Gut microbiota as a separate body system

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Microbiocenosis of various ecological niches of the human body has been studied for many years around the world. In this article, gut microbiota is considered as a separate system of the human body. The relevance of this issue is due to importance of microbiota for the human body. Gut microflora performs various essential functions: participates in digestion, vitamins, hormones and biologically active substances synthesis. Microbiota influences our health, immune response against various adverse factors and formation of the primary prevention of diseases starting from infancy. Human microbiome is a large community of bacteria, viruses and fungi. Development of molecular and genetic testing expanded our knowledge about taxonomic composition of microbiomes and their role and functions in the human body. Undoubtedly, bowel has the most diverse spectrum of microorganisms that needs further investigation. Moreover, modern advances in medical science make it possible to consider gut microbiotope as a new organ or system of the body with its typical features: integrity and divisibility, stable connections, organization and emergence. The purpose of this review is to prove that gut microbiota is a separate functioning system of the human body.

Keywords:

microbiota

functions

intestine

organ

Authors:

Yudina Yu.V.

I.M. Sechenov First Moscow State Medical University, Ministry of Health of Russia, Moscow, Russia

Korsunsky A.A.

Federal State Autonomous Educational Institution of Higher Education «I.M. Sechenov First Moscow State Medical University» of the Ministry of Health of the Russian Federation, Moscow, Russia;
G.N. Speransky City Children’s Clinical Hospital No 9, Moscow Healthcare Department, Moscow, Russia

Aminova A.I.

Sechenov First Moscow State Medical University of the Ministry of Health of Russia, Moscow, Russia;
Speransky Children’s Clinical Hospital of the Moscow Department of Health, Moscow, Russia

Abdullaeva G.D.

OOO 'Medkvadrat', Moscow, Russia

Prodeus A.P.

N.I. Pirogov Russian National Research Medical University, Ministry of Health of Russia, Moscow, Russia;
G.N. Speransky City Children’s Clinical Hospital Nine, Moscow Healthcare Department, Moscow, Russia

List of references:

