Human Gut Microbiome as an Indicator of Human Health

Authors

DOI:

https://doi.org/10.20535/ibb.2021.5.4.244375

Keywords:

human intestine, gut microbiome, coronavirus, immune response, drug metabolism

Abstract

The undeniable achievement in the study of the gut microbiome as an association of different microorganisms, including viruses, that colonize various organs and systems of the body, is the establishment of the fact that some diseases that were consmicrobiotaidered as non-infectious can also be transmitted through microorganisms. This resulted in the gut microbiome being called a forgotten organ that could serve as an additional and kind of missing link for a more objective and better diagnosis and treatment of many diseases that were not considered infectious. The rapid development of gut microbiome research in recent years not only is connected with better understanding of the functioning of the microbiome by the scientific community, but also inseparable from the strategic support of each country. Global investment in researches, related to the human microbiome, has exceeded $1.7 billion over the past decade. These researches contribute to the development of new diagnostic methods and therapeutic interventions. Our review is dedicated to the analysis of the possibilities of application of the human gut microbiome for the diagnosis of diseases, and the role of the intestines in the provocation and causing of certain diseases. Significant differences in the composition and diversity of the human microbiome are shown depending on geographical location and the change of socio-economic formations towards a gradual decrease in the diversity of the gut microbiome due to three stages of human population’s existence: food production, agriculture and industrial urban life. We analyze the influence of dietary patterns, various diseases (including malignant neoplasms) and viral infections (in particular, coronavirus) on the gut microbiome. And vice versa – the influence of the gut microbiome on the drugs effect and their metabolism, which affects the host's immune response and course of the disease.

References

Shreiner AB, Kao JY, Young VB. The gut microbiome in health and in disease. Curr Opin Gastroenterol. 2015;31(1):69-75. DOI: 10.1097/MOG.0000000000000139

O'Hara AM, Shanahan F. The gut flora as a forgotten organ. EMBO Rep. 2006;7(7):688-93. DOI: 10.1038/sj.embor.7400731

Li D, Gao C, Zhang F, Yang R, Lan C, Ma Y, et al. Seven facts and five initiatives for gut microbiome research. Protein Cell. 2020;11(6):391-400. DOI: 10.1007/s13238-020-00697-8

Belizário JE, Napolitano M. Human microbiomes and their roles in dysbiosis, common diseases, and novel therapeutic ap-proaches. Front Microbiol. 2015;6:1050. DOI: 10.3389/fmicb.2015.01050

Sender R, Fuchs S, Milo R. Are we really vastly outnumbered? Revisiting the ratio of bacterial to host cells in humans? Cell. 2016;164(3):337-40. DOI: 10.1016/j.cell.2016.01.013

Gilbert JA, Blaser MJ, Caporaso JG, Jansson JK., Lynch SV, Knight R. Current understanding of the human microbi-ome. Nature Med. 2018;24(4):392-400. DOI: 10.1038/nm.4517

Rastelli M, Cani PD, Knauf C. The gut microbiome influences host endocrine functions. Endocrine Rev. 2019;40(5):1271-84. DOI: 10.1210/er.2018-00280

Lloyd-Price J, Abu-Ali G, Huttenhower C. The healthy human microbiome. Genome Med. 2016;8(1):51. DOI: 10.1186/s13073-016-0307-y

Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486(7402):207. DOI: 10.1038/nature11234

Odamaki T, Kato K, Sugahara H, Hashikura N, Takahashi S, Xiao J-Z, et al. Age-related changes in gut microbiota com-position from newborn to centenarian: a cross sectional study. BMC Microbiol. 2016;16(1):90. DOI: 10.1186/s12866-016-0708-5

Dekaboruah E, Suryavanshi M, Chettri D, Verma AK. Human microbiome: an academic update on human body site spe-cific surveillance and its possible role. Arch Microbiol. 2020;202(8):2147-67. DOI: 10.1007/s00203-020-01931-x

