Processes 2019, 7,97
Abbreviations
The following abbreviations are used in this manuscript:
ATPM
ATP maintenance
BT
Bacteroides thetaiotaomicron
CD
Clostridium difficile
CDI
Clostridium difficile infection
DFBAlab Dynamic flux balance analysis laboratory
EC
Escherichia coli
FBA
Flux balance analysis
FP
Faecalibacterium prausnitzii
IBD
Inflammatory bowel diseases
LP
Linear program
MDM
Minimal defined media
OA
Organic acid
ODE
Ordinary differential equation
PDE
Partial differential equation
SCFA
Short chain fatty acid
References
1.
Gill, S.R.; Pop, M.; DeBoy, R.T.; Eckburg, P.B.; Turnbaugh, P.J.; Samuel, B.S.; Gordon, J.I.; Relman, D.A.;
Fraser-Liggett, C.M.; Nelson, K.E. Metagenomic analysis of the human distal gut microbiome. Science 2006,
312, 1355–1359. [CrossRef][PubMed]
2.
Bäckhed, F.; Ley, R.E.; Sonnenburg, J.L.; Peterson, D.A.; Gordon, J.I. Host-bacterial mutualism in the human
intestine. Science 2005, 307, 1915–1920. [CrossRef][PubMed]
3.
Macpherson, A.J.; Harris, N.L. Interactions between commensal intestinal bacteria and the immune system.
Nat. Rev. Immunol. 2004, 4, 478–485. [CrossRef][PubMed]
4.
Bäumler, A.J.; Sperandio, V. Interactions between the microbiota and pathogenic bacteria in the gut. Nature
2016, 535, 85–93. [CrossRef][PubMed]
5.
Den Besten, G.; van Eunen, K.; Groen, A.K.; Venema, K.; Reijngoud, D.J.; Bakker, B.M. The role of short-chain
fatty acids in the interplay between diet, gut microbiota, and host energy metabolism. J. Lipid Res. 2013,
54, 2325–2340. [CrossRef][PubMed]
6.
Macfarlane, S.; Steed, H.; Macfarlane, G.T. Intestinal bacteria and inflammatory bowel disease. Crit. Rev.
Clin. Lab. Sci. 2009, 46, 25–54. [CrossRef][PubMed]
7.
Morrison, D.J.; Preston, T. Formation of short chain fatty acids by the gut microbiota and their impact on
human metabolism. Gut Microbes 2016, 7, 189–200. [CrossRef][PubMed]
8.
Rajili´ c-Stojanovi´ c, M.; Smidt, H.; De Vos, W.M. Diversity of the human gastrointestinal tract microbiota
revisited. Environ. Microbiol. 2007, 9, 2125–2136. [CrossRef]
9.
Zoetendal, E.; Rajili´ c-Stojanovi´ c, M.; De Vos, W. High-throughput diversity and functionality analysis of the
gastrointestinal tract microbiota. Gut 2008, 57, 1605–1615. [CrossRef]
10. Gerritsen, J.; Smidt, H.; Rijkers, G.T.; Vos, W.M. Intestinal microbiota in human health and disease: The impact
of probiotics. Genes Nutr. 2011, 6, 209. [CrossRef]
11. Young, V.B.; Schmidt, T.M. Antibiotic-associated diarrhea accompanied by large-scale alterations in the
composition of the fecal microbiota. J. Clin. Microbiol. 2004, 42, 1203–1206. [CrossRef][PubMed]
12. Brown, K.; DeCoffe, D.; Molcan, E.; Gibson, D.L. Diet-induced dysbiosis of the intestinal microbiota and the
effects on immunity and disease. Nutrients 2012, 4, 1095–1119. [CrossRef][PubMed]
13. Anitha, M.; Reichardt, F.; Tabatabavakili, S.; Nezami, B.G.; Chassaing, B.; Mwangi, S.; Vijay-Kumar, M.;
Gewirtz, A.; Srinivasan, S. Intestinal dysbiosis contributes to the delayed gastrointestinal transit in high-fat
diet fed mice. CMGH Cell. Mol. Gastroenterol. Hepatol. 2016, 2, 328–339. [CrossRef][PubMed]
14. Alou, M.T.; Lagier, J.C.; Raoult, D. Diet influence on the gut microbiota and dysbiosis related to nutritional
disorders. Hum. Microb. J. 2016, 1, 3–11. [CrossRef]
35
Abbreviations
The following abbreviations are used in this manuscript:
ATPM
ATP maintenance
BT
Bacteroides thetaiotaomicron
CD
Clostridium difficile
CDI
Clostridium difficile infection
DFBAlab Dynamic flux balance analysis laboratory
EC
Escherichia coli
FBA
Flux balance analysis
FP
Faecalibacterium prausnitzii
IBD
Inflammatory bowel diseases
LP
Linear program
MDM
Minimal defined media
OA
Organic acid
ODE
Ordinary differential equation
PDE
Partial differential equation
SCFA
Short chain fatty acid
References
1.
