1932
0
  1. Home
  2. A-Z Publications
  3. Annual Review of Microbiology
  4. Volume 76, 2022
  5. Article

Annual Review of Microbiology

Volume 76, 2022

Translating Microbiome Research From and To the Clinic

Abstract

Extensive research has elucidated the influence of the gut microbiota on human health and disease susceptibility and resistance. We review recent clinical and laboratory-based experimental studies associating the gut microbiota with certain human diseases. We also highlight ongoing translational advances that manipulate the gut microbiota to treat human diseases and discuss opportunities and challenges in translating microbiome research from and to the bedside.

Keyword(s): clinical trials, immune checkpoint inhibitor, infectious diseases, inflammatory bowel disease, microbiome, microbiota, translational research, transplantation
Loading

Article metrics loading...

/content/journals/10.1146/annurev-micro-041020-022206
2022-09-08
2024-04-20
Loading full text...

Full text loading...

/deliver/fulltext/micro/76/1/annurev-micro-041020-022206.html?itemId=/content/journals/10.1146/annurev-micro-041020-022206&mimeType=html&fmt=ahah

Literature Cited

  1. 1.
    Abt MC, McKenney PT, Pamer EG. 2016. Clostridium difficile colitis: pathogenesis and host defence. Nat. Rev. Microbiol. 14:10609–20
     [Google Scholar]
  2. 2.
    Adeolu M, Alnajar S, Naushad S, Gupta RS. 2016. Genome-based phylogeny and taxonomy of the “Enterobacteriales”: proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov. Int. J. Syst. Evol. Microbiol. 66:125575–99
     [Google Scholar]
  3. 3.
    Aitken SL, Sahasrabhojane PV, Kontoyiannis DP, Savidge TC, Arias CA et al. 2021. Alterations of the oral microbiome and cumulative carbapenem exposure are associated with Stenotrophomonas maltophilia infection in patients with acute myeloid leukemia receiving chemotherapy. Clin. Infect. Dis. 72:91507–13
     [Google Scholar]
  4. 4.
    Alavi S, Mitchell JD, Cho JY, Liu R, Macbeth JC, Hsiao A. 2020. Interpersonal gut microbiome variation drives susceptibility and resistance to cholera infection. Cell 181:71533–46.e13
     [Google Scholar]
  5. 5.
    Alexeev EE, Lanis JM, Kao DJ, Campbell EL, Kelly CJ et al. 2018. Microbiota-derived indole metabolites promote human and murine intestinal homeostasis through regulation of interleukin-10 receptor. Am. J. Pathol. 188:51183–94
     [Google Scholar]
  6. 6.
    Antonopoulos DA, Huse SM, Morrison HG, Schmidt TM, Sogin ML, Young VB. 2009. Reproducible community dynamics of the gastrointestinal microbiota following antibiotic perturbation. Infect. Immun. 77:62367–75
     [Google Scholar]
  7. 7.
    Ao TT, Feasey NA, Gordon MA, Keddy KH, Angulo FJ, Crump JA. 2015. Global burden of invasive nontyphoidal salmonella disease; 2010. Emerg. Infect. Dis 21:6941–49
     [Google Scholar]
  8. 8.
    Arpaia N, Campbell C, Fan X, Dikiy S, Van Der Veeken J et al. 2013. Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation. Nature 504:7480451–55
     [Google Scholar]
  9. 9.
    Arrieta MC, Walter J, Finlay BB. 2016. Human microbiota–associated mice: a model with challenges. Cell Host Microbe 19:5575–78
     [Google Scholar]
  10. 10.
    Ashraf MF, Ashraf MF, Tageldin O, Nassar Y, Batool A. 2021. Fecal microbiota transplantation in patients with recurrent Clostridium difficile infection: a four-year single-center retrospective review. Gastroenterol. Res. 14:4237–43
     [Google Scholar]
  11. 11.
    Barker AK, Duster M, Valentine S, Hess T, Archbald-Pannone L et al. 2017. A randomized controlled trial of probiotics for Clostridium difficile infection in adults (PICO). J. Antimicrob. Chemother. 72:113177–80
     [Google Scholar]
  12. 12.
    Bartlett JG, Onderdonk AB, Cisneros RL, Kasper DL. 1977. Clindamycin-associated colitis due to a toxin-producing species of Clostridium in hamsters. J. Infect. Dis. 136:5701–5
     [Google Scholar]
  13. 13.
    Baruch EN, Youngster I, Ben-Betzalel G, Ortenberg R, Lahat A et al. 2021. Fecal microbiota transplant promotes response in immunotherapy-refractory melanoma patients. Science 371:6529602–9
     [Google Scholar]
  14. 14.
    Battaglioli EJ, Hale VL, Chen J, Jeraldo P, Ruiz-Mojica C et al. 2018. Clostridioides difficile uses amino acids associated with gut microbial dysbiosis in a subset of patients with diarrhea. Sci. Transl. Med. 10:7019
     [Google Scholar]
  15. 15.
    Ben-Ami R, Rodríguez-Baño J, Arslan H, Pitout JDD, Quentin C et al. 2009. A multinational survey of risk factors for infection with extended-spectrum β-lactamase-producing Enterobacteriaceae in nonhospitalized patients. Clin. Infect. Dis. 49:5682–90
     [Google Scholar]
  16. 16.
    Beresford-Jones BS, Forster SC, Stares MD, Notley G, Viciani E et al. 2022. The Mouse Gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping. Cell Host Microbe 30:1124–38.e8
     [Google Scholar]
  17. 17.
    Bezabih YM, Sabiiti W, Alamneh E, Bezabih A, Peterson GM et al. 2021. The global prevalence and trend of human intestinal carriage of ESBL-producing Escherichia coli in the community. J. Antimicrob. Chemother. 76:122–29
     [Google Scholar]
  18. 18.
    Biagi E, Franceschi C, Rampelli S, Severgnini M, Ostan R et al. 2016. Gut microbiota and extreme longevity. Curr. Biol 26:111480–85
     [Google Scholar]
  19. 19.
    Bohnhoff M, Miller CP, Martin WR. 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. 120:5805–16
     [Google Scholar]
  20. 20.
    Boursi B, Mamtani R, Haynes K, Yang YX. 2015. The effect of past antibiotic exposure on diabetes risk. Eur. J. Endocrinol. 172:6639–48
     [Google Scholar]
  21. 21.
    Britton GJ, Contijoch EJ, Mogno I, Vennaro OH, Llewellyn SR et al. 2019. Microbiotas from humans with inflammatory bowel disease alter the balance of gut Th17 and RORγt+ regulatory T cells and exacerbate colitis in mice. Immunity 50:1212–24.e4
     [Google Scholar]
  22. 22.
    Brook I, Frazier EH. 2000. Aerobic and anaerobic microbiology in intra-abdominal infections associated with diverticulitis. J. Med. Microbiol. 49:9827–30
     [Google Scholar]
  23. 23.
    Brouwer MSM, Roberts AP, Hussain H, Williams RJ, Allan E, Mullany P 2013. Horizontal gene transfer converts non-toxigenic Clostridium difficile strains into toxin producers. Nat. Commun. 4:2601
     [Google Scholar]
  24. 24.
