Processes 2019, 7,97
57. Spor, A.; Koren, O.; Ley, R. Unravelling the effects of the environment and host genotype on the gut
microbiome. Nat. Rev. Microbiol. 2011, 9, 279–290. [CrossRef]
58. De Filippo, C.; Cavalieri, D.; Di Paola, M.; Ramazzotti, M.; Poullet, J.B.; Massart, S.; Collini, S.; Pieraccini, G.;
Lionetti, P. Impact of diet in shaping gut microbiota revealed by a comparative study in children from
Europe and rural Africa. Proc. Natl. Acad. Sci. USA 2010, 107, 14691–14696. [CrossRef]
59. Byrne, C.; Chambers, E.; Morrison, D.; Frost, G. The role of short chain fatty acids in appetite regulation and
energy homeostasis. Int. J. Obes. 2015, 39, 1331–1338. [CrossRef]
60. Campbell, J.M.; Fahey, G.C.; Wolf, B.W. Selected indigestible oligosaccharides affect large bowel mass, cecal
and fecal short-chain fatty acids, pH and microflora in rats. J. Nutr. 1997, 127, 130–136. [CrossRef]
61. Theriot, C.M.; Koenigsknecht, M.J.; Carlson Jr, P.E.; Hatton, G.E.; Nelson, A.M.; Li, B.; Huffnagle, G.B.; Li, J.Z.;
Young, V.B. Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility
to Clostridium difficile infection. Nat. Commun. 2014, 5, 3114. [CrossRef][PubMed]
62. Utzschneider, K.M.; Kratz, M.; Damman, C.J.; Hullarg, M. Mechanisms linking the gut microbiome and
glucose metabolism. J. Clin. Endocrinol. Metab. 2016, 101, 1445–1454. [CrossRef][PubMed]
63. Carmody, R.N.; Gerber, G.K.; Luevano, J.M.; Gatti, D.M.; Somes, L.; Svenson, K.L.; Turnbaugh, P.J. Diet
dominates host genotype in shaping the murine gut microbiota. Cell Host Microbe 2015, 17, 72–84. [CrossRef]
[PubMed]
64. Zhang, X.; Shen, D.; Fang, Z.; Jie, Z.; Qiu, X.; Zhang, C.; Chen, Y.; Ji, L. Human gut microbiota changes reveal
the progression of glucose intolerance. PLoS ONE 2013, 8, e71108. [CrossRef][PubMed]
65. Jackson, S.; Calos, M.; Myers, A.; Self, W.T. Analysis of proline reduction in the nosocomial pathogen
Clostridium difficile. J. Bacteriol. 2006, 188, 8487–8495. [CrossRef][PubMed]
66. Karlsson, S.; Burman, L.G.; Åkerlund, T. Suppression of toxin production in Clostridium difficile VPI 10463 by
amino acids. Microbiology 1999, 145, 1683–1693. [CrossRef][PubMed]
67. Neumann-Schaal, M.; Hofmann, J.D.; Will, S.E.; Schomburg, D. Time-resolved amino acid uptake of
Clostridium difficile 630∆erm and concomitant fermentation product and toxin formation. BMC Microbiol.
2015, 15, 281. [CrossRef][PubMed]
68. Antonopoulos, D.A.; Huse, S.M.; Morrison, H.G.; Schmidt, T.M.; Sogin, M.L.; Young, V.B. Reproducible
community dynamics of the gastrointestinal microbiota following antibiotic perturbation. Infect. Immunity
2009, 77, 2367–2375. [CrossRef][PubMed]
69. Antharam, V.C.; Li, E.C.; Ishmael, A.; Sharma, A.; Mai, V.; Rand, K.H.; Wang, G.P. Intestinal dysbiosis and
depletion of butyrogenic bacteria in Clostridium difficile infection and nosocomial diarrhea. J. Clin. Microbiol.