Walter J, Ley R. The human gut microbiome: ecology and recent evolutionary changes. Annu Rev Microbiol. 2011;65(1):411-29. DOI: 10.1146/annurev-micro-090110-102830

Brito IL, Yilmaz S, Huang K, Xu L, Jupiter SD, Jenkins AP, et al. Mobile genes in the human microbiome are struc-tured from global to individual scales. Nature. 2016;535(7612):435-9. DOI: 10.1038/nature18927

DiGiulio DB, Callahan BJ, McMurdie PJ, Costello EK, Lyell DJ, Robaczewska A, et al. Temporal and spatial variation of the human microbiota during pregnancy. Proc Natl Acad Sci USA. 2015;112(35):11060-5. DOI: 10.1073/pnas.1502875112

Rinninella E, Raoul P, Cintoni M, Franceschi F, Miggiano GAD, Gasbarrini A, et al. What is the healthy gut microbiota composition? A changing ecosystem across age, environment, diet, and diseases. Microorganisms. 2019;7(1):10-4. DOI: 10.3390/microorganisms7010014

Paisse S, Valle C, Servant F, Courtney M, Burcelin R, Amar J, Lelouvier B. Comprehensive description of blood microbiome from healthy donors assessed by 16S targeted metagenomic sequencing. Transfusion. 2016;56(5):1138-47. DOI: 10.1111/trf.13477

Gupta VK, Paul S, Dutta C. Geography, ethnicity or subsistence-specific variations in human microbiome composition and diversity. Front Microbiol. 2017;8:1162. DOI: 10.3389/fmicb.2017.01162

Sankaranarayanan K, Ozga AT, Warinner C, Tito RY, Obregon-Tito AJ, Xu J, et al. Gut microbiome diversity among cheyenne and arapaho individuals from Western Oklahoma. Curr Biol. 2015;25(24):3161-9. DOI: 10.1016/j.cub.2015.10.060

Rampelli S, Schnorr SL, Consolandi C, Turroni S, Severgnini M, Peano P, et al. Metagenome sequencing of the hadza hunter-gatherer gut microbiota. Curr Biol. 2015;25(13):1682-93. DOI: 10.1016/j.cub.2015.04.055

Gomez A, Petrzelkova KJ, Burns MB, Yeoman CJ, Amato KR, Vlckova K, et al. Gut microbiome of coexisting BaAka pygmies and bantu reflects gradients of traditional subsistence patterns. Cell Rep. 2016;14(9):2142-53. DOI: 10.1016/j.celrep.2016.02.013

Greenhill AR, Tsuji H, Ogata K, Natsuhara K, Morita A, Soli K, et al. Characterization of the gut microbiota of Papua New Guineans using reverse transcription quantitative PCR. PLoS One. 2015;10(2):427. DOI: 10.1371/journal.pone.0117427

Morton ER, Lynch J, Froment A, Lafosse S, Heyer E, Przeworski M, et al. Variation in rural african gut microbiota is strongly correlated with colonization by entamoeba and subsistence. PLoS Genet. 2015;11(11):30. DOI: 10.1371/journal.pgen.1005658

How ethnicity and geography affect your microbiome. [Internet]. GUTXY. 2021 [cited 2021 Nov 10]. Available from: https://www.gutxy.com/blog/how-ethnicity-and-geography-affect-your-microbiome

Harrison CA, Taren D. How poverty affects diet to shape the microbiota and chronic disease. Nat Rev Immunol. 2018;18(4):279-87. DOI: 10.1038/nri.2017.121

Perry RJ, Peng L, Barry NA, Cline GW, Zhang D, Cardone RL, et al. Acetate mediates a microbiome-brain-beta-cell axis to promote metabolic syndrome. Nature. 2016;534(7606):213-7. DOI: 10.1038/nature18309

De Filippis F, Pellegrini N, Vannini L, Jeffery IB, La Storia A, Laghi L, et al. High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome. Gut. 2016;65(11):1812-21. DOI: 10.1136/gutjnl-2015-309957