    Brown EM, Ke X, Hitchcock D, Jeanfavre S, Avila-Pacheco J et al. 2019. Bacteroides-derived sphingolipids are critical for maintaining intestinal homeostasis and symbiosis. Cell Host Microbe 25:5668–80.e7
     [Google Scholar]
  25. 25.
    Buffie CG, Bucci V, Stein RR, McKenney PT, Ling L et al. 2015. Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature 517:7533205–8
     [Google Scholar]
  26. 26.
    Byrd AL, Belkaid Y, Segre JA. 2018. The human skin microbiome. Nat. Rev. Microbiol. 16:3143–55
     [Google Scholar]
  27. 27.
    Caballero S, Carter R, Ke X, Sušac B, Leiner IM et al. 2015. Distinct but spatially overlapping intestinal niches for vancomycin-resistant Enterococcus faecium and carbapenem-resistant Klebsiella pneumoniae. PLOS Pathog 11:9e1005132
     [Google Scholar]
  28. 28.
    Caballero S, Kim S, Carter RA, Leiner IM, Sušac B et al. 2017. Cooperating commensals restore colonization resistance to vancomycin-resistant Enterococcus faecium. Cell Host Microbe 21:5592–602.e4
     [Google Scholar]
  29. 29.
    Caminero A, Galipeau HJ, McCarville JL, Johnston CW, Bernier SP et al. 2016. Duodenal bacteria from patients with celiac disease and healthy subjects distinctly affect gluten breakdown and immunogenicity. Gastroenterology 151:4670–83
     [Google Scholar]
  30. 30.
    CDC (Cent. Dis. Control Prev.) 2019. Antibiotic resistance threats in the United States Rep., CDC Washington, DC:
  31. 31.
    Chaput N, Lepage P, Coutzac C, Soularue E, Le Roux K et al. 2017. Baseline gut microbiota predicts clinical response and colitis in metastatic melanoma patients treated with ipilimumab. Ann. Oncol. 28:61368–79
     [Google Scholar]
  32. 32.
    Chen J, Wright K, Davis JM, Jeraldo P, Marietta EV et al. 2016. An expansion of rare lineage intestinal microbes characterizes rheumatoid arthritis. Genome Med 8:43
     [Google Scholar]
  33. 33.
    Chen N, Zhou M, Dong X, Qu J, Gong F et al. 2020. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study. Lancet 395:10223507–13
     [Google Scholar]
  34. 34.
    Claesson MJ, Jeffery IB, Conde S, Power SE, O'Connor EM et al. 2012. Gut microbiota composition correlates with diet and health in the elderly. Nature 488:7410178–84
     [Google Scholar]
  35. 35.
    Clerkin KJ, Fried JA, Raikhelkar J, Sayer G, Griffin JM et al. 2020. COVID-19 and cardiovascular disease. Circulation 141:1648–55
     [Google Scholar]
  36. 36.
    Cornely OA, Crook DW, Esposito R, Poirier A, Somero MS et al. 2012. Fidaxomicin versus vancomycin for infection with Clostridium difficile in Europe, Canada, and the USA: a double-blind, non-inferiority, randomised controlled trial. Lancet Infect. Dis. 12:4281–89
     [Google Scholar]
  37. 37.
    Davar D, Dzutsev AK, McCulloch JA, Rodrigues RR, Chauvin J-M et al. 2021. Fecal microbiota transplant overcomes resistance to anti-PD-1 therapy in melanoma patients. Science 371:6529595–602
     [Google Scholar]
  38. 38.
    De Lange KM, Moutsianas L, Lee JC, Lamb CA, Luo Y et al. 2017. Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease. Nat. Genet. 49:2256–61
     [Google Scholar]
  39. 39.
    De Wolfe TJ, Eggers S, Barker AK, Kates AE, Dill-McFarland KA et al. 2018. Oral probiotic combination of Lactobacillus and Bifidobacterium alters the gastrointestinal microbiota during antibiotic treatment for Clostridium difficile infection. PLOS ONE 13:9e0204253
     [Google Scholar]
  40. 40.
    DeFilipp Z, Bloom PP, Torres Soto M, Mansour MK, Sater MRA et al. 2019. Drug-resistant E. coli bacteremia transmitted by fecal microbiota transplant. N. Engl. J. Med. 381:212043–50
     [Google Scholar]
  41. 41.
    Denkel LA, Maechler F, Schwab F, Kola A, Weber A et al. 2020. Infections caused by extended-spectrum β-lactamase-producing Enterobacterales after rectal colonization with ESBL-producing Escherichia coli or Klebsiella pneumoniae. Clin. Microbiol. Infect. 26:81046–51
     [Google Scholar]
  42. 42.
    Devkota S, Wang Y, Musch MW, Leone V, Fehlner-Peach H et al. 2012. Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10−/− mice. Nature 487:7405104–8
     [Google Scholar]
  43. 43.
    Donskey CJ, Chowdhry TK, Hecker MT, Hoyen CK, Hanrahan JA et al. 2000. Effect of antibiotic therapy on the density of vancomycin-resistant enterococci in the stool of colonized patients. N. Engl. J. Med. 343:261925–32
     [Google Scholar]
  44. 44.
    Dubin K, Pamer EG. 2017. Enterococci and their interactions with the intestinal microbiome. Microbiol. Spectr. 5:6 https://doi.org/10.1128/microbiolspec.BAD-0014-2016
    [Crossref] [Google Scholar]
  45. 45.
    Dubin KA, Mathur D, McKenney PT, Taylor BP, Littmann ER et al. 2019. Diversification and evolution of vancomycin-resistant Enterococcus faecium during intestinal domination. Infect. Immun. 87:7e00102
     [Google Scholar]
  46. 46.
    Echols RM, Tosiello RL, Haverstock DC, Tice AD. 1999. Demographic, clinical, and treatment parameters influencing the outcome of acute cystitis. Clin. Infect. Dis. 29:1113–19
     [Google Scholar]
  47. 47.
    Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L et al. 2005. Diversity of the human intestinal microbial flora. Science 308:57281635–38
     [Google Scholar]
  48. 48.
    Eiseman B, Silen W, Bascom GS, Kauvar AJ. 1958. Fecal enema as an adjunct in the treatment of pseudomembranous enterocolitis. Surgery 44:5854–59
     [Google Scholar]
  49. 49.
    Escherich T. 1885. Die Darmbakterien des Neugeborenen und Säuglings. Fortschr. Med. 3:515–22
     [Google Scholar]
  50. 50.
    Feehley T, Plunkett CH, Bao R, Choi Hong SM, Culleen E et al. 2019. Healthy infants harbor intestinal bacteria that protect against food allergy. Nat. Med. 25:3448–53
     [Google Scholar]
  51. 51.
    Fluckiger A, Daillère R, Sassi M, Sixt BS, Liu P et al. 2020. Cross-reactivity between tumor MHC class I–restricted antigens and an enterococcal bacteriophage. Science 369:6506936–42
     [Google Scholar]
  52. 52.
    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 528:7581262–66
     [Google Scholar]
  53. 53.
