Processes 2019, 7,97
15. Agus, A.; Denizot, J.; Thévenot, J.; Martinez-Medina, M.; Massier, S.; Sauvanet, P.; Bernalier-Donadille, A.;
Denis, S.; Hofman, P.; Bonnet, R.; et al. Western diet induces a shift in microbiota composition enhancing
susceptibility to Adherent-Invasive E. coli infection and intestinal inflammation. Sci. Rep. 2016, 6, 19032.
[CrossRef][PubMed]
16. Theriot, C.M.; Bowman, A.A.; Young, V.B. Antibiotic-induced alterations of the gut microbiota alter
secondary bile acid production and allow for Clostridium difficile spore germination and outgrowth in the
large intestine. MSphere 2016, 1, e00045-15. [CrossRef]
17. Winter, S.E.; Winter, M.G.; Xavier, M.N.; Thiennimitr, P.; Poon, V.; Keestra, A.M.; Laughlin, R.C.; Gomez, G.;
Wu, J.; Lawhon, S.D.; et al. Host-derived nitrate boosts growth of E. coli in the inflamed gut. Science 2013,
339, 708–711. [CrossRef]
18. Frank, D.N.; Amand, A.L.S.; Feldman, R.A.; Boedeker, E.C.; Harpaz, N.; Pace, N.R. Molecular-phylogenetic
characterization of microbial community imbalances in human inflammatory bowel diseases. Proc. Natl.
Acad. Sci. USA 2007, 104, 13780–13785. [CrossRef][PubMed]
19. Ley, R.E.; Turnbaugh, P.J.; Klein, S.; Gordon, J.I. Microbial ecology: Human gut microbes associated with
obesity. Nature 2006, 444, 1022–1023. [CrossRef][PubMed]
20. Carding, S.; Verbeke, K.; Vipond, D.T.; Corfe, B.M.; Owen, L.J. Dysbiosis of the gut microbiota in disease.
Microb. Ecol. Health Dis. 2015, 26, 26191. [CrossRef]
21. Surawicz, C.M.; Brandt, L.J.; Binion, D.G.; Ananthakrishnan, A.N.; Curry, S.R.; Gilligan, P.H.; McFarland,
L.V.; Mellow, M.; Zuckerbraun, B.S. Guidelines for diagnosis, treatment, and prevention of Clostridium
difficile infections. Am. J. Gastroenterol. 2013, 108, 478. [CrossRef][PubMed]
22. Shim, J.K.; Johnson, S.; Samore, M.H.; Bliss, D.Z.; Gerding, D.N. Primary symptomless colonisation by
Clostridium difficile and decreased risk of subsequent diarrhoea. Lancet 1998, 351, 633–636. [CrossRef]
23. Kyne, L.; Warny, M.; Qamar, A.; Kelly, C.P. Asymptomatic carriage of Clostridium difficile and serum levels of
IgG antibody against toxin A. N. Engl. J. Med. 2000, 342, 390–397. [CrossRef][PubMed]
24. Barbut, F.; Petit, J.C. Epidemiology of Clostridium difficile-associated infections. Clin. Microbiol. Infect. 2001,
7, 405–410. [CrossRef]
25. Kato, H.; Kita, H.; Karasawa, T.; Maegawa, T.; Koino, Y.; Takakuwa, H.; Saikai, T.; Kobayashi, K.;
Yamagishi, T.; Nakamura, S. Colonisation and transmission of Clostridium difficile in healthy individuals
examined by PCR ribotyping and pulsed-field gel electrophoresis. J. Med. Microbiol. 2001, 50, 720–727.
