1932

Abstract

Food has a major impact on all aspects of health. Recent data suggest that food composition can also affect susceptibility to infections by enteropathogenic bacteria. Here, we discuss how food may alter the microbiota as well as mucosal defenses and how this can affect infection. Typhimurium diarrhea serves as a paradigm, and complementary evidence comes from other pathogens. We discuss the effects of food composition on colonization resistance, host defenses, and the infection process as well as the merits and limitations of mouse models and experimental foods, which are available to decipher the underlying mechanisms.

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2020-09-08
2024-06-17
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Literature Cited

  1. 1. 
    Ackermann M, Stecher B, Freed NE, Songhet P, Hardt WD, Doebeli M 2008. Self-destructive cooperation mediated by phenotypic noise. Nature 454:987–90
    [Google Scholar]
  2. 2. 
    Aghaali M, Mohebi S, Heydari H 2015. Prevalence of asymptomatic brucellosis in children 7 to 12 years old. Interdiscip. Perspect. Infect. Dis. 2015:187369
    [Google Scholar]
  3. 3. 
    Alva-Murillo N, Ochoa-Zarzosa A, Lopez-Meza JE 2012. Short chain fatty acids (propionic and hexanoic) decrease Staphylococcus aureus internalization into bovine mammary epithelial cells and modulate antimicrobial peptide expression. Vet. Microbiol. 155:324–31
    [Google Scholar]
  4. 4. 
    Anderson KL, Salyers AA. 1989. Biochemical evidence that starch breakdown by Bacteroides thetaiotaomicron involves outer membrane starch-binding sites and periplasmic starch-degrading enzymes. J. Bacteriol. 171:3192–98
    [Google Scholar]
  5. 5. 
    Arike L, Holmen-Larsson J, Hansson GC 2017. Intestinal Muc2 mucin O-glycosylation is affected by microbiota and regulated by differential expression of glycosyltranferases. Glycobiology 27:318–28
    [Google Scholar]
  6. 6. 
    Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T et al. 2011. Enterotypes of the human gut microbiome. Nature 473:174–80
    [Google Scholar]
  7. 7. 
    Axelrad JE, Olen O, Askling J, Lebwohl B, Khalili H et al. 2019. Gastrointestinal infection increases odds of inflammatory bowel disease in a nationwide case-control study. Clin. Gastroenterol. Hepatol. 17:1311–22.e7
    [Google Scholar]
  8. 8. 
    Bakkeren E, Huisman JS, Fattinger SA, Hausmann A, Furter M et al. 2019. Salmonella persisters promote the spread of antibiotic resistance plasmids in the gut. Nature 573:276–80
    [Google Scholar]
  9. 9. 
    Baquero F, Moreno F. 1984. The microcins. FEMS Microbiol. Lett. 23:117–24
    [Google Scholar]
  10. 10. 
    Barthel M, Hapfelmeier S, Quintanilla-Martinez L, Kremer M, Rohde M et al. 2003. Pretreatment of mice with streptomycin provides a Salmonella enterica serovar Typhimurium colitis model that allows analysis of both pathogen and host. Infect. Immun. 71:2839–58
    [Google Scholar]
  11. 11. 
    Basler M, Ho BT, Mekalanos JJ 2013. Tit-for-tat: type VI secretion system counterattack during bacterial cell-cell interactions. Cell 152:884–94
    [Google Scholar]
  12. 12. 
    Baxter NT, Schmidt AW, Venkataraman A, Kim KS, Waldron C, Schmidt TM 2019. Dynamics of human gut microbiota and short-chain fatty acids in response to dietary interventions with three fermentable fibers. mBio 10:e02566–18
    [Google Scholar]
  13. 13. 
    Benkerroum N, Sandine WE. 1988. Inhibitory action of nisin against Listeria monocytogenes. J. Dairy Sci 71:3237–45
    [Google Scholar]
  14. 14. 
    Bergstrom KS, Kissoon-Singh V, Gibson DL, Ma C, Montero M et al. 2010. Muc2 protects against lethal infectious colitis by disassociating pathogenic and commensal bacteria from the colonic mucosa. PLOS Pathog 6:e1000902
    [Google Scholar]
  15. 15. 
    Berry S, Valdes A, Davies R, Khatib HA, Delahanty L et al. 2019. Large inter-individual variation in postprandial lipemia following a mixed meal in over 1000 twins and singletons from the UK and US: the PREDICT I study (OR19–06–19). Curr. Dev. Nutr. 3:Suppl. 1 nzz046.OR19-06-19
    [Google Scholar]
  16. 16. 
    Black RE, Levine MM, Clements ML, Hughes TP, Blaser MJ 1988. Experimental Campylobacter jejuni infection in humans. J. Infect. Dis. 157:472–79
    [Google Scholar]
  17. 17. 
    Bortolussi R. 2008. Listeriosis: a primer. CMAJ 179:795–97
    [Google Scholar]
  18. 18. 
    Bosak J, Micenkova L, Hrala M, Pomorska K, Kunova Bosakova M et al. 2018. Colicin FY inhibits pathogenic Yersinia enterocolitica in mice. Sci. Rep. 8:12242
    [Google Scholar]
  19. 19. 
    Brandl K, Plitas G, Mihu CN, Ubeda C, Jia T et al. 2008. Vancomycin-resistant enterococci exploit antibiotic-induced innate immune deficits. Nature 455:804–7
    [Google Scholar]
  20. 20. 
    Brandl K, Plitas G, Schnabl B, DeMatteo RP, Pamer EG 2007. MyD88-mediated signals induce the bactericidal lectin RegIIIγ and protect mice against intestinal Listeria monocytogenes infection. J. Exp. Med. 204:1891–900
    [Google Scholar]
  21. 21. 
    Bronner DN, Faber F, Olsan EE, Byndloss MX, Sayed NA et al. 2018. Genetic ablation of butyrate utilization attenuates gastrointestinal Salmonella disease. Cell Host Microbe 23:266–73.e4
    [Google Scholar]
  22. 22. 
    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 25:668–80.e7
    [Google Scholar]
  23. 23. 
    Brugiroux S, Beutler M, Pfann C, Garzetti D, Ruscheweyh HJ et al. 2016. Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium. Nat. Microbiol. 2:16215
    [Google Scholar]
  24. 24. 
    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 517:205–8
    [Google Scholar]
  25. 25. 
    Byndloss MX, Olsan EE, Rivera-Chavez F, Tiffany CR, Cevallos SA et al. 2017. Microbiota-activated PPAR-γ signaling inhibits dysbiotic Enterobacteriaceae expansion. Science 357:570–75
    [Google Scholar]
  26. 26. 
    Carmody RN, Bisanz JE, Bowen BP, Maurice CF, Lyalina S et al. 2019. Cooking shapes the structure and function of the gut microbiome. Nat. Microbiol. 4:122052–63
    [Google Scholar]
  27. 27. 
    Carmody RN, Gerber GK, Luevano JM Jr, Gatti DM, Somes L et al. 2015. Diet dominates host genotype in shaping the murine gut microbiota. Cell Host Microbe 17:72–84
    [Google Scholar]
  28. 28. 
    Cash HL, Whitham CV, Behrendt CL, Hooper LV 2006. Symbiotic bacteria direct expression of an intestinal bactericidal lectin. Science 313:1126–30
    [Google Scholar]
  29. 29. 
    Cent. Dis. Control Prev 2012. Pathogens causing US foodborne illnesses, hospitalizations, and deaths, 2000–2008 Fact sheet, Cent. Dis. Control Prev Atlanta, GA: www.cdc.gov/foodborneburden/PDFs/pathogens-complete-list-01-12.pdf
    [Google Scholar]
  30. 30. 