    Frankel AE, Coughlin LA, Kim J, Froehlich TW, Xie Y et al. 2017. Metagenomic shotgun sequencing and unbiased metabolomic profiling identify specific human gut microbiota and metabolites associated with immune checkpoint therapy efficacy in melanoma patients. Neoplasia 19:10848–55
     [Google Scholar]
  54. 54.
    Franzosa EA, Sirota-Madi A, Avila-Pacheco J, Fornelos N, Haiser HJ et al. 2019. Gut microbiome structure and metabolic activity in inflammatory bowel disease. Nat. Microbiol. 4:2293–305
     [Google Scholar]
  55. 55.
    Freeman JM, Kossoff EH. 2010. Ketosis and the ketogenic diet, 2010: advances in treating epilepsy and other disorders. Adv. Pediatr 57:1315–29
     [Google Scholar]
  56. 56.
    Fujino S, Andoh A, Bamba S, Ogawa A, Hata K et al. 2003. Increased expression of interleukin 17 in inflammatory bowel disease. Gut 52:165–70
     [Google Scholar]
  57. 57.
    Furusawa Y, Obata Y, Fukuda S, Endo TA, Nakato G et al. 2013. Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells. Nature 504:7480446–50
     [Google Scholar]
  58. 58.
    Gao F, Zheng KI, Wang XB, Sun QF, Pan KH et al. 2020. Obesity is a risk factor for greater COVID-19 severity. Diabetes Care 43:7e72–74
     [Google Scholar]
  59. 59.
    Gerding DN, Meyer T, Lee C, Cohen SH, Murthy UK et al. 2015. Administration of spores of nontoxigenic Clostridium difficile strain M3 for prevention of recurrent C. difficile infection: a randomized clinical trial. JAMA 313:171719–27
     [Google Scholar]
  60. 60.
    Gevers D, Kugathasan S, Denson LA, Vázquez-Baeza Y, Van Treuren W et al. 2014. The treatment-naive microbiome in new-onset Crohn's disease. Cell Host Microbe 15:3382–92
     [Google Scholar]
  61. 61.
    Ghorbani Y, Schwenger KJP, Allard JP. 2021. Manipulation of intestinal microbiome as potential treatment for insulin resistance and type 2 diabetes. Eur. J. Nutr. 60:52361–79
     [Google Scholar]
  62. 62.
    Gjonbalaj M, Keith JW, Do MH, Hohl TM, Pamer EG, Becattini S. 2020. Antibiotic degradation by commensal microbes shields pathogens. Infect. Immun. 88:4e00012
     [Google Scholar]
  63. 63.
    Gopalakrishnan V, Spencer CN, Nezi L, Reuben A, Andrews MC et al. 2018. Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients. Science 359:637197–103
     [Google Scholar]
  64. 64.
    Gough E, Shaikh H, Manges AR. 2011. Systematic review of intestinal microbiota transplantation (fecal bacteriotherapy) for recurrent Clostridium difficile infection. Clin. Infect. Dis. 53:10994–1002
     [Google Scholar]
  65. 65.
    Goyal P, Choi JJ, Pinheiro LC, Schenck EJ, Chen R et al. 2020. Clinical characteristics of Covid-19 in New York City. N. Engl. J. Med 382:242372–74
     [Google Scholar]
  66. 66.
    Griffin ME, Espinosa J, Becker JL, Luo J-D, Carroll TS et al. 2021. Enterococcus peptidoglycan remodeling promotes checkpoint inhibitor cancer immunotherapy. Science 373:65581040–46
     [Google Scholar]
  67. 67.
    Gu S, Chen Y, Wu Z, Chen Y, Gao H et al. 2020. Alterations of the gut microbiota in patients with coronavirus disease 2019 or H1N1 influenza. Clin. Infect. Dis. 71:102669–78
     [Google Scholar]
  68. 68.
    Guan W, Ni Z, Hu Y, Liang W, Ou C et al. 2020. Clinical characteristics of coronavirus disease 2019 in China. N. Engl. J. Med. 382:181708–20
     [Google Scholar]
  69. 69.
    Gupta A, Osadchiy V, Mayer EA. 2020. Brain–gut–microbiome interactions in obesity and food addiction. Nat. Rev. Gastroenterol. Hepatol. 17:11655–72
     [Google Scholar]
  70. 70.
    Haak BW, Littmann ER, Chaubard J-L, Pickard AJ, Fontana E et al. 2018. Impact of gut colonization with butyrate-producing microbiota on respiratory viral infection following allo-HCT. Blood 131:262978–86
     [Google Scholar]
  71. 71.
    Hall AB, Yassour M, Sauk J, Garner A, Jiang X et al. 2017. A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients. Genome Med 9:103
     [Google Scholar]
  72. 72.
    Hall IC, O'Toole E. 1935. Intestinal flora in new-born infants: with a description of a new pathogenic anaerobe, Bacillus difficilis. Am. J. Dis. Child. 49:2390–402
     [Google Scholar]
  73. 73.
    Hang S, Paik D, Yao L, Kim E, Jamma T et al. 2019. Bile acid metabolites control TH17 and Treg cell differentiation. Nature 576:7785143–48
     [Google Scholar]
  74. 74.
    Harris B, Morjaria SM, Littmann ER, Geyer AI, Stover DE et al. 2016. Gut microbiota predict pulmonary infiltrates after allogeneic hematopoietic cell transplantation. Am. J. Respir. Crit. Care Med. 194:4450–63
     [Google Scholar]
  75. 75.
    Henke MT, Kenny DJ, Cassilly CD, Vlamakis H, Xavier RJ, Clardy J. 2019. Ruminococcus gnavus, a member of the human gut microbiome associated with Crohn's disease, produces an inflammatory polysaccharide. PNAS 116:2612672–77
     [Google Scholar]
  76. 76.
    Henn MR, O'Brien EJ, Diao L, Feagan BG, Sandborn WJ et al. 2021. A phase 1b safety study of SER-287, a spore-based microbiome therapeutic, for active mild to moderate ulcerative colitis. Gastroenterology 160:1115–27.e30
     [Google Scholar]
  77. 77.
    Hentges DJ, Freter R. 1962. In vivo and in vitro antagonism of intestinal bacteria against Shigella flexneri. I. Correlation between various tests. J. Infect. Dis. 110:130–37
     [Google Scholar]
  78. 78.
    Hooton TM, Bradley SF, Cardenas DD, Colgan R, Geerlings SE et al. 2010. Diagnosis, prevention, and treatment of catheter-associated urinary tract infection in adults: 2009 International Clinical Practice Guidelines from the Infectious Diseases Society of America. Clin. Infect. Dis. 50:5625–63
     [Google Scholar]
  79. 79.
    Hsiao A, Ahmed AMS, Subramanian S, Griffin NW, Drewry LL et al. 2014. Members of the human gut microbiota involved in recovery from Vibrio cholerae infection. Nature 515:7527423–26
     [Google Scholar]
  80. 80.
    Hu B, Huang S, Yin L. 2021. The cytokine storm and COVID-19. J. Med. Virol. 93:1250–56
     [Google Scholar]
  81. 81.
