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Microbiome and Diseases: Pathogen Infection

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Abstract

The host and the intestinal microbiota contribute in manifold ways to an immune balance and defense against diseases and pathogens. Infectious diseases of the intestine are major diseases which severely threaten individual and global health. Enteropathogenic agents causing infectious diseases have evolved specific tactics how they interact with the host and with the microbiota simultaneously. This chapter characterizes the main players of the intestinal niche, which contribute to the well-being of the host and can ward off or limit pathogenic invaders. It also illustrates, using a few prominent and well-studied examples, how intestinal pathogenic agents can interact with both the host and the microbiota in order to promote their own expansion, to overcome the defenses by the resident microbiota and the mucosal barrier, and how they finally cause disease. This chapter also introduces novel ways how to treat intestinal infections by addressing the microbiota.

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References

  • Allsopp, L. P., Wood, T. E., Howard, S. A., Maggiorelli, F., Nolan, L. M., Wettstadt, S., & Filloux, A. (2017). RsmA and AmrZ orchestrate the assembly of all three type VI secretion systems in Pseudomonas aeruginosa. Proceedings of the National Academy of Sciences of the United States of America, 114, 7707–7712.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Alvarez-Curto, E., & Milligan, G. (2016). Metabolism meets immunity: The role of free fatty acid receptors in the immune system. Biochemical Pharmacology, 114, 3–13.

    Article  PubMed  CAS  Google Scholar 

  • Anderson, M. C., Vonaesch, P., Saffarian, A., Marteyn, B. S., & Sansonetti, P. J. (2017). Shigella sonnei encodes a functional T6SS used for interbacterial competition and niche occupancy. Cell Host and Microbe, 21, 769–776.e3.

    Article  PubMed  CAS  Google Scholar 

  • Arike, L., & Hansson, G. C. (2016). The densely O-glycosylated MUC2 mucin protects the intestine and provides food for the commensal bacteria. Journal of Molecular Biology, 428, 3221–3229.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D. R., Fernandes, G. R., Tap, J., Bruls, T., Batto, J.-M., et al. (2011). Enterotypes of the human gut microbiome. Nature, 473, 174–180.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Avril, T., Wagner, E. R., Willison, H. J., & Crocker, P. R. (2006). Sialic acid-binding immunoglobulin-like lectin 7 mediates selective recognition of sialylated glycans expressed on Campylobacter jejuni lipooligosaccharides. Infection and Immunity, 74, 4133–4141.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Awad, W. A., Dublecz, F., Hess, C., Dublecz, K., Khayal, B., Aschenbach, J. R., & Hess, M. (2016). Campylobacter jejuni colonization promotes the translocation of Escherichia coli to extra-intestinal organs and disturbs the short-chain fatty acids profiles in the chicken gut. Poultry Science, 95, 2259–2265.

    Article  PubMed  CAS  Google Scholar 

  • Azevedo, M., Eriksson, S., Mendes, N., Serpa, J., Figueiredo, C., Resende, L. P., Ruvoën-Clouet, N., Haas, R., Borén, T., Le Pendu, J., et al. (2008). Infection by Helicobacter pylori expressing the BabA adhesin is influenced by the secretor phenotype. The Journal of Pathology, 215, 308–316.

    Article  PubMed  CAS  Google Scholar 

  • Bansil, R., & Turner, B. S. (2017). The biology of mucus: Composition, synthesis and organization. Advanced Drug Delivery Reviews, 124, 3–15.

    Article  PubMed  CAS  Google Scholar 

  • Basler, M., Ho, B. T., & Mekalanos, J. J. (2013). Tit-for-tat: Type VI secretion system counterattack during bacterial cell-cell interactions. Cell, 152, 884–894.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Bax, M., Kuijf, M. L., Heikema, A. P., van Rijs, W., Bruijns, S. C. M., García-Vallejo, J. J., Crocker, P. R., Jacobs, B. C., van Vliet, S. J., & van Kooyk, Y. (2011). Campylobacter jejuni lipooligosaccharides modulate dendritic cell-mediated T cell polarization in a sialic acid linkage-dependent manner. Infection and Immunity, 79, 2681–2689.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Baxter, M., & Colville, A. (2016). Adverse events in faecal microbiota transplant: A review of the literature. The Journal of Hospital Infection, 92, 117–127.

    Article  PubMed  CAS  Google Scholar 

  • Beery, J. T., Hugdahl, M. B., & Doyle, M. P. (1988). Colonization of gastrointestinal tracts of chicks by Campylobacter jejuni. Applied and Environmental Microbiology, 54, 2365–2370.

    PubMed  PubMed Central  CAS  Google Scholar 

  • Behnsen, J., Jellbauer, S., Wong, C. P., Edwards, R. A., George, M. D., Ouyang, W., & Raffatellu, M. (2014). The cytokine IL-22 promotes pathogen colonization by suppressing related commensal bacteria. Immunity, 40, 262–273.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Birchenough, G. M. H., Johansson, M. E. V., Gustafsson, J. K., Bergström, J. H., & Hansson, G. C. (2015). New developments in goblet cell mucus secretion and function. Mucosal Immunology, 8, 712–719.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Blaser, M. J. (2016). Antibiotic use and its consequences for the normal microbiome. Science, 352, 544–545.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Blaut, M., & Clavel, T. (2007). Metabolic diversity of the intestinal microbiota: Implications for health and disease. The Journal of Nutrition, 137, 751S–755S.

    Article  PubMed  CAS  Google Scholar 

  • Bohnhoff, M., Drake, B. L., & Miller, C. P. (1954). Effect of streptomycin on susceptibility of intestinal tract to experimental Salmonella infection. Proceedings of the Society for Experimental Biology and Medicine, 86, 132–137.

    Article  PubMed  CAS  Google Scholar 

  • Bohnhoff, M., Miller, C. P., & Martin, W. R. (1964). Resistance of the mouse’s intestinal tract to experimental Salmonella infection. I. Factors which interfere with the initiation of infection by oral inoculation. The Journal of Experimental Medicine, 120, 805–816.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Brooks, P. T., Brakel, K. A., Bell, J. A., Bejcek, C. E., Gilpin, T., Brudvig, J. M., & Mansfield, L. S. (2017). Transplanted human fecal microbiota enhanced Guillain Barré syndrome autoantibody responses after Campylobacter jejuni infection in C57BL/6 mice. Microbiome, 5, 92.

    Article  PubMed  PubMed Central  Google Scholar 

  • Browne, H. (2016). Antibiotics, gut bugs and the young. Nature Reviews. Microbiology, 14, 336.

    Article  PubMed  CAS  Google Scholar 

  • Brugiroux, S., Beutler, M., Pfann, C., Garzetti, D., Ruscheweyh, H.-J., Ring, D., Diehl, M., Herp, S., Lötscher, Y., Hussain, S., et al. (2016). Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium. Nature Microbiology, 2, 16215.

    Article  PubMed  CAS  Google Scholar 

  • Buck, M. D., Sowell, R. T., Kaech, S. M., & Pearce, E. L. (2017). Metabolic instruction of immunity. Cell, 169, 570–586.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Buffie, C. G., & Pamer, E. G. (2013). Microbiota-mediated colonization resistance against intestinal pathogens. Nature Reviews. Immunology, 13, 790–801.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Buffie, C. G., Bucci, V., Stein, R. R., McKenney, P. T., Ling, L., Gobourne, A., No, D., Liu, H., Kinnebrew, M., Viale, A., et al. (2015). Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature, 517, 205–208.