    Cerqueira FM, Photenhauer AL, Pollet RM, Brown HA, Koropatkin NM 2019. Starch digestion by gut bacteria: crowdsourcing for carbs. Trends Microbiol 28:295–108
    [Google Scholar]
  31. 31. 
    Chan JM, Bhinder G, Sham HP, Ryz N, Huang T et al. 2013. CD4+ T cells drive goblet cell depletion during Citrobacter rodentium infection. Infect. Immun. 81:4649–58
    [Google Scholar]
  32. 32. 
    Chatterjee A, Johnson CN, Luong P, Hullahalli K, McBride SW et al. 2019. Bacteriophage resistance alters antibiotic-mediated intestinal expansion of enterococci. Infect. Immun. 87:6e00085–19
    [Google Scholar]
  33. 33. 
    Chatzidaki-Livanis M, Geva-Zatorsky N, Comstock LE 2016. Bacteroides fragilis type VI secretion systems use novel effector and immunity proteins to antagonize human gut Bacteroidales species. PNAS 113:3627–32
    [Google Scholar]
  34. 34. 
    Chen T, Leung RK, Zhou Z, Liu R, Zhang X, Zhang L 2014. Investigation of key interventions for shigellosis outbreak control in China. PLOS ONE 9:e95006
    [Google Scholar]
  35. 35. 
    Choi SH, Kim Y, Oh S, Oh S, Chun T, Kim SH 2014. Inhibitory effect of skatole (3-methylindole) on enterohemorrhagic Escherichia coli O157:H7 ATCC 43894 biofilm formation mediated by elevated endogenous oxidative stress. Lett. Appl. Microbiol. 58:454–61
    [Google Scholar]
  36. 36. 
    Chung H, Pamp SJ, Hill JA, Surana NK, Edelman SM et al. 2012. Gut immune maturation depends on colonization with a host-specific microbiota. Cell 149:1578–93
    [Google Scholar]
  37. 37. 
    Connolly JP, Gabrielsen M, Goldstone RJ, Grinter R, Wang D et al. 2016. A highly conserved bacterial D-serine uptake system links host metabolism and virulence. PLOS Pathog 12:e1005359
    [Google Scholar]
  38. 38. 
    Corr SC, Li Y, Riedel CU, O'Toole PW, Hill C, Gahan CG 2007. Bacteriocin production as a mechanism for the antiinfective activity of Lactobacillus salivarius UCC118. PNAS 104:7617–21
    [Google Scholar]
  39. 39. 
    Costea PI, Hildebrand F, Arumugam M, Backhed F, Blaser MJ et al. 2018. Enterotypes in the landscape of gut microbial community composition. Nat. Microbiol. 3:8–16
    [Google Scholar]
  40. 40. 
    Cremer J, Arnoldini M, Hwa T 2017. Effect of water flow and chemical environment on microbiota growth and composition in the human colon. PNAS 114:6438–43
    [Google Scholar]
  41. 41. 
    Cremer J, Segota I, Yang CY, Arnoldini M, Sauls JT et al. 2016. Effect of flow and peristaltic mixing on bacterial growth in a gut-like channel. PNAS 113:11414–19
    [Google Scholar]
  42. 42. 
    Croxen MA, Law RJ, Scholz R, Keeney KM, Wlodarska M, Finlay BB 2013. Recent advances in understanding enteric pathogenic Escherichia coli. Clin. Microbiol. Rev 26:822–80
    [Google Scholar]
  43. 43. 
    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
    [Google Scholar]
  44. 44. 
    Deriu E, Liu JZ, Pezeshki M, Edwards RA, Ochoa RJ et al. 2013. Probiotic bacteria reduce Salmonella Typhimurium intestinal colonization by competing for iron. Cell Host Microbe 14:26–37
    [Google Scholar]
  45. 45. 
    Desai MS, Seekatz AM, Koropatkin NM, Kamada N, Hickey CA et al. 2016. A dietary fiber-deprived gut microbiota degrades the colonic mucus barrier and enhances pathogen susceptibility. Cell 167:1339–53.e21
    [Google Scholar]
  46. 46. 
    Dessein R, Gironella M, Vignal C, Peyrin-Biroulet L, Sokol H et al. 2009. Toll-like receptor 2 is critical for induction of Reg3β expression and intestinal clearance of Yersinia pseudotuberculosis. Gut 58:771–76
    [Google Scholar]
  47. 47. 
    Dewhirst FE, Chien CC, Paster BJ, Ericson RL, Orcutt RP et al. 1999. Phylogeny of the defined murine microbiota: altered Schaedler flora. Appl. Environ. Microbiol. 65:3287–92
    [Google Scholar]
  48. 48. 
    Dhital S, Warren FJ, Butterworth PJ, Ellis PR, Gidley MJ 2017. Mechanisms of starch digestion by α-amylase—structural basis for kinetic properties. Crit. Rev. Food Sci. Nutr. 57:875–92
    [Google Scholar]
  49. 49. 
    Diard M, Bakkeren E, Cornuault JK, Moor K, Hausmann A et al. 2017. Inflammation boosts bacteriophage transfer between Salmonella spp. Science 355:1211–15
    [Google Scholar]
  50. 50. 
    Diard M, Garcia V, Maier L, Remus-Emsermann MN, Regoes RR et al. 2013. Stabilization of cooperative virulence by the expression of an avirulent phenotype. Nature 494:353–56
    [Google Scholar]
  51. 51. 
    Duan Y, Llorente C, Lang S, Brandl K, Chu H et al. 2019. Bacteriophage targeting of gut bacterium attenuates alcoholic liver disease. Nature 575:505–11
    [Google Scholar]
  52. 52. 
    Ducarmon QR, Zwittink RD, Hornung BVH, van Schaik W, Young VB, Kuijper EJ 2019. Gut microbiota and colonization resistance against bacterial enteric infection. Microbiol. Mol. Biol. Rev. 83:3e00007–19
    [Google Scholar]
  53. 53. 
    Duerkop BA, Kleiner M, Paez-Espino D, Zhu W, Bushnell B et al. 2018. Murine colitis reveals a disease-associated bacteriophage community. Nat. Microbiol. 3:1023–31
    [Google Scholar]
  54. 54. 
    Earle KA, Billings G, Sigal M, Lichtman JS, Hansson GC et al. 2015. Quantitative imaging of gut microbiota spatial organization. Cell Host Microbe 18:478–88
    [Google Scholar]
  55. 55. 
    Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L et al. 2005. Diversity of the human intestinal microbial flora. Science 308:1635–38
    [Google Scholar]
  56. 56. 
    El Kaoutari A, Armougom F, Gordon JI, Raoult D, Henrissat B 2013. The abundance and variety of carbohydrate-active enzymes in the human gut microbiota. Nat. Rev. Microbiol. 11:497–504
    [Google Scholar]
  57. 57. 
    Endt K, Stecher B, Chaffron S, Slack E, Tchitchek N et al. 2010. The microbiota mediates pathogen clearance from the gut lumen after non-typhoidal Salmonella diarrhea. PLOS Pathog 6:e1001097
    [Google Scholar]
  58. 58. 
    Enserink R, Scholts R, Bruijning-Verhagen P, Duizer E, Vennema H et al. 2014. High detection rates of enteropathogens in asymptomatic children attending day care. PLOS ONE 9:e89496
    [Google Scholar]
  59. 59. 
