Indian Journal of Microbiology

, Volume 58, Issue 1, pp 3–7 | Cite as

Gut-Bioreactor and Human Health in Future

  • Hemant J. PurohitEmail author
Review Article


Gut-microbiome provides the complementary metabolic potential to the human system. To understand the active participation and the performance of the microbial community in human health, the concept of gut as a plug-flow reactor with the fed-batch mode of operation can provide better insight. The concept suggests the virtual compartmentalized gut with sequential stratification of the microbial community in response to a typical host genotype. It also provides the analysis plan for gut microbiome; and its relevance in developing health management options under the identified clinical conditions.


Gut microbiome Plug-flow reactor Microbial diversity Human health SNP 



The authors thank the Director, CSIR-NEERI for providing constant support and infrastructure for the research work; and manuscript has institute’s publication reference number KRC\2017\Dec\EBGD\2.


  1. 1.
    Mutch DM, Wahli W, Williamson G (2005) Nutrigenomics and nutrigenetics: the emerging faces of nutrition. FASEB 19:1602–1616. CrossRefGoogle Scholar
  2. 2.
    Gill SR, Pop M, DeBoy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, Gordon JI, Relman DA, Fraser-Liggett CM, Nelson KE (2006) Metagenomic analysis of the human distal gut microbiome. Science 312:1355–1359. CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Segre JA, Salafsky N (2016) Hominid superorganisms. Science 353:350–351. CrossRefPubMedGoogle Scholar
  4. 4.
    Sender R, Fuchs S, Milo R (2016) Revised estimates for the number of human and bacteria cells in the body. PLoS Biol 14:e1002533. CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Flint HJ, Scott KP, Louis P, Duncan SH (2012) The role of the gut microbiota in nutrition and health. Nat Rev Gastroenterol Hepatol 9:577–589. CrossRefPubMedGoogle Scholar
  6. 6.
    Zeevi D, Korem T, Zmora N, Israeli D, Rothschild D, Weinberger A, Ben-Yacov O, Lador D, Avnit-Sagi T, Lotan-Pompan M, Suez J, Mahdi JA, Matot E, Malka G, Kosower N, Rein M, Zilberman-Schapira G, Dohnalová L, Pevsner-Fischer M, Bikovsky R, Halpern Z, Elinav E, Segal E (2015) Personalized nutrition by prediction of glycemic esponses. Cell 163:1079–1094. CrossRefPubMedGoogle Scholar
  7. 7.
    Porter NT, Martens EC (2017) The critical roles of polysaccharides in gut microbial ecology and physiology. Annu Rev Microbiol 71:349–369. CrossRefPubMedGoogle Scholar
  8. 8.
    Kau AL, Ahern PP, Griffin NW, Goodman AL, Gordon JI (2011) Human nutrition, the gut microbiome and the immune system. Nature 474:327–336. CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Cencič A, Langerholc T (2010) Functional cell models of the gut and their applications in food microbiology—a review. Int J Food Microbiol 141:S4–S14. CrossRefPubMedGoogle Scholar
  10. 10.
    Flint HJ, Duncan SH, Louis P (2017) The impact of nutrition on intestinal bacterial communities. Curr Opin Microbiol 38:59–65. CrossRefPubMedGoogle Scholar
  11. 11.
    Wissenbach DK, Oliphant K, Rolle-Kampczyk U, Yen S, Höke H, Baumann S, Haange SB, Verdu EF, Allen-Vercoe E, von Bergen M (2016) Optimization of metabolomics of defined in vitro gut microbial ecosystems. Int J Med Microbiol 306:280–900. CrossRefPubMedGoogle Scholar
  12. 12.
    Gevers D, Kugathasan S, Knights D, Kostic AD, Knight R, Xavier RJ (2017) A microbiome foundation for the study of Crohn’s disease. Cell Host Microbe 21:301–304. CrossRefPubMedGoogle Scholar
  13. 13.
    Halfvarson J, Brislawn CJ, Lamendella R, Vázquez-Baeza Y, Walters WA, Bramer LM, D’Amato M, Bonfiglio F, McDonald D, Gonzalez A, McClure EE (2017) Dynamics of the human gut microbiome in inflammatory bowel disease. Nat Microbiol 2:17004. CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Kamada N, Seo SU, Chen GY, Núñez G (2013) Role of the gut microbiota in immunity and inflammatory disease. Nat Rev Immunol 13:321–335. CrossRefPubMedGoogle Scholar
  15. 15.
    Malaisé Y, Menard S, Cartier C, Gaultier E, Lasserre F, Lencina C, Harkat C, Geoffre N, Lakhal L, Castan I, Olier M (2017) Gut dysbiosis and impairment of immune system homeostasis in perinatally-exposed mice to Bisphenol A precede obese phenotype development. Sci Rep 7:14472. CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Xu P, Hong F, Wang J, Wang J, Zhao X, Wang S, Xue T, Xu J, Zheng X, Zhai Y (2017) DBZ is a putative PPARγ agonist that prevents high fat diet-induced obesity, insulin resistance and gut dysbiosis. Biochim Biophys Acta Gen Subj 1861:2690–2701. CrossRefGoogle Scholar
