The Composition and Functions of Human Gut Symbiotic Microbiota

  • Boris A. Shenderov
  • Alexander V. Sinitsa
  • Mikhail M. Zakharchenko
  • Christine Lang


From the contemporary perspective, the human organism should be viewed as the most complex “superorganism”, a symbiotic community of eukaryotic, prokaryotic cells including archaebacteria, and viruses (Ugolev 1991, Lederberg 2000). The microbial component of this community is represented by the aggregate of sets of microbiocenoses characterized by a definite composition and occupying the respective biotope in the human organism which is open to the environment (skin, nasopharynx, mouth cavity, respiratory and gastrointestinal tracts, genitourinary system mucosa). In any microbiocenosis one can distinguish widespread species, the so-called characteristic or dominating (core) species (autochthonous, indigenous symbiotic microbiota) and additional or accidental species (transitory allochthonous microbiota). The number of characteristic species is relatively not too big, but to make up for it, they are always well-represented. The “metagenome” of this “superorganism” consists of the Homo sapiens genes proper and the genes of microorganisms colonizing human body. The genome of every human being is quite stable (except for the changes in genes related to the immune system, the metabolism of various dietary substrates or xenobiotic destruction, neoplasms); the microbiome, on the other hand, undergoes rather profound changes in the course of a lifetime (Gilbert et al. 2016).