    Faith JJ, McNulty NP, Rey FE, Gordon JI 2011. Predicting a human gut microbiota's response to diet in gnotobiotic mice. Science 333:101–4
    [Google Scholar]
  60. 60. 
    Faundez G, Figueroa G, Troncoso M, Cabello FC 1988. Characterization of enteroinvasive Escherichia coli strains isolated from children with diarrhea in Chile. J. Clin. Microbiol. 26:928–32
    [Google Scholar]
  61. 61. 
    FELASA Work. Group Revis. Guidel. Health Monit. Rodents Rabbits, Mähler Convenor M, Berard M, Feinstein R, Gallagher A, et al. 2014. FELASA recommendations for the health monitoring of mouse, rat, hamster, guinea pig and rabbit colonies in breeding and experimental units. Lab. Anim 48:178–92 Erratum. 2015. Lab. Anim. 49:88
    [Google Scholar]
  62. 62. 
    Fischbach MA, Sonnenburg JL. 2011. Eating for two: how metabolism establishes interspecies interactions in the gut. Cell Host Microbe 10:336–47
    [Google Scholar]
  63. 63. 
    Fischer S, Kittler S, Klein G, Glunder G 2013. Impact of a single phage and a phage cocktail application in broilers on reduction of Campylobacter jejuni and development of resistance. PLOS ONE 8:e78543
    [Google Scholar]
  64. 64. 
    Flint HJ, Bayer EA, Rincon MT, Lamed R, White BA 2008. Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis. Nat. Rev. Microbiol. 6:121–31
    [Google Scholar]
  65. 65. 
    Frazao N, Sousa A, Lassig M, Gordo I 2019. Horizontal gene transfer overrides mutation in Escherichia coli colonizing the mammalian gut. PNAS 116:17906–15
    [Google Scholar]
  66. 66. 
    Fukuda S, Toh H, Hase K, Oshima K, Nakanishi Y et al. 2011. Bifidobacteria can protect from enteropathogenic infection through production of acetate. Nature 469:543–47
    [Google Scholar]
  67. 67. 
    Furter M, Sellin ME, Hansson GC, Hardt WD 2019. Mucus architecture and near-surface swimming affect distinct Salmonella Typhimurium infection patterns along the murine intestinal tract. Cell Rep 27:2665–78.e3
    [Google Scholar]
  68. 68. 
    Garcia-Gutierrez E, Mayer MJ, Cotter PD, Narbad A 2019. Gut microbiota as a source of novel antimicrobials. Gut Microbes 10:1–21
    [Google Scholar]
  69. 69. 
    Garud NR, Good BH, Hallatschek O, Pollard KS 2019. Evolutionary dynamics of bacteria in the gut microbiome within and across hosts. PLOS Biol 17:e3000102
    [Google Scholar]
  70. 70. 
    Garzetti D, Brugiroux S, Bunk B, Pukall R, McCoy KD et al. 2017. High-quality whole-genome sequences of the oligo-mouse-microbiota bacterial community. Genome Announc 5:42e00758-17
    [Google Scholar]
  71. 71. 
    Giannattasio A, Guarino A, Lo Vecchio A 2016. Management of children with prolonged diarrhea. F1000Research 5:206
    [Google Scholar]
  72. 72. 
    Gielda LM, DiRita VJ. 2012. Zinc competition among the intestinal microbiota. mBio 3:e00171-12
    [Google Scholar]
  73. 73. 
    Glass RI, Stoll BJ, Huq MI, Struelens MJ, Blaser M, Kibriya AK 1983. Epidemiologic and clinical features of endemic Campylobacter jejuni infection in Bangladesh. J. Infect. Dis. 148:292–96
    [Google Scholar]
  74. 74. 
    Glenwright AJ, Pothula KR, Bhamidimarri SP, Chorev DS, Basle A et al. 2017. Structural basis for nutrient acquisition by dominant members of the human gut microbiota. Nature 541:407–11
    [Google Scholar]
  75. 75. 
    Goldberg EL, Molony RD, Kudo E, Sidorov S, Kong Y et al. 2019. Ketogenic diet activates protective γδ T cell responses against influenza virus infection. Sci. Immunol. 4:41eaav2026
    [Google Scholar]
  76. 76. 
    Grif K, Hein I, Wagner M, Brandl E, Mpamugo O et al. 2001. Prevalence and characterization of Listeria monocytogenes in the feces of healthy Austrians. Wien. Klin. Wochenschr. 113:737–42
    [Google Scholar]
  77. 77. 
    Guo C, Xie S, Chi Z, Zhang J, Liu Y et al. 2016. Bile acids control inflammation and metabolic disorder through inhibition of NLRP3 inflammasome. Immunity 45:802–16
    [Google Scholar]
  78. 78. 
    Hang S, Paik D, Yao L, Kim E, Trinath J et al. 2019. Bile acid metabolites control TH17 and Treg cell differentiation. Nature 576:7785143–48 Erratum. 2020. Nature 579(7798):E7
    [Google Scholar]
  79. 79. 
    Hansen NW, Sams A. 2018. The microbiotic highway to health—new perspective on food structure, gut microbiota, and host inflammation. Nutrients 10:111590
    [Google Scholar]
  80. 80. 
    Hapfelmeier S, Muller AJ, Stecher B, Kaiser P, Barthel M et al. 2008. Microbe sampling by mucosal dendritic cells is a discrete, MyD88-independent step in ΔinvG S. Typhimurium colitis. J. Exp. Med. 205:437–50
    [Google Scholar]
  81. 81. 
    Hapfelmeier S, Stecher B, Barthel M, Kremer M, Muller AJ et al. 2005. The Salmonella pathogenicity island (SPI)-2 and SPI-1 type III secretion systems allow Salmonella serovar Typhimurium to trigger colitis via MyD88-dependent and MyD88-independent mechanisms. J. Immunol. 174:1675–85
    [Google Scholar]
  82. 82. 
    Hennet T, Borsig L. 2016. Breastfed at Tiffany's. Trends Biochem. Sci. 41:508–18
    [Google Scholar]
  83. 83. 
    Herp S, Brugiroux S, Garzetti D, Ring D, Jochum LM et al. 2019. Mucispirillum schaedleri antagonizes Salmonella virulence to protect mice against colitis. Cell Host Microbe 25:681–94.e8
    [Google Scholar]
  84. 84. 
    Hillman ET, Lu H, Yao T, Nakatsu CH 2017. Microbial ecology along the gastrointestinal tract. Microbes Environ 32:300–13
    [Google Scholar]
  85. 85. 
    Hoces D, Arnoldini M, Diard M, Loverdo C, Slack E 2020. Growing, evolving and sticking in a flowing environment: understanding IgA interactions with bacteria in the gut. Immunology 159:52–62
    [Google Scholar]
  86. 86. 
    Hochbaum AI, Kolodkin-Gal I, Foulston L, Kolter R, Aizenberg J, Losick R 2011. Inhibitory effects of d-amino acids on Staphylococcus aureus biofilm development. J. Bacteriol. 193:5616–22
    [Google Scholar]
  87. 87. 
    Hossain MA, Hasan KZ, Albert MJ 1994. Shigella carriers among non-diarrhoeal children in an endemic area of shigellosis in Bangladesh. Trop. Geogr. Med. 46:40–42
    [Google Scholar]
  88. 88. 
    Hu J, Torres AG. 2015. Enteropathogenic Escherichia coli: foe or innocent bystander. Clin. Microbiol. Infect. 21:729–34
    [Google Scholar]
  89. 89. 