    Article  PubMed  CAS  Google Scholar 

  • Cascales, E., & Cambillau, C. (2012). Structural biology of type VI secretion systems. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 367, 1102–1111.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Chessa, D., Winter, M. G., Jakomin, M., & Baumler, A. J. (2009). Salmonella enterica serotype Typhimurium Std fimbriae bind terminal alpha(1,2)fucose residues in the cecal mucosa. Molecular Microbiology, 71, 864–875.

    Article  PubMed  CAS  Google Scholar 

  • Cho, I., Yamanishi, S., Cox, L., Methé, B. A., Zavadil, J., Li, K., Gao, Z., Mahana, D., Raju, K., Teitler, I., et al. (2012). Antibiotics in early life alter the murine colonic microbiome and adiposity. Nature, 488, 621–626.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Chung, H., Pamp, S. J., Hill, J. A., Surana, N. K., Edelman, S. M., Troy, E. B., Reading, N. C., Villablanca, E. J., Wang, S., Mora, J. R., et al. (2012). Gut immune maturation depends on colonization with a host-specific microbiota. Cell, 149, 1578–1593.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Cianfanelli, F. R., Monlezun, L., & Coulthurst, S. J. (2016). Aim, load, fire: The type VI secretion system, a bacterial nanoweapon. Trends in Microbiology, 24, 51–62.

    Article  PubMed  CAS  Google Scholar 

  • Clavel, T., Lagkouvardos, I., & Stecher, B. (2017). From complex gut communities to minimal microbiomes via cultivation. Current Opinion in Microbiology, 38, 148–155.

    Article  PubMed  CAS  Google Scholar 

  • Coddens, A., Diswall, M., Angström, J., Breimer, M. E., Goddeeris, B., Cox, E., & Teneberg, S. (2009). Recognition of blood group ABH type 1 determinants by the FedF adhesin of F18-fimbriated Escherichia coli. The Journal of Biological Chemistry, 284, 9713–9726.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Collins, J., Robinson, C., Danhof, H., Knetsch, C. W., van Leeuwen, H. C., Lawley, T. D., Auchtung, J. M., & Britton, R. A. (2018). Dietary trehalose enhances virulence of epidemic Clostridium difficile. Nature, 553, 291–294.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Costea, P. I., Hildebrand, F., Manimozhiyan, A., Bäckhed, F., Blaser, M. J., Bushman, F. D., de Vos, W. M., Ehrlich, S. D., Fraser, C. M., Hattori, M., et al. (2018). Enterotypes in the landscape of gut microbial community composition. Nature Microbiology, 3, 8–16.

    Article  PubMed  CAS  Google Scholar 

  • Cotter, P. D., Ross, R. P., & Hill, C. (2013). Bacteriocins – a viable alternative to antibiotics? Nature Reviews. Microbiology, 11, 95–105.

    Article  PubMed  CAS  Google Scholar 

  • Cowardin, C. A., Buonomo, E. L., Saleh, M. M., Wilson, M. G., Burgess, S. L., Kuehne, S. A., Schwan, C., Eichhoff, A. M., Koch-Nolte, F., Lyras, D., et al. (2016). The binary toxin CDT enhances Clostridium difficile virulence by suppressing protective colonic eosinophilia. Nature Microbiology, 1, 16108.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Cresci, G. A. M., Mayor, P. C., & Thompson, S. A. (2017). Effect of butyrate and Lactobacillus GG on a butyrate receptor and transporter during Campylobacter jejuni exposure. FEMS Microbiology Letters, 364. https://doi.org/10.1093/femsle/fnx046.

  • Dall’Olio, F., Malagolini, N., Chiricolo, M., Trinchera, M., & Harduin-Lepers, A. (2014). The expanding roles of the Sd(a)/Cad carbohydrate antigen and its cognate glycosyltransferase B4GALNT2. Biochimica et Biophysica Acta, 1840, 443–453.

    Article  PubMed  CAS  Google Scholar 

  • Day, C. J., Tiralongo, J., Hartnell, R. D., Logue, C.-A., Wilson, J. C., von Itzstein, M., & Korolik, V. (2009). Differential carbohydrate recognition by Campylobacter jejuni strain 11168: Influences of temperature and growth conditions. PLoS One, 4, e4927.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Day, C. J., Semchenko, E. A., & Korolik, V. (2012). Glycoconjugates play a key role in Campylobacter jejuni infection: Interactions between host and pathogen. Frontiers in Cellular and Infection Microbiology, 2, 9.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Day, C. J., Tram, G., Hartley-Tassell, L. E., Tiralongo, J., & Korolik, V. (2013). Assessment of glycan interactions of clinical and avian isolates of Campylobacter jejuni. BMC Microbiology, 13, 228.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Day, C. J., Tran, E. N., Semchenko, E. A., Tram, G., Hartley-Tassell, L. E., Ng, P. S. K., King, R. M., Ulanovsky, R., McAtamney, S., Apicella, M. A., et al. (2015). Glycan:glycan interactions: High affinity biomolecular interactions that can mediate binding of pathogenic bacteria to host cells. Proceedings of the National Academy of Sciences of the United States of America, 112, E7266–E7275.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • de Vries, S. P., Gupta, S., Baig, A., Wright, E., Wedley, A., Jensen, A. N., Lora, L. L., Humphrey, S., Skovgard, H., Macleod, K., et al. (2017). Genome-wide fitness analyses of the foodborne pathogen Campylobacter jejuni in in vitro and in vivo models. Scientific Reports, 7, 1251.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Donia, M. S., & Fischbach, M. A. (2015). HUMAN MICROBIOTA. Small molecules from the human microbiota. Science, 349, 1254766.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Donia, M. S., Cimermancic, P., Schulze, C. J., Wieland Brown, L. C., Martin, J., Mitreva, M., Clardy, J., Linington, R. G., & Fischbach, M. A. (2014). A systematic analysis of biosynthetic gene clusters in the human microbiome reveals a common family of antibiotics. Cell, 158, 1402–1414.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ekmekciu, I., von Klitzing, E., Fiebiger, U., Escher, U., Neumann, C., Bacher, P., Scheffold, A., Kühl, A. A., Bereswill, S., & Heimesaat, M. M. (2017). Immune responses to broad-spectrum antibiotic treatment and fecal microbiota transplantation in mice. Frontiers in Immunology, 8, 397.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Eren, A. M., Morrison, H. G., Lescault, P. J., Reveillaud, J., Vineis, J. H., & Sogin, M. L. (2015). Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences. The ISME Journal, 9, 968–979.

    Article  PubMed  CAS  Google Scholar 

  • Ermund, A., Schütte, A., Johansson, M. E. V., Gustafsson, J. K., & Hansson, G. C. (2013). Studies of mucus in mouse stomach, small intestine, and colon. I. Gastrointestinal mucus layers have different properties depending on location as well as over the Peyer’s patches. American Journal of Physiology. Gastrointestinal and Liver Physiology, 305, G341–G347.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Esan, O. B., Pearce, M., van Hecke, O., Roberts, N., Collins, D. R. J., Violato, M., McCarthy, N., Perera, R., & Fanshawe, T. R. (2017). Factors associated with sequelae of Campylobacter and non-typhoidal Salmonella infections: A systematic review. EBio Medicine, 15, 100–111.