Li JM, Yu R, Zhang LP, Wen SY, Wang SJ, Zhang XY, et al. Dietary fructose-induced gut dysbiosis promotes mouse hippocampal neuroinflammation: a benefit of short-chain fatty acids. Microbiome. 2019;7(1). DOI: 10.1186/s40168-019-0713-7

Zhu S, Jiang Y, Xu K, Cui M, Ye W, Zhao G, et al. The progress of gut microbiome research related to brain disorders. J Neuroinflammation. 2020;17(1):25. DOI: 10.1186/s12974-020-1705-z

Duvallet C, Gibbons SM, Gurry T, Irizarry RA, Alm EJ. Meta-analysis of gut microbiome studies identifies disease-specific and shared responses. Nat Commun. 2017;8(1):1784. DOI: 10.1038/s41467-017-01973-8

Trials A. The Future of Microbiome Research [Internet]. News-Medical.net. 2021 [cited 2021 Nov 10]. Available from: https://www.news-medical.net/news/20201026/The-Future-of-Microbiome-Research.aspx

Brennan CA, Garrett WS. Gut microbiota, inflammation, and colorectal cancer. Annu Rev Microbiol. 2016;70(1):395-411. DOI: 10.1146/annurev-micro-102215-095513

Shang FM, Liu HL. Fusobacterium nucleatum and colorectal cancer: a review. World J Gastrointest Oncol. 2018;10(3):71-81. DOI: 10.4251/wjgo.v10.i3.71

Planas R, Santos R, Tomas-Ojer P, Cruciani C, Lutterotti A, Faigle W, et al. GDP-l-fucose synthase is a CD4+ T cell-specific autoantigen in DRB3 patients with multiple sclerosis. Sci Transl Med. 2018;10(462):eaat4301. DOI: 10.1126/scitranslmed.aat4301

Maini Rekdal V, Bess EN, Bisanz JE, Turnbaugh PJ, Balskus EP. Discovery and inhibition of an interspecies gut bacterial pathway for Levodopa metabolism. Science. 2019;364(6445):eaau6323. DOI: 10.1126/science.aau6323

Zimmermann M, Zimmermann-Kogadeeva M, Wegmann R, Goodman AL. Mapping human microbiome drug metabo-lism by gut bacteria and their genes. Nature. 2019;570(7762):462-7. DOI: 10.1038/s41586-019-1291-3

Gurung M, Li Z, You H, Rodrigues R, Jump DB, Morgun A, et al. Role of gut microbiota in type 2 diabetes pathophysi-ology. EBioMedicine. 2020;51:102590. DOI: 10.1016/j.ebiom.2019.11.051

Tilg H, Zmora N, Adolph TE, Elinav E. The intestinal microbiota fuelling metabolic inflammation. Nat Rev Immunol. 2019;20(1):40-54. DOI: 10.1038/s41577-019-0198-4

Winek K, Dirnagl U, Meisel A. The gut microbiome as therapeutic target in central nervous system diseases: implications for stroke. Neurotherapeutics. 2016;13(4):762-74. DOI: 10.1007/s13311-016-0475-x

He Y, Wang J, Li F, Shi Y. Main clinical features of COVID-19 and potential prognostic and therapeutic value of the microbiota in SARS-CoV-2 infections. Front Microbiol. 2020;11:1302. DOI: 10.3389/fmicb.2020.01302

Hepworth MR, Fung TC, Masur SH, Kelsen JR, Mcconnell FM, Dubrot J, et al. Group 3 innate lymphoid cells mediate intestinal selection of commensal bacteria-specific CD4+ T cells. Science. 2015;348(6238):1031-5. DOI: 10.1126/science.aaa4812

Gut reaction: How the gut microbiome may inuence the severity of COVID-19 [Internet]. 2021 [cited 2021 Nov 10]. Available from: https://medicalxpress.com/news/2020-06-gut-reactionmicrobiome-severity-covid-.html

Zuo T, Zhang F, Lui GCY, Yeoh YK, Li AYL, Zhan H, et al. Alterations in gut microbiota of patients with COVID-19 during time of hospitalization. Gastroenterology. 2020;159(3):944-55. DOI: 10.1053/j.gastro.2020.05.048