    Hugenholtz F, de Vos WM 2018. Mouse models for human intestinal microbiota research: a critical evaluation. Cell Mol. Life Sci. 75:149–60
    [Google Scholar]
  90. 90. 
    Hung CC, Garner CD, Slauch JM, Dwyer ZW, Lawhon SD et al. 2013. The intestinal fatty acid propionate inhibits Salmonella invasion through the post-translational control of HilD. Mol. Microbiol. 87:1045–60
    [Google Scholar]
  91. 91. 
    Ivanov II, Atarashi K, Manel N, Brodie EL, Shima T et al. 2009. Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell 139:485–98
    [Google Scholar]
  92. 92. 
    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 24:296–307.e7
    [Google Scholar]
  93. 93. 
    Janssen R, Krogfelt KA, Cawthraw SA, van Pelt W, Wagenaar JA, Owen RJ 2008. Host-pathogen interactions in Campylobacter infections: the host perspective. Clin. Microbiol. Rev. 21:505–18
    [Google Scholar]
  94. 94. 
    Jertborn M, Haglind P, Iwarson S, Svennerholm AM 1990. Estimation of symptomatic and asymptomatic Salmonella infections. Scand. J. Infect. Dis. 22:451–55
    [Google Scholar]
  95. 95. 
    Jimenez AG, Ellermann M, Abbott W, Sperandio V 2020. Diet-derived galacturonic acid regulates virulence and intestinal colonization in enterohaemorrhagic Escherichia coli and Citrobacter rodentium. Nat. Microbiol 5:2368–78
    [Google Scholar]
  96. 96. 
    Johansson ME, Hansson GC. 2016. Immunological aspects of intestinal mucus and mucins. Nat. Rev. Immunol. 16:639–49
    [Google Scholar]
  97. 97. 
    Johansson ME, Jakobsson HE, Holmen-Larsson J, Schutte A, Ermund A et al. 2015. Normalization of host intestinal mucus layers requires long-term microbial colonization. Cell Host Microbe 18:582–92
    [Google Scholar]
  98. 98. 
    Johansson ME, Larsson JM, Hansson GC 2011. The two mucus layers of colon are organized by the MUC2 mucin, whereas the outer layer is a legislator of host-microbial interactions. PNAS 108:Suppl. 14659–65
    [Google Scholar]
  99. 99. 
    Jones SA, Gibson T, Maltby RC, Chowdhury FZ, Stewart V et al. 2011. Anaerobic respiration of Escherichia coli in the mouse intestine. Infect. Immun. 79:4218–26
    [Google Scholar]
  100. 100. 
    Journet L, Cascales E. 2016. The type VI secretion system in Escherichia coli and related species. EcoSal Plus 7:1 https://doi.org/10.1128/ecosalplus.ESP-0009-2015
    [Crossref] [Google Scholar]
  101. 101. 
    Kaiser P, Diard M, Stecher B, Hardt WD 2012. The streptomycin mouse model for Salmonella diarrhea: functional analysis of the microbiota, the pathogen's virulence factors, and the host's mucosal immune response. Immunol. Rev. 245:56–83
    [Google Scholar]
  102. 102. 
    Kamada N, Kim YG, Sham HP, Vallance BA, Puente JL et al. 2012. Regulated virulence controls the ability of a pathogen to compete with the gut microbiota. Science 336:1325–29
    [Google Scholar]
  103. 103. 
    Kirk MD, Pires SM, Black RE, Caipo M, Crump JA et al. 2015. World Health Organization estimates of the global and regional disease burden of 22 foodborne bacterial, protozoal, and viral diseases, 2010: a data synthesis. PLOS Med 12:e1001921
    [Google Scholar]
  104. 104. 
    Kitamoto S, Alteri CJ, Rodrigues M, Nagao-Kitamoto H, Sugihara K et al. 2020. Dietary l-serine confers a competitive fitness advantage to Enterobacteriaceae in the inflamed gut. Nat. Microbiol. 5:116–25
    [Google Scholar]
  105. 105. 
    Klose CS, Kiss EA, Schwierzeck V, Ebert K, Hoyler T et al. 2013. A T-bet gradient controls the fate and function of CCR6-RORγt+ innate lymphoid cells. Nature 494:261–65
    [Google Scholar]
  106. 106. 
    Klurfeld DM, Davis CD, Karp RW, Allen-Vercoe E, Chang EB et al. 2018. Considerations for best practices in studies of fiber or other dietary components and the intestinal microbiome. Am. J. Physiol. Endocrinol. Metab. 315:E1087–97
    [Google Scholar]
  107. 107. 
    Kohli N, Crisp Z, Riordan R, Li M, Alaniz RC, Jayaraman A 2018. The microbiota metabolite indole inhibits Salmonella virulence: involvement of the PhoPQ two-component system. PLOS ONE 13:e0190613
    [Google Scholar]
  108. 108. 
    Kolodziejczyk AA, Zheng D, Elinav E 2019. Diet-microbiota interactions and personalized nutrition. Nat. Rev. Microbiol. 17:12742–53
    [Google Scholar]
  109. 109. 
    Krych L, Hansen CH, Hansen AK, van den Berg FW, Nielsen DS 2013. Quantitatively different, yet qualitatively alike: a meta-analysis of the mouse core gut microbiome with a view towards the human gut microbiome. PLOS ONE 8:e62578
    [Google Scholar]
  110. 110. 
    Kurdi P, Kawanishi K, Mizutani K, Yokota A 2006. Mechanism of growth inhibition by free bile acids in lactobacilli and bifidobacteria. J. Bacteriol. 188:1979–86
    [Google Scholar]
  111. 111. 
    Kurtz DM, Glascoe R, Caviness G, Locklear J, Whiteside T et al. 2018. Acrylamide production in autoclaved rodent feed. J. Am. Assoc. Lab. Anim. Sci. 57:6703–11
    [Google Scholar]
  112. 112. 
    Kushugulova A, Forslund SK, Costea PI, Kozhakhmetov S, Khassenbekova Z et al. 2018. Metagenomic analysis of gut microbial communities from a Central Asian population. BMJ Open 8:e021682
    [Google Scholar]
  113. 113. 
    Laaveri T, Antikainen J, Pakkanen SH, Kirveskari J, Kantele A 2016. Prospective study of pathogens in asymptomatic travellers and those with diarrhoea: aetiological agents revisited. Clin. Microbiol. Infect. 22:535–41
    [Google Scholar]
  114. 114. 
    Lamichhane-Khadka R, Frye JG, Porwollik S, McClelland M, Maier RJ 2011. Hydrogen-stimulated carbon acquisition and conservation in Salmonella enterica serovar Typhimurium. J. Bacteriol. 193:5824–32
    [Google Scholar]
  115. 115. 
    Lamichhane-Khadka R, Kwiatkowski A, Maier RJ 2010. The Hyb hydrogenase permits hydrogen-dependent respiratory growth of Salmonella enterica serovar Typhimurium. mBio 1:5e00284-10a
    [Google Scholar]
  116. 116. 
    Lamont RJ, Postlethwaite R. 1986. Carriage of Listeria monocytogenes and related species in pregnant and non-pregnant women in Aberdeen, Scotland. J. Infect. 13:187–93
    [Google Scholar]
  117. 117. 
    Las Heras V, Clooney AG, Ryan FJ, Cabrera-Rubio R, Casey PG et al. 2019. Short-term consumption of a high-fat diet increases host susceptibility to Listeria monocytogenes infection. Microbiome 7:7
    [Google Scholar]
  118. 118. 