    Hylemon PB, Melone PD, Franklund CV, Lund E, Bjorkhem I. 1991. Mechanism of intestinal 7α-dehydroxylation of cholic acid: evidence that allo-deoxycholic acid is an inducible side-product. J. Lipid Res. 32:189–96
     [Google Scholar]
  82. 82.
    Isaac S, Scher JU, Djukovic A, Jiménez N, Littman DR et al. 2017. Short- and long-term effects of oral vancomycin on the human intestinal microbiota. J. Antimicrob. Chemother. 72:1128–36
     [Google Scholar]
  83. 83.
    Jacobson A, Lam L, Rajendram M, Tamburini F, Honeycutt J et al. 2018. A gut commensal–produced metabolite mediates colonization resistance to salmonella infection. Cell Host Microbe 24:2296–307.e7
     [Google Scholar]
  84. 84.
    Jenq RR, Taur Y, Devlin SM, Ponce DM, Goldberg JD et al. 2015. Intestinal Blautia is associated with reduced death from graft-versus-host disease. Biol. Blood Marrow Transplant. 21:81373–83
     [Google Scholar]
  85. 85.
    Johnson S, Lavergne V, Skinner AM, Gonzales-Luna AJ, Garey KW et al. 2021. Clinical practice guideline by the Infectious Diseases Society of America (IDSA) and Society for Healthcare Epidemiology of America (SHEA): 2021 focused update guidelines on management of Clostridioides difficile infection in adults. Clin. Infect. Dis. 73:5e1029–44
     [Google Scholar]
  86. 86.
    Jostins L, Ripke S, Weersma RK, Duerr RH, McGovern DP et al. 2012. Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature 491:7422119–24
     [Google Scholar]
  87. 87.
    Kalaora S, Nagler A, Nejman D, Alon M, Barbolin C et al. 2021. Identification of bacteria-derived HLA-bound peptides in melanoma. Nature 592:7852138–43
     [Google Scholar]
  88. 88.
    Kalil AC, Metersky ML, Klompas M, Muscedere J, Sweeney DA et al. 2016. Management of adults with hospital-acquired and ventilator-associated pneumonia: 2016 clinical practice guidelines by the Infectious Diseases Society of America and the American Thoracic Society. Clin. Infect. Dis. 63:5e61–111
     [Google Scholar]
  89. 89.
    Kang JD, Myers CJ, Harris SC, Kakiyama G, Lee IK et al. 2019. Bile acid 7α-dehydroxylating gut bacteria secrete antibiotics that inhibit Clostridium difficile: role of secondary bile acids. Cell Chem. Biol. 26:127–34.e4
     [Google Scholar]
  90. 90.
    Kao D, Wong K, Franz R, Cochrane K, Sherriff K et al. 2021. The effect of a microbial ecosystem therapeutic (MET-2) on recurrent Clostridioides difficile infection: a phase 1, open-label, single-group trial. Lancet Gastroenterol. Hepatol. 6:4282–91
     [Google Scholar]
  91. 91.
    Karasawa T, Ikoma S, Yamakawa K, Nakamura S. 1995. A defined growth medium for Clostridium difficile. Microbiology 141:2371–75
     [Google Scholar]
  92. 92.
    Kassam Z, Lee CH, Yuan Y, Hunt RH. 2013. Fecal microbiota transplantation for Clostridium difficile infection: systematic review and meta-analysis. Am. J. Gastroenterol. 108:4500–8
     [Google Scholar]
  93. 93.
    Kato K, Nagao M, Miyamoto K, Oka K, Takahashi M et al. 2017. Longitudinal analysis of the intestinal microbiota in liver transplantation. Transplant. Direct 3:4e144
     [Google Scholar]
  94. 94.
    Kelly CR, Yen EF, Grinspan AM, Kahn SA, Atreja A et al. 2021. Fecal microbiota transplantation is highly effective in real-world practice: initial results from the FMT National Registry. Gastroenterology 160:1183–92.e3
     [Google Scholar]
  95. 95.
    Kim B, Wang YC, Hespen CW, Espinosa J, Salje J et al. 2019. Enterococcus faecium secreted antigen A generates muropeptides to enhance host immunity and limit bacterial pathogenesis. eLife 8:e45343
     [Google Scholar]
  96. 96.
    Kim SG, Becattini S, Moody TU, Shliaha PV, Littmann ER et al. 2019. Microbiota-derived lantibiotic restores resistance against vancomycin-resistant Enterococcus. Nature 572:7771665–69
     [Google Scholar]
  97. 97.
    Kotloff KL, Winickoff JP, Ivanoff B, Clemens JD, Swerdlow DL et al. 1999. Global burden of Shigella infections: implications for vaccine development and implementation of control strategies. Bull. World Health Organ. 77:8651–66
     [Google Scholar]
  98. 98.
    Lamas B, Hernandez-Galan L, Galipeau HJ, Constante M, Clarizio A et al. 2020. Aryl hydrocarbon receptor ligand production by the gut microbiota is decreased in celiac disease leading to intestinal inflammation. Sci. Transl. Med. 12:566eaba0624
     [Google Scholar]
  99. 99.
    Lamas B, Richard ML, Leducq V, Pham HP, Michel ML et al. 2016. CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands. Nat. Med. 22:6598–605
     [Google Scholar]
  100. 100.
    Lamers MM, Beumer J, van der Vaart J, Knoops K, Puschhof J et al. 2020. SARS-CoV-2 productively infects human gut enterocytes. Science 369:649950–54
     [Google Scholar]
  101. 101.
    Lavoie S, Conway KL, Lassen KG, Jijon HB, Pan H et al. 2019. The Crohn's disease polymorphism, ATG16L1 T300A, alters the gut microbiota and enhances the local Th1/Th17 response. eLife 8:e39982
     [Google Scholar]
  102. 102.
    Lee JR, Huang J, Magruder M, Zhang LT, Gong C et al. 2019. Butyrate-producing gut bacteria and viral infections in kidney transplant recipients: a pilot study. Transpl. Infect. Dis. 21:6e13180
     [Google Scholar]
  103. 103.
    Lee SH, Cho SY, Yoon Y, Park C, Sohn J et al. 2021. Bifidobacterium bifidum strains synergize with immune checkpoint inhibitors to reduce tumour burden in mice. Nat. Microbiol. 6:3277–88
     [Google Scholar]
  104. 104.
    Lehmann CJ, Pho MT, Pitrak D, Ridgway JP, Pettit NN. 2021. Community-acquired coinfection in coronavirus disease 2019: a retrospective observational experience. Clin. Infect. Dis. 72:81450–52
     [Google Scholar]
  105. 105.
    Lewis BB, Buffie CG, Carter RA, Leiner I, Toussaint NC et al. 2015. Loss of microbiota-mediated colonization resistance to Clostridium difficile infection with oral vancomycin compared with metronidazole. J. Infect. Dis. 212:101656–65
     [Google Scholar]
  106. 106.
    Li W, Hang S, Fang Y, Bae S, Zhang Y et al. 2021. A bacterial bile acid metabolite modulates Treg activity through the nuclear hormone receptor NR4A1. Cell Host Microbe 29:91366–77.e9
     [Google Scholar]
  107. 107.