[CrossRef][PubMed]
26. Ozaki, E.; Kato, H.; Kita, H.; Karasawa, T.; Maegawa, T.; Koino, Y.; Matsumoto, K.; Takada, T.; Nomoto, K.;
Tanaka, R.; et al. Clostridium difficile colonization in healthy adults: transient colonization and correlation
with enterococcal colonization. J. Med. Microbiol. 2004, 53, 167–172. [CrossRef]
27. Poutanen, S.M.; Simor, A.E. Clostridium difficile-associated diarrhea in adults. Can. Med. Assoc. J. 2004,
171, 51–58. [CrossRef]
28. Furuya-Kanamori, L.; Marquess, J.; Yakob, L.; Riley, T.V.; Paterson, D.L.; Foster, N.F.; Huber, C.A.;
Clements, A.C. Asymptomatic Clostridium difficile colonization: epidemiology and clinical implications.
BMC Infect. Dis. 2015, 15, 516. [CrossRef][PubMed]
29. Chang, J.Y.; Antonopoulos, D.A.; Kalra, A.; Tonelli, A.; Khalife, W.T.; Schmidt, T.M.; Young, V.B. Decreased
diversity of the fecal microbiome in recurrent Clostridium difficile-associated diarrhea. J. Infect. Dis. 2008,
197, 435–438. [CrossRef]
30. Bartlett, J.G. Clostridium difficile: History of its role as an enteric pathogen and the current state of knowledge
about the organism. Clin. Infect. Dis. 1994, 18, S265–S272. [CrossRef]
31. Pérez-Cobas, A.E.; Moya, A.; Gosalbes, M.J.; Latorre, A. Colonization resistance of the gut microbiota against
Clostridium difficile. Antibiotics 2015, 4, 337–357. [CrossRef][PubMed]
32. Pothoulakis, C. Pathogenesis of Clostridium difficile-associated diarrhoea. Eur. J. Gastroenterol. Hepatol. 1996,
8, 1041–1047. [CrossRef][PubMed]
33. Theriot, C.M.; Young, V.B. Interactions between the gastrointestinal microbiome and Clostridium difficile.
Annu. Rev. Microbiol. 2015, 69, 445–461. [CrossRef][PubMed]
34. Mylonakis, E.; Ryan, E.T.; Calderwood, S.B. Clostridium difficile-associated diarrhea: A review. Arch. Intern. Med.
2001, 161, 525–533. [CrossRef][PubMed]
36
15. Agus, A.; Denizot, J.; Thévenot, J.; Martinez-Medina, M.; Massier, S.; Sauvanet, P.; Bernalier-Donadille, A.;
Denis, S.; Hofman, P.; Bonnet, R.; et al. Western diet induces a shift in microbiota composition enhancing
susceptibility to Adherent-Invasive E. coli infection and intestinal inflammation. Sci. Rep. 2016, 6, 19032.
[CrossRef][PubMed]
16. Theriot, C.M.; Bowman, A.A.; Young, V.B. Antibiotic-induced alterations of the gut microbiota alter
secondary bile acid production and allow for Clostridium difficile spore germination and outgrowth in the
large intestine. MSphere 2016, 1, e00045-15. [CrossRef]
17. Winter, S.E.; Winter, M.G.; Xavier, M.N.; Thiennimitr, P.; Poon, V.; Keestra, A.M.; Laughlin, R.C.; Gomez, G.;
Wu, J.; Lawhon, S.D.; et al. Host-derived nitrate boosts growth of E. coli in the inflamed gut. Science 2013,
339, 708–711. [CrossRef]
18. Frank, D.N.; Amand, A.L.S.; Feldman, R.A.; Boedeker, E.C.; Harpaz, N.; Pace, N.R. Molecular-phylogenetic
characterization of microbial community imbalances in human inflammatory bowel diseases. Proc. Natl.