    Lawhon SD, Maurer R, Suyemoto M, Altier C 2002. Intestinal short-chain fatty acids alter Salmonella typhimurium invasion gene expression and virulence through BarA/SirA. Mol. Microbiol. 46:1451–64
    [Google Scholar]
  119. 119. 
    Leatham MP, Banerjee S, Autieri SM, Mercado-Lubo R, Conway T, Cohen PS 2009. Precolonized human commensal Escherichia coli strains serve as a barrier to E. coli O157:H7 growth in the streptomycin-treated mouse intestine. Infect. Immun. 77:2876–86
    [Google Scholar]
  120. 120. 
    Lee JH, Cho HS, Kim Y, Kim JA, Banskota S et al. 2013. Indole and 7-benzyloxyindole attenuate the virulence of Staphylococcus aureus. Appl. Microbiol. Biotechnol 97:4543–52
    [Google Scholar]
  121. 121. 
    Ley RE, Backhed F, Turnbaugh P, Lozupone CA, Knight RD, Gordon JI 2005. Obesity alters gut microbial ecology. PNAS 102:11070–75
    [Google Scholar]
  122. 122. 
    Li T, Lu X, Yang X 2013. Stachyose-enriched α-galacto-oligosaccharides regulate gut microbiota and relieve constipation in mice. J. Agric. Food Chem. 61:11825–31
    [Google Scholar]
  123. 123. 
    Lim B, Zimmermann M, Barry NA, Goodman AL 2017. Engineered regulatory systems modulate gene expression of human commensals in the gut. Cell 169:547–58.e15
    [Google Scholar]
  124. 124. 
    Litvak Y, Baumler AJ. 2019. The founder hypothesis: a basis for microbiota resistance, diversity in taxa carriage, and colonization resistance against pathogens. PLOS Pathog 15:e1007563
    [Google Scholar]
  125. 125. 
    Litvak Y, Byndloss MX, Baumler AJ 2018. Colonocyte metabolism shapes the gut microbiota. Science 362:6418eaat9076
    [Google Scholar]
  126. 126. 
    Litvak Y, Mon KKZ, Nguyen H, Chanthavixay G, Liou M et al. 2019. Commensal Enterobacteriaceae protect against Salmonella colonization through oxygen competition. Cell Host Microbe 25:128–39.e5
    [Google Scholar]
  127. 127. 
    Louis P, Flint HJ. 2017. Formation of propionate and butyrate by the human colonic microbiota. Environ. Microbiol. 19:29–41
    [Google Scholar]
  128. 128. 
    Lozer DM, Souza TB, Monfardini MV, Vicentini F, Kitagawa SS et al. 2013. Genotypic and phenotypic analysis of diarrheagenic Escherichia coli strains isolated from Brazilian children living in low socioeconomic level communities. BMC Infect. Dis. 13:418
    [Google Scholar]
  129. 129. 
    MacGowan AP, Bowker K, McLauchlin J, Bennett PM, Reeves DS 1994. The occurrence and seasonal changes in the isolation of Listeria spp. in shop bought food stuffs, human faeces, sewage and soil from urban sources. Int. J. Food Microbiol. 21:325–34
    [Google Scholar]
  130. 130. 
    MacIntyre DL, Miyata ST, Kitaoka M, Pukatzki S 2010. The Vibrio cholerae type VI secretion system displays antimicrobial properties. PNAS 107:19520–24
    [Google Scholar]
  131. 131. 
    Macpherson AJ, Harris NL. 2004. Interactions between commensal intestinal bacteria and the immune system. Nat. Rev. Immunol. 4:478–85
    [Google Scholar]
  132. 132. 
    Maier L, Barthel M, Stecher B, Maier RJ, Gunn JS, Hardt WD 2014. Salmonella Typhimurium strain ATCC14028 requires H2-hydrogenases for growth in the gut, but not at systemic sites. PLOS ONE 9:e110187
    [Google Scholar]
  133. 133. 
    Maier L, Pruteanu M, Kuhn M, Zeller G, Telzerow A et al. 2018. Extensive impact of non-antibiotic drugs on human gut bacteria. Nature 555:623–28
    [Google Scholar]
  134. 134. 
    Maier L, Vyas R, Cordova CD, Lindsay H, Schmidt TS et al. 2013. Microbiota-derived hydrogen fuels Salmonella Typhimurium invasion of the gut ecosystem. Cell Host Microbe 14:641–51
    [Google Scholar]
  135. 135. 
    Maier RJ. 2005. Use of molecular hydrogen as an energy substrate by human pathogenic bacteria. Biochem. Soc. Trans. 33:83–85
    [Google Scholar]
  136. 136. 
    Makki K, Deehan EC, Walter J, Backhed F 2018. The impact of dietary fiber on gut microbiota in host health and disease. Cell Host Microbe 23:705–15
    [Google Scholar]
  137. 137. 
    Maltby R, Leatham-Jensen MP, Gibson T, Cohen PS, Conway T 2013. Nutritional basis for colonization resistance by human commensal Escherichia coli strains HS and Nissle 1917 against E. coli O157:H7 in the mouse intestine. PLOS ONE 8:e53957
    [Google Scholar]
  138. 138. 
    Mamantopoulos M, Ronchi F, McCoy KD, Wullaert A 2018. Inflammasomes make the case for littermate-controlled experimental design in studying host-microbiota interactions. Gut Microbes 9:374–81
    [Google Scholar]
  139. 139. 
    Marion S, Studer N, Desharnais L, Menin L, Escrig S et al. 2019. In vitro and in vivo characterization of Clostridium scindens bile acid transformations. Gut Microbes 10:481–503
    [Google Scholar]
  140. 140. 
    Martens EC, Lowe EC, Chiang H, Pudlo NA, Wu M et al. 2011. Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts. PLOS Biol 9:e1001221
    [Google Scholar]
  141. 141. 
    Marteyn B, West NP, Browning DF, Cole JA, Shaw JG et al. 2010. Modulation of Shigella virulence in response to available oxygen in vivo. Nature 465:355–58
    [Google Scholar]
  142. 142. 
    Martinez-Guryn K, Hubert N, Frazier K, Urlass S, Musch MW et al. 2018. Small intestine microbiota regulate host digestive and absorptive adaptive responses to dietary lipids. Cell Host Microbe 23:458–69.e5
    [Google Scholar]
  143. 143. 
    Martinez I, Muller CE, Walter J 2013. Long-term temporal analysis of the human fecal microbiota revealed a stable core of dominant bacterial species. PLOS ONE 8:e69621
    [Google Scholar]
  144. 144. 
    McCormack WM, Islam MS, Fahimuddin M, Mosley WH 1969. A community study of inapparent cholera infections. Am. J. Epidemiol. 89:658–64
    [Google Scholar]
  145. 145. 
    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 25:695–705.e5
    [Google Scholar]
  146. 146. 
    McNorton MM, Maier RJ. 2012. Roles of H2 uptake hydrogenases in Shigella flexneri acid tolerance. Microbiology 158:2204–12
    [Google Scholar]
  147. 147. 
    Megraud F, Boudraa G, Bessaoud K, Bensid S, Dabis F et al. 1990. Incidence of Campylobacter infection in infants in western Algeria and the possible protective role of breast feeding. Epidemiol. Infect. 105:73–78
    [Google Scholar]
  148. 148. 
    Miki T, Goto R, Fujimoto M, Okada N, Hardt WD 2017. The bactericidal lectin RegIIIβ prolongs gut colonization and enteropathy in the streptomycin mouse model for Salmonella diarrhea. Cell Host Microbe 21:195–207
    [Google Scholar]
  149. 149. 