    Google Scholar 

  • Faber, F., Tran, L., Byndloss, M. X., Lopez, C. A., Velazquez, E. M., Kerrinnes, T., Nuccio, S.-P., Wangdi, T., Fiehn, O., Tsolis, R. M., et al. (2016). Host-mediated sugar oxidation promotes post-antibiotic pathogen expansion. Nature, 534, 697–699.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Faber, F., Thiennimitr, P., Spiga, L., Byndloss, M. X., Litvak, Y., Lawhon, S., Andrews-Polymenis, H. L., Winter, S. E., & Bäumler, A. J. (2017). Respiration of microbiota-derived 1,2-propanediol drives Salmonella expansion during Colitis. PLoS Pathogens, 13, e1006129.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Faïs, T., Delmas, J., Serres, A., Bonnet, R., & Dalmasso, G. (2016). Impact of CDT toxin on human diseases. Toxins, 8. https://doi.org/10.3390/toxins8070220.

  • Gantois, I., Ducatelle, R., Pasmans, F., Haesebrouck, F., Hautefort, I., Thompson, A., Hinton, J. C., & Van Immerseel, F. (2006). Butyrate specifically down-regulates salmonella pathogenicity island 1 gene expression. Applied and Environmental Microbiology, 72, 946–949.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Gao, B., Vorwerk, H., Huber, C., Lara-Tejero, M., Mohr, J., Goodman, A. L., Eisenreich, W., Galán, J. E., & Hofreuter, D. (2017). Metabolic and fitness determinants for in vitro growth and intestinal colonization of the bacterial pathogen Campylobacter jejuni. PLoS Biology, 15, e2001390.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Gerding, D. N., Johnson, S., Rupnik, M., & Aktories, K. (2014). Clostridium difficile binary toxin CDT: Mechanism, epidemiology, and potential clinical importance. Gut Microbes, 5, 15–27.

    Article  PubMed  Google Scholar 

  • Gerlach, R. G., Jackel, D., Stecher, B., Wagner, C., Lupas, A., Hardt, W. D., & Hensel, M. (2007). Salmonella Pathogenicity Island 4 encodes a giant non-fimbrial adhesin and the cognate type 1 secretion system. Cellular Microbiology, 9, 1834–1850.

    Article  PubMed  CAS  Google Scholar 

  • Geva-Zatorsky, N., Sefik, E., Kua, L., Pasman, L., Tan, T. G., Ortiz-Lopez, A., Yanortsang, T. B., Yang, L., Jupp, R., Mathis, D., et al. (2017). Mining the human gut microbiota for immunomodulatory organisms. Cell, 168, 928–943.e11.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Gibson, T. E., Bashan, A., Cao, H.-T., Weiss, S. T., & Liu, Y.-Y. (2016). On the origins and control of community types in the human microbiome. PLoS Computational Biology, 12, e1004688.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Gilbert, M., Karwaski, M.-F., Bernatchez, S., Young, N. M., Taboada, E., Michniewicz, J., Cunningham, A.-M., & Wakarchuk, W. W. (2002). The genetic bases for the variation in the lipo-oligosaccharide of the mucosal pathogen, Campylobacter jejuni. Biosynthesis of sialylated ganglioside mimics in the core oligosaccharide. The Journal of Biological Chemistry, 277, 327–337.

    Article  PubMed  CAS  Google Scholar 

  • Godschalk, P. C. R., Heikema, A. P., Gilbert, M., Komagamine, T., Ang, C. W., Glerum, J., Brochu, D., Li, J., Yuki, N., Jacobs, B. C., et al. (2004). The crucial role of Campylobacter jejuni genes in anti-ganglioside antibody induction in Guillain-Barre syndrome. The Journal of Clinical Investigation, 114, 1659–1665.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Goodrich, J. K., Waters, J. L., Poole, A. C., Sutter, J. L., Koren, O., Blekhman, R., Beaumont, M., Van Treuren, W., Knight, R., Bell, J. T., et al. (2014). Human genetics shape the gut microbiome. Cell, 159, 789–799.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Goodrich, J. K., Davenport, E. R., Waters, J. L., Clark, A. G., & Ley, R. E. (2016a). Cross-species comparisons of host genetic associations with the microbiome. Science, 352, 532–535.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Goodrich, J. K., Davenport, E. R., Beaumont, M., Jackson, M. A., Knight, R., Ober, C., Spector, T. D., Bell, J. T., Clark, A. G., & Ley, R. E. (2016b). Genetic determinants of the gut microbiome in UK twins. Cell Host and Microbe, 19, 731–743.

    Article  PubMed  CAS  Google Scholar 

  • Goto, Y., Obata, T., Kunisawa, J., Sato, S., Ivanov, I. I., Lamichhane, A., Takeyama, N., Kamioka, M., Sakamoto, M., Matsuki, T., et al. (2014). Innate lymphoid cells regulate intestinal epithelial cell glycosylation. Science, 345, 1254009.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Goto, Y., Uematsu, S., & Kiyono, H. (2016). Epithelial glycosylation in gut homeostasis and inflammation. Nature Immunology, 17, 1244–1251.

    Article  PubMed  CAS  Google Scholar 

  • Grassl, G. A., & Finlay, B. B. (2008). Pathogenesis of enteric Salmonella infections. Current Opinion in Gastroenterology, 24, 22–26.

    Article  PubMed  CAS  Google Scholar 

  • Gripp, E., Hlahla, D., Didelot, X., Kops, F., Maurischat, S., Tedin, K., Alter, T., Ellerbroek, L., Schreiber, K., Schomburg, D., et al. (2011). Closely related Campylobacter jejuni strains from different sources reveal a generalist rather than a specialist lifestyle. BMC Genomics, 12, 584.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Guerry, P., Ewing, C. P., Hickey, T. E., Prendergast, M. M., & Moran, A. P. (2000). Sialylation of lipooligosaccharide cores affects immunogenicity and serum resistance of Campylobacter jejuni. Infection and Immunity, 68, 6656–6662.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Günther, C., Josenhans, C., & Wehkamp, J. (2016). Crosstalk between microbiota, pathogens and the innate immune responses. International Journal of Medical Microbiology, 306, 257–265.

    Article  PubMed  CAS  Google Scholar 

  • Hansson, G. C. (2012). Role of mucus layers in gut infection and inflammation. Current Opinion in Microbiology, 15, 57–62.

    Article  PubMed  CAS  Google Scholar 

  • Hegarty, J. W., Guinane, C. M., Ross, R. P., Hill, C., & Cotter, P. D. (2016). Bacteriocin production: A relatively unharnessed probiotic trait? F1000Research, 5, 2587.

    Article  PubMed  PubMed Central  Google Scholar 

  • Heikema, A. P., Jacobs, B. C., Horst-Kreft, D., Huizinga, R., Kuijf, M. L., Endtz, H. P., Samsom, J. N., & van Wamel, W. J. B. (2013). Siglec-7 specifically recognizes Campylobacter jejuni strains associated with oculomotor weakness in Guillain-Barré syndrome and Miller Fisher syndrome. Clinical Microbiology and Infection, 19, E106–E112.

    Article  PubMed  CAS  Google Scholar 

  • Hiergeist, A., Reischl, U., Priority Program 1656 Intestinal Microbiota Consortium/quality assessment participants, & Gessner, A. (2016). Multicenter quality assessment of 16S ribosomal DNA-sequencing for microbiome analyses reveals high inter-center variability. International Journal of Medical Microbiology, 306, 334–342.

