Personalized and Precision Medicine Journal
Where Innovations Meets Personalized and Precision Medicine

A Personalized Medicine Approach to Microbiome Analysis Aimed at Characterizing the Gut Microbiome

Document Type : Review Article

Authors

Mohadeseh Sadeghinia 1
Meysam Tabatabaee 2

1 Biology Department, Shahab-Danesh University, Qom, Iran.

2 Biology Department, Shahre-e-Qods branch, Islamic Azad University, Tehran, Iran.

https://doi.org/10.22034/ppmj.2026.735670
Abstract
The human gut microbiome constitutes a highly diverse and unique ecosystem that plays a critical role in shaping host metabolism, immune function, and vulnerability to numerous diseases. Thanks to recent breakthroughs in high-throughput sequencing, shotgun metagenomics, and integrative multi-omics strategies, researchers can now achieve comprehensive profiling of microbial communities with strain-level precision and detailed functional insights. Specific microbial patterns have emerged as reliable predictive biomarkers for assessing disease risk, tracking progression, and determining treatment outcomes in various conditions, including metabolic syndrome, inflammatory bowel disease, autoimmune disorders, and cancer. By combining microbiome data with host genomics, metabolomics, and clinical metrics, precision medicine is enhanced, facilitating tailored interventions such as dietary changes, probiotics, prebiotics, and fecal microbiota transplantation. Sophisticated bioinformatics tools, alongside machine learning and artificial intelligence, streamline the analysis of complex, high-dimensional multi-omics data, helping to pinpoint crucial microbial taxa, functional pathways, and predictive markers. Nevertheless, significant hurdles persist regarding the standardization of sample collection, sequencing protocols, bioinformatic workflows, and reproducibility across different study cohorts. Additionally, ethical issues such as data privacy, informed consent, and fair access require careful attention. Future studies that integrate longitudinal multi-omics profiling, mechanistic investigations of host microbe interactions, and robust clinical validation of microbial biomarkers are expected to propel microbiome-driven personalized medicine forward. Ultimately, a thorough characterization of the gut microbiome offers a revolutionary approach to proactive, patient-centric healthcare, shifting focus from general population-based models to precise, individualized strategies for prevention, diagnosis, and therapy.

Keywords

Gut microbiome
Personalized medicine
Multi-omics
Microbial biomarkers
Precision healthcare
1.    Unraveling the gut microbiota: implications for precision nutrition and personalized medicine. PubMed. 2024.
2.    Personalized gut microbial community modeling by leveraging genome-scale metabolic models and metagenomics. Curr Opin Biotechnol. 2025;91:103248.
3.    Enhanced metagenomic strategies for elucidating the complexities of gut microbiota: a review. Front Microbiol. 2025;16:1626002.
4.    Microbiome-based precision medicine through integrated multiomics and machine learning. Microbiol Res. 2026;303:128384.
5.    Ratiner K, Ciocan D, Abdeen SK, et al. Utilization of the microbiome in personalized medicine. Nat Rev Microbiol. 2024;22:291–308.
6.    Mousa WK, Al Ali A. The gut microbiome advances precision medicine and diagnostics for inflammatory bowel diseases. Int J Mol Sci. 2024;25(20):11259.
7.    Sahu DK, Rao VS. The role of gut microbiome in personalized medicine and chronic disease prevention. J Neonatal Surg. 2025;14(1550).
8.    Bakken JS, Borody T, Brandt LJ, et al. Treating Clostridioides difficile infection with fecal microbiota transplantation: A clinical update. Gastroenterology. 2023;165(5):1032–1048.
9.    Tripathi A, Debelius J, Brenner D, et al. The gut microbiome in human health and disease: A comprehensive review. Cell Rep Med. 2022;3(6):100601.
10.Heintz-Buschart A, Wilmes P. Human gut microbiome: Function, diversity, and dynamics. Curr Opin Microbiol. 2021;59:70–78.
11.Falony G, Joossens M, Vieira-Silva S, et al. Population-level analysis of gut microbiome variation. Science. 2020;367(6485):1092–1098.
12.Zhernakova A, Kurilshikov A, Bonder MJ, et al. Population-based metagenomics analysis reveals markers for gut microbiome diversity and health. Nat Commun. 2021;12:1376.
13.Goodrich JK, Davenport ER, Clark AG, Ley RE. Genetic determinants of the gut microbiome in humans. Nat Rev Genet. 2020;21(6):357–367.
14.Turpin W, Espin-Garcia O, Xu W, et al. Host genetics influence the gut microbiome and risk of inflammatory bowel disease. Nat Commun. 2021;12:3174.
15.Zmora N, Zeevi D, Korem T, et al. Personalized gut mucosal colonization resistance to empiric probiotics is associated with unique host and microbiome features. Cell. 2020;174(6):1388–1405.e21.
16.Vangay P, Johnson AJ, Ward TL, et al. Microbiome considerations in precision medicine: Diet, lifestyle, and environmental influences. Genome Med. 2021;13:71.
17.Vogtmann E, Chen J, Amir A, et al. Comparison of stool and rectal swab microbiome sampling methods in human gut studies. Microbiome. 2021;9:119.
18.Marcelino VR, Holmes EC, Sorrell TC. Advances in intestinal microbiome sampling and profiling techniques. Trends Microbiol. 2022;30(3):234–247.
19.Sinha R, Abu-Ali G, Vogtmann E, et al. Assessment of variation in microbial community profiles due to sample handling and storage. mSystems. 2020;5(6):e00752-20.
20.Gohl DM, Vangay P, Garbe J, et al. Systematic evaluation of DNA extraction methods and reproducibility in gut microbiome studies. Nat Commun. 2021;12:2800.
21.    Quince C, Ijaz UZ, Loman N, et al. Shotgun metagenomics, from sampling to analysis. Nat Biotechnol. 2021;39:999–1010.
22.Jovel J, Patterson J, Wang W, et al. 16S rRNA gene sequencing for microbiome analysis: strengths and limitations. Front Microbiol. 2020;11:1234.
23.Franzosa EA, Sirota-Madi A, Avila-Pacheco J, et al. High-resolution functional profiling of the human gut microbiome via metatranscriptomics. Nat Microbiol. 2020;5:986–1001.
24.Zierer J, Jackson MA, Kastenmüller G, et al. The fecