Denman SE, Morrison M, Yu Z, Doré J. 61.  et al. 2010. Dysbiosis of fecal microbiota in Crohn's disease patients as revealed by a custom phylogenetic microarray. Inflamm. Bowel Dis. 16:122034–42 [Google Scholar]
  62. Kelly CP, Pothoulakis C, LaMont JT. 62.  1994. Clostridium difficile colitis. N. Engl. J. Med. 330:4257–62 [Google Scholar]
  63. Kline KA, Fälker S, Dahlberg S, Normark S, Henriques-Normark B. 63.  2009. Bacterial adhesins in host-microbe interactions. Cell Host Microbe 5:6580–92 [Google Scholar]
  64. Kovatcheva-Datchary P, Zoetendal EG, Venema K, de Vos WM, Smidt H. 64.  2009. Tools for the tract: understanding the functionality of the gastrointestinal tract. Ther. Adv. Gastroenterol. 2:49–22 [Google Scholar]
  65. Kwon J-W, Kim B-J, Song Y, Seo J-H, Kim T-H. 65.  et al. 2011. Changes in the prevalence of childhood asthma in Seoul from 1995 to 2008 and its risk factors. Allergy Asthma Immunol. Res. 3:127–33 [Google Scholar]
  66. Lane JA, Murray LJ, Harvey IM, Donovan JL, Nair P, Harvey RF. 66.  2011. Randomised clinical trial: Helicobacter pylori eradication is associated with a significantly increased body mass index in a placebo-controlled study. Aliment. Pharmacol. Ther. 33:8922–29 [Google Scholar]
  67. Lepage P, Häsler R, Spehlmann ME, Rehman A, Zvirbliene A. 67.  et al. 2011. Twin study indicates loss of interaction between microbiota and mucosa of patients with ulcerative colitis. Gastroenterology 141:1227–36 [Google Scholar]
  68. Levy J. 68.  2000. The effects of antibiotic use on gastrointestinal function. Am. J. Gastroenterol. 95:Suppl. 1S8–10 [Google Scholar]
  69. Ley RE, Bäckhed F, Turnbaugh P, Lozupone CA, Knight RD, Gordon JI. 69.  2005. Obesity alters gut microbial ecology. Proc. Natl. Acad. Sci. USA 102:3111070–75 [Google Scholar]
  70. Ley RE, Peterson DA, Gordon JI. 70.  2006. Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 124:4837–48 [Google Scholar]
  71. Liévin V, Peiffer I, Hudault S, Rochat F, Brassart D. 71.  et al. 2000. Bifidobacterium strains from resident infant human gastrointestinal microflora exert antimicrobial activity. Gut 47:5646–52 [Google Scholar]
  72. Linsell WD, Fletcher AP. 72.  1950. Laboratory and clinical experience with terramycin hydrochloride. Br. Med. J. 2:46901190–95 [Google Scholar]
  73. Lupp C, Robertson ML, Wickham ME, Sekirov I, Champion OL. 73.  et al. 2007. Host-mediated inflammation disrupts the intestinal microbiota and promotes the overgrowth of Enterobacteriaceae. Cell Host Microbe 2:2119–29 [Google Scholar]
  74. Mai X-M, Kull I, Wickman M, Bergstrom A. 74.  2010. Antibiotic use in early life and development of allergic diseases: respiratory infection as the explanation. Clin. Exp. Allergy 40:81230–37 [Google Scholar]
  75. Manichanh C, Rigottier-Gois L, Bonnaud E, Gloux K, Pelletier E. 75.  et al. 2006. Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach. Gut 55:2205–11 [Google Scholar]
  76. Martens EC, Roth R, Heuser JE, Gordon JI. 76.  2009. Coordinate regulation of glycan degradation and polysaccharide capsule biosynthesis by a prominent human gut symbiont. J. Biol. Chem. 284:2718445–57 [Google Scholar]
  77. Martinez-Martinez RE, Abud-Mendoza C, Patiño-Marin N, Rizo-Rodríguez JC, Little JW, Loyola-Rodríguez JP. 77.  2009. Detection of periodontal bacterial DNA in serum and synovial fluid in refractory rheumatoid arthritis patients. J. Clin. Periodontol. 36:121004–10 [Google Scholar]
  78. Mazmanian SK, Liu CH, Tzianabos AO, Kasper DL. 78.  2005. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell 122:1107–18 [Google Scholar]
  79. Mazmanian SK, Round JL, Kasper DL. 79.  2008. A microbial symbiosis factor prevents intestinal inflammatory disease. Nature 453:620–25 [Google Scholar]
  80. McCall CE, Sanders WE, Boring JR, Brachman PS, Wikingsson M. 80.  1964. Delineation of chronic carriers of Salmonella derby within an institution for incurables. Antimicrob. Agents Chemother. 10:717–21 [Google Scholar]
  81. McFarland LV. 81.  2008. Update on the changing epidemiology of Clostridium difficile-associated disease. Nat. Clin. Pract. Gastroenterol. Hepatol. 5:140–48 [Google Scholar]
  82. McFarland LV, Mulligan ME, Kwok RY, Stamm WE. 82.  1989. Nosocomial acquisition of Clostridium difficile infection. N. Engl. J. Med. 320:4204–10 [Google Scholar]
  83. Mentula S, Harmoinen J, Heikkila M, Westermarck E, Rautio M. 83.  et al. 2005. Comparison between cultured small-intestinal and fecal microbiotas in beagle dogs. Appl. Environ. Microbiol. 71:84169–75 [Google Scholar]
  84. Million M, Angelakis E, Paul M, Armougom F, Leibovici L, Raoult D. 84.  2012. Comparative meta-analysis of the effect of Lactobacillus species on weight gain in humans and animals. Microb. Pathog. 53:2100–8 [Google Scholar]
  85. Moore PR, Evenson A. 85.  1946. Use of sulfasuxidine, streptothricin, and streptomycin in nutritional studies with the chick. J. Biol. Chem. 165:2437–41 [Google Scholar]
  86. Most H, Miller JW, Grossman EJ. 86.  1950. Treatment of amebiasis with bacitracin and other antibiotics. Am. J. Trop. Med. Hyg. 30:4491–97 [Google Scholar]
  87. Ng KM, Ferreyra JA, Higginbottom SK, Lynch JB, Kashyap PC. 87.  et al. 2013. Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens. Nature 502:746996–99 [Google Scholar]
  88. NIH HMP Working Group, Peterson J, Garges S, Giovanni M, McInnes P. 88.  et al. 2009. The NIH Human Microbiome Project. Genome Res. 19:122317–23 [Google Scholar]
  89. Nord CE. 89.  1993. The effect of antimicrobial agents on the ecology of the human intestinal microflora. Vet. Microbiol. 35:3–4193–97 [Google Scholar]
  90. O’Hara AM, Shanahan F. 90.  2006. The gut flora as a forgotten organ. EMBO Rep. 7:7688–93 [Google Scholar]
  91. Olszak T, An D, Zeissig S, Vera MP, Richter J. 91.  et al. 2012. Microbial exposure during early life has persistent effects on natural killer T cell function. Science 336:6080489–93 [Google Scholar]
  92. Penders J, Thijs C, Vink C, Stelma FF, Snijders B. 92.  et al. 2006. Factors influencing the composition of the intestinal microbiota in early infancy. Pediatrics 118:2511–21 [Google Scholar]
  93. Pirzada OM, McGaw J, Taylor CJ, Everard ML. 93.  2003. Improved lung function and body mass index associated with long-term use of Macrolide antibiotics. J. Cystic Fibrosis 2:269–71 [Google Scholar]
  94. Pothoulakis C, LaMont JT. 94.  1993. Clostridium difficile colitis and diarrhea. Gastroenterol. Clin. N. Am. 22:3623–37 [Google Scholar]
  95. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS. 95.  et al. 2010. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:728559–65 [Google Scholar]
  96. Rakoff-Nahoum S, Paglino J, Eslami-Varzaneh F, Edberg S, Medzhitov R. 96.  2004. Recognition of commensal microflora by Toll-like receptors is required for intestinal homeostasis. Cell 118:2229–41 [Google Scholar]
  97. Risnes KR, Belanger K, Murk W, Bracken MB. 97.  2011. Antibiotic exposure by 6 months and asthma and allergy at 6 years: findings in a cohort of 1,401 US children. Am. J. Epidemiol. 173:3310–18 [Google Scholar]
  98. Roesch LFW, Lorca GL, Casella G, Giongo A, Naranjo A. 98.  et al. 2009. Culture-independent identification of gut bacteria correlated with the onset of diabetes in a rat model. ISME J. 3:5536–48 [Google Scholar]
  99. Rosenthal SL. 99.  1969. Exacerbation of Salmonella enteritis due to ampicillin. N. Engl. J. Med. 280:3147–48 [Google Scholar]
  100. Russell SL, Gold MJ, Hartmann M, Willing BP, Thorson L. 100.  et al. 2012. Early life antibiotic-driven changes in microbiota enhance susceptibility to allergic asthma. EMBO Rep. 13:5440–47 [Google Scholar]
  101. Russell SL, Gold MJ, Willing BP, Thorson L, McNagny KM, Finlay BB. 101.  2013. Perinatal antibiotic treatment affects murine microbiota, immune responses and allergic asthma. Gut Microbes 4:2158–64 [Google Scholar]
  102. Ruutu M, Thomas G, Steck R, Degli-Esposti MA, Zinkernagel MS. 102.  et al. 2012. β-glucan triggers spondylarthritis and Crohn's disease–like ileitis in SKG mice. Arthritis Rheum. 64:72211–22 [Google Scholar]
  103. Saiman L, Marshall BC, Mayer-Hamblett N, Burns JL, Quittner AL. 103.  et al. 2003. Azithromycin in patients with cystic fibrosis chronically infected with Pseudomonas aeruginosa: a randomized controlled trial. JAMA 290:131749–56 [Google Scholar]
  104. Salman S, Rogerson SJ, Kose K, Griffin S, Gomorai S. 104.  et al. 2010. Pharmacokinetic properties of azithromycin in pregnancy. Antimicrob. Agents Chemother. 54:1360–66 [Google Scholar]
  105. Saroglou G, Bisno AL. 105.  1978. Salmonella bacteremia and gastroenteritis after oral ampicillin therapy for gonorrhea. South. Med. J. 71:8964–65 [Google Scholar]
  106. Scher JU, Sczesnak A, Longman RS, Segata N, Ubeda C. 106.  et al. 2013. Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis. eLife 2:e01202 [Google Scholar]
  107. Schneeman BO. 107.  2002. Gastrointestinal physiology and functions. Br. J. Nutr. 88:Suppl. 2S159–63 [Google Scholar]
  108. Sekirov I, Tam NM, Jogova M, Robertson ML, Li Y. 108.  et al. 2008. Antibiotic-induced perturbations of the intestinal microbiota alter host susceptibility to enteric infection. Infect. Immun. 76:104726–36 [Google Scholar]
  109. Shim JK, Johnson S, Samore MH, Bliss DZ, Gerding DN. 109.  1998. Primary symptomless colonisation by Clostridium difficile and decreased risk of subsequent diarrhoea. Lancet 351:9103633–36 [Google Scholar]
  110. Sokol H, Pigneur B, Watterlot L, Lakhdari O, Bermúdez-Humarán LG. 110.  et al. 2008. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc. Natl. Acad. Sci. USA 105:4316731–36 [Google Scholar]
  111. Sokol H, Seksik P, Furet JP, Firmesse O, Nion-Larmurier I. 111.  et al. 2009. Low counts of Faecalibacterium prausnitzii in colitis microbiota. Inflamm. Bowel Dis. 15:81183–89 [Google Scholar]
  112. Sommer F, Bäckhed F. 112.  2013. The gut microbiota—masters of host development and physiology. Nat. Rev. Microbiol. 11:4227–38 [Google Scholar]
  113. Sonnenburg JL, Angenent LT, Gordon JI. 113.  2004. Getting a grip on things: How do communities of bacterial symbionts become established in our intestine?. Nat. Immunol. 5:6569–73 [Google Scholar]
  114. Southern KW, Barker PM, Solis-Moya A, Patel L. 114.  2012. Macrolide antibiotics for cystic fibrosis. Cochrane Database Syst. Rev. 11:CD002203 [Google Scholar]
  115. Stecher B, Robbiani R, Walker AW, Westendorf AM, Barthel M. 115.  et al. 2007. Salmonella enterica serovar Typhimurium exploits inflammation to compete with the intestinal microbiota. PLoS Biol. 5:102177–89 [Google Scholar]
  116. Sydora BC, Tavernini MM, Doyle JSG, Fedorak RN. 116.  2005. Association with selected bacteria does not cause enterocolitis in IL-10 gene-deficient mice despite a systemic immune response. Dig. Dis. Sci. 50:5905–13 [Google Scholar]
  117. Tamboli CP, Neut C, Desreumaux P, Colombel JF. 117.  2004. Dysbiosis in inflammatory bowel disease. Gut 53:11–4 [Google Scholar]
  118. Tedesco FJ, Barton RW, Alpers DH. 118.  1974. Clindamycin-associated colitis: a prospective study. Ann. Intern. Med. 81:4429–33 [Google Scholar]
  119. Thavagnanam S, Fleming J, Bromley A, Shields MD, Cardwell CR. 119.  2008. A meta-analysis of the association between caesarean section and childhood asthma. Clin. Exp. Allergy 38:4629–33 [Google Scholar]
  120. Thuny F, Richet H, Casalta J-P, Angelakis E, Habib G, Raoult D. 120.  2010. Vancomycin treatment of infective endocarditis is linked with recently acquired obesity. PLoS ONE 5:2) e9074 [Google Scholar]
  121. Trasande L, Blustein J, Liu M, Corwin E, Cox LM, Blaser MJ. 121.  2013. Infant antibiotic exposures and early-life body mass. Int. J. Obes. 37:116–23 [Google Scholar]
  122. Turnbaugh PJ, Bäckhed F, Fulton L, Gordon JI. 122.  2008. Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe 3:4213–23 [Google Scholar]
  123. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A. 123.  et al. 2009. A core gut microbiome in obese and lean twins. Nature 457:7228480–84 [Google Scholar]
  124. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. 124.  2006. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444:71221027–31 [Google Scholar]
  125. Vaahtovuo J, Munukka E, Korkeamäki M, Luukkainen R, Toivanen P. 125.  2008. Fecal microbiota in early rheumatoid arthritis. J. Rheumatol. 35:81500–5 [Google Scholar]
  126. van Nimwegen FA, Penders J, Stobberingh EE, Postma DS, Koppelman GH. 126.  et al. 2011. Mode and place of delivery, gastrointestinal microbiota, and their influence on asthma and atopy. J. Allergy Clin. Immunol. 128:5948–55.e3 [Google Scholar]
  127. Vebø HC, Sekelja M, Nestestog R, Storrø O, Johnsen R. 127.  et al. 2011. Temporal development of the infant gut microbiota in immunoglobulin E-sensitized and nonsensitized children determined by the GA-map infant array. Clin. Vaccine Immunol. 18:81326–35 [Google Scholar]
  128. Warny M, Pepin J, Fang A, Killgore G, Thompson A. 128.  et al. 2005. Toxin production by an emerging strain of Clostridium difficile associated with outbreaks of severe disease in North America and Europe. Lancet 366:94911079–84 [Google Scholar]
  129. Willing BP, Dicksved J, Halfvarson J, Andersson AF, Lucio M. 129.  et al. 2010. A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes. Gastroenterology 139:61844–54.e1 [Google Scholar]
  130. Willing BP, Vacharaksa A, Croxen M, Thanachayanont T, Finlay BB. 130.  2011. Altering host resistance to infections through microbial transplantation. PLoS ONE 6:10e26988 [Google Scholar]
  131. Wlodarska M, Willing B, Keeney KM, Menendez A, Bergstrom KS. 131.  et al. 2011. Antibiotic treatment alters the colonic mucus layer and predisposes the host to exacerbated Citrobacter rodentium-induced colitis. Infect. Immun. 79:41536–45 [Google Scholar]
  132. Young VB, Schmidt TM. 132.  2004. Antibiotic-associated diarrhea accompanied by large-scale alterations in the composition of the fecal microbiota. J. Clin. Microbiol. 42:31203–6 [Google Scholar]
  133. Zhang H, DiBaise JK, Zuccolo A, Kudrna D, Braidotti M. 133.  et al. 2009. Human gut microbiota in obesity and after gastric bypass. Proc. Natl. Acad. Sci. USA 106:72365–70 [Google Scholar]
  134. Zoetendal EG, Rajilić-Stojanović M, de Vos WM. 134.  2008. High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota. Gut 57:111605–15 [Google Scholar]
  135. Zuo H-J, Xie Z-M, Zhang W-W, Li Y-R, Wang W. 135.  et al. 2011. Gut bacteria alteration in obese people and its relationship with gene polymorphism. World J. Gastroenterol. 17:81076–81 [Google Scholar]
/content/journals/10.1146/annurev-micro-091313-103456
Loading
/content/journals/10.1146/annurev-micro-091313-103456
Loading

Data & Media loading...

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error