    Article  PubMed  CAS  Google Scholar 

  • Hildebrand, F., Nguyen, T. L. A., Brinkman, B., Yunta, R. G., Cauwe, B., Vandenabeele, P., Liston, A., & Raes, J. (2013). Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice. Genome Biology, 14, R4.

    Article  PubMed  PubMed Central  Google Scholar 

  • Ho, B. T., Dong, T. G., & Mekalanos, J. J. (2014). A view to a kill: The bacterial type VI secretion system. Cell Host and Microbe, 15, 9–21.

    Article  PubMed  CAS  Google Scholar 

  • Humphrey, S., Chaloner, G., Kemmett, K., Davidson, N., Williams, N., Kipar, A., Humphrey, T., & Wigley, P. (2014). Campylobacter jejuni is not merely a commensal in commercial broiler chickens and affects bird welfare. MBio, 5, e01364-01314.

    Article  CAS  Google Scholar 

  • Iovine, N. M., Pursnani, S., Voldman, A., Wasserman, G., Blaser, M. J., & Weinrauch, Y. (2008). Reactive nitrogen species contribute to innate host defense against Campylobacter jejuni. Infection and Immunity, 76, 986–993.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Iwasaki, A., & Medzhitov, R. (2015). Control of adaptive immunity by the innate immune system. Nature Immunology, 16, 343–353.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Jäger, S., Stange, E. F., & Wehkamp, J. (2013). Inflammatory bowel disease: An impaired barrier disease. Langenbeck’s Archives of Surgery, 398, 1–12.

    Article  PubMed  Google Scholar 

  • Jennings, E., Thurston, T. L. M., & Holden, D. W. (2017). Salmonella SPI-2 type III secretion system effectors: Molecular mechanisms and physiological consequences. Cell Host and Microbe, 22, 217–231.

    Article  PubMed  CAS  Google Scholar 

  • Jervis, A. J., Butler, J. A., Lawson, A. J., Langdon, R., Wren, B. W., & Linton, D. (2012). Characterization of the structurally diverse N-linked glycans of Campylobacter species. Journal of Bacteriology, 194, 2355–2362.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Johansson, M. E. V., & Hansson, G. C. (2016). Immunological aspects of intestinal mucus and mucins. Nature Reviews. Immunology, 16, 639–649.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Johansson, M. E. V., Ambort, D., Pelaseyed, T., Schütte, A., Gustafsson, J. K., Ermund, A., Subramani, D. B., Holmén-Larsson, J. M., Thomsson, K. A., Bergström, J. H., et al. (2011). Composition and functional role of the mucus layers in the intestine. Cellular and Molecular Life Sciences, 68, 3635–3641.

    Article  PubMed  CAS  Google Scholar 

  • Johansson, M. E. V., Sjövall, H., & Hansson, G. C. (2013). The gastrointestinal mucus system in health and disease. Nature Reviews. Gastroenterology & Hepatology, 10, 352–361.

    Article  CAS  Google Scholar 

  • Joshi, A., Kostiuk, B., Rogers, A., Teschler, J., Pukatzki, S., & Yildiz, F. H. (2017). Rules of engagement: The type VI secretion system in Vibrio cholerae. Trends in Microbiology, 25, 267–279.

    Article  PubMed  CAS  Google Scholar 

  • Juge, N. (2012). Microbial adhesins to gastrointestinal mucus. Trends in Microbiology, 20, 30–39.

    Article  PubMed  CAS  Google Scholar 

  • Kaiser, P., Diard, M., Stecher, B., & Hardt, W.-D. (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. Immunological Reviews, 245, 56–83.

    Article  PubMed  CAS  Google Scholar 

  • Kampmann, C., Dicksved, J., Engstrand, L., & Rautelin, H. (2016). Composition of human faecal microbiota in resistance to Campylobacter infection. Clinical Microbiology and Infection, 22, 61–61.

    Article  PubMed  Google Scholar 

  • Kernbauer, E., Ding, Y., & Cadwell, K. (2014). An enteric virus can replace the beneficial function of commensal bacteria. Nature, 516, 94–98.

    PubMed  PubMed Central  CAS  Google Scholar 

  • Kilcoyne, M., Twomey, M. E., Gerlach, J. Q., Kane, M., Moran, A. P., & Joshi, L. (2014). Campylobacter jejuni strain discrimination and temperature-dependent glycome expression profiling by lectin microarray. Carbohydrate Research, 389, 123–133.

    Article  PubMed  CAS  Google Scholar 

  • Kim, S., Covington, A., & Pamer, E. G. (2017). The intestinal microbiota: Antibiotics, colonization resistance, and enteric pathogens. Immunological Reviews, 279, 90–105.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Klaas, M., Oetke, C., Lewis, L. E., Erwig, L. P., Heikema, A. P., Easton, A., Willison, H. J., & Crocker, P. R. (2012). Sialoadhesin promotes rapid proinflammatory and type I IFN responses to a sialylated pathogen, Campylobacter jejuni. Journal of Immunology (Baltimore, MD), 1950(189), 2414–2422.

    Google Scholar 

  • Knights, D., Ward, T. L., McKinlay, C. E., Miller, H., Gonzalez, A., McDonald, D., & Knight, R. (2014). Rethinking “enterotypes”. Cell Host and Microbe, 16, 433–437.

    Article  PubMed  CAS  Google Scholar 

  • Koenig, J. E., Spor, A., Scalfone, N., Fricker, A. D., Stombaugh, J., Knight, R., Angenent, L. T., & Ley, R. E. (2011). Succession of microbial consortia in the developing infant gut microbiome. Proceedings of the National Academy of Sciences of the United States of America, 108(Suppl 1), 4578–4585.

    Article  PubMed  Google Scholar 

  • Kubinak, J. L., & Round, J. L. (2016). Do antibodies select a healthy microbiota? Nature Reviews. Immunology, 16, 767–774.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lagier, J.-C., Armougom, F., Million, M., Hugon, P., Pagnier, I., Robert, C., Bittar, F., Fournous, G., Gimenez, G., Maraninchi, M., et al. (2012). Microbial culturomics: Paradigm shift in the human gut microbiome study. Clinical Microbiology and Infection, 18, 1185–1193.

    Article  PubMed  CAS  Google Scholar 

  • Lagkouvardos, I., Pukall, R., Abt, B., Foesel, B. U., Meier-Kolthoff, J. P., Kumar, N., Bresciani, A., Martínez, I., Just, S., Ziegler, C., et al. (2016). The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota. Nature Microbiology, 1, 16131.

    Article  PubMed  CAS  Google Scholar 

  • Lardone, R. D., Yuki, N., Irazoqui, F. J., & Nores, G. A. (2016). Individual restriction of fine specificity variability in anti-GM1 IgG antibodies associated with Guillain-Barré syndrome. Scientific Reports, 6, 19901.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lawley, T. D., & Walker, A. W. (2013). Intestinal colonization resistance. Immunology, 138, 1–11.

    Article  PubMed  CAS  Google Scholar 

  • Lawley, T. D., Clare, S., Walker, A. W., Stares, M. D., Connor, T. R., Raisen, C., Goulding, D., Rad, R., Schreiber, F., Brandt, C., et al. (2012). Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice. PLoS Pathogens, 8, e1002995.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Le Chatelier, E., Nielsen, T., Qin, J., Prifti, E., Hildebrand, F., Falony, G., Almeida, M., Arumugam, M., Batto, J.-M., Kennedy, S., et al. (2013). Richness of human gut microbiome correlates with metabolic markers. Nature, 500, 541–546.