  17. 17.
    Pindjakova J, Sartini C, Lo Re O, Rappa F, Coupe B, Lelouvier B, Pazienza V, Vinciguerra M (2017) Gut dysbiosis and adaptive immune response in diet-induced obesity vs. systemic inflammation. Front Microbiol 8:1157. CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Dzutsev A, Badger JH, Perez-Chanona E, Roy S, Salcedo R, Smith CK, Trinchieri G (2017) Microbes and cancer. Ann Rev Immunol 35:199–228. CrossRefGoogle Scholar
  19. 19.
    Hooper LV, Littman DR, Macpherson AJ (2012) Interactions between the microbiota and the immune system. Science 336:1268–1273. CrossRefPubMedPubMedCentralGoogle Scholar
  20. 20.
    Lee WJ, Hase K (2014) Gut microbiota-generated metabolites in animal health and disease. Nat Chem Biol 10:416–424. CrossRefPubMedGoogle Scholar
  21. 21.
    Kurilshikov A, Wijmenga C, Fu J, Zhernakova A (2017) Host genetics and gut microbiome: challenges and perspectives. Trends Immunol 38:633–647. CrossRefPubMedGoogle Scholar
  22. 22.
    Ronen M, Shabtai Y, Guterman H (2002) Optimization of feeding profile for a fed-batch bioreactor by an evolutionary algorithm. J Biotechnol 97:253–263.,00106-2 CrossRefPubMedGoogle Scholar
  23. 23.
    Hu P, Hsieh MH, Lei MJ, Cui B, Chiu SK, Tzeng CM (2016) A simple algorithm for population classification. Sci Rep 6:23491. CrossRefPubMedPubMedCentralGoogle Scholar
  24. 24.
    Gulhane M, Pandit P, Khardenavis A, Singh D, Purohit H (2017) Study of microbial community plasticity for anaerobic digestion of vegetable waste in anaerobic baffled reactor. Renew Energy 101:59–66. CrossRefGoogle Scholar
  25. 25.
    Carding S, Verbeke K, Vipond DT, Corfe BM, Owen LJ (2015) Dysbiosis of the gut microbiota in disease. Microb Ecol Health Dis 26:26191. PubMedGoogle Scholar
  26. 26.
    Coyte KZ, Schluter J, Foster KR (2015) The ecology of the microbiome: networks, competition, and stability. Science 350:663–666. CrossRefPubMedGoogle Scholar
  27. 27.
    Franzosa EA, Huang K, Meadow JF, Gevers D, Lemon KP, Bohannan BJ, Huttenhower C (2015) Identifying personal microbiomes using metagenomic codes. Proc Natl Acad Sci 112:E2930–E2938. CrossRefPubMedPubMedCentralGoogle Scholar
  28. 28.
    Wang K, Gaitsch H, Poon H, Cox NJ, Rzhetsky A (2017) Classification of common human diseases derived from shared genetic and environmental determinants. Nat Genet 49:1319–1325. CrossRefPubMedGoogle Scholar
  29. 29.
    Annalisa N, Alessio T, Claudette TD, Erald V, Antonino DL, Nicola DD (2014) Gut microbioma population: an indicator really sensible to any change in age, diet, metabolic syndrome, and life-style. Mediat Inflamm. Google Scholar
  30. 30.
    Luceri C, Bigagli E, Pitozzi V, Giovannelli L (2017) A nutrigenomics approach for the study of anti-aging interventions: olive oil phenols and the modulation of gene and microRNA expression profiles in mouse brain. Eur J Nutr 56:865–877. CrossRefPubMedGoogle Scholar
  31. 31.
    Meng Q, Ying Z, Noble E, Zhao Y, Agrawal R, Mikhail A, Zhuang Y, Tyagi E, Zhang Q, Lee JH, Morselli M (2016) Systems nutrigenomics reveals brain gene networks linking metabolic and brain disorders. EBioMedicine 7:157–166. CrossRefPubMedPubMedCentralGoogle Scholar
  32. 32.
    Noble EE, Hsu TM, Kanoski SE (2017) Gut to brain dysbiosis: mechanisms linking Western Diet consumption, the microbiome, and cognitive impairment. Front Behav Neurosci 11:9. CrossRefPubMedPubMedCentralGoogle Scholar
  33. 33.
    Vogt NM, Kerby RL, Dill-McFarland KA, Harding SJ, Merluzzi AP, Johnson SC, Carlsson CM, Asthana S, Zetterberg H, Blennow K, Bendlin BB (2017) Gut microbiome alterations in Alzheimer’s disease. Sci Rep 7:13537. CrossRefPubMedPubMedCentralGoogle Scholar
  34. 34.
    Mallick H, Ma S, Franzosa EA, Vatanen T, Morgan XC, Huttenhower C (2017) Experimental design and quantitative analysis of microbial community multiomics. Genome Biol 18:228. CrossRefPubMedPubMedCentralGoogle Scholar
  35. 35.
    Moorthy AS, Eberl HJ (2017) compuGUT: an in silico platform for simulating intestinal fermentation. SoftwareX 6:237–242. CrossRefGoogle Scholar
  36. 36.
    Liotta F, Chatellier P, Esposito G, Fabbricino M, Van Hullebusch ED, Lens PN (2014) Hydrodynamic mathematical modelling of aerobic plug flow and non-ideal flow reactors: a critical and historical review. Crit Rev Environ Sci Technol 44:2642–2673. CrossRefGoogle Scholar

Copyright information

© Association of Microbiologists of India 2017

Authors and Affiliations

  1. 1.Environmental Biotechnology and Genomic DivisionNational Environmental Engineering Research Institute, (CSIR-NEERI)NagpurIndia

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