Possibilities and Prospects of Modification of the Intestinal Microbiome
https://doi.org/10.20514/2226-6704-2022-12-5-341-351
Abstract
The gut microbiome is a variable system that not only adapts to signals and information coming from humans, but also affects its host due to a complex system of interactions of living microorganisms, phages, viruses, plasmids, mobile genetic elements, molecules synthesized by microorganisms, including their structural elements (nucleic acids, proteins, lipids, polysaccharides), metabolites (signaling molecules, toxins, organic and inorganic molecules) and molecules synthesized by the human body. Modification or modulation of the microbiome by correcting the diet, the intensity of physical activity, the appointment of components of personalized products (prebiotics, probiotics, paraprobiotics, postbiotics, autoprobiotics) can lead to changes in species diversity, the metabolic profile of the intestinal microbiome and the regulation of metabolic processes, local and systemic response to infectious diseases, drug metabolism, the activity of many organs and systems due to the presence of physiological axes “gut microbiome–central nervous system”, “gut microbiome–liver”, “gut microbiome–kidneys” and some others. New, targeted directions of modification of the intestinal microbiome are being studied, which consist in targeted exposure to pathogenic microorganisms, including intracellular and resistant to antibacterial drugs.
The dynamic nature of the intestinal microbiome, the ability to change and adapt under the influence of some of the studied factors opens up new promising areas of medical prevention and treatment of somatic and mental diseases. Undoubtedly, the modification of the microbiome for clinical purposes is aimed at improving human health. However, individual, not always predictable, changes in the microbiome in response to modifying factors may be due to the uniqueness of the species composition and functional potential of microorganisms in each person.
About the Authors
E. G. MalaevaBelarus
Ekaterina G. Malaeva
Gomel
Competing Interests:
Авторы заявляют, что данная работа, её тема, предмет и содержание не затрагивают конкурирующих интересов
I. O. Stoma
Belarus
Gomel
Competing Interests:
Авторы заявляют, что данная работа, её тема, предмет и содержание не затрагивают конкурирующих интересов
References
1. Fassarella M., Blaak E.E., Penders J., et al. Gut microbiome stability and resilience: elucidating the response to perturbations in order to modulate gut health. Gut. 2021; 70(3): 595–605. https://doi.org/10.1136/gutjnl-2020-321747
2. Sitkin S.I., Tkachenko E.I., Vahitov T.Ya. Metabolic intestinal dysbiosis and its biomarkers. Experimental and Clinical Gastroenterology. 2015; 124(12): 6–29 [In Russian].
3. Stoma I.O. Microbiome in medicine. Moscow, GEOTAR-Media. 2020; 320 p. [In Russian].
4. Malaeva E.G. Urinary tract infections and microbiota. Health and Ecology Issues. 2021; 18(3): 5–14 [In Russian]. https://doi.org/10.51523/2708-6011.2021-18-3-1
5. Quigley E.M.М., Gajula P. Recent advances in modulating the microbiome. F1000Res. 2020; 27(9). https://doi.org/10.12688/f1000research.20204.1
6. Danilenko V.N., Ilyasov R.A., Yunes R.A., et al. Zhebrakov readings X. Minsk, Institute of Genetics and Cytology of the National Academy of Sciences of Belarus. 2021; 68 p. [In Russian].
7. Kolodziejczyk A.A., Zheng D., Elinav E. Diet-microbiota interactions and personalized nutrition. Nature Reviews Microbiology. 2019; 17(12): 742–753. https://doi.org/10.1038/s41579-019-0256-8
8. Belzer C., Chia L.W., Aalvink S., et al. Microbial metabolic networks at the mucus layer lead to diet-independent butyrate and vitamin B12 production by intestinal symbionts. mBio. 2017; 8(5): e00770–00717. https://doi.org/10.1128/mBio.00770-17
9. Sassone-Corsi M., Nuccio S.-P., Liu H., et al. Microcins mediate competition among Enterobacteriaceae in the inflamed gut. Nature. 2016; 540: 280–283. https://doi.org/10.1038/nature20557
10. Papenfort K., Bassler B.L. Quorum sensing signal-response systems in gram-negative bacteria. Nature Reviews Microbiology. 2016; 14(9): 576–588. https://doi.org/10.1038/nrmicro.2016.89
11. Perez-Carrasco V., Soriano-Lerma A., Soriano M., et al. Urinary Microbiome: yin and yang of the urinary tract. Frontiers in Cellular and Infection Microbiology. 2021; 11: 617002. https://doi.org/10.3389/fcimb.2021.617002