    Livanos AE, Greiner TU, Vangay P, Pathmasiri W, Stewart D et al. 2016. Antibiotic-mediated gut microbiome perturbation accelerates development of type 1 diabetes in mice. Nat. Microbiol. 1:16140
     [Google Scholar]
  108. 108.
    Livermore DM, Brown DFJ. 2001. Detection of β-lactamase-mediated resistance. J. Antimicrob. Chemother. 48:Suppl. 159–64
     [Google Scholar]
  109. 109.
    Machiels K, Joossens M, Sabino J, de Preter V, Arijs I et al. 2014. A decrease of the butyrate-producing species Roseburia hominis and Faecalibacterium prausnitzii defines dysbiosis in patients with ulcerative colitis. Gut 63:81275–83
     [Google Scholar]
  110. 110.
    Maeda Y, Kurakawa T, Umemoto E, Motooka D, Ito Y et al. 2016. Dysbiosis contributes to arthritis development via activation of autoreactive T cells in the intestine. Arthritis Rheumatol 68:112646–61
     [Google Scholar]
  111. 111.
    Mager LF, Burkhard R, Pett N, Cooke NCA, Brown K et al. 2020. Microbiome-derived inosine modulates response to checkpoint inhibitor immunotherapy. Science 369:65101481–89
     [Google Scholar]
  112. 112.
    Magruder M, Edusei E, Zhang L, Albakry S, Satlin MJ et al. 2020. Gut commensal microbiota and decreased risk for Enterobacteriaceae bacteriuria and urinary tract infection. Gut Microbes 12:1805281
     [Google Scholar]
  113. 113.
    Mantovani A, Byrne CD, Zheng MH, Targher G. 2020. Diabetes as a risk factor for greater COVID-19 severity and in-hospital death: a meta-analysis of observational studies. Nutr. Metab. Cardiovasc. Dis. 30:81236–48
     [Google Scholar]
  114. 114.
    Matson V, Fessler J, Bao R, Chongsuwat T, Zha Y et al. 2018. The commensal microbiome is associated with anti-PD-1 efficacy in metastatic melanoma patients. Science 359:6371104–8
     [Google Scholar]
  115. 115.
    McGovern BH, Ford CB, Henn MR, Pardi DS, Khanna S et al. 2021. SER-109, an investigational microbiome drug to reduce recurrence after Clostridioides difficile infection: lessons learned from a phase 2 trial. Clin. Infect. Dis. 72:122132–40
     [Google Scholar]
  116. 116.
    McKenney PT, Yan J, Vaubourgeix J, Becattini S, Lampen N et al. 2019. intestinal bile acids induce a morphotype switch in vancomycin-resistant Enterococcus that facilitates intestinal colonization. Cell Host Microbe 25:5695–705.e5
     [Google Scholar]
  117. 117.
    Méric G, Hitchings MD, Pascoe B, Sheppard SK. 2016. From Escherich to the Escherichia coli genome. Lancet Infect. Dis. 16:6634–36
     [Google Scholar]
  118. 118.
    Mermel LA, Allon M, Bouza E, Craven DE, Flynn P et al. 2009. Clinical practice guidelines for the diagnosis and management of intravascular catheter–related infection: 2009 update by the Infectious Diseases Society of America. Clin. Infect. Dis. 49:11–45
     [Google Scholar]
  119. 119.
    Midani FS, Weil AA, Chowdhury F, Begum YA, Khan AI et al. 2018. Human gut microbiota predicts susceptibility to Vibrio cholerae infection. J. Infect. Dis. 218:4645–53
     [Google Scholar]
  120. 120.
    Milani C, Duranti S, Bottacini F, Casey E, Turroni F et al. 2017. The first microbial colonizers of the human gut: composition, activities, and health implications of the infant gut microbiota. Microbiol. Mol. Biol. Rev. 81:4e00036
     [Google Scholar]
  121. 121.
    Moayyedi P, Surette MG, Kim PT, Libertucci J, Wolfe M et al. 2015. Fecal microbiota transplantation induces remission in patients with active ulcerative colitis in a randomized controlled trial. Gastroenterology 149:1102–9.e6
     [Google Scholar]
  122. 122.
    Morais LH, Schreiber HL, Mazmanian SK. 2021. The gut microbiota-brain axis in behaviour and brain disorders. Nat. Rev. Microbiol. 19:4241–55
     [Google Scholar]
  123. 123.
    Morrison DJ, Preston T. 2016. Formation of short chain fatty acids by the gut microbiota and their impact on human metabolism. Gut Microbes 7:3189–200
     [Google Scholar]
  124. 124.
    Mundt JO. 1963. Occurrence of enterococci in animals in a wild environment. Appl. Microbiol. 11:2136–40
     [Google Scholar]
  125. 125.
    Nelson RE, Hatfield KM, Wolford H, Samore MH, Scott RD et al. 2021. National estimates of healthcare costs associated with multidrug-resistant bacterial infections among hospitalized patients in the United States. Clin. Infect. Dis. 72:Suppl. 1S17–26
     [Google Scholar]
  126. 126.
    Nicholson MR, Mitchell PD, Alexander E, Ballal S, Bartlett M et al. 2020. Efficacy of fecal microbiota transplantation for Clostridium difficile infection in children. Clin. Gastroenterol. Hepatol. 18:3612–19.e1
     [Google Scholar]
  127. 127.
    Nissle A. 1916. Über die Grundlagen einer neuen ursächlichen Bekämpfung der pathologischen Darmflora. Dtsch. Med. Wochenschr. 42:1181–84
     [Google Scholar]
  128. 128.
    Oh PL, Martínez I, Sun Y, Walter J, Peterson DA, Mercer DF. 2012. Characterization of the ileal microbiota in rejecting and nonrejecting recipients of small bowel transplants. Am. J. Transplant. 12:3753–62
     [Google Scholar]
  129. 129.
    Omenetti S, Pizarro TT. 2015. The Treg/Th17 axis: a dynamic balance regulated by the gut microbiome. Front. Immunol. 6:639
     [Google Scholar]
  130. 130.
    Onderdonk AB, Cisneros RL, Bartlett JG. 1980. Clostridium difficile in gnotobiotic mice. Infect. Immun. 28:1277–82
     [Google Scholar]
  131. 131.
    Orenstein R, Dubberke E, Hardi R, Ray A, Mullane K et al. 2016. Safety and durability of RBX2660 (microbiota suspension) for recurrent Clostridium difficile infection: results of the PUNCH CD study. Clin. Infect. Dis. 62:5596–602
     [Google Scholar]
  132. 132.
    Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO 2007. Development of the human infant intestinal microbiota. PLOS Biol 5:7e177
     [Google Scholar]
  133. 133.
    Pan L, Mu M, Yang P, Sun Y, Wang R et al. 2020. Clinical characteristics of COVID-19 patients with digestive symptoms in Hubei, China: a descriptive, cross-sectional, multicenter study. Am. J. Gastroenterol. 115:5766–73
     [Google Scholar]
  134. 134.