    Article  PubMed  CAS  Google Scholar 

  • Ley, R. E., Lozupone, C. A., Hamady, M., Knight, R., & Gordon, J. I. (2008). Worlds within worlds: Evolution of the vertebrate gut microbiota. Nature Reviews. Microbiology, 6, 776–788.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lim, M. Y., Rho, M., Song, Y.-M., Lee, K., Sung, J., & Ko, G. (2014). Stability of gut enterotypes in Korean monozygotic twins and their association with biomarkers and diet. Scientific Reports, 4, 7348.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lindesmith, L., Moe, C., Marionneau, S., Ruvoen, N., Jiang, X., Lindblad, L., Stewart, P., LePendu, J., & Baric, R. (2003). Human susceptibility and resistance to Norwalk virus infection. Nature Medicine, 9, 548–553.

    Article  PubMed  CAS  Google Scholar 

  • Lindner, C., Thomsen, I., Wahl, B., Ugur, M., Sethi, M. K., Friedrichsen, M., Smoczek, A., Ott, S., Baumann, U., Suerbaum, S., et al. (2015). Diversification of memory B cells drives the continuous adaptation of secretory antibodies to gut microbiota. Nature Immunology, 16, 880–888.

    Article  PubMed  CAS  Google Scholar 

  • Liu, J. Z., Jellbauer, S., Poe, A. J., Ton, V., Pesciaroli, M., Kehl-Fie, T. E., Restrepo, N. A., Hosking, M. P., Edwards, R. A., Battistoni, A., et al. (2012). Zinc sequestration by the neutrophil protein calprotectin enhances Salmonella growth in the inflamed gut. Cell Host and Microbe, 11, 227–239.

    Article  PubMed  CAS  Google Scholar 

  • Liu, Y. W., Denkmann, K., Kosciow, K., Dahl, C., & Kelly, D. J. (2013). Tetrathionate stimulated growth of Campylobacter jejuni identifies a new type of bi-functional tetrathionate reductase (TsdA) that is widely distributed in bacteria. Molecular Microbiology, 88, 173–188.

    Article  PubMed  CAS  Google Scholar 

  • Lopez, C. A., Winter, S. E., Rivera-Chavez, F., Xavier, M. N., Poon, V., Nuccio, S. P., Tsolis, R. M., & Baumler, A. J. (2012). Phage-mediated acquisition of a type III secreted effector protein boosts growth of salmonella by nitrate respiration. MBio, 3. https://doi.org/10.1128/mBio.00143-12.

  • Lu, Q., Li, S., & Shao, F. (2015). Sweet talk: Protein glycosylation in bacterial interaction with the host. Trends in Microbiology, 23, 630–641.

    Article  PubMed  CAS  Google Scholar 

  • Lustri, B. C., Sperandio, V., & Moreira, C. G. (2017). Bacterial chat: Intestinal metabolites and signals in host-microbiota-pathogen interactions. Infection and Immunity, 85. https://doi.org/10.1128/IAI.00476-17.

  • Macpherson, A. J., & McCoy, K. D. (2015). Standardised animal models of host microbial mutualism. Mucosal Immunology, 8, 476–486.

    Article  PubMed  CAS  Google Scholar 

  • Madhavan, T. P., & Sakellaris, H. (2015). Colonization factors of enterotoxigenic Escherichia coli. Advances in Applied Microbiology, 90, 155–197.

    Article  PubMed  Google Scholar 

  • Maier, L., Vyas, R., Cordova, C. D., Lindsay, H., Schmidt, T. S. B., Brugiroux, S., Periaswamy, B., Bauer, R., Sturm, A., Schreiber, F., et al. (2013). Microbiota-derived hydrogen fuels Salmonella typhimurium invasion of the gut ecosystem. Cell Host and Microbe, 14, 641–651.

    Article  PubMed  CAS  Google Scholar 

  • McCoy, K. D., Ronchi, F., & Geuking, M. B. (2017). Host-microbiota interactions and adaptive immunity. Immunological Reviews, 279, 63–69.

    Article  PubMed  CAS  Google Scholar 

  • McGovern, D. P., Jones, M. R., Taylor, K. D., Marciante, K., Yan, X., Dubinsky, M., Ippoliti, A., Vasiliauskas, E., Berel, D., Derkowski, C., et al. (2010). Fucosyltransferase 2 (FUT2) non-secretor status is associated with Crohn’s disease. Human Molecular Genetics, 19, 3468–3476.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • McGuckin, M. A., Lindén, S. K., Sutton, P., & Florin, T. H. (2011). Mucin dynamics and enteric pathogens. Nature Reviews. Microbiology, 9, 265–278.

    Article  PubMed  CAS  Google Scholar 

  • Miller, C. P., Bohnhoff, M., & Drake, B. L. (1954). The effect of antibiotic therapy on susceptibility to an experimental enteric infection. Transactions of the Association of American Physicians, 67, 156–161.

    PubMed  CAS  Google Scholar 

  • Mills, S., Shanahan, F., Stanton, C., Hill, C., Coffey, A., & Ross, R. P. (2013). Movers and shakers: Influence of bacteriophages in shaping the mammalian gut microbiota. Gut Microbes, 4, 4–16.

    Article  PubMed  PubMed Central  Google Scholar 

  • Minot, S., Bryson, A., Chehoud, C., Wu, G. D., Lewis, J. D., & Bushman, F. D. (2013). Rapid evolution of the human gut virome. Proceedings of the National Academy of Sciences of the United States of America, 110, 12450–12455.

    Article  PubMed  PubMed Central  Google Scholar 

  • Molnár, A., Hess, C., Pál, L., Wágner, L., Awad, W. A., Husvéth, F., Hess, M., & Dublecz, K. (2015). Composition of diet modifies colonization dynamics of Campylobacter jejuni in broiler chickens. Journal of Applied Microbiology, 118, 245–254.

    Article  PubMed  CAS  Google Scholar 

  • Montalban-Arques, A., De Schryver, P., Bossier, P., Gorkiewicz, G., Mulero, V., Gatlin, D. M., & Galindo-Villegas, J. (2015). Selective manipulation of the gut microbiota improves immune status in vertebrates. Frontiers in Immunology, 6, 512.

    Article  PubMed  PubMed Central  Google Scholar 

  • Moonens, K., Bouckaert, J., Coddens, A., Tran, T., Panjikar, S., De Kerpel, M., Cox, E., Remaut, H., & De Greve, H. (2012). Structural insight in histo-blood group binding by the F18 fimbrial adhesin FedF. Molecular Microbiology, 86, 82–95.

    Article  PubMed  CAS  Google Scholar 

  • Morgan, X. C., & Huttenhower, C. (2014). Meta’omic analytic techniques for studying the intestinal microbiome. Gastroenterology, 146, 1437–1448.e1.

    Article  PubMed  CAS  Google Scholar 

  • Morrison, D. J., & Preston, T. (2016). Formation of short chain fatty acids by the gut microbiota and their impact on human metabolism. Gut Microbes, 7, 189–200.

    Article  PubMed  PubMed Central  Google Scholar 

  • Muraoka, W. T., & Zhang, Q. (2011). Phenotypic and genotypic evidence for L-fucose utilization by Campylobacter jejuni. Journal of Bacteriology, 193, 1065–1075.