Wang J, Zhao S, Liu M, Zhao Z, Xu Y, Wang P, et al. ACE2 expression by colonic epithelial cells is associated with viral infection, immunity and energy metabolism. medRxiv [Preprint] 2020. DOI: 10.1101/2020.02.05.20020545

Chan JW, Kok KH, Zhu Z, Chu H, To KKW, Yuan S, et al. Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan. Emerg Microbes Infect. 2020;9(1):221-36. DOI: 10.1080/22221751.2020.1719902

Zhou J, Li C, Zhao G, Chu H, Wang D, Yan HHN, et al. Human intestinal tract serves as an alternative infection route for Middle East respiratory syndrome coronavirus. Sci Adv. 2017;3(11):15. DOI: 10.1126/sciadv.aao4966

Xiao F, Tang M, Zheng X, Liu Y, Li X, Shan H. Evidence for gastrointestinal infection of SARS-CoV-2. Gastroenterol-ogy. 2020;158(6):1831-3. DOI: 10.1053/j.gastro.2020.02.055

Gou W, Fu Y, Yue L, Chen GD, Cai X, Shuai M, et al. Gut microbiota may underlie the predisposition of healthy indi-viduals to COVID-19. J Genet Genom. 2021;48(9):792-802. DOI: 10.1016/j.jgg.2021.04.002

Jones VG, Mills M, Suarez D, Hogan CA, Yeh D, Segal JB, et al. COVID-19 and Kawasaki disease: novel virus and nov-el case. Hosp Pediatr. 2020;10(6):537-40. DOI: 10.1542/hpeds.2020-0123

Cat L. The decade of the microbiome [Internet]. Forbes. 2021 [cited 2021 Nov 10]. Available from: https://www.forbes.com/sites/linhanhcat/2019/12/31/decade-of-the-microbiome/?sh=2458a4c29961

Stripling J, Rodriguez M. Current evidence in delivery and therapeutic uses of fecal microbiota transplantation in human diseases-Clostridium difficile disease and beyond. Am J Med Sci. 2018;356(5):424-32. DOI: 10.1016/j.amjms.2018.08.010

Safety Alert Regarding the Use of FMT & Risk of Serious Adverse Events [Internet]. U.S. Food and Drug Administration. 2021 [cited 2021 Nov 10]. Available from: https://www.fda.gov/vaccines-blood-biologics/safety-availability-biologics/safety-alert-regarding-use-fecal-microbiota-transplantation-and-risk-serious-adverse-events-likely

Sberro H, Fremin BJ, Zlitni S, Edfors F, Greenfield N, Snyder MP, et al. Large-scale analyses of human microbiomes reveal thousands of small, novel genes. Cell. 2019;178(5):1245-59. DOI: 10.1016/j.cell.2019.07.016

Wilmanski T, Rappaport N, Earls JC, Magis AT, Manor O, Lovejoy J, et al. Blood metabolome predicts gut microbiome α-diversity in humans. Nat Biotechnol. 2019;37(10):1217-28. DOI: 10.1038/s41587-019-0233-9

Turroni S, Brigidi P, Cavalli A, Candela M. Microbiota–host transgenomic metabolism, bioactive molecules from the in-side. J Med Chem. 2018;61(1):47-61. DOI: 10.1021/acs.jmedchem.7b00244

Wang L, Ravichandran V, Yin Y, Yin J, Zhang Y. Natural products from mammalian gut microbiota. Trends Biotechnol. 2019;37(5):492-504. DOI: 10.1016/j.tibtech.2018.10.003

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Published

2021-12-23

How to Cite

1.
Ivanova A, Yalovenko O, Dugan A. Human Gut Microbiome as an Indicator of Human Health. Innov Biosyst Bioeng [Internet]. 2021Dec.23 [cited 2024Apr.18];5(4):207-19. Available from: http://ibb.kpi.ua/article/view/244375

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