    Pantell RH, Roberts KB, Adams WG, Dreyer BP, Kuppermann N et al. 2021. Evaluation and management of well-appearing febrile infants 8 to 60 days old. Pediatrics 148:2e2021052228
     [Google Scholar]
  135. 135.
    Papanicolas LE, Gordon DL, Wesselingh SL, Rogers GB. 2020. Improving risk-benefit in faecal transplantation through microbiome screening. Trends Microbiol 28:5331–39
     [Google Scholar]
  136. 136.
    Paramsothy S, Paramsothy R, Rubin DT, Kamm MA, Kaakoush NO et al. 2017. Faecal microbiota transplantation for inflammatory bowel disease: a systematic review and meta-analysis. J. Crohn's Colitis 11:101180–99
     [Google Scholar]
  137. 137.
    Paun A, Yau C, Meshkibaf S, Daigneault MC, Marandi L et al. 2019. Association of HLA-dependent islet autoimmunity with systemic antibody responses to intestinal commensal bacteria in children. Sci. Immunol. 4:32aau8125
     [Google Scholar]
  138. 138.
    Peled JU, Gomes ALC, Devlin SM, Littmann ER, Taur Y et al. 2020. Microbiota as predictor of mortality in allogeneic hematopoietic-cell transplantation. N. Engl. J. Med. 382:9822–34
     [Google Scholar]
  139. 139.
    Peng Y, Liang S, Poonsuk K, On H, Li SW et al. 2021. Role of gut microbiota in travel-related acquisition of extended spectrum β-lactamase-producing Enterobacteriaceae. J. Travel Med. 28:3taab022
     [Google Scholar]
  140. 140.
    Petrof EO, Gloor GB, Vanner SJ, Weese SJ, Carter D et al. 2013. Stool substitute transplant therapy for the eradication of Clostridium difficile infection: “rePOOPulating” the gut. Microbiome 1:3
     [Google Scholar]
  141. 141.
    Pranata R, Lim MA, Huang I, Raharjo SB, Lukito AA. 2020. Hypertension is associated with increased mortality and severity of disease in COVID-19 pneumonia: a systematic review, meta-analysis and meta-regression. J. Renin-Angiotensin-Aldosterone Syst. 21:2147032032092689
     [Google Scholar]
  142. 142.
    de Preter V, Machiels K, Joossens M, Arijs I, Matthys C et al. 2015. Faecal metabolite profiling identifies medium-chain fatty acids as discriminating compounds in IBD. Gut 64:3447–58
     [Google Scholar]
  143. 143.
    Pruss KM, Sonnenburg JL. 2021. C. difficile exploits a host metabolite produced during toxin-mediated disease. Nature 593:7858261–65
     [Google Scholar]
  144. 144.
    Quévrain E, Maubert MA, Michon C, Chain F, Marquant R et al. 2016. Identification of an anti-inflammatory protein from Faecalibacterium prausnitzii, a commensal bacterium deficient in Crohn's disease. Gut 65:3415–25
     [Google Scholar]
  145. 145.
    Rangan KJ, Pedicord VA, Wang Y-C, Kim B, Lu Y et al. 2016. A secreted bacterial peptidoglycan hydrolase enhances tolerance to enteric pathogens. Science 353:63061434–37
     [Google Scholar]
  146. 146.
    Rawson TM, Moore LSP, Zhu N, Ranganathan N, Skolimowska K et al. 2020. Bacterial and fungal coinfection in individuals with coronavirus: a rapid review to support COVID-19 antimicrobial prescribing. Clin. Infect. Dis. 71:92459–68
     [Google Scholar]
  147. 147.
    Reddy P, Malczynski M, Obias A, Reiner S, Jin N et al. 2007. Screening for extended-spectrum β-lactamase-producing Enterobacteriaceae among high-risk patients and rates of subsequent bacteremia. Clin. Infect. Dis. 45:7846–52
     [Google Scholar]
  148. 148.
    Reeves AE, Theriot CM, Bergin IL, Huffnagle GB, Schloss PD, Young VB. 2011. The interplay between microbiome dynamics and pathogen dynamics in a murine model of Clostridium difficile infection. Gut Microbes 2:3145–58
     [Google Scholar]
  149. 149.
    Rehaume LM, Mondot S, de Cárcer DA, Velasco J, Benham H et al. 2014. ZAP-70 genotype disrupts the relationship between microbiota and host, leading to spondyloarthritis and ileitis in SKG mice. Arthritis Rheumatol 66:102780–92
     [Google Scholar]
  150. 150.
    Ridlon JM, Kang DJ, Hylemon PB. 2006. Bile salt biotransformations by human intestinal bacteria. J. Lipid Res. 47:2241–59
     [Google Scholar]
  151. 151.
    Rivas MA, Beaudoin M, Gardet A, Stevens C, Sharma Y et al. 2011. Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease. Nat. Genet. 43:111066–73
     [Google Scholar]
  152. 152.
    Rogers AWL, Tsolis RM, Bäumler AJ. 2021. Salmonella versus the microbiome. Microbiol. Mol. Biol. Rev. 85:1e00027
     [Google Scholar]
  153. 153.
    Rosser EC, Piper CJM, Matei DE, Blair PA, Rendeiro AF et al. 2020. Microbiota-derived metabolites suppress arthritis by amplifying aryl-hydrocarbon receptor activation in regulatory B cells. Cell Metab 31:4837–51.e10
     [Google Scholar]
  154. 154.
    Routy B, Le Chatelier E, Derosa L, Duong CPM, Alou MT et al. 2018. Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors. Science 359:637191–97
     [Google Scholar]
  155. 155.
    Santoru ML, Piras C, Murgia A, Palmas V, Camboni T et al. 2017. Cross sectional evaluation of the gut-microbiome metabolome axis in an Italian cohort of IBD patients. Sci. Rep. 7:9523
     [Google Scholar]
  156. 156.
    Sato Y, Atarashi K, Plichta DR, Arai Y, Sasajima S et al. 2021. Novel bile acid biosynthetic pathways are enriched in the microbiome of centenarians. Nature 599:7885458–64
     [Google Scholar]
  157. 157.
    Schaedler RW, Dubs R, Costello R. 1965. Association of germfree mice with bacteria isolated from normal mice. J. Exp. Med. 122:177–82
     [Google Scholar]
  158. 158.
    Scher JU, Sczesnak A, Longman RS, Segata N, Ubeda C et al. 2013. Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis. eLife 2:e01202
     [Google Scholar]
  159. 159.
    Schirmer M, Garner A, Vlamakis H, Xavier RJ. 2019. Microbial genes and pathways in inflammatory bowel disease. Nat. Rev. Microbiol. 17:8497–511
     [Google Scholar]
  160. 160.
    Schwan A, Sjölin S, Trottestam U, Aronsson B. 1984. Relapsing Clostridium difficile enterocolitis cured by rectal infusion of normal faeces. Scand. . J. Infect. Dis. 16:2211–15
     [Google Scholar]
  161. 161.
    Seal D, Borriello SP, Barclay F, Welch A, Piper M, Bonnycastle M. 1987. Treatment of relapsing Clostridium difficile diarrhoea by administration of a non-toxigenic strain. Eur. J. Clin. Microbiol. 6:151–53
     [Google Scholar]
  162. 162.