    Article  PubMed  CAS  Google Scholar 

  • Ng, K. M., Ferreyra, J. A., Higginbottom, S. K., Lynch, J. B., Kashyap, P. C., Gopinath, S., Naidu, N., Choudhury, B., Weimer, B. C., Monack, D. M., et al. (2013). Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens. Nature, 502, 96–99.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Nguyen, T. L., Vieira-Silva, S., Liston, A., & Raes, J. (2015). How informative is the mouse for human gut microbiota research? Disease Models and Mechanisms, 8, 1–16.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Nuttal, G., & Thierfelder, H. (1895). Thierisches Leben ohne Bakterien im Verdauungskanal. Hoppe-Seyler’s Zeitschrift für Physiologische Chemie, 21, 109–121.

    Article  Google Scholar 

  • O’Neill, L. A. J., Kishton, R. J., & Rathmell, J. (2016). A guide to immunometabolism for immunologists. Nature Reviews. Immunology, 16, 553–565.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ohno, H. (2016). Intestinal M cells. Journal of Biochemistry, 159, 151–160.

    Article  PubMed  CAS  Google Scholar 

  • Okai, S., Usui, F., Ohta, M., Mori, H., Kurokawa, K., Matsumoto, S., Kato, T., Miyauchi, E., Ohno, H., & Shinkura, R. (2017). Intestinal IgA as a modulator of the gut microbiota. Gut Microbes, 8, 486–492.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Okoro, C. K., Kingsley, R. A., Connor, T. R., Harris, S. R., Parry, C. M., Al-Mashhadani, M. N., Kariuki, S., Msefula, C. L., Gordon, M. A., de Pinna, E., et al. (2012). Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa. Nature Genetics, 44, 1215–1221.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Olsan, E. E., Byndloss, M. X., Faber, F., Rivera-Chávez, F., Tsolis, R. M., & Bäumler, A. J. (2017). Colonization resistance: The deconvolution of a complex trait. The Journal of Biological Chemistry, 292, 8577–8581.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Pabst, O., Cerovic, V., & Hornef, M. (2016). Secretory IgA in the coordination of establishment and maintenance of the microbiota. Trends in Immunology, 37, 287–296.

    Article  PubMed  CAS  Google Scholar 

  • Pacheco, A. R., Curtis, M. M., Ritchie, J. M., Munera, D., Waldor, M. K., Moreira, C. G., & Sperandio, V. (2012). Fucose sensing regulates bacterial intestinal colonization. Nature, 492, 113–117.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Palm, N. W., de Zoete, M. R., & Flavell, R. A. (2015). Immune-microbiota interactions in health and disease. Clinical Immunology (Orlando, Florida), 159, 122–127.

    Article  CAS  Google Scholar 

  • Perdicchio, M., Ilarregui, J. M., Verstege, M. I., Cornelissen, L. A. M., Schetters, S. T. T., Engels, S., Ambrosini, M., Kalay, H., Veninga, H., den Haan, J. M. M., et al. (2016). Sialic acid-modified antigens impose tolerance via inhibition of T-cell proliferation and de novo induction of regulatory T cells. Proceedings of the National Academy of Sciences of the United States of America, 113, 3329–3334.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Perez-Lopez, A., Behnsen, J., Nuccio, S.-P., & Raffatellu, M. (2016). Mucosal immunity to pathogenic intestinal bacteria. Nature Reviews. Immunology, 16, 135–148.

    Article  PubMed  CAS  Google Scholar 

  • Phongsisay, V. (2016). The immunobiology of Campylobacter jejuni: Innate immunity and autoimmune diseases. Immunobiology, 221, 535–543.

    Article  PubMed  CAS  Google Scholar 

  • Phongsisay, V., Hara, H., & Fujimoto, S. (2015). Toll-like receptors recognize distinct proteinase-resistant glycoconjugates in Campylobacter jejuni and Escherichia coli. Molecular Immunology, 64, 195–203.

    Article  PubMed  CAS  Google Scholar 

  • Pickard, J. M., Maurice, C. F., Kinnebrew, M. A., Abt, M. C., Schenten, D., Golovkina, T. V., Bogatyrev, S. R., Ismagilov, R. F., Pamer, E. G., Turnbaugh, P. J., et al. (2014). Rapid fucosylation of intestinal epithelium sustains host-commensal symbiosis in sickness. Nature, 514, 638–641.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Planer, J. D., Peng, Y., Kau, A. L., Blanton, L. V., Ndao, I. M., Tarr, P. I., Warner, B. B., & Gordon, J. I. (2016). Development of the gut microbiota and mucosal IgA responses in twins and gnotobiotic mice. Nature, 534, 263–266.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Price-Carter, M., Tingey, J., Bobik, T. A., & Roth, J. R. (2001). The alternative electron acceptor tetrathionate supports B12-dependent anaerobic growth of Salmonella enterica serovar typhimurium on ethanolamine or 1,2-propanediol. Journal of Bacteriology, 183, 2463–2475.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Próchnicki, T., & Latz, E. (2017). Inflammasomes on the crossroads of innate immune recognition and metabolic control. Cell Metabolism, 26, 71–93.

    Article  PubMed  CAS  Google Scholar 

  • Pukatzki, S., Ma, A. T., Revel, A. T., Sturtevant, D., & Mekalanos, J. J. (2007). Type VI secretion system translocates a phage tail spike-like protein into target cells where it cross-links actin. Proceedings of the National Academy of Sciences of the United States of America, 104, 15508–15513.

    Article  PubMed  PubMed Central  Google Scholar 

  • Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., Yamada, T., et al. (2010). A human gut microbial gene catalogue established by metagenomic sequencing. Nature, 464, 59–65.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Raffatellu, M., George, M. D., Akiyama, Y., Hornsby, M. J., Nuccio, S.-P., Paixao, T. A., Butler, B. P., Chu, H., Santos, R. L., Berger, T., et al. (2009). Lipocalin-2 resistance confers an advantage to Salmonella enterica serotype Typhimurium for growth and survival in the inflamed intestine. Cell Host and Microbe, 5, 476–486.

    Article  PubMed  CAS  Google Scholar 

  • Rakoff-Nahoum, S., Paglino, J., Eslami-Varzaneh, F., Edberg, S., & Medzhitov, R. (2004). Recognition of commensal microflora by toll-like receptors is required for intestinal homeostasis. Cell, 118, 229–241.

    Article  CAS  PubMed  Google Scholar 

  • Ramachandran, G., Panda, A., Higginson, E. E., Ateh, E., Lipsky, M. M., Sen, S., Matson, C. A., Permala-Booth, J., DeTolla, L. J., & Tennant, S. M. (2017). Virulence of invasive Salmonella Typhimurium ST313 in animal models of infection. PLoS Neglected Tropical Diseases, 11, e0005697.

    Article  PubMed  PubMed Central  Google Scholar 

  • Rausch, P., Steck, N., Suwandi, A., Seidel, J. A., Künzel, S., Bhullar, K., Basic, M., Bleich, A., Johnsen, J. M., Vallance, B. A., et al. (2015). Expression of the blood-group-related gene B4galnt2 alters susceptibility to Salmonella infection. PLoS Pathogens, 11, e1005008.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ringot-Destrez, B., Kalach, N., Mihalache, A., Gosset, P., Michalski, J.-C., Léonard, R., & Robbe-Masselot, C. (2017). How do they stick together? Bacterial adhesins implicated in the binding of bacteria to the human gastrointestinal mucins. Biochemical Society Transactions, 45, 389–399.