12. Dubourg G., Morand A., Mekhalif F., et al. Deciphering the urinary microbiota repertoire by culturomics reveals mostly anaerobic bacteria from the gut. Frontiers in Microbiology. 2020; 11: 513305. https://doi.org/10.3389/fmicb.2020.513305
13. Tariq R., Pardi D.S., Tosh P.K., et al. Fecal microbiota transplantation for recurrent Clostridicum difficile infection reduces recurrent urinary tract infection frequency. Clinical Infectious Diseases. 2017; 65 (10): 1745–1747. https://doi.org/10.1093/cid/cix618
14. Dahl W.J., Rivero M.D., Lambert J.M. Diet, nutrients and the microbiome. Progress in Molecular Biology and Translational Science. 2020; 171: 237–263. https://doi.org/10.1016/bs.pmbts.2020.04.006
15. So D., Whelan K., Rossi M., et al. Dietary fiber intervention on gut microbiota composition in healthy adults: a systematic review and meta-analysis. American Journal of Clinical Nutrition. 2018; 107(6): 965–983. https://doi.org/10.1093/ajcn/nqy041
16. Costea P.I., Hildebrand F., Arumugam M., et al. Enterotypes in the landscape of gut microbial community composition. Nature Microbiology. 2018; 3(1): 8–16. https://doi.org/10.1038/s41564-017-0072-8
17. Ruiz-Ojeda F.J., Plaza-Diaz J., Saez-Lara M.J., et al. Effects of sweeteners on the gut microbiota: a review of experimental studies and clinical trials. Advances in Nutrition. 2019; 10: s31–s48. https://doi.org/10.1093/advances/nmy037
18. David L.A., Maurice C.F., Carmody R.N., et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014; 505: 559–563. https://doi.org/10.1038/nature12820
19. Wan Y., Wang F., Yuan J., et al. Effects of dietary fat on gut microbiota and faecal metabolites, and their relationship with cardiometabolic risk factors: a 6-month randomized controlled-feeding trial. Gut. 2019; 68(8): 1417–1429. https://doi.org/10.1136/gutjnl-2018-317609
20. Palleja A., Mikkelsen K.H., Forslund S.K., et al. Recovery of gut microbiota of healthy adults following antibiotic exposure. Nature Microbiology. 2018; 3: 1255–1265. https://doi.org/10.1038/s41564-018-0257-9
21. Tosti V., Bertozzi B., Fontana L. Health benefits of the mediterranean diet: metabolic and molecular mechanisms. The Journals of Gerontology Series A Biological Sciences and Medical Sciences. 2018; 73(3): 318–326. https://doi.org/10.1093/gerona/glx227
22. Kahleova H., Levin S., Barnard N. Cardio-metabolic benefits of plant-based diets. Nutrients. 2017; 9(8): 848. https://doi.org/10.3390/nu9080848
23. Shikany J.M., Demmer R.T., Johnson A.J., et al. Association of dietary patterns with the gut microbiota in older, community-dwelling men. American Journal of Clinical Nutrition. 2019; 110(4): 1003–1014. https://doi.org/10.1093/ajcn/nqz174
24. Tett A., Huang K.D., Asnicar F., et al. The Prevotella copri complex comprises four distinct clades underrepresented in Westernized populations. Cell Host Microbe. 2019; 26(5): 666–679. https://doi.org/10.1016/j.chom.2019.08.018
25. Meslier V., Laiola M., Roager H.M., et al. Mediterranean diet intervention in overweight and obese subjects lowers plasma cholesterol and causes changes in the gut microbiome and metabolome independently of energy intake. Gut. 2020; 69(7): 1258–1268. https://doi.org/10.1136/gutjnl-2019-320438
26. Barrett H.L., Gomez-Arango L.F., Wilkinson S.A., et al. A vegetarian diet is a major determinant of gut microbiota composition in early pregnancy. Nutrients. 2018; 10(7): 890. https://doi.org/10.3390/nu10070890
27. De Angelis M., Ferrocino I., Calabrese F.M., et al. Diet influences the functions of the human intestinal microbiome. Scientific Reports. 2020; 10(1): 4247. https://doi.org/10.1038/s41598-020-61192-y
28. Zhang Y., Zhou S., Zhou Y., et al. Altered gut microbiome composition in children with refractory epilepsy after ketogenic diet. Epilepsy research. 2018; 145: 163–168. https://doi.org/10.1016/j.eplepsyres.2018.06.015
29. Murtaza N., Burke L.M., Vlahovich N., et al. The effects of dietary pattern during intensified training on stool microbiota of elite race walkers. Nutrients. 2019; 11(2): 261. https://doi.org/10.3390/nu11020261
30. Pedersini P., Turroni S., Villafañe J.H. Gut microbiota and physical activity: is there an evidence-based link? Science of the Total Environment. 2020; 727: 138648. https://doi.org/10.1016/j.scitotenv.2020.138648
