Processes 2019, 7,97
79. Sorg, J.A.; Sonenshein, A.L. Bile salts and glycine as cogerminants for Clostridium difficile spores. J. Bacteriol.
2008, 190, 2505–2512. [CrossRef][PubMed]
80. Sorg, J.A.; Sonenshein, A.L. Inhibiting the initiation of Clostridium difficile spore germination using analogs
of chenodeoxycholic acid, a bile acid. J. Bacteriol. 2010, 192, 4983–4990. [CrossRef][PubMed]
81. Allegretti, J.R.; Kearney, S.; Li, N.; Bogart, E.; Bullock, K.; Gerber, G.K.; Bry, L.; Clish, C.B.; Alm, E.; Korzenik, J.
Recurrent Clostridium difficile infection associates with distinct bile acid and microbiome profiles. Aliment.
Pharmacol. Ther. 2016, 43, 1142–1153. [CrossRef][PubMed]
82. Wilson, K.H.; Kennedy, M.J.; Fekety, F.R. Use of sodium taurocholate to enhance spore recovery on a medium
selective for Clostridium difficile. J. Clin. Microbiol. 1982, 15, 443–446. [PubMed]
83. Buggy, B.; Hawkins, C.; Fekety, R. Effect of adding sodium taurocholate to selective media on the recovery
of Clostridium difficile from environmental surfaces. J. Clin. Microbiol. 1985, 21, 636–637. [PubMed]
84. Wilson, K.H. Efficiency of various bile salt preparations for stimulation of Clostridium difficile spore
germination. J. Clin. Microbiol. 1983, 18, 1017–1019. [PubMed]
85. Seekatz, A.M.; Young, V.B. Clostridium difficile and the microbiota. J. Clin. Investig. 2014, 124, 4182–4189.
[CrossRef]
86. Thursby, E.; Juge, N. Introduction to the human gut microbiota. Biochem. J. 2017, 474, 1823–1836. [CrossRef]
87. Engevik, M.A.; Engevik, K.A.; Yacyshyn, M.B.; Wang, J.; Hassett, D.J.; Darien, B.; Yacyshyn, B.R.; Worrell, R.T.
Human Clostridium difficile infection: Inhibition of NHE3 and microbiota profile. Am. J. Physiol. Gastrointest.
Liver Physiol. 2015, 308, G497–G509. [CrossRef]
88. Dannheim, H.; Will, S.E.; Schomburg, D.; Neumann-Schaal, M. Clostridioides difficile 630∆erm in silico and
in vivo–quantitative growth and extensive polysaccharide secretion. FEBS Open Biol. 2017, 7, 602–615.
[CrossRef]
89. Heinken, A.; Sahoo, S.; Fleming, R.M.; Thiele, I. Systems-level characterization of a host-microbe metabolic
symbiosis in the mammalian gut. Gut Microbes 2013, 4, 28–40. [CrossRef]
90. Heinken, A.; Khan, M.T.; Paglia, G.; Rodionov, D.A.; Harmsen, H.J.; Thiele, I. Functional metabolic map of
Faecalibacterium prausnitzii, a beneficial human gut microbe. J. Bacteriol. 2014, 196, 3289–3302. [CrossRef]
91. Baumler, D.J.; Peplinski, R.G.; Reed, J.L.; Glasner, J.D.; Perna, N.T. The evolution of metabolic networks of
E. coli. BMC Syst. Biol. 2011, 5, 182. [CrossRef][PubMed]
92. Henson, M.A.; Phalak, P. Suboptimal community growth mediated through metabolite cross-feeding
promotes species diversity in the gut microbiota. PLoS Comput. Biol. 2018, 14, e1006558. [CrossRef]
[PubMed]