    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. 81:4e00036-17
    [Google Scholar]
  150. 150. 
    Misselwitz B, Butter M, Verbeke K, Fox MR 2019. Update on lactose malabsorption and intolerance: pathogenesis, diagnosis and clinical management. Gut 68:2080–91
    [Google Scholar]
  151. 151. 
    Momose Y, Hirayama K, Itoh K 2008. Competition for proline between indigenous Escherichia coli and E. coli O157:H7 in gnotobiotic mice associated with infant intestinal microbiota and its contribution to the colonization resistance against E. coli O157:H7. Antonie Van Leeuwenhoek 94:165–71
    [Google Scholar]
  152. 152. 
    Moor K, Diard M, Sellin ME, Felmy B, Wotzka SY et al. 2017. High-avidity IgA protects the intestine by enchaining growing bacteria. Nature 544:498–502
    [Google Scholar]
  153. 153. 
    Moor K, Wotzka SY, Toska A, Diard M, Hapfelmeier S, Slack E 2016. Peracetic acid treatment generates potent inactivated oral vaccines from a broad range of culturable bacterial species. Front. Immunol. 7:34
    [Google Scholar]
  154. 154. 
    Morita-Ishihara T, Iyoda S, Iguchi A, Ohnishi M 2016. Secondary Shiga toxin-producing Escherichia coli infection, Japan, 2010–2012. Emerg. Infect. Dis. 22:2181–84
    [Google Scholar]
  155. 155. 
    Muller HE. 1990. Listeria isolations from feces of patients with diarrhea and from healthy food handlers. Infection 18:97–99
    [Google Scholar]
  156. 156. 
    Nagengast FM, Grubben MJ, van Munster IP 1995. Role of bile acids in colorectal carcinogenesis. Eur. J. Cancer 31A:1067–70
    [Google Scholar]
  157. 157. 
    Nataro JP, Mai V, Johnson J, Blackwelder WC, Heimer R et al. 2006. Diarrheagenic Escherichia coli infection in Baltimore, Maryland, and New Haven, Connecticut. Clin. Infect. Dis. 43:402–7
    [Google Scholar]
  158. 158. 
    Nezami BG, Mwangi SM, Lee JE, Jeppsson S, Anitha M et al. 2014. MicroRNA 375 mediates palmitate-induced enteric neuronal damage and high-fat diet-induced delayed intestinal transit in mice. Gastroenterology 146:473–83.e3
    [Google Scholar]
  159. 159. 
    Ng KM, Ferreyra JA, Higginbottom SK, Lynch JB, Kashyap PC et al. 2013. Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens. Nature 502:96–99
    [Google Scholar]
  160. 160. 
    Nguyen B, Cuenca Vera M, Hartl J, Gül E, Bauer Ret al 2020. Import of aspartate and malate by DcuABC drives H2/fumarate respiration to promote initial Salmonella gut-lumen colonization in mice. Cell Host Microbe 27:6922–36.e
    [Google Scholar]
  161. 161. 
    Nguyen TL, Vieira-Silva S, Liston A, Raes J 2015. How informative is the mouse for human gut microbiota research. Dis. Model. Mech. 8:1–16
    [Google Scholar]
  162. 162. 
    Nuesch-Inderbinen MT, Hofer E, Hachler H, Beutin L, Stephan R 2013. Characteristics of enteroaggregative Escherichia coli isolated from healthy carriers and from patients with diarrhoea. J. Med. Microbiol. 62:1828–34
    [Google Scholar]
  163. 163. 
    Ochoa TJ, Ecker L, Barletta F, Mispireta ML, Gil AI et al. 2009. Age-related susceptibility to infection with diarrheagenic Escherichia coli among infants from periurban areas in Lima, Peru. Clin. Infect. Dis. 49:1694–702
    [Google Scholar]
  164. 164. 
    Olaimat AN, Al-Holy MA, Shahbaz HM, Al-Nabulsi AA, Abu Ghoush MH et al. 2018. Emergence of antibiotic resistance in Listeria monocytogenes isolated from food products: a comprehensive review. Compr. Rev. Food Sci. Food Saf. 17:1277–92
    [Google Scholar]
  165. 165. 
    Olesen B, Neimann J, Bottiger B, Ethelberg S, Schiellerup P et al. 2005. Etiology of diarrhea in young children in Denmark: a case-control study. J. Clin. Microbiol. 43:3636–41
    [Google Scholar]
  166. 166. 
    Onwuezobe IA, Oshun PO, Odigwe CC 2012. Antimicrobials for treating symptomatic non-typhoidal Salmonella infection. Cochrane Database Syst. Rev. 11:CD001167
    [Google Scholar]
  167. 167. 
    Pai CH, Gillis F, Tuomanen E, Marks MI 1984. Placebo-controlled double-blind evaluation of trimethoprim-sulfamethoxazole treatment of Yersinia enterocolitica gastroenteritis. J. Pediatr. 104:308–11
    [Google Scholar]
  168. 168. 
    Pandiyan P, Bhaskaran N, Zou M, Schneider E, Jayaraman S, Huehn J 2019. Microbiome dependent regulation of Tregs and Th17 cells in mucosa. Front. Immunol. 10:426
    [Google Scholar]
  169. 169. 
    Patnode ML, Beller ZW, Han ND, Cheng J, Peters SL et al. 2019. Interspecies competition impacts targeted manipulation of human gut bacteria by fiber-derived glycans. Cell 179:59–73.e13
    [Google Scholar]
  170. 170. 
    Pazzaglia G, Bourgeois AL, el Diwany K, Nour N, Badran N, Hablas R 1991. Campylobacter diarrhoea and an association of recent disease with asymptomatic shedding in Egyptian children. Epidemiol. Infect. 106:77–82
    [Google Scholar]
  171. 171. 
    Pellizzon MA, Ricci MR. 2018. The common use of improper control diets in diet-induced metabolic disease research confounds data interpretation: the fiber factor. Nutr. Metab. 15:3
    [Google Scholar]
  172. 172. 
    Pukatzki S, Ma AT, Revel AT, Sturtevant D, Mekalanos JJ 2007. Type VI secretion system translocates a phage tail spike-like protein into target cells where it cross-links actin. PNAS 104:15508–13
    [Google Scholar]
  173. 173. 
    Qadri MH, Ai-Gamdi MA, Al-Harfi RA 1995. Asymptomatic Salmonella, Shigella and intestinal parasites among primary school children in the eastern province. J. Fam. Community Med. 2:36–40
    [Google Scholar]
  174. 174. 
    Rea MC, Sit CS, Clayton E, O'Connor PM, Whittal RM et al. 2010. Thuricin CD, a posttranslationally modified bacteriocin with a narrow spectrum of activity against Clostridium difficile. PNAS 107:9352–57
    [Google Scholar]
  175. 175. 
    Rivera-Chavez F, Zhang LF, Faber F, Lopez CA, Byndloss MX et al. 2016. Depletion of butyrate-producing Clostridia from the gut microbiota drives an aerobic luminal expansion of Salmonella. Cell Host Microbe 19:443–54
    [Google Scholar]
  176. 176. 
    Rodriguez JM, Murphy K, Stanton C, Ross RP, Kober OI et al. 2015. The composition of the gut microbiota throughout life, with an emphasis on early life. Microb. Ecol. Health Dis. 26:26050
    [Google Scholar]
  177. 177. 
    Roe AJ, O'Byrne C, McLaggan D, Booth IR 2002. Inhibition of Escherichia coli growth by acetic acid: a problem with methionine biosynthesis and homocysteine toxicity. Microbiology 148:2215–22
    [Google Scholar]
  178. 178. 