31. Mailing L.J., Allen J.M., Buford T.W., et al. Exercise and the gut microbiome: a review of the evidence, potential mechanisms, and implications for human health. Exercise and sport sciences reviews. 2019; 47(2): 75–85. https://doi.org/10.1249/JES.0000000000000183
32. de Sire A., de Sire R., Petito V., et al. Gut-joint Axis: the role of physical exercise on gut microbiota modulation in older people with osteoarthritis. Nutrients. 2020; 12(2): 574. https://doi.org/10.3390/nu12020574
33. Rashid M.-U., Weintraub A., Nord C.E. Development of antimicrobial resistance in the normal anaerobic microbiota during one year after administration of clindamycin or ciprofloxacin. Anaerobe. 2015; 31: 72–77. https://doi.org/10.1016/j.anaerobe.2014.10.004
34. Panda S., El khader I., Casellas F., et al. Short-term effect of antibiotics on human gut microbiota. PLoS One. 2014; 9(4): e95476. https://doi.org/10.1371/journal.pone.0095476
35. Reijnders D., Goossens G.H., Hermes G.D., et al. Effects of gut microbiota manipulation by antibiotics on host metabolism in obese humans: a randomized double-blind placebo-controlled trial. Cell metabolism. 2016; 24: 63–74. https://doi.org/10.1016/j.cmet.2016.06.016
36. Kim S., Covington A., Pamer E.G. The intestinal microbiota: antibiotics, colonization resistance, and enteric pathogens. Immunological reviews. 2017; 279: 90–105. https://doi.org/10.1111/imr.12563
37. Willmann M., Vehreschild M.JGT., Biehl L.M., et al. Distinct impact of antibiotics on the gut microbiome and resistome: a longitudinal multicenter cohort study. BMC biology. 2019; 17: 76. https://doi.org/10.1186/s12915-019-0692-y
38. Kriss M., Hazleton K.Z., Nusbacher N.M., et al. Low diversity gut microbiota dysbiosis: drivers, functional implications and recovery. Current Opinion in Microbiology. 2018; 44: 34–40. https://doi.org/10.1016/j.mib.2018.07.003
39. Nataraj B.H., Shivanna S.K., Rao P., et al. Evolutionary concepts in the functional biotics arena: a mini-review. Food Science and Biotechnology. 2020; 16(30): 487–496. https://doi.org/10.1007/s10068-020-00818-3
40. Reid G., Gadir A.A., Dhir R. Probiotics: reiterating what they are and what they are not. Frontiers in microbiology. 2019; 12(10): P. 424. https://doi.org/10.3389/fmicb.2019.00424
41. Zendeboodi F., Khorshidian N., Mortazavian A.M., et al. Probiotic: conceptualization from a new approach. Current Opinion in Food Science. 2020; 32: 103–123. https://doi.org/10.1016/j.cofs.2020.03.009
42. Farup P.G., Jacobsen M., Ligaarden S.C., et al. Probiotics, symptoms, and gut microbiota: what are the relations? A randomized controlled trial in subjects with irritable bowel syndrome. Gastroenterology Research and Practice. 2012: 214102. https://doi.org/10.1155/2012/214102
43. Wang J.W., Kuo C.H., Kuo F.C., et al. Fecal microbiota transplantation: review and update. Journal of the Formosan Medical Association. 2019; 118: S23–S31. https://doi.org/10.1016/j.jfma.2018.08.011
44. Cammarota G., Ianiro G., Tilg H., et al. European consensus conference on faecal microbiota transplantation in clinical practice. Gut. 2017; 66(4): 569–580. https://doi.org/10.1136/gutjnl-2016-313017
45. Yakupova A.A., Abdulhakov S.R., Safin A.G., et al. Fecal microbiota transplantation: criteria for donor selection, preparation and storage of biomaterial (review of current recommendations). Therapeutic Archive. 2021; 93(2): 215–221 [In Russian]. https://doi.org/10.26442/00403660.2021.02.200615
46. Suvorov A., Karaseva A., Kotyleva M., et al. Autoprobiotics as an approach for restoration of personalised microbiota. Frontiers in Microbiology. 2018; 9: 1869. https://doi.org/10.3389/fmicb.2018.01869
47. Zheng D.W., Pan P., Chen K.W., et al. An orally delivered microbial cocktail for the removal of nitrogenous metabolic waste in animal models of kidney failure. Nature Biomedical Engineering. 2020; 4(9): 853–862. https://doi.org/10.1038/s41551-020-0582-1
48. Scheiman J., Luber J.M., Chavkin T.A., et al. Meta-omics analysis of elite athletes identifies a performance-enhancing microbe that functions via lactate metabolism. Nature Medicine. 2019; 25(7): 1104–1109. https://doi.org/10.1038/s41591-019-0485-4
Review
For citations:
Malaeva E.G., Stoma I.O. Possibilities and Prospects of Modification of the Intestinal Microbiome. The Russian Archives of Internal Medicine. 2022;12(5):341-351. https://doi.org/10.20514/2226-6704-2022-12-5-341-351