93. Ouwerkerk, J.P.; de Vos, W.M.; Belzer, C. Glycobiome: Bacteria and mucus at the epithelial interface.
Best Pract. Res. Clin. Gastroenterol. 2013, 27, 25–38. [CrossRef][PubMed]
94. Ross, C.L.; Spinler, J.K.; Savidge, T.C. Structural and functional changes within the gut microbiota and
susceptibility to Clostridium difficile infection. Anaerobe 2016, 41, 37–43. [CrossRef][PubMed]
95. Browne, H.P.; Forster, S.C.; Anonye, B.O.; Kumar, N.; Neville, B.A.; Stares, M.D.; Goulding, D.; Lawley, T.D.
Culturing of ‘unculturable’human microbiota reveals novel taxa and extensive sporulation. Nature 2016,
533, 543–546. [CrossRef][PubMed]
96. Staley, C.; Weingarden, A.R.; Khoruts, A.; Sadowsky, M.J. Interaction of gut microbiota with bile acid
metabolism and its influence on disease states. Appl. Microbiol. Biotechnol. 2017, 101, 47–64. [CrossRef]
[PubMed]
97. Myers, S.P. The causes of intestinal dysbiosis: A review. Altern. Med. Rev. 2004, 9, 180–197.
98. Singh, R.K.; Chang, H.W.; Yan, D.; Lee, K.M.; Ucmak, D.; Wong, K.; Abrouk, M.; Farahnik, B.; Nakamura, M.;
Zhu, T.H.; et al. Influence of diet on the gut microbiome and implications for human health. J. Transl. Med.
2017, 15, 73. [CrossRef]
99. Kamada, N.; Chen, G.Y.; Inohara, N.; Núñez, G. Control of pathogens and pathobionts by the gut microbiota.
Nat. Immunol. 2013, 14, 685–690. [CrossRef]
100. Weingarden, A.R.; Chen, C.; Bobr, A.; Yao, D.; Lu, Y.; Nelson, V.M.; Sadowsky, M.J.; Khoruts, A. Microbiota
transplantation restores normal fecal bile acid composition in recurrent Clostridium difficile infection. Am. J.
Physiol. Gastrointest. Liver Physiol. 2013, 306, G310–G319. [CrossRef]
101. Heinken, A.; Thiele, I. Systematic prediction of health-relevant human-microbial co-metabolism through a
computational framework. Gut Microbes 2015, 6, 120–130. [CrossRef][PubMed]
39
79. Sorg, J.A.; Sonenshein, A.L. Bile salts and glycine as cogerminants for Clostridium difficile spores. J. Bacteriol.
2008, 190, 2505–2512. [CrossRef][PubMed]
80. Sorg, J.A.; Sonenshein, A.L. Inhibiting the initiation of Clostridium difficile spore germination using analogs
of chenodeoxycholic acid, a bile acid. J. Bacteriol. 2010, 192, 4983–4990. [CrossRef][PubMed]
81. Allegretti, J.R.; Kearney, S.; Li, N.; Bogart, E.; Bullock, K.; Gerber, G.K.; Bry, L.; Clish, C.B.; Alm, E.; Korzenik, J.
Recurrent Clostridium difficile infection associates with distinct bile acid and microbiome profiles. Aliment.
Pharmacol. Ther. 2016, 43, 1142–1153. [CrossRef][PubMed]
82. Wilson, K.H.; Kennedy, M.J.; Fekety, F.R. Use of sodium taurocholate to enhance spore recovery on a medium
selective for Clostridium difficile. J. Clin. Microbiol. 1982, 15, 443–446. [PubMed]
83. Buggy, B.; Hawkins, C.; Fekety, R. Effect of adding sodium taurocholate to selective media on the recovery
of Clostridium difficile from environmental surfaces. J. Clin. Microbiol. 1985, 21, 636–637. [PubMed]
84. Wilson, K.H. Efficiency of various bile salt preparations for stimulation of Clostridium difficile spore
germination. J. Clin. Microbiol. 1983, 18, 1017–1019. [PubMed]
85. Seekatz, A.M.; Young, V.B. Clostridium difficile and the microbiota. J. Clin. Investig. 2014, 124, 4182–4189.
[CrossRef]
86. Thursby, E.; Juge, N. Introduction to the human gut microbiota. Biochem. J. 2017, 474, 1823–1836. [CrossRef]
87. Engevik, M.A.; Engevik, K.A.; Yacyshyn, M.B.; Wang, J.; Hassett, D.J.; Darien, B.; Yacyshyn, B.R.; Worrell, R.T.
Human Clostridium difficile infection: Inhibition of NHE3 and microbiota profile. Am. J. Physiol. Gastrointest.