    Article  PubMed  CAS  Google Scholar 

  • Robinson, C. M., & Pfeiffer, J. K. (2014). Viruses and the microbiota. Annual Review of Virology, 1, 55–69.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ruiz-Palacios, G. M., Cervantes, L. E., Ramos, P., Chavez-Munguia, B., & Newburg, D. S. (2003). Campylobacter jejuni binds intestinal H(O) antigen (Fuc alpha 1, 2Gal beta 1, 4GlcNAc), and fucosyloligosaccharides of human milk inhibit its binding and infection. The Journal of Biological Chemistry, 278, 14112–14120.

    Article  PubMed  CAS  Google Scholar 

  • Sana, T. G., Flaugnatti, N., Lugo, K. A., Lam, L. H., Jacobson, A., Baylot, V., Durand, E., Journet, L., Cascales, E., & Monack, D. M. (2016). Salmonella Typhimurium utilizes a T6SS-mediated antibacterial weapon to establish in the host gut. Proceedings of the National Academy of Sciences of the United States of America, 113, E5044–E5051.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Sankar, S. A., Lagier, J.-C., Pontarotti, P., Raoult, D., & Fournier, P.-E. (2015). The human gut microbiome, a taxonomic conundrum. Systematic and Applied Microbiology, 38, 276–286.

    Article  PubMed  CAS  Google Scholar 

  • Sassone-Corsi, M., & Raffatellu, M. (2013). A hydrogen boost for salmonella. Cell Host and Microbe, 14, 603–604.

    Article  PubMed  CAS  Google Scholar 

  • Sassone-Corsi, M., Nuccio, S.-P., Liu, H., Hernandez, D., Vu, C. T., Takahashi, A. A., Edwards, R. A., & Raffatellu, M. (2016). Microcins mediate competition among Enterobacteriaceae in the inflamed gut. Nature, 540, 280–283.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Sears, C. L. (2009). Enterotoxigenic Bacteroides fragilis: A rogue among symbiotes. Clinical Microbiology Reviews, 22, 349–369 Table of Contents.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Sperandio, B., Fischer, N., & Sansonetti, P. J. (2015). Mucosal physical and chemical innate barriers: Lessons from microbial evasion strategies. Seminars in Immunology, 27, 111–118.

    Article  PubMed  CAS  Google Scholar 

  • Spiga, L., Winter, M. G., Furtado de Carvalho, T., Zhu, W., Hughes, E. R., Gillis, C. C., Behrendt, C. L., Kim, J., Chessa, D., Andrews-Polymenis, H. L., et al. (2017). An oxidative central metabolism enables Salmonella to utilize microbiota-derived succinate. Cell Host and Microbe, 22, 291–301.e6.

    Article  PubMed  CAS  Google Scholar 

  • St Charles, J. L., Bell, J. A., Gadsden, B. J., Malik, A., Cooke, H., Van de Grift, L. K., Kim, H. Y., Smith, E. J., & Mansfield, L. S. (2017). Guillain Barré syndrome is induced in non-obese diabetic (NOD) mice following Campylobacter jejuni infection and is exacerbated by antibiotics. Journal of Autoimmunity, 77, 11–38.

    Article  PubMed  CAS  Google Scholar 

  • Stahl, M., Friis, L. M., Nothaft, H., Liu, X., Li, J., Szymanski, C. M., & Stintzi, A. (2011). L-fucose utilization provides Campylobacter jejuni with a competitive advantage. Proceedings of the National Academy of Sciences of the United States of America, 108, 7194–7199.

    Article  PubMed  PubMed Central  Google Scholar 

  • Staubach, F., Künzel, S., Baines, A. C., Yee, A., McGee, B. M., Bäckhed, F., Baines, J. F., & Johnsen, J. M. (2012). Expression of the blood-group-related glycosyltransferase B4galnt2 influences the intestinal microbiota in mice. The ISME Journal, 6, 1345–1355.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Stecher, B., & Hardt, W. D. (2011). Mechanisms controlling pathogen colonization of the gut. Current Opinion in Microbiology, 14, 82–91.

    Article  PubMed  CAS  Google Scholar 

  • Stecher, B., Barthel, M., Schlumberger, M. C., Haberli, L., Rabsch, W., Kremer, M., & Hardt, W. D. (2008). Motility allows S. Typhimurium to benefit from the mucosal defence. Cellular Microbiology, 10, 1166–1180.

    Article  PubMed  CAS  Google Scholar 

  • Stecher, B., Berry, D., & Loy, A. (2013). Colonization resistance and microbial ecophysiology: Using gnotobiotic mouse models and single-cell technology to explore the intestinal jungle. FEMS Microbiology Reviews, 37, 793–829.

    Article  PubMed  CAS  Google Scholar 

  • Stephenson, H. N., John, C. M., Naz, N., Gundogdu, O., Dorrell, N., Wren, B. W., Jarvis, G. A., & Bajaj-Elliott, M. (2013). Campylobacter jejuni lipooligosaccharide sialylation, phosphorylation, and amide/ester linkage modifications fine-tune human Toll-like receptor 4 activation. The Journal of Biological Chemistry, 288, 19661–19672.

    Article  PubMed  CAS  Google Scholar 

  • Stephenson, H. N., Mills, D. C., Jones, H., Milioris, E., Copland, A., Dorrell, N., Wren, B. W., Crocker, P. R., Escors, D., & Bajaj-Elliott, M. (2014). Pseudaminic acid on Campylobacter jejuni flagella modulates dendritic cell IL-10 expression via Siglec-10 receptor: A novel flagellin-host interaction. The Journal of Infectious Diseases, 210, 1487–1498.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Struwe, W. B., Gough, R., Gallagher, M. E., Kenny, D. T., Carrington, S. D., Karlsson, N. G., & Rudd, P. M. (2015). Identification of O-glycan structures from chicken intestinal mucins provides insight into Campylobactor jejuni pathogenicity. Molecular and Cellular Proteomics, 14, 1464–1477.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Szymanski, C. M., & Gaynor, E. C. (2012). How a sugary bug gets through the day: Recent developments in understanding fundamental processes impacting Campylobacter jejuni pathogenesis. Gut Microbes, 3, 135–144.

    Article  PubMed  PubMed Central  Google Scholar 

  • Tailford, L. E., Crost, E. H., Kavanaugh, D., & Juge, N. (2015). Mucin glycan foraging in the human gut microbiome. Frontiers in Genetics, 6, 81.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Tan, T. G., Sefik, E., Geva-Zatorsky, N., Kua, L., Naskar, D., Teng, F., Pasman, L., Ortiz-Lopez, A., Jupp, R., Wu, H.-J. J., et al. (2016). Identifying species of symbiont bacteria from the human gut that, alone, can induce intestinal Th17 cells in mice. Proceedings of the National Academy of Sciences of the United States of America, 113, E8141–E8150.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Thaiss, C. A., Zmora, N., Levy, M., & Elinav, E. (2016). The microbiome and innate immunity. Nature, 535, 65–74.

    Article  PubMed  CAS  Google Scholar 

  • Thiennimitr, P., Winter, S. E., Winter, M. G., Xavier, M. N., Tolstikov, V., Huseby, D. L., Sterzenbach, T., Tsolis, R. M., Roth, J. R., & Bäumler, A. J. (2011). Intestinal inflammation allows Salmonella to use ethanolamine to compete with the microbiota. Proceedings of the National Academy of Sciences of the United States of America, 108, 17480–17485.