Sender R, Fuchs S, Milo R. Revised Estimates for the Number of Human and Bacteria Cells in the Body. PLoS Biology. 2016; 14(8):e1002533. https://doi.org/10.1371/journal.pbio.1002533
Li J, Jia H, Cai X, Zhong H, Feng Q, Sunagawa S, Arumugam M, Kultima JR, Prifti E, Nielsen T, Juncker AS, Manichanh C, Chen B, Zhang W, Levenez F, Wang J, Xu X, Xiao L, Liang S, Zhang D, Zhang Z, Chen W, Zhao H, Al-Aama JY, Edris S, Yang H, Wang J, Hansen T, Nielsen HB, Brunak S, Kristiansen K, Guarner F, Pedersen O, Doré J, Ehrlich SD; MetaHIT Consortium, Bork P, Wang J. An integrated catalog of reference genes in the human gut microbiome. Nature Biotechnology. 2014;32(8):834-841. https://doi.org/10.1038/nbt.2942
Moya A, Ferrer M. Functional Redundancy-Induced Stability of Gut Microbiota Subjected to Disturbance. Trends in Microbiology. 2016;24(5):402-413. https://doi.org/10.1016/j.tim.2016.02.002
Chen T, Yu W-H, Izard J, Baranova OV, Lakshmanan A, Dewhirst FE. The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information. Database: the Journal of Biological Databases and Curation. 2010;2010:baq013. https://doi.org/10.1093/database/baq013
Costalonga M, Herzberg MC. The oral microbiome and the immunobiology of periodontal disease and caries. Immunology Letters. 2014;162(2):22-38. https://doi.org/10.1016/j.imlet.2014.08.017
Di Pilato V, Freschi G, Ringressi MN, Pallecchi L, Rossolini GM, Bechi P. The esophageal microbiota in health and disease. Annals of the New York Academy of Sciences. 2016;1381(1):21-33. https://doi.org/10.1111/nyas.13127
Ianiro G, Molina-Infante J, Gasbarrini A. Gastric Microbiota. Helicobacter. 2015;20:68-71. https://doi.org/10.1111/hel.12260
Saltykova IV, Petrov VA, Logacheva MD, Ivanova PG, Merzlikin NV, Sazonov AE, Ogorodova LM, Brindley PJ. Biliary Microbiota, Gallstone Disease and Infection with Opisthorchis felineus. PLOS Neglected Tropical Diseases. 2016;10(7):e0004809. https://doi.org/10.1371/journal.pntd.0004809
Pereira P, Aho V, Arola J, Boyd S, Jokelainen K, Paulin L, Auvinen P, Färkkilä M. Bile microbiota in primary sclerosing cholangitis: Impact on disease progression and development of biliary dysplasia. PLoS One. 2017;12(8):e0182924. https://doi.org/10.1371/journal.pone.0182924
Falony G, Joossens M, Vieira-Silva S, Wang J, Darzi Y, Faust K, Kurilshikov A, Bonder MJ, Valles-Colomer M, Vandeputte D, Tito RY, Chaffron S, Rymenans L, Verspecht C, De Sutter L, Lima-Mendez G, D’hoe K, Jonckheere K, Homola D, Garcia R, Tigchelaar EF, Eeckhaudt L, Fu J, Henckaerts L, Zhernakova A, Wijmenga C, Raes J. Population-level analysis of gut microbiome variation. Science. 2016;352(6285):560-564. https://doi.org/10.1126/science.aad3503
Thursby E, Juge N. Introduction to the human gut microbiota. Biochemical Journal. 2017;474(11):1823-1836. https://doi.org/10.1042/bcj20160510
Ardissone AN, de la Cruz DM, Davis-Richardson AG, Rechcigl KT, Li N, Drew JC, Murgas-Torrazza R, Sharma R, Hudak ML, Triplett EW, Neu J. Meconium microbiome analysis identifies bacteria correlated with premature birth. PLoS One. 2014;9(3):e90784. https://doi.org/10.1371/journal.pone.0090784
Moles L, Gómez M, Heilig H, Bustos G, Fuentes S, de Vos W, Fernández L, Rodríguez JM, Jiménez E. Bacterial diversity in meconium of preterm neonates and evolution of their fecal microbiota during the first month of life. PLoS One. 2013;8(6):e66986. https://doi.org/10.1371/journal.pone.0066986
Rautava S, Kainonen E, Salminen S, Isolauri E. Maternal probiotic supplementation during pregnancy and breast-feeding reduces the risk of eczema in the infant. Journal of Allergy and Clinical Immunology. 2012;130:1355-1360. https://doi.org/10.1016/j.jaci.2012.09.003