Liver Physiol. 2015, 308, G497–G509. [CrossRef]
88. Dannheim, H.; Will, S.E.; Schomburg, D.; Neumann-Schaal, M. Clostridioides difficile 630∆erm in silico and
in vivo–quantitative growth and extensive polysaccharide secretion. FEBS Open Biol. 2017, 7, 602–615.
[CrossRef]
89. Heinken, A.; Sahoo, S.; Fleming, R.M.; Thiele, I. Systems-level characterization of a host-microbe metabolic
symbiosis in the mammalian gut. Gut Microbes 2013, 4, 28–40. [CrossRef]
90. Heinken, A.; Khan, M.T.; Paglia, G.; Rodionov, D.A.; Harmsen, H.J.; Thiele, I. Functional metabolic map of
Faecalibacterium prausnitzii, a beneficial human gut microbe. J. Bacteriol. 2014, 196, 3289–3302. [CrossRef]
91. Baumler, D.J.; Peplinski, R.G.; Reed, J.L.; Glasner, J.D.; Perna, N.T. The evolution of metabolic networks of
E. coli. BMC Syst. Biol. 2011, 5, 182. [CrossRef][PubMed]
92. Henson, M.A.; Phalak, P. Suboptimal community growth mediated through metabolite cross-feeding
promotes species diversity in the gut microbiota. PLoS Comput. Biol. 2018, 14, e1006558. [CrossRef]
[PubMed]
93. Ouwerkerk, J.P.; de Vos, W.M.; Belzer, C. Glycobiome: Bacteria and mucus at the epithelial interface.
Best Pract. Res. Clin. Gastroenterol. 2013, 27, 25–38. [CrossRef][PubMed]
94. Ross, C.L.; Spinler, J.K.; Savidge, T.C. Structural and functional changes within the gut microbiota and
susceptibility to Clostridium difficile infection. Anaerobe 2016, 41, 37–43. [CrossRef][PubMed]
95. Browne, H.P.; Forster, S.C.; Anonye, B.O.; Kumar, N.; Neville, B.A.; Stares, M.D.; Goulding, D.; Lawley, T.D.
Culturing of ‘unculturable’human microbiota reveals novel taxa and extensive sporulation. Nature 2016,
533, 543–546. [CrossRef][PubMed]
96. Staley, C.; Weingarden, A.R.; Khoruts, A.; Sadowsky, M.J. Interaction of gut microbiota with bile acid
metabolism and its influence on disease states. Appl. Microbiol. Biotechnol. 2017, 101, 47–64. [CrossRef]
[PubMed]
97. Myers, S.P. The causes of intestinal dysbiosis: A review. Altern. Med. Rev. 2004, 9, 180–197.
98. Singh, R.K.; Chang, H.W.; Yan, D.; Lee, K.M.; Ucmak, D.; Wong, K.; Abrouk, M.; Farahnik, B.; Nakamura, M.;
Zhu, T.H.; et al. Influence of diet on the gut microbiome and implications for human health. J. Transl. Med.
2017, 15, 73. [CrossRef]
99. Kamada, N.; Chen, G.Y.; Inohara, N.; Núñez, G. Control of pathogens and pathobionts by the gut microbiota.
Nat. Immunol. 2013, 14, 685–690. [CrossRef]
100. Weingarden, A.R.; Chen, C.; Bobr, A.; Yao, D.; Lu, Y.; Nelson, V.M.; Sadowsky, M.J.; Khoruts, A. Microbiota
transplantation restores normal fecal bile acid composition in recurrent Clostridium difficile infection. Am. J.
Physiol. Gastrointest. Liver Physiol. 2013, 306, G310–G319. [CrossRef]
101. Heinken, A.; Thiele, I. Systematic prediction of health-relevant human-microbial co-metabolism through a
computational framework. Gut Microbes 2015, 6, 120–130. [CrossRef][PubMed]
39