    Article  PubMed  PubMed Central  Google Scholar 

  • Thursby, E., & Juge, N. (2017). Introduction to the human gut microbiota. Biochemical Journal, 474, 1823–1836.

    Article  PubMed  CAS  Google Scholar 

  • Turonova, H., Neu, T. R., Ulbrich, P., Pazlarova, J., & Tresse, O. (2016). The biofilm matrix of Campylobacter jejuni determined by fluorescence lectin-binding analysis. Biofouling, 32, 597–608.

    Article  PubMed  CAS  Google Scholar 

  • Ursell, L. K., Metcalf, J. L., Parfrey, L. W., & Knight, R. (2012). Defining the human microbiome. Nutrition Reviews, 70(Suppl 1), S38–S44.

    Article  PubMed  Google Scholar 

  • van der Heijden, J., & Finlay, B. B. (2012). Type III effector-mediated processes in Salmonella infection. Future Microbiology, 7, 685–703.

    Article  PubMed  CAS  Google Scholar 

  • van Sorge, N. M., Bleumink, N. M. C., van Vliet, S. J., Saeland, E., van der Pol, W.-L., van Kooyk, Y., & van Putten, J. P. M. (2009). N-glycosylated proteins and distinct lipooligosaccharide glycoforms of Campylobacter jejuni target the human C-type lectin receptor MGL. Cellular Microbiology, 11, 1768–1781.

    Article  PubMed  CAS  Google Scholar 

  • Verster, A. J., Ross, B. D., Radey, M. C., Bao, Y., Goodman, A. L., Mougous, J. D., & Borenstein, E. (2017). The landscape of type VI secretion across human gut microbiomes reveals its role in community composition. Cell Host and Microbe, 22, 411–419.e4.

    Article  PubMed  CAS  Google Scholar 

  • Vogt, S. L., Peña-Díaz, J., & Finlay, B. B. (2015). Chemical communication in the gut: Effects of microbiota-generated metabolites on gastrointestinal bacterial pathogens. Anaerobe, 34, 106–115.

    Article  PubMed  CAS  Google Scholar 

  • Vorwerk, H., Mohr, J., Huber, C., Wensel, O., Schmidt-Hohagen, K., Gripp, E., Josenhans, C., Schomburg, D., Eisenreich, W., & Hofreuter, D. (2014). Utilization of host-derived cysteine-containing peptides overcomes the restricted sulphur metabolism of Campylobacter jejuni. Molecular Microbiology, 93, 1224–1245.

    PubMed  CAS  Google Scholar 

  • Vorwerk, H., Huber, C., Mohr, J., Bunk, B., Bhuju, S., Wensel, O., Spröer, C., Fruth, A., Flieger, A., Schmidt-Hohagen, K., et al. (2015). A transferable plasticity region in Campylobacter coli allows isolates of an otherwise non-glycolytic food-borne pathogen to catabolize glucose. Molecular Microbiology, 98, 809–830.

    Article  PubMed  CAS  Google Scholar 

  • Wagley, S., Newcombe, J., Laing, E., Yusuf, E., Sambles, C. M., Studholme, D. J., La Ragione, R. M., Titball, R. W., & Champion, O. L. (2014). Differences in carbon source utilisation distinguish Campylobacter jejuni from Campylobacter coli. BMC Microbiology, 14, 262.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Wagner, C., Barlag, B., Gerlach, R. G., Deiwick, J., & Hensel, M. (2014). The Salmonella enterica giant adhesin SiiE binds to polarized epithelial cells in a lectin-like manner. Cellular Microbiology, 16, 962–975.

    Article  PubMed  CAS  Google Scholar 

  • Winter, S. E., & Bäumler, A. J. (2011). A breathtaking feat: To compete with the gut microbiota, Salmonella drives its host to provide a respiratory electron acceptor. Gut Microbes, 2, 58–60.

    Article  PubMed  PubMed Central  Google Scholar 

  • Winter, S. E., Thiennimitr, P., Winter, M. G., Butler, B. P., Huseby, D. L., Crawford, R. W., Russell, J. M., Bevins, C. L., Adams, L. G., Tsolis, R. M., et al. (2010). Gut inflammation provides a respiratory electron acceptor for Salmonella. Nature, 467, 426–429.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Wu, S., Rhee, K.-J., Albesiano, E., Rabizadeh, S., Wu, X., Yen, H.-R., Huso, D. L., Brancati, F. L., Wick, E., McAllister, F., et al. (2009). A human colonic commensal promotes colon tumorigenesis via activation of T helper type 17 T cell responses. Nature Medicine, 15, 1016–1022.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., Magris, M., Hidalgo, G., Baldassano, R. N., Anokhin, A. P., et al. (2012). Human gut microbiome viewed across age and geography. Nature, 486, 222–227.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Yin, Y., Fan, B., Liu, W., Ren, R., Chen, H., Bai, S., Zhu, L., Sun, G., Yang, Y., & Wang, X. (2017). Investigation into the stability and culturability of Chinese enterotypes. Scientific Reports, 7, 7947.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Young, N. M., Brisson, J. R., Kelly, J., Watson, D. C., Tessier, L., Lanthier, P. H., Jarrell, H. C., Cadotte, N., St Michael, F., Aberg, E., et al. (2002). Structure of the N-linked glycan present on multiple glycoproteins in the Gram-negative bacterium, Campylobacter jejuni. The Journal of Biological Chemistry, 277, 42530–42539.

    Article  PubMed  CAS  Google Scholar 

  • Young, K. T., Davis, L. M., & Dirita, V. J. (2007). Campylobacter jejuni: Molecular biology and pathogenesis. Nature Reviews. Microbiology, 5, 665–679.

    Article  PubMed  CAS  Google Scholar 

  • Yrios, J. W., & Balish, E. (1986). Pathogenesis of Campylobacter spp. in athymic and euthymic germfree mice. Infection and Immunity, 53, 384–392.

    PubMed  PubMed Central  CAS  Google Scholar 

  • Yurist-Doutsch, S., Arrieta, M.-C., Vogt, S. L., & Finlay, B. B. (2014). Gastrointestinal microbiota-mediated control of enteric pathogens. Annual Review of Genetics, 48, 361–382.

    Article  PubMed  CAS  Google Scholar 

  • Zasloff, M. (2002). Antimicrobial peptides in health and disease. The New England Journal of Medicine, 347, 1199–1200.

    Article  PubMed  Google Scholar 

  • Zhu, W., Winter, M. G., Byndloss, M. X., Spiga, L., Duerkop, B. A., Hughes, E. R., Büttner, L., de Lima Romão, E., Behrendt, C. L., Lopez, C. A., et al. (2018). Precision editing of the gut microbiota ameliorates colitis. Nature, 553, 208–211.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zumbrun, S. D., Melton-Celsa, A. R., Smith, M. A., Gilbreath, J. J., Merrell, D. S., & O’Brien, A. D. (2013). Dietary choice affects Shiga toxin-producing Escherichia coli (STEC) O157:H7 colonization and disease. Proceedings of the National Academy of Sciences of the United States of America, 110, E2126–E2133.

    Article  PubMed  PubMed Central  Google Scholar 

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Josenhans, C., Grassl, G.A. (2018). Microbiome and Diseases: Pathogen Infection. In: Haller, D. (eds) The Gut Microbiome in Health and Disease. Springer, Cham. https://doi.org/10.1007/978-3-319-90545-7_14

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