    Rogier EW, Frantz AL, Bruno ME, Kaetzel CS 2014. Secretory IgA is concentrated in the outer layer of colonic mucus along with gut bacteria. Pathogens 3:390–403
    [Google Scholar]
  179. 179. 
    Ross BD, Verster AJ, Radey MC, Schmidtke DT, Pope CE et al. 2019. Human gut bacteria contain acquired interbacterial defence systems. Nature 575:224–28
    [Google Scholar]
  180. 180. 
    Rosshart SP, Vassallo BG, Angeletti D, Hutchinson DS, Morgan AP et al. 2017. Wild mouse gut microbiota promotes host fitness and improves disease resistance. Cell 171:1015–28.e13
    [Google Scholar]
  181. 181. 
    Rothschild D, Weissbrod O, Barkan E, Kurilshikov A, Korem T et al. 2018. Environment dominates over host genetics in shaping human gut microbiota. Nature 555:210–15
    [Google Scholar]
  182. 182. 
    Russell AB, Hood RD, Bui NK, LeRoux M, Vollmer W, Mougous JD 2011. Type VI secretion delivers bacteriolytic effectors to target cells. Nature 475:343–47
    [Google Scholar]
  183. 183. 
    Sannasiddappa TH, Lund PA, Clarke SR 2017. In vitro antibacterial activity of unconjugated and conjugated bile salts on Staphylococcus aureus. Front. Microbiol 8:1581
    [Google Scholar]
  184. 184. 
    Sasabe J, Miyoshi Y, Rakoff-Nahoum S, Zhang T, Mita M et al. 2016. Interplay between microbial d-amino acids and host d-amino acid oxidase modifies murine mucosal defence and gut microbiota. Nat. Microbiol. 1:16125
    [Google Scholar]
  185. 185. 
    Sassone-Corsi M, Nuccio SP, Liu H, Hernandez D, Vu CT et al. 2016. Microcins mediate competition among Enterobacteriaceae in the inflamed gut. Nature 540:280–83
    [Google Scholar]
  186. 186. 
    Satoh-Takayama N, Vosshenrich CA, Lesjean-Pottier S, Sawa S, Lochner M et al. 2008. Microbial flora drives interleukin 22 production in intestinal NKp46+ cells that provide innate mucosal immune defense. Immunity 29:958–70
    [Google Scholar]
  187. 187. 
    Schirmer M, Garner A, Vlamakis H, Xavier RJ 2019. Microbial genes and pathways in inflammatory bowel disease. Nat. Rev. Microbiol. 17:497–511
    [Google Scholar]
  188. 188. 
    Schnupf P, Gaboriau-Routhiau V, Sansonetti PJ, Cerf-Bensussan N 2017. Segmented filamentous bacteria, Th17 inducers and helpers in a hostile world. Curr. Opin. Microbiol. 35:100–9
    [Google Scholar]
  189. 189. 
    Simonsen J, Molbak K, Falkenhorst G, Krogfelt KA, Linneberg A, Teunis PF 2009. Estimation of incidences of infectious diseases based on antibody measurements. Stat. Med. 28:1882–95
    [Google Scholar]
  190. 190. 
    Simonsen J, Strid MA, Molbak K, Krogfelt KA, Linneberg A, Teunis P 2008. Sero-epidemiology as a tool to study the incidence of Salmonella infections in humans. Epidemiol. Infect. 136:895–902
    [Google Scholar]
  191. 191. 
    Smith HW, Huggins MB. 1983. Effectiveness of phages in treating experimental Escherichia coli diarrhoea in calves, piglets and lambs. J. Gen. Microbiol. 129:2659–75
    [Google Scholar]
  192. 192. 
    Smith K, McCoy KD, Macpherson AJ 2007. Use of axenic animals in studying the adaptation of mammals to their commensal intestinal microbiota. Semin. Immunol. 19:59–69
    [Google Scholar]
  193. 193. 
    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 341:569–73
    [Google Scholar]
  194. 194. 
    Smits SA, Leach J, Sonnenburg ED, Gonzalez CG, Lichtman JS et al. 2017. Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania. Science 357:802–6
    [Google Scholar]
  195. 195. 
    Songhet P, Barthel M, Stecher B, Muller AJ, Kremer M et al. 2011. Stromal IFN-γR-signaling modulates goblet cell function during Salmonella Typhimurium infection. PLOS ONE 6:e22459
    [Google Scholar]
  196. 196. 
    Sonnenburg ED, Smits SA, Tikhonov M, Higginbottom SK, Wingreen NS, Sonnenburg JL 2016. Diet-induced extinctions in the gut microbiota compound over generations. Nature 529:212–15
    [Google Scholar]
  197. 197. 
    Stecher B, Chaffron S, Kappeli R, Hapfelmeier S, Freedrich S et al. 2010. Like will to like: Abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria. PLOS Pathog 6:e1000711
    [Google Scholar]
  198. 198. 
    Stecher B, Denzler R, Maier L, Bernet F, Sanders MJ et al. 2012. Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae. PNAS 109:1269–74
    [Google Scholar]
  199. 199. 
    Stecher B, Hardt WD. 2008. The role of microbiota in infectious disease. Trends Microbiol 16:107–14
    [Google Scholar]
  200. 200. 
    Stecher B, Hardt WD. 2011. Mechanisms controlling pathogen colonization of the gut. Curr. Opin. Microbiol. 14:82–91
    [Google Scholar]
  201. 201. 
    Stecher B, Macpherson AJ, Hapfelmeier S, Kremer M, Stallmach T, Hardt WD 2005. Comparison of Salmonella enterica serovar Typhimurium colitis in germfree mice and mice pretreated with streptomycin. Infect. Immun. 73:3228–41
    [Google Scholar]
  202. 202. 
    Stelter C, Kappeli R, Konig C, Krah A, Hardt WD et al. 2011. Salmonella-induced mucosal lectin RegIIIβ kills competing gut microbiota. PLOS ONE 6:e20749
    [Google Scholar]
  203. 203. 
    Stephan R, Joutsen S, Hofer E, Sade E, Bjorkroth J et al. 2013. Characteristics of Yersinia enterocolitica biotype 1A strains isolated from patients and asymptomatic carriers. Eur. J. Clin. Microbiol. Infect. Dis. 32:869–75
    [Google Scholar]
  204. 204. 
    Stewart CJ, Ajami NJ, O'Brien JL, Hutchinson DS, Smith DP et al. 2018. Temporal development of the gut microbiome in early childhood from the TEDDY study. Nature 562:583–88
    [Google Scholar]
  205. 205. 
    Studer N, Desharnais L, Beutler M, Brugiroux S, Terrazos MA et al. 2016. Functional intestinal bile acid 7α-dehydroxylation by Clostridiumscindens associated with protection from Clostridium difficile infection in a gnotobiotic mouse model. Front. Cell Infect. Microbiol. 6:191
    [Google Scholar]
  206. 206. 
    Sturm A, Heinemann M, Arnoldini M, Benecke A, Ackermann M et al. 2011. The cost of virulence: retarded growth of Salmonella Typhimurium cells expressing type III secretion system 1. PLOS Pathog 7:e1002143
    [Google Scholar]
  207. 207. 
    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
    [Google Scholar]
  208. 208. 
    Takeuchi A. 1967. Electron microscope studies of experimental Salmonella infection. I. Penetration into the intestinal epithelium by Salmonella typhimurium. Am. J. Pathol 50:109–36
    [Google Scholar]
  209. 209. 