Gill, S.R.; Pop, M.; DeBoy, R.T.; Eckburg, P.B.; Turnbaugh, P.J.; Samuel, B.S.; Gordon, J.I.; Relman, D.A.;
Fraser-Liggett, C.M.; Nelson, K.E. Metagenomic analysis of the human distal gut microbiome. Science 2006,
312, 1355–1359. [CrossRef][PubMed]
2.
Bäckhed, F.; Ley, R.E.; Sonnenburg, J.L.; Peterson, D.A.; Gordon, J.I. Host-bacterial mutualism in the human
intestine. Science 2005, 307, 1915–1920. [CrossRef][PubMed]
3.
Macpherson, A.J.; Harris, N.L. Interactions between commensal intestinal bacteria and the immune system.
Nat. Rev. Immunol. 2004, 4, 478–485. [CrossRef][PubMed]
4.
Bäumler, A.J.; Sperandio, V. Interactions between the microbiota and pathogenic bacteria in the gut. Nature
2016, 535, 85–93. [CrossRef][PubMed]
5.
Den Besten, G.; van Eunen, K.; Groen, A.K.; Venema, K.; Reijngoud, D.J.; Bakker, B.M. The role of short-chain
fatty acids in the interplay between diet, gut microbiota, and host energy metabolism. J. Lipid Res. 2013,
54, 2325–2340. [CrossRef][PubMed]
6.
Macfarlane, S.; Steed, H.; Macfarlane, G.T. Intestinal bacteria and inflammatory bowel disease. Crit. Rev.
Clin. Lab. Sci. 2009, 46, 25–54. [CrossRef][PubMed]
7.
Morrison, D.J.; Preston, T. Formation of short chain fatty acids by the gut microbiota and their impact on
human metabolism. Gut Microbes 2016, 7, 189–200. [CrossRef][PubMed]
8.
Rajili´ c-Stojanovi´ c, M.; Smidt, H.; De Vos, W.M. Diversity of the human gastrointestinal tract microbiota
revisited. Environ. Microbiol. 2007, 9, 2125–2136. [CrossRef]
9.
Zoetendal, E.; Rajili´ c-Stojanovi´ c, M.; De Vos, W. High-throughput diversity and functionality analysis of the
gastrointestinal tract microbiota. Gut 2008, 57, 1605–1615. [CrossRef]
10. Gerritsen, J.; Smidt, H.; Rijkers, G.T.; Vos, W.M. Intestinal microbiota in human health and disease: The impact
of probiotics. Genes Nutr. 2011, 6, 209. [CrossRef]
11. Young, V.B.; Schmidt, T.M. Antibiotic-associated diarrhea accompanied by large-scale alterations in the
composition of the fecal microbiota. J. Clin. Microbiol. 2004, 42, 1203–1206. [CrossRef][PubMed]
12. Brown, K.; DeCoffe, D.; Molcan, E.; Gibson, D.L. Diet-induced dysbiosis of the intestinal microbiota and the
effects on immunity and disease. Nutrients 2012, 4, 1095–1119. [CrossRef][PubMed]
13. Anitha, M.; Reichardt, F.; Tabatabavakili, S.; Nezami, B.G.; Chassaing, B.; Mwangi, S.; Vijay-Kumar, M.;
Gewirtz, A.; Srinivasan, S. Intestinal dysbiosis contributes to the delayed gastrointestinal transit in high-fat
diet fed mice. CMGH Cell. Mol. Gastroenterol. Hepatol. 2016, 2, 328–339. [CrossRef][PubMed]
14. Alou, M.T.; Lagier, J.C.; Raoult, D. Diet influence on the gut microbiota and dysbiosis related to nutritional
disorders. Hum. Microb. J. 2016, 1, 3–11. [CrossRef]
35