    Shen NT, Maw A, Tmanova LL, Pino A, Ancy K et al. 2017. Timely use of probiotics in hospitalized adults prevents Clostridium difficile infection: a systematic review with meta-regression analysis. Gastroenterology 152:81889–900.e9
     [Google Scholar]
  163. 163.
    Shono Y, Docampo MD, Peled JU, Perobelli SM, Velardi E et al. 2016. Increased GVHD-related mortality with broad-spectrum antibiotic use after allogeneic hematopoietic stem cell transplantation in human patients and mice. Sci. Transl. Med. 8:339339ra71
     [Google Scholar]
  164. 164.
    Shoulders MD, Raines RT. 2009. Collagen structure and stability. Annu. Rev. Biochem. 78:929–58
     [Google Scholar]
  165. 165.
    Sivan A, Corrales L, Hubert N, Williams JB, Aquino-Michaels K et al. 2015. Commensal Bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy. Science 350:62641084–89
     [Google Scholar]
  166. 166.
    Smillie CS, Sauk J, Gevers D, Friedman J, Sung J et al. 2018. Strain tracking reveals the determinants of bacterial engraftment in the human gut following fecal microbiota transplantation. Cell Host Microbe 23:2229–40.e5
     [Google Scholar]
  167. 167.
    Smith PM, Howitt MR, Panikov N, Michaud M, Gallini CA et al. 2013. The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis. Science 341:6145569–73
     [Google Scholar]
  168. 168.
    Snydman DR, Jacobus NV, McDermott LA, Ruthazer R, Golan Y et al. 2007. National survey on the susceptibility of Bacteroides fragilis group: report and analysis of trends in the United States from 1997 to 2004. Antimicrob. Agents Chemother. 51:51649–55
     [Google Scholar]
  169. 169.
    Sokol H, Pigneur B, Watterlot L, Lakhdari O, Bermúdez-Humarán LG et al. 2008. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. PNAS 105:4316731–36
     [Google Scholar]
  170. 170.
    Song X, Sun X, Oh SF, Wu M, Zhang Y et al. 2020. Microbial bile acid metabolites modulate gut RORγ+ regulatory T cell homeostasis. Nature 577:7790410–15
     [Google Scholar]
  171. 171.
    Sonnenborn U. 2016. Escherichia coli strain Nissle 1917—from bench to bedside and back: history of a special Escherichia coli strain with probiotic properties. FEMS Microbiol. Lett. 363:19212
     [Google Scholar]
  172. 172.
    Sorbara MT, Dubin K, Littmann ER, Moody TU, Fontana E et al. 2019. Inhibiting antibiotic-resistant Enterobacteriaceae by microbiota-mediated intracellular acidification. J. Exp. Med. 216:184–98
     [Google Scholar]
  173. 173.
    Sorbara MT, Littmann ER, Fontana E, Moody TU, Kohout CE et al. 2020. Functional and genomic variation between human-derived isolates of Lachnospiraceae reveals inter- and intra-species diversity. Cell Host Microbe 28:1134–46.e4
     [Google Scholar]
  174. 174.
    Sorg JA, Sonenshein AL. 2009. Chenodeoxycholate is an inhibitor of Clostridium difficile spore germination. J. Bacteriol. 191:31115–17
     [Google Scholar]
  175. 175.
    Spinler JK, Brown A, Ross CL, Boonma P, Conner ME, Savidge TC. 2016. Administration of probiotic kefir to mice with Clostridium difficile infection exacerbates disease. Anaerobe 40:54–57
     [Google Scholar]
  176. 176.
    Stefka AT, Feehley T, Tripathi P, Qiu J, McCoy K et al. 2014. Commensal bacteria protect against food allergen sensitization. PNAS 111:3613145–50
     [Google Scholar]
  177. 177.
    Stein-Thoeringer CK, Nichols KB, Lazrak A, Docampo MD, Slingerland AE et al. 2019. Lactose drives Enterococcus expansion to promote graft-versus-host disease. Science 366:64691143–49
     [Google Scholar]
  178. 178.
    Stoma I, Littmann ER, Peled JU, Giralt S, van den Brink MRM et al. 2021. Compositional flux within the intestinal microbiota and risk for bloodstream infection with gram-negative bacteria. Clin. Infect. Dis. 73:11e4627–35
     [Google Scholar]
  179. 179.
    Tack DM, Ray L, Griffin PM, Cieslak PR, Dunn J et al. 2020. Preliminary incidence and trends of infections with pathogens transmitted commonly through food—Foodborne Diseases Active Surveillance Network, 10 U.S. sites, 2016–2019. Morb. Mortal. Wkly. Rep. 69:17509–14
     [Google Scholar]
  180. 180.
    Takahashi K, Nishida A, Fujimoto T, Fujii M, Shioya M et al. 2016. Reduced abundance of butyrate-producing bacteria species in the fecal microbial community in Crohn's disease. Digestion 93:159–65
     [Google Scholar]
  181. 181.
    Tanaka JS, Young RR, Heston SM, Jenkins K, Spees LP et al. 2020. Anaerobic antibiotics and the risk of graft-versus-host disease after allogeneic hematopoietic stem cell transplantation. Biol. Blood Marrow Transplant. 26:112053–60
     [Google Scholar]
  182. 182.
    Tang H-J, Hsieh C-F, Chang P-C, Chen J-J, Lin Y-H et al. 2016. Clinical significance of community- and healthcare-acquired carbapenem-resistant Enterobacteriaceae isolates. PLOS ONE 11:3e0151897
     [Google Scholar]
  183. 183.
    Taur Y, Coyte K, Schluter J, Robilotti E, Figueroa C et al. 2018. Reconstitution of the gut microbiota of antibiotic-treated patients by autologous fecal microbiota transplant. Sci. Transl. Med. 10:460eaap9489
     [Google Scholar]
  184. 184.
    Taur Y, Xavier JB, Lipuma L, Ubeda C, Goldberg J et al. 2012. Intestinal domination and the risk of bacteremia in patients undergoing allogeneic hematopoietic stem cell transplantation. Clin. Infect. Dis. 55:7905–14
     [Google Scholar]
  185. 185.
    Taur Y, Xavier JB, Lipuma L, Ubeda C, Goldberg J et al. 2012. Intestinal domination and the risk of bacteremia in patients undergoing allogeneic hematopoietic stem cell transplantation. Clin. Infect. Dis. 55:7905–14
     [Google Scholar]
  186. 186.
    Taurog JD, Richardson JA, Croft JT, Simmons WA, Zhou M et al. 1994. The germfree state prevents development of gut and joint inflammatory disease in HLA-B27 transgenic rats. J. Exp. Med. 180:62359–64
     [Google Scholar]
  187. 187.
    Terveer EM, van Gool T, Ooijevaar RE, Sanders IMJG, Boeije-Koppenol E et al. 2020. Human transmission of blastocystis by fecal microbiota transplantation without development of gastrointestinal symptoms in recipients. Clin. Infect. Dis. 71:102630–36
     [Google Scholar]
  188. 188.