2013, 51, 2884–2892. [CrossRef]
70. Vincent, C.; Manges, A. Antimicrobial use, human gut microbiota and Clostridium difficile colonization and
infection. Antibiotics 2015, 4, 230–253. [CrossRef]
71. Schippa, S.; Conte, M.P. Dysbiotic events in gut microbiota: Impact on human health. Nutrients 2014,
6, 5786–5805. [CrossRef]
72. Tamboli, C.; Neut, C.; Desreumaux, P.; Colombel, J. Dysbiosis in inflammatory bowel disease. Gut 2004,
53, 1–4. [CrossRef][PubMed]
73. Honda, K.; Littman, D.R. The microbiome in infectious disease and inflammation. Annu. Rev. Immunol.
2012, 30, 759–795. [CrossRef][PubMed]
74. Ling, Z.; Liu, X.; Jia, X.; Cheng, Y.; Luo, Y.; Yuan, L.; Wang, Y.; Zhao, C.; Guo, S.; Li, L.; et al. Impacts of
infection with different toxigenic Clostridium difficile strains on faecal microbiota in children. Sci. Rep. 2014,
4, 7485. [CrossRef][PubMed]
75. Ridlon, J.M.; Kang, D.J.; Hylemon, P.B. Bile salt biotransformations by human intestinal bacteria. J. Lipid Res.
2006, 47, 241–259. [CrossRef]
76. Setchell, K.; Lawson, A.; Tanida, N.; Sjövall, J. General methods for the analysis of metabolic profiles of bile
acids and related compounds in feces. J. Lipid Res. 1983, 24, 1085–1100. [PubMed]
77. Winston, J.A.; Theriot, C.M. Impact of microbial derived secondary bile acids on colonization resistance
against Clostridium difficile in the gastrointestinal tract. Anaerobe 2016, 41, 44–50. [CrossRef][PubMed]
78. Rea, M.C.; Dobson, A.; O’Sullivan, O.; Crispie, F.; Fouhy, F.; Cotter, P.D.; Shanahan, F.; Kiely, B.; Hill, C.;
Ross, R.P. Effect of broad-and narrow-spectrum antimicrobials on Clostridium difficile and microbial diversity
in a model of the distal colon. Proc. Natl. Acad. Sci. USA 2011, 108, 4639–4644. [CrossRef]
38
57. Spor, A.; Koren, O.; Ley, R. Unravelling the effects of the environment and host genotype on the gut
microbiome. Nat. Rev. Microbiol. 2011, 9, 279–290. [CrossRef]
58. De Filippo, C.; Cavalieri, D.; Di Paola, M.; Ramazzotti, M.; Poullet, J.B.; Massart, S.; Collini, S.; Pieraccini, G.;
Lionetti, P. Impact of diet in shaping gut microbiota revealed by a comparative study in children from
Europe and rural Africa. Proc. Natl. Acad. Sci. USA 2010, 107, 14691–14696. [CrossRef]
59. Byrne, C.; Chambers, E.; Morrison, D.; Frost, G. The role of short chain fatty acids in appetite regulation and
energy homeostasis. Int. J. Obes. 2015, 39, 1331–1338. [CrossRef]
60. Campbell, J.M.; Fahey, G.C.; Wolf, B.W. Selected indigestible oligosaccharides affect large bowel mass, cecal
and fecal short-chain fatty acids, pH and microflora in rats. J. Nutr. 1997, 127, 130–136. [CrossRef]
61. Theriot, C.M.; Koenigsknecht, M.J.; Carlson Jr, P.E.; Hatton, G.E.; Nelson, A.M.; Li, B.; Huffnagle, G.B.; Li, J.Z.;
Young, V.B. Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility
to Clostridium difficile infection. Nat. Commun. 2014, 5, 3114. [CrossRef][PubMed]
62. Utzschneider, K.M.; Kratz, M.; Damman, C.J.; Hullarg, M. Mechanisms linking the gut microbiome and
glucose metabolism. J. Clin. Endocrinol. Metab. 2016, 101, 1445–1454. [CrossRef][PubMed]
63. Carmody, R.N.; Gerber, G.K.; Luevano, J.M.; Gatti, D.M.; Somes, L.; Svenson, K.L.; Turnbaugh, P.J. Diet
dominates host genotype in shaping the murine gut microbiota. Cell Host Microbe 2015, 17, 72–84. [CrossRef]
[PubMed]
64. Zhang, X.; Shen, D.; Fang, Z.; Jie, Z.; Qiu, X.; Zhang, C.; Chen, Y.; Ji, L. Human gut microbiota changes reveal
the progression of glucose intolerance. PLoS ONE 2013, 8, e71108. [CrossRef][PubMed]
65. Jackson, S.; Calos, M.; Myers, A.; Self, W.T. Analysis of proline reduction in the nosocomial pathogen
Clostridium difficile. J. Bacteriol. 2006, 188, 8487–8495. [CrossRef][PubMed]
66. Karlsson, S.; Burman, L.G.; Åkerlund, T. Suppression of toxin production in Clostridium difficile VPI 10463 by
amino acids. Microbiology 1999, 145, 1683–1693. [CrossRef][PubMed]
67. Neumann-Schaal, M.; Hofmann, J.D.; Will, S.E.; Schomburg, D. Time-resolved amino acid uptake of
Clostridium difficile 630∆erm and concomitant fermentation product and toxin formation. BMC Microbiol.