Acad. Sci. USA 2007, 104, 13780–13785. [CrossRef][PubMed]
19. Ley, R.E.; Turnbaugh, P.J.; Klein, S.; Gordon, J.I. Microbial ecology: Human gut microbes associated with
obesity. Nature 2006, 444, 1022–1023. [CrossRef][PubMed]
20. Carding, S.; Verbeke, K.; Vipond, D.T.; Corfe, B.M.; Owen, L.J. Dysbiosis of the gut microbiota in disease.
Microb. Ecol. Health Dis. 2015, 26, 26191. [CrossRef]
21. Surawicz, C.M.; Brandt, L.J.; Binion, D.G.; Ananthakrishnan, A.N.; Curry, S.R.; Gilligan, P.H.; McFarland,
L.V.; Mellow, M.; Zuckerbraun, B.S. Guidelines for diagnosis, treatment, and prevention of Clostridium
difficile infections. Am. J. Gastroenterol. 2013, 108, 478. [CrossRef][PubMed]
22. Shim, J.K.; Johnson, S.; Samore, M.H.; Bliss, D.Z.; Gerding, D.N. Primary symptomless colonisation by
Clostridium difficile and decreased risk of subsequent diarrhoea. Lancet 1998, 351, 633–636. [CrossRef]
23. Kyne, L.; Warny, M.; Qamar, A.; Kelly, C.P. Asymptomatic carriage of Clostridium difficile and serum levels of
IgG antibody against toxin A. N. Engl. J. Med. 2000, 342, 390–397. [CrossRef][PubMed]
24. Barbut, F.; Petit, J.C. Epidemiology of Clostridium difficile-associated infections. Clin. Microbiol. Infect. 2001,
7, 405–410. [CrossRef]
25. Kato, H.; Kita, H.; Karasawa, T.; Maegawa, T.; Koino, Y.; Takakuwa, H.; Saikai, T.; Kobayashi, K.;
Yamagishi, T.; Nakamura, S. Colonisation and transmission of Clostridium difficile in healthy individuals
examined by PCR ribotyping and pulsed-field gel electrophoresis. J. Med. Microbiol. 2001, 50, 720–727.
[CrossRef][PubMed]
26. Ozaki, E.; Kato, H.; Kita, H.; Karasawa, T.; Maegawa, T.; Koino, Y.; Matsumoto, K.; Takada, T.; Nomoto, K.;
Tanaka, R.; et al. Clostridium difficile colonization in healthy adults: transient colonization and correlation
with enterococcal colonization. J. Med. Microbiol. 2004, 53, 167–172. [CrossRef]
27. Poutanen, S.M.; Simor, A.E. Clostridium difficile-associated diarrhea in adults. Can. Med. Assoc. J. 2004,
171, 51–58. [CrossRef]
28. Furuya-Kanamori, L.; Marquess, J.; Yakob, L.; Riley, T.V.; Paterson, D.L.; Foster, N.F.; Huber, C.A.;
Clements, A.C. Asymptomatic Clostridium difficile colonization: epidemiology and clinical implications.
BMC Infect. Dis. 2015, 15, 516. [CrossRef][PubMed]
29. Chang, J.Y.; Antonopoulos, D.A.; Kalra, A.; Tonelli, A.; Khalife, W.T.; Schmidt, T.M.; Young, V.B. Decreased
diversity of the fecal microbiome in recurrent Clostridium difficile-associated diarrhea. J. Infect. Dis. 2008,
197, 435–438. [CrossRef]
30. Bartlett, J.G. Clostridium difficile: History of its role as an enteric pathogen and the current state of knowledge
about the organism. Clin. Infect. Dis. 1994, 18, S265–S272. [CrossRef]
31. Pérez-Cobas, A.E.; Moya, A.; Gosalbes, M.J.; Latorre, A. Colonization resistance of the gut microbiota against
Clostridium difficile. Antibiotics 2015, 4, 337–357. [CrossRef][PubMed]
32. Pothoulakis, C. Pathogenesis of Clostridium difficile-associated diarrhoea. Eur. J. Gastroenterol. Hepatol. 1996,
8, 1041–1047. [CrossRef][PubMed]
33. Theriot, C.M.; Young, V.B. Interactions between the gastrointestinal microbiome and Clostridium difficile.
Annu. Rev. Microbiol. 2015, 69, 445–461. [CrossRef][PubMed]
34. Mylonakis, E.; Ryan, E.T.; Calderwood, S.B. Clostridium difficile-associated diarrhea: A review. Arch. Intern. Med.
2001, 161, 525–533. [CrossRef][PubMed]
36