    Theriot CM, Koenigsknecht MJ, Carlson PE, Hatton GE, Nelson AM et al. 2014. Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection. Nat. Commun. 5:3114
     [Google Scholar]
  189. 189.
    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 444:71221027–31
     [Google Scholar]
  190. 190.
    Tvede M, Rask-Madsen J. 1989. Bacteriotherapy for chronic relapsing Clostridium difficile diarrhoea in six patients. Lancet 333:86481156–60
     [Google Scholar]
  191. 191.
    van Duin D, Doi Y. 2017. The global epidemiology of carbapenemase-producing Enterobacteriaceae. Virulence 8:4460–69
     [Google Scholar]
  192. 192.
    van Nood E, Vrieze A, Nieuwdorp M, Fuentes S, Zoetendal EG et al. 2013. Duodenal infusion of donor feces for recurrent Clostridium difficile. N. Engl. J. Med. 368:5407–15
     [Google Scholar]
  193. 193.
    Vandeputte D, Kathagen G, D'Hoe K, Vieira-Silva S, Valles-Colomer M et al. 2017. Quantitative microbiome profiling links gut community variation to microbial load. Nature 551:7681507–11
     [Google Scholar]
  194. 194.
    Vatanen T, Kostic AD, D'Hennezel E, Siljander H, Franzosa EA et al. 2016. Variation in microbiome LPS immunogenicity contributes to autoimmunity in humans. Cell 165:4842–53
     [Google Scholar]
  195. 195.
    Vétizou M, Pitt JM, Daillère R, Lepage P, Waldschmitt N et al. 2015. Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota. Science 350:62641079–84
     [Google Scholar]
  196. 196.
    Vila AV, Imhann F, Collij V, Jankipersadsing SA, Gurry T et al. 2018. Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome. Sci. Transl. Med. 10:472eaap8914
     [Google Scholar]
  197. 197.
    Walter J, Armet AM, Finlay BB, Shanahan F. 2020. Establishing or exaggerating causality for the gut microbiome: lessons from human microbiota-associated rodents. Cell 180:2221–32
     [Google Scholar]
  198. 198.
    Wang D, Hu B, Hu C, Zhu F, Liu X et al. 2020. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China. JAMA 323:111061–69
     [Google Scholar]
  199. 199.
    Weingarden AR, Chen C, Bobr A, Yao D, Lu Y et al. 2014. Microbiota transplantation restores normal fecal bile acid composition in recurrent Clostridium difficile infection. Am. J. Physiol. Gastrointest. Liver Physiol. 306:4310–19
     [Google Scholar]
  200. 200.
    Weinstock DM, Conlon M, Iovino C, Aubrey T, Gudiol C et al. 2007. Colonization, bloodstream infection, and mortality caused by vancomycin-resistant Enterococcus early after allogeneic hematopoietic stem cell transplant. Biol. Blood Marrow Transplant. 13:5615–21
     [Google Scholar]
  201. 201.
    Wilson KH. 1993. The microecology of Clostridium difficile. Clin. Infect. Dis. 16:Suppl. 4S214–18
     [Google Scholar]
  202. 202.
    Wilson KH, Kennedy MJ, Fekety FR. 1982. Use of sodium taurocholate to enhance spore recovery on a medium selective for Clostridium difficile. J. Clin. Microbiol. 15:3443–46
     [Google Scholar]
  203. 203.
    Wilson KH, Perini F. 1988. Role of competition for nutrients in suppression of Clostridium difficile by the colonic microflora. Infect. Immun. 56:102610–14
     [Google Scholar]
  204. 204.
    Wilson KH, Sheagren JN, Freter R. 1985. Population dynamics of ingested Clostridium difficile in the gastrointestinal tract of the Syrian hamster. J. Infect. Dis. 151:2355–61
     [Google Scholar]
  205. 205.
    Wilson KH, Silva J, Fekety FR. 1981. Suppression of Clostridium difficile by normal hamster cecal flora and prevention of antibiotic-associated cecitis. Infect. Immun. 34:2626–28
     [Google Scholar]
  206. 206.
    Wlodarska M, Luo C, Kolde R, d'Hennezel E, Annand JW et al. 2017. Indoleacrylic acid produced by commensal Peptostreptococcus species suppresses inflammation. Cell Host Microbe 22:125–37.e6
     [Google Scholar]
  207. 207.
    Wu H, Esteve E, Tremaroli V, Khan MT, Caesar R et al. 2017. Metformin alters the gut microbiome of individuals with treatment-naive type 2 diabetes, contributing to the therapeutic effects of the drug. Nat. Med. 23:7850–58
     [Google Scholar]
  208. 208.
    Wu H, Tremaroli V, Schmidt C, Lundqvist A, Olsson LM et al. 2020. The gut microbiota in prediabetes and diabetes: a population-based cross-sectional study. Cell Metab 32:3379–90.e3
     [Google Scholar]
  209. 209.
    Yang T, Santisteban MM, Rodriguez V, Li E, Ahmari N et al. 2015. Gut dysbiosis is linked to hypertension. Hypertension 65:61331–40
     [Google Scholar]
  210. 210.
    Yilmaz B, Juillerat P, Øyås O, Ramon C, Bravo FD et al. 2019. Microbial network disturbances in relapsing refractory Crohn's disease. Nat. Med. 25:2323–36
     [Google Scholar]
  211. 211.
    Zhang C, Wu Z, Li JW, Zhao H, Wang GQ. 2020. Cytokine release syndrome in severe COVID-19: Interleukin-6 receptor antagonist tocilizumab may be the key to reduce mortality. Int. J. Antimicrob. Agents 55:5105954
     [Google Scholar]
  212. 212.
    Zhang L, Bahl MI, Roager HM, Fonvig CE, Hellgren LI et al. 2017. Environmental spread of microbes impacts the development of metabolic phenotypes in mice transplanted with microbial communities from humans. ISME J 11:3676–90
     [Google Scholar]
  213. 213.
    Zhang S, Palazuelos-Munoz S, Balsells EM, Nair H, Chit A, Kyaw MH. 2016. Cost of hospital management of Clostridium difficile infection in United States—a meta-analysis and modelling study. BMC Infect. Dis. 16:447
     [Google Scholar]
  214. 214.
    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. 21:8895–905
     [Google Scholar]
  215. 215.
    Zhang ZJ, Pedicord VA, Peng T, Hang HC. 2020. Site-specific acylation of a bacterial virulence regulator attenuates infection. Nat. Chem. Biol. 16:195–103
     [Google Scholar]
  216. 216.
    Zhao L, Zhang F, Ding X, Wu G, Lam YY et al. 2018. Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes. Science 359:63801151–56
     [Google Scholar]
  217. 217.
    Zuo T, Zhang F, Lui GCY, Yeoh YK, Li AYL et al. 2020. Alterations in gut microbiota of patients with COVID-19 during time of hospitalization. Gastroenterology 159:3944–55.e8
     [Google Scholar]
/content/journals/10.1146/annurev-micro-041020-022206
Loading
  • Article Type: Review Article

Most Cited Most Cited RSS feed

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