  1. Bik EM, Ugalde JA, Cousins J, Goddard AD, Richman J, Apte ZS. Microbial biotransformations in the human distal gut. British J Pharmacology. 2018;175(24):4404–4414. doi: Scholar
  2. Blum HE. The human microbiome. Advan Med Science. 2017;62:414–420. doi: Scholar
  3. Braune A, Blaut M. Bacterial species involved in the conversion of dietary flavonoids in the human gut. Gut microbes. 2016;7:216–234. doi: Scholar
  4. Cani PD, Delzenne NM. Gut microflora as a target for energy and metabolic homeostasis. Curr Opin Clin Nutr Metab Care. 2007;10(6):729–734. doi: Scholar
  5. Carding S, Verbeke K, Vipond DT, Corfe BM, Owen LJ. Dysbiosis of the gut microbiota in disease. Microb Ecol Health Dis. 2015;26:26191. doi: Scholar
  6. Charbonneau MR, Blanton LV, Di Giulio DB, Relan DA, Lebrilla CB, Mills DA, Gordon JI. A microbial perspective of human developmental biology. Nature. 2016;535:48–55. doi: Scholar
  7. Chernevskaya EA, Beloborodova NV. Gut microbiome in critical illness (Review). General Reanimatology. 2018;14(5):96–119. Scholar
  8. Chervinets YuV, Chervinets VM, Shenderov BA. The modern view on the biotechnological potential of human symbiotic microbiota. Upper Volga medical journal. 2018;17(1):19–26 (in Russian).Google Scholar
  9. Dietert RR, Dietert JM. The microbiome and sustainable healthcare. Healthcare. 2015;3:100–129. doi: Scholar
  10. Donaldson GP, Lee SM, Mazmanian SK. Gut biogeography of the bacterial microbiota. Nat Rev Microbiol. 2016;14(1):20–32. doi: Scholar
  11. Dorrestein PC, Mazmanian SK, Knight R. Finding the missing links among metabolites, microbes, and the host. Immunity. 2014;40:824–832. doi: Scholar
  12. Faith JJ, Guruge JL, Charbonneau M, Subramanian S, Seedorf H et al. The long-term stability of the human gut microbiota. Science. 2013;341(6141):1237439. doi: Scholar
  13. Falony G, Joossens M, Vieira-Silva S, Wang J, Darzi Y et al. Population-level analysis of gut microbiome variation. Science. 2016;352(6285):560–564. doi: Scholar
  14. Franzosa EA, Huang K, Meadow JF, Gevers D, Lemon KP et al. Identifying personal microbiomes using metagenomic codes. Peoc Natl Acad Sci. 2015;112:2930–8. doi: Scholar
  15. Freitas M, Tavan E, Cayuela C et al. Host-pathogens cross-talk. Indigenous bacteria and probiotics also play the game. Biol Cell. 2003;95(8):503–506.CrossRefGoogle Scholar
  16. Gao D, Gao Z, Zhu G. Antioxidant effects of Lactobacillus plantarum via activation of transcription factor Nrf2. Food Funct. 2013;4:982–989.CrossRefGoogle Scholar
  17. Gilbert JA, Quinn RA, Debelius J, Morton J, Garg N et al. Microbiome-wide association studies link dynamic microbial consortia to disease. Nature. 2016;535:94–103. doi: Scholar
  18. Ilinskaya ON, Ulyanova VV, Yarullina DR, Gataullin IG. Secretome of intestinal Bacilli; a nature guard against pathologies. Front Microbiol. 2017;8:1666. doi: Scholar
  19. Lagier JC, Million M, Hugon P, Armougom F, Raoult D. Human gut microbiota: repertoire and variations. Front Cell Infect Microbiol. 2012;2:136. doi: Scholar
  20. Lederberg J. Infectious history. Science. 2000;288(5464):287–293. doi: Scholar
  21. Lyu Q, Hsu C-C. Can diet influence our health by altering intestinal microbiota-derived fecal metabolites? mSystems. 2018;3(2):e00187–17. doi: Scholar
  22. Maguire M, Maguire G. Gut dysbiosis, leaky gut, and intestinal epithelial proliferation in neurological disorders: towards the development of a new therapeutic using amino acids, prebiotics, probiotics, and postbiotics. Rev Neurosci. 2019;30(2):179–201. doi: Scholar
  23. Meisel JC, Grice EA. The human microbiome. Chapter 4. In: Ginsburg G, Willard H, editors. Genomic and Precision Medicine (Third Edition). Elsevier Inc; 2017. p. 63–77. doi: Scholar
  24. Mimee M, Citorik RJ, Lu TK. Microbiome therapeutics-Advances and challenges. Adv Drug Deliv Rev. 2016;105(Pt A):44–54. doi: Scholar
  25. Nicholson JK, Holmes E, Kinross J, Gibson G, Jia W, Pettersson S. Host-Gut microbiota metabolic interactions. Science. 2012;336(6086):1262–1267. doi: Scholar
  26. Proal AD, Lindseth IA, Marshall TG. Microbe-Microbe and Host-Microbe Interactions Drive Microbiome Dysbiosis and Inflammatory Processes. Discovery Medicine. 2017;23(124):51–60.Google Scholar
  27. Sitkin SI, Tkachenko EI, Vakhitov TYa. Phylo-metabolic nucleus of an intestinal microbiota. Almanac of clinical medicine. 2015;40:12–34 (in Russian).Google Scholar
  28. Sonnenburg JL, Backhed F. Diet-microbiota interactions as moderators of human metabolism. Nature. 2016;535(7610):56–64. doi: Scholar
  29. Suvorov A. Gut microbiota, probiotics, and human health. Bioscience of Microbiota, Food and Health. 2013;32(3):81–91. doi: Scholar
  30. The Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486(7402):207–214. doi: Scholar
  31. Ugolev AM. Theory of adequate nutrition and trophology. Leningrad: Nauka; 1991. (in Russian).Google Scholar
  32. Vakhitov TYa, Sitkin SI. The concept of superorganism in biology and medicine. Experimental & clinical gastroenterology. 2014;107(7):72–85 (in Russian).Google Scholar
  33. Voreades N, Kozil A, Weir TL. Diet and the development of the human intestinal microbiome. Front Microbiol. 2014;5:1–9. doi: Scholar
  34. Yadav M, Verma MK, Chauhan NS. A review of metabolic potential of human gut microbiome in human nutrition. Arch Microbiol. 2018;200(2):203–217. doi: Scholar
  35. Zhernakova A, Kurilshikov A, Bonder MJ, Tigchelaar EF, Schirmer M et al. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science. 2016;352(6285):565–569. doi: Scholar

Copyright information

© Springer Nature Switzerland AG 2020

Authors and Affiliations

  • Boris A. Shenderov
    • 1
  • Alexander V. Sinitsa
    • 2
  • Mikhail M. Zakharchenko
    • 2
  • Christine Lang
    • 3
  1. 1.Research Laboratory for Design & Implementation of Personalized Nutrition-Related Product & DietsK.G. Razumovsky University of Technology & ManagementMoscowRussia
  2. 2.Kraft Ltd.St. PetersburgRussia
  3. 3.MBCC GroupBerlinGermany

Personalised recommendations