Aagaard K, Ma J, Antony KM, Ganu R, Petrosino J, Versalovic J. The placenta harbors a unique microbiome. Science Translational Medicine. 2014;6(237):237ra65. https://doi.org/10.1126/scitranslmed.3008599
Hu J, Nomura Y, Bashir A, Fernandez-Hernandez H, Itzkowitz S, Pei Z, Stone J, Loudon H, Peter I. Diversified microbiota of meconium is affected by maternal diabetes status. PLoS One. 2013;8(11):e78257. https://doi.org/10.1371/journal.pone.0078257
Mackie RI, Sghir A, Gaskins HR. Developmental microbial ecology of the neonatal gastrointestinal tract. American Journal of Clinical Nutrition. 1999;69(5):1035S-1045S. https://doi.org/10.1093/ajcn/69.5.1035s
Maksimova OV, Gervazieva VB, Zverev VV. Gut microbiota and allergic disease. Zhurnal mikrobiologii, epidemiologii i immunobiologii. 2014;3:49-60. (In Russ.) https://doi.org/10.4172/2155-9597.1000179
MacIntyre DA, Chandiramani M, Lee YS, Kindinger L, Smith A, Angelopoulos N, Lehne B, Arulkumaran S, Brown R, Teoh TG, Holmes E, Nicoholson JK, Marchesi JR, Bennett PR. The vaginal microbiome during pregnancy and the postpartum period in a European population. Scientific Reports. 2015;5:8988. https://doi.org/10.1038/srep08988
Nikolaeva IV, Tsaregorodtsev AD, Shaykhieva GS. Formation of intestinal microbiota of the child and the factors influencing this process. Rossijskij vestnik perinatologii i pediatrii. 2018;63(3):13-18. (In Russ.) https://doi.org/10.21508/1027-4065-2018-63-3-13-18
Dogra S, Sakwinska O, Soh SE, Ngom-Bru C, Brück WM, Berger B, Brüssow H, Lee YS, Yap F, Chong YS, Godfrey KM, Holbrook JD; GUSTO Study Group. Dynamics of infant gut microbiota are influenced by delivery mode and gestational duration and are associated with subsequent adiposity. MBio. 2015;6(1):e02419-14. https://doi.org/10.1128/mbio.02419-14
Adlerberth I, Lindberg E, Aberg N, Hesselmar B, Saalman R, Strannegård IL, Wold AE. Reduced enterobacterial and increased staphylococcal colonization of the infantile bowel: an effect of hygienic lifestyle? Pediatric research. 2006;59(1):96-101. https://doi.org/10.1203/01.pdr.0000191137.12774.b2
Soto A, Martín V, Jiménez E, Mader I, Rodríguez JM, Fernández L. Lactobacilli and bifidobacteria in human breast milk: influence of antibiotherapy and other host and clinical factors. Journal of Pediatric Gastroenterology and Nutrition. 2014;59(1):78-88. https://doi.org/10.1097/mpg.0000000000000347
Jost T, Lacroix C, Braegger C, Chassard C. Assessment of bacterial diversity in breast milk using culture-dependent and culture-independent approaches. British Journal of Nutrition. 2013;110(7):1253-1262. https://doi.org/10.1017/s0007114513000597
Marcobal A, Barboza M, Sonnenburg ED, Pudlo N, Martens EC, Desai P, Lebrilla CB, Weimer BC, Mills DA, German JB, Sonnenburg JL. Bacteroides in the infant gut consume milk oligosaccharides via mucus-utilization pathways. Cell Host and Microbe. 2011;10(5):507-514. https://doi.org/10.1016/j.chom.2011.10.007
Tanaka S, Kobayashi T, Songjinda P, Tateyama A, Tsubouchi M, Kiyohara C, Shirakawa T, Sonomoto K, Nakayama J. Influence of antibiotic exposure in the early postnatal period on the development of intestinal microbiota. FEMS Immunology and Medical Microbiology. 2009;56(1):80-87. https://doi.org/10.1111/j.1574-695x.2009.00553.x
Shreiner AB, Kao JY, Young VB. The gut microbiome in health and in disease. Current Opinion in Gastroenterology. 2015;31(1):69-75. https://doi.org/10.1097/mog.0000000000000139
Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Doré J; MetaHIT Consortium, Antolín M, Artiguenave F, Blottiere HM, Almeida M, Brechot C, Cara C, Chervaux C, Cultrone A, Delorme C, Denariaz G, Dervyn R, Foerstner KU, Friss C, van de Guchte M, Guedon E, Haimet F, Huber W, van Hylckama-Vlieg J, Jamet A, Juste C, Kaci G, Knol J, Lakhdari O, Layec S, Le Roux K, Maguin E, Mérieux A, Melo Minardi R, M’rini C, Muller J, Oozeer R, Parkhill J, Renault P, Rescigno M, Sanchez N, Sunagawa S, Torrejon A, Turner K, Vandemeulebrouck G, Varela E, Winogradsky Y, Zeller G, Weissenbach J, Ehrlich SD, Bork P. Enterotypes of the human gut microbiome. Nature. 2011;473(7346):174-180. https://doi.org/10.1038/nature09944
Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD, Lewis JD. Linking long-term dietary patterns with gut microbial enterotypes. Science. 2011;334(6052):105-108. https://doi.org/10.1126/science.1208344
Lim MY, Rho M, Song YM, Lee K, Sung J, Ko G. Stability of gut enterotypes in Korean mono-zygotic twins and their association with bio-markers and diet. Scientific Reports. 2014;4:7348. https://doi.org/10.1038/srep07348
Popenko AS. Bioinformatsionnoe issledovanie taksonomicheskogo sostava mikrobioty kishechnika cheloveka. Diss. … kand. biol. nauk. M. 2014. (In Russ.)
Yong E. Gut microbial «enterotypes» become less clear-cut. Nature. March 2012. Accessed November 08, 2019. Available at: http://www.nature.com/news/gut-microbial-enterotypes-become-less-clear-cut-1.10276 https://doi.org/10.1038/nature.2012.10276
Patrascu O, Béguet-Crespel F, Marinelli L, Le Chatelier E, Abraham AL, Leclerc M, Klopp C, Terrapon N, Henrissat B, Blottière HM, Doré J, Béra-Maillet C. A fibrolytic potential in the human ileum mucosal microbiota revealed by functional metagenomic. Scientific Reports. 2017;7(1):40248. https://doi.org/10.1038/srep40248
Derrien M, Collado MC, Ben-Amor K, Salminen S, de Vos WM. The Mucin degrader Akkermansia muciniphila is an abundant resident of the human intestinal tract. Applied and Environmental Microbiology. 2008;74(5):1646-1648. https://doi.org/10.1128/aem.01226-07
Chen T, Long W, Zhang C, Liu S, Zhao L, Hamaker BR. Fiber-utilizing capacity varies in Prevotella — versus Bacteroides — dominated gut microbiota. Scientific Reports. 2017;7(1):2594. https://doi.org/10.1038/s41598-017-02995-4
Ríos-Covián D, Ruas-Madiedo P, Margolles A, Gueimonde M, de los Reyes-Gavilán CG, Salazar N. Intestinal Short Chain Fatty Acids and their Link with Diet and Human Health. Frontiers in Microbiology. 2016;7:185. https://doi.org/10.3389/fmicb.2016.00185
Sitkin S, Tkachenko E, Vakhitov T, Oreshko L, Zhigalova T. Oral butyrate plus inulin improve serum metabolomic profile and gut microbiota composition in ulcerative colitis and celiac disease. Journal of Crohns and Colitis. 2014;8(Suppl 1):232. https://doi.org/10.1016/s1873-9946(14)60519-5
Ridlon JM, Kang DJ, Hylemon PB, Bajaj JS. Bile acids and the gut microbiome. Current Opinion in Gastroenterology. 2014;30(3):332-338. https://doi.org/10.1097/mog.0000000000000057
De Aguiar Vallim TQ, Tarling EJ, Edwards PA. Pleiotropic roles of bile acids in metabolism. Cell Metabolism. 2013;17(5):657-669. https://doi.org/10.1016/j.cmet.2015.01.007
Hooper LV, Wong MH, Thelin A, Hansson L, Falk PG, Gordon JI. Molecular Analysis of Commensal Host-Microbial Relationships in the Intestine. Science. 2001;291(5505):881-884. https://doi.org/10.1126/science.291.5505.881
Davila AM, Blachier F, Gotteland M, Andriamihaja M, Benetti PH, Sanz Y, Tomé D. Intestinal luminal nitrogen metabolism: Role of the gut microbiota and consequences for the host. Pharmacological Research. 2013;68(1):95-107. https://doi.org/10.1016/j.phrs.2012.11.005
Dai Z-L, Wu G, Zhu W-Y. Amino acid metabolism in intestinal bacteria: links between gut ecology and host health. Frontiers in Bioscience. 2011;16:1768-1786. https://doi.org/10.2741/3820
