Intestinal microbiome: basics of diagnostics for maintaining health
DOI:
https://doi.org/10.14739/2310-1210.2025.2.322064Keywords:
gut microbiome, GA-map dysbiosis test, microbiota diagnostics, 16S rRNA sequencing, metagenomic analysis, clinical validation, dysbiosis, personalized medicine, microbial diversityAbstract
Aim. To examine the impact of the gut microbiome on human health, as well as modern methods of its diagnosis, determining the role of modern diagnostic tests as a tool for assessing the microbiota state and its importance in personalized medicine.
Materials and methods. A literature search was conducted in scientometric databases, including PubMed, Scopus, Web of Science, and Google Scholar, using the keywords: gut microbiome, microbiota diagnostics, GA-map dysbiosis test, fecal microbiota. The analysis included over 30 sources from specialized scientific literature.
Results. The article covers the role of gut microbiome diagnostics in maintaining human health by presenting a comprehensive analysis of modern diagnostic methods, their comparative advantages and disadvantages, with a focus on the GA-map dysbiosis test as an innovative standardized approach. The authors review the historical context, dating all the way back to the Hippocrates’ views, and trace the evolution of microbiome studies to modern technological advances. Particular attention is paid to key aspects of microbiome composition, including recent changes in the nomenclature of bacterial phyla and the issues of various diagnostic method standardization.
The article discusses the stages of development and clinical validation of the GA-map diagnostic test, emphasizing its advantages in providing standardized and reproducible results. The clinical application and interpretation of the test results are analyzed, demonstrating the importance of the test for personalized medicine approaches. The study reinforces the importance of understanding the gut microbiota for disease prevention and treatment, suggesting that standardized diagnostic methods such as GA-map could significantly improve clinical outcomes.
Conclusions. The importance of maintaining microbiota balance for disease prevention has been emphasized. The GA-map dysbiosis test has demonstrated high accuracy and reproducibility allowing physicians to develop individualized nutrition and treatment recommendations and making it a key tool in modern medicine aimed at a personalized therapeutic approach.
References
Kasselman LJ, Vernice NA, DeLeon J, Reiss AB. The gut microbiome and elevated cardiovascular risk in obesity and autoimmunity. Atherosclerosis. 2018;271:203-13. doi: https://doi.org/10.1016/j.atherosclerosis.2018.02.036
Groen RN, de Clercq NC, Nieuwdorp M, Hoenders HJ, Groen AK. Gut microbiota, metabolism and psychopathology: A critical review and novel perspectives. Crit Rev Clin Lab Sci. 2018;55(4):283-93. doi: https://doi.org/10.1080/10408363.2018.1463507
Hills RD Jr, Pontefract BA, Mishcon HR, Black CA, Sutton SC, Theberge CR. Gut Microbiome: Profound Implications for Diet and Disease. Nutrients. 2019;11(7):1613. doi: https://doi.org/10.3390/nu11071613
Gonçalves P, Araújo JR, Di Santo JP. A Cross-Talk Between Microbiota-Derived Short-Chain Fatty Acids and the Host Mucosal Immune System Regulates Intestinal Homeostasis and Inflammatory Bowel Disease. Inflamm Bowel Dis. 2018;24(3):558-572. doi: https://doi.org/10.1093/ibd/izx029
Integrative HMP (iHMP) Research Network Consortium. The Integrative Human Microbiome Project. Nature. 2019;569(7758):641-8. doi: https://doi.org/10.1038/s41586-019-1238-8
Creasy HH, Felix V, Aluvathingal J, Crabtree J, Ifeonu O, Matsumura J, et al. HMPDACC: a Human Microbiome Project Multi-omic data resource. Nucleic Acids Res. 2021;49(D1):D734-42. doi: https://doi.org/10.1093/nar/gkaa996
Yoo JY, Groer M, Dutra SV, Sarkar A, McSkimming DI. Gut Microbiota and Immune System Interactions. Microorganisms. 2020;8(10):1587. doi: https://doi.org/10.3390/microorganisms8101587
Chambers ES, Preston T, Frost G, Morrison DJ. Role of Gut Microbiota-Generated Short-Chain Fatty Acids in Metabolic and Cardiovascular Health. Curr Nutr Rep. 2018;7(4):198-206. doi: https://doi.org/10.1007/s13668-018-0248-8
Cheng HY, Ning MX, Chen DK, Ma WT. Interactions Between the Gut Microbiota and the Host Innate Immune Response Against Pathogens. Front Immunol. 2019;10:607. doi: https://doi.org/10.3389/fimmu.2019.00607
Magne F, Gotteland M, Gauthier L, Zazueta A, Pesoa S, Navarrete P, et al. The Firmicutes/Bacteroidetes Ratio: A Relevant Marker of Gut Dysbiosis in Obese Patients? Nutrients. 2020;12(5):1474. doi: https://doi.org/10.3390/nu12051474
Sun Y, Zhang S, Nie Q, He H, Tan H, Geng F, et al. Gut firmicutes: Relationship with dietary fiber and role in host homeostasis. Crit Rev Food Sci Nutr. 2023;63(33):12073-88. doi: https://doi.org/10.1080/10408398.2022.2098249
Binda C, Lopetuso LR, Rizzatti G, Gibiino G, Cennamo V, Gasbarrini A. Actinobacteria: A relevant minority for the maintenance of gut homeostasis. Dig Liver Dis. 2018;50(5):421-8. doi: https://doi.org/10.1016/j.dld.2018.02.012
Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res. 2022;50(D1):D801-7. doi: https://doi.org/10.1093/nar/gkab902
Oren A, Garrity GM. Notification of changes in taxonomic opinion previously published outside the IJSEM. Int J Syst Evol Microbiol. 2018;68(1):7-8. doi: https://doi.org/10.1099/ijsem.0.002502
Oren A, Garrity GM. Valid publication of the names of forty-two phyla of prokaryotes. Int J Syst Evol Microbiol. 2021;71(10). doi: https://doi.org/10.1099/ijsem.0.005056
Regueira-Iglesias A, Balsa-Castro C, Blanco-Pintos T, Tomás I. Critical review of 16S rRNA gene sequencing workflow in microbiome studies: From primer selection to advanced data analysis. Mol Oral Microbiol. 2023;38(5):347-99. doi: https://doi.org/10.1111/omi.12434
Zhang L, Chen F, Zeng Z, Xu M, Sun F, Yang L, et al. Advances in Metagenomics and Its Application in Environmental Microorganisms. Front Microbiol. 2021;12:766364. doi: https://doi.org/10.3389/fmicb.2021.766364
Kool J, Tymchenko L, Shetty SA, Fuentes S. Reducing bias in microbiome research: Comparing methods from sample collection to sequencing. Front Microbiol. 2023;14:1094800. doi: https://doi.org/10.3389/fmicb.2023.1094800
Tourlousse DM, Narita K, Miura T, Sakamoto M, Ohashi A, Shiina K, et al. Validation and standardization of DNA extraction and library construction methods for metagenomics-based human fecal microbiome measurements. Microbiome. 2021;9(1):95. doi: https://doi.org/10.1186/s40168-021-01048-3
Casén C, Vebø HC, Sekelja M, Hegge FT, Karlsson MK, Ciemniejewska E, et al. Deviations in human gut microbiota: a novel diagnostic test for determining dysbiosis in patients with IBS or IBD. Aliment Pharmacol Ther. 2015;42(1):71-83. doi: https://doi.org/10.1111/apt.13236
Vatn S, Carstens A, Kristoffersen AB, Bergemalm D, Casén C, Moen AE, et al. Faecal microbiota signatures of IBD and their relation to diagnosis, disease phenotype, inflammation, treatment escalation and anti-TNF response in a European Multicentre Study (IBD-Character). Scand J Gastroenterol. 2020;55(10):1146-56. doi: https://doi.org/10.1080/00365521.2020.1803396. Epub 2020 Aug 11. PMID: 32780604.
Lavelle A, Sokol H. Gut microbiota-derived metabolites as key actors in inflammatory bowel disease. Nat Rev Gastroenterol Hepatol. 2020;17(4):223-37. doi: https://doi.org/10.1038/s41575-019-0258-z
Gravdal K, Kirste KH, Grzelak K, Kirubakaran GT, Leissner P, Saliou A, et al. Exploring the gut microbiota in patients with pre-diabetes and treatment naïve diabetes type 2 - a pilot study. BMC Endocr Disord. 2023;23(1):179. doi: https://doi.org/10.1186/s12902-023-01432-0
Vatn S, Carstens A, Kristoffersen AB, Bergemalm D, Casén C, Moen AE, et al. Faecal microbiota signatures of IBD and their relation to diagnosis, disease phenotype, inflammation, treatment escalation and anti-TNF response in a European Multicentre Study (IBD-Character). Scand J Gastroenterol. 2020;55(10):1146-56. doi: https://doi.org/10.1080/00365521.2020.1803396
Algera JP, Magnusson MK, Öhman L, Störsrud S, Simrén M, Törnblom H. Randomised controlled trial: effects of gluten-free diet on symptoms and the gut microenvironment in irritable bowel syndrome. Aliment Pharmacol Ther. 2022;56(9):1318-1327. doi: https://doi.org/10.1111/apt.17239
Telle-Hansen VH, Gaundal L, Bastani N, Rud I, Byfuglien MG, Gjøvaag T, et al. Replacing saturated fatty acids with polyunsaturated fatty acids increases the abundance of Lachnospiraceae and is associated with reduced total cholesterol levels-a randomized controlled trial in healthy individuals. Lipids Health Dis. 2022;21(1):92. doi: https://doi.org/10.1186/s12944-022-01702-1
Mazzawi T, Hausken T, Refsnes PF, Hatlebakk JG, Lied GA. The Effect of Anaerobically Cultivated Human Intestinal Microbiota Compared to Fecal Microbiota Transplantation on Gut Microbiota Profile and Symptoms of Irritable Bowel Syndrome, a Double-Blind Placebo-Controlled Study. Microorganisms. 2022;10(9):1819. doi: https://doi.org/10.3390/microorganisms10091819
Gaundal L, Myhrstad MC, Rud I, Gjøvaag T, Byfuglien MG, Retterstøl K, et al. Gut microbiota is associated with dietary intake and metabolic markers in healthy individuals. Food Nutr Res. 2022;66. doi: https://doi.org/10.29219/fnr.v66.8580
Kumar A, Gravdal K, Segal JP, Steed H, Brookes MJ, Al-Hassi HO. Variability in the Pre-Analytical Stages Influences Microbiome Laboratory Analyses. Genes (Basel). 2022;13(6):1069. doi: https://doi.org/10.3390/genes13061069
El-Salhy M, Winkel R, Casen C, Hausken T, Gilja OH, Hatlebakk JG. Efficacy of Fecal Microbiota Transplantation for Patients With Irritable Bowel Syndrome at 3 Years After Transplantation. Gastroenterology. 2022;163(4):982-994.e14. doi: https://doi.org/10.1053/j.gastro.2022.06.020
Jin Y, Dong H, Xia L, Yang Y, Zhu Y, Shen Y, et al. The Diversity of Gut Microbiome is Associated With Favorable Responses to Anti-Programmed Death 1 Immunotherapy in Chinese Patients With NSCLC. J Thorac Oncol. 2019;14(8):1378-89. doi: https://doi.org/10.1016/j.jtho.2019.04.007
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