2015, 15, 281. [CrossRef][PubMed]
68. Antonopoulos, D.A.; Huse, S.M.; Morrison, H.G.; Schmidt, T.M.; Sogin, M.L.; Young, V.B. Reproducible
community dynamics of the gastrointestinal microbiota following antibiotic perturbation. Infect. Immunity
2009, 77, 2367–2375. [CrossRef][PubMed]
69. Antharam, V.C.; Li, E.C.; Ishmael, A.; Sharma, A.; Mai, V.; Rand, K.H.; Wang, G.P. Intestinal dysbiosis and
depletion of butyrogenic bacteria in Clostridium difficile infection and nosocomial diarrhea. J. Clin. Microbiol.
2013, 51, 2884–2892. [CrossRef]
70. Vincent, C.; Manges, A. Antimicrobial use, human gut microbiota and Clostridium difficile colonization and
infection. Antibiotics 2015, 4, 230–253. [CrossRef]
71. Schippa, S.; Conte, M.P. Dysbiotic events in gut microbiota: Impact on human health. Nutrients 2014,
6, 5786–5805. [CrossRef]
72. Tamboli, C.; Neut, C.; Desreumaux, P.; Colombel, J. Dysbiosis in inflammatory bowel disease. Gut 2004,
53, 1–4. [CrossRef][PubMed]
73. Honda, K.; Littman, D.R. The microbiome in infectious disease and inflammation. Annu. Rev. Immunol.
2012, 30, 759–795. [CrossRef][PubMed]
74. Ling, Z.; Liu, X.; Jia, X.; Cheng, Y.; Luo, Y.; Yuan, L.; Wang, Y.; Zhao, C.; Guo, S.; Li, L.; et al. Impacts of
infection with different toxigenic Clostridium difficile strains on faecal microbiota in children. Sci. Rep. 2014,
4, 7485. [CrossRef][PubMed]
75. Ridlon, J.M.; Kang, D.J.; Hylemon, P.B. Bile salt biotransformations by human intestinal bacteria. J. Lipid Res.
2006, 47, 241–259. [CrossRef]
76. Setchell, K.; Lawson, A.; Tanida, N.; Sjövall, J. General methods for the analysis of metabolic profiles of bile
acids and related compounds in feces. J. Lipid Res. 1983, 24, 1085–1100. [PubMed]
77. Winston, J.A.; Theriot, C.M. Impact of microbial derived secondary bile acids on colonization resistance
against Clostridium difficile in the gastrointestinal tract. Anaerobe 2016, 41, 44–50. [CrossRef][PubMed]
78. Rea, M.C.; Dobson, A.; O’Sullivan, O.; Crispie, F.; Fouhy, F.; Cotter, P.D.; Shanahan, F.; Kiely, B.; Hill, C.;
Ross, R.P. Effect of broad-and narrow-spectrum antimicrobials on Clostridium difficile and microbial diversity
in a model of the distal colon. Proc. Natl. Acad. Sci. USA 2011, 108, 4639–4644. [CrossRef]
38