Fischbach MA, Segre JA. Signaling in Host-Associated Microbial Communities. Cell. 2016;164(6):1288-1300. https://doi.org/10.1016/j.cell.2016.02.037
Holzer P, Farzi A. Neuropeptides and the microbiota-gut-brain axis. Advances in Experimental Medicine and Biology. 2014;817:195-219. https://doi.org/10.1007/978-1-4939-0897-4_9
Tiso M, Schechter AN. Nitrate Reduction to Nitrite, Nitric Oxide and Ammonia by Gut Bacteria under Physiological Conditions. PLoS One. 2015;10(3):e0119712. https://doi.org/10.1371/journal.pone.0119712
Tomasova L, Konopelski P, Ufnal M. Gut Bacteria and Hydrogen Sulfide: The New Old Players in Circulatory System Homeostasis. Molecules. 2016;21(11):1558. https://doi.org/10.3390/molecules21111558
Shenderov BA. Funktsional’noe pitanie i ego rol’ v profilaktike metabolicheskogo sindroma. M.: DeLiPrint; 2008. (In Russ.)
Sivaprakasam S, Bhutia YD, Ramachandran S, Ganapathy V. Cell-Surface and Nuclear Receptors in the Colon as Targets for Bacterial Metabolites and Its Relevance to Colon Health. Nutrients. 2017;9(8):856. https://doi.org/10.3390/nu9080856
Cohen LJ, Han S, Huang Y-H, Brady SF. Identification of the Colicin V Bacteriocin Gene Cluster by Functional Screening of a Human Microbiome Metagenomic Library. ACS Infectious Diseases. 2018;4(1):27-32. https://doi.org/10.1021/acsinfecdis.7b00081
Hamer HM, Jonkers D, Venema K, Vanhoutvin S, Troost FJ, Brummer R-J. Review article: the role of butyrate on colonic function. Alimentary Pharmacology and Therapeutics. 2007;27(2):104-119. https://doi.org/10.1111/j.1365-2036.2007.03562.x
Jung T-H, Park JH, Jeon W-M, Han K-S. Butyrate modulates bacterial adherence on LS174T human colorectal cells by stimulating mucin secretion and MAPK signaling pathway. Nutrition Research and Practice. 2015;9(4):343-349. https://doi.org/10.4162/nrp.2015.9.4.343
Macfarlane GT, Macfarlane S. Bacteria, colonic fermentation, and gastrointestinal health. Journal of AOAC International. 2012;95(1):50-60. https://doi.org/10.5740/jaoacint.sge_macfarlane
Fernando MR, Saxena A, Reyes J-L, McKay DM. Butyrate enhances antibacterial effects while suppressing other features of alternative activation in IL-4-induced macrophages. American Journal of Physiology: Gastrointestinal and Liver Physiology. 2016;310(10):G822-G831. https://doi.org/10.1152/ajpgi.00440.2015
Bindels LB, Dewulf EM, Delzenne NM. GPR43/FFA2: physiopathological relevance and therapeutic prospects. Trends in Pharmacological Sciences. 2013;34(4):226-232. https://doi.org/10.1016/j.tips.2013.02.002
Ang Z, Ding JL. GPR41 and GPR43 in Obesity and Inflammation — Protective or Causative? Frontiers in Immunology. 2016;7:28. https://doi.org/10.3389/fimmu.2016.00028
Schiffrin EJ, Rochat F, Link-Amster H, Aeschlimann JM, Donnet-Hughes A. Immunomodulation of blood cells following the ingestion of lactic acid bacteria. Journal of Dairy Science. 1995;78:491-497. https://doi.org/10.3168/jds.s0022-0302(95)76659-0
Stiemsma L, Reynolds L, Turvey S, Finlay B. The hygiene hypothesis: current perspectives and future therapies. ImmunoTargets and Therapy. 2015;4:143-157. https://doi.org/10.2147/itt.s61528
Dinan TG, Cryan JF. The Microbiome-Gut-Brain Axis in Health and Disease. Gastroenterology Clinics of North America. 2017;46(1):77-89. https://doi.org/10.1016/j.gtc.2016.09.007
Kramer P, Bressan P. Humans as Superorganisms: How Microbes, Viruses, Imprinted Genes, and Other Selfish Entities Shape Our Behavior. Perspectives on Psychological Science. 2015;10(4):464-481. https://doi.org/10.1177/1745691615583131

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