    Taylor DN, Echeverria P, Sethabutr O, Pitarangsi C, Leksomboon U et al. 1988. Clinical and microbiologic features of Shigella and enteroinvasive Escherichia coli infections detected by DNA hybridization. J. Clin. Microbiol. 26:1362–66
    [Google Scholar]
  210. 210. 
    Thanissery R, Winston JA, Theriot CM 2017. Inhibition of spore germination, growth, and toxin activity of clinically relevant C. difficile strains by gut microbiota derived secondary bile acids. Anaerobe 45:86–100
    [Google Scholar]
  211. 211. 
    Tinevez JY, Arena ET, Anderson M, Nigro G, Injarabian L et al. 2019. Shigella-mediated oxygen depletion is essential for intestinal mucosa colonization. Nat. Microbiol. 4:2001–9
    [Google Scholar]
  212. 212. 
    Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, Gordon JI 2009. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci. Transl. Med. 1:6ra14
    [Google Scholar]
  213. 213. 
    Tunio A, Taciak M, Barszcz M, Paradziej-Łukowicz J, Olędzka I et al. 2014. Thermal sterilization affects the content of selected compounds in diets for laboratory animals. J. Anim. Feed Sci. 23:351–60
    [Google Scholar]
  214. 214. 
    Uchimura Y, Wyss M, Brugiroux S, Limenitakis JP, Stecher B et al. 2016. Complete genome sequences of 12 species of stable defined moderately diverse mouse microbiota 2. Genome Announc 4:5e00951-16
    [Google Scholar]
  215. 215. 
    Vaishnava S, Behrendt CL, Ismail AS, Eckmann L, Hooper LV 2008. Paneth cells directly sense gut commensals and maintain homeostasis at the intestinal host-microbial interface. PNAS 105:20858–63
    [Google Scholar]
  216. 216. 
    Van Deun K, Pasmans F, Van Immerseel F, Ducatelle R, Haesebrouck F 2008. Butyrate protects Caco-2 cells from Campylobacter jejuni invasion and translocation. Br. J. Nutr. 100:480–84
    [Google Scholar]
  217. 217. 
    Velazquez EM, Nguyen H, Heasley KT, Saechao CH, Gil LM et al. 2019. Endogenous Enterobacteriaceae underlie variation in susceptibility to Salmonella infection. Nat. Microbiol. 4:61057–64
    [Google Scholar]
  218. 218. 
    Venkataraman A, Sieber JR, Schmidt AW, Waldron C, Theis KR, Schmidt TM 2016. Variable responses of human microbiomes to dietary supplementation with resistant starch. Microbiome 4:33
    [Google Scholar]
  219. 219. 
    Vukomanovic M, Zunic V, Kunej S, Jancar B, Jeverica S et al. 2017. Nano-engineering the antimicrobial spectrum of lantibiotics: activity of nisin against Gram negative bacteria. Sci. Rep. 7:4324
    [Google Scholar]
  220. 220. 
    Wang J, Lang T, Shen J, Dai J, Tian L, Wang X 2019. Core gut bacteria analysis of healthy mice. Front. Microbiol. 10:887
    [Google Scholar]
  221. 221. 
    Watanabe M, Fukiya S, Yokota A 2017. Comprehensive evaluation of the bactericidal activities of free bile acids in the large intestine of humans and rodents. J. Lipid Res. 58:1143–52
    [Google Scholar]
  222. 222. 
    Wenneras C, Erling V. 2004. Prevalence of enterotoxigenic Escherichia coli-associated diarrhoea and carrier state in the developing world. J. Health Popul. Nutr. 22:370–82
    [Google Scholar]
  223. 223. 
    Wexler AG, Bao Y, Whitney JC, Bobay LM, Xavier JB et al. 2016. Human symbionts inject and neutralize antibacterial toxins to persist in the gut. PNAS 113:3639–44
    [Google Scholar]
  224. 224. 
    Willmann M, Vehreschild M, Biehl LM, Vogel W, Dorfel D et al. 2019. Distinct impact of antibiotics on the gut microbiome and resistome: a longitudinal multicenter cohort study. BMC Biol 17:76
    [Google Scholar]
  225. 225. 
    Wotzka SY, Kreuzer M, Maier L, Arnoldini M, Nguyen BD et al. 2019. Escherichia coli limits Salmonella Typhimurium infections after diet shifts and fat-mediated microbiota perturbation in mice. Nat. Microbiol. 4:122164–74
    [Google Scholar]
  226. 226. 
    Wotzka SY, Nguyen BD, Hardt WD 2017. Salmonella Typhimurium diarrhea reveals basic principles of enteropathogen infection and disease-promoted DNA exchange. Cell Host Microbe 21:443–54
    [Google Scholar]
  227. 227. 
    Wrzosek L, Ciocan D, Borentain P, Spatz M, Puchois V et al. 2018. Transplantation of human microbiota into conventional mice durably reshapes the gut microbiota. Sci. Rep. 8:6854
    [Google Scholar]
  228. 228. 
    Yang Y, Feye KM, Shi Z, Pavlidis HO, Kogut M et al. 2019. A historical review on antibiotic resistance of foodborne Campylobacter. Front. Microbiol 10:1509
    [Google Scholar]
  229. 229. 
    Yen M, Cairns LS, Camilli A 2017. A cocktail of three virulent bacteriophages prevents Vibrio cholerae infection in animal models. Nat. Commun. 8:14187
    [Google Scholar]
  230. 230. 
    Ze X, Duncan SH, Louis P, Flint HJ 2012. Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon. ISME J 6:1535–43
    [Google Scholar]
  231. 231. 
    Zeng H, Chi H. 2015. Metabolic control of regulatory T cell development and function. Trends Immunol 36:3–12
    [Google Scholar]
  232. 232. 
    Zhang K, Riba A, Nietschke M, Torow N, Repnik U et al. 2018. Minimal SPI1-T3SS effector requirement for Salmonella enterocyte invasion and intracellular proliferation in vivo. PLOS Pathog 14:e1006925
    [Google Scholar]
  233. 233. 
    Zhang Y, Zhang Y. 2007. Formation and reduction of acrylamide in Maillard reaction: a review based on the current state of knowledge. Crit. Rev. Food Sci. Nutr. 47:521–42
    [Google Scholar]
  234. 234. 
    Zhao S, Lieberman TD, Poyet M, Kauffman KM, Gibbons SM et al. 2019. Adaptive evolution within gut microbiomes of healthy people. Cell Host Microbe 25:656–67.e8
    [Google Scholar]
  235. 235. 
    Zhao Y, Yu YB. 2016. Intestinal microbiota and chronic constipation. SpringerPlus 5:1130
    [Google Scholar]
  236. 236. 
    Zhen Q, Lu Y, Yuan X, Qiu Y, Xu J et al. 2013. Asymptomatic brucellosis infection in humans: implications for diagnosis and prevention. Clin. Microbiol. Infect. 19:E395–97
    [Google Scholar]
  237. 237. 
    Zhong Y, Cantwell A, Dube PH 2010. Transforming growth factor β and CD25 are important for controlling systemic dissemination following Yersinia enterocolitica infection of the gut. Infect. Immun. 78:3716–25
    [Google Scholar]
  238. 238. 
    Zmora N, Zilberman-Schapira G, Suez J, Mor U, Dori-Bachash M et al. 2018. Personalized gut mucosal colonization resistance to empiric probiotics is associated with unique host and microbiome features. Cell 174:1388–405.e21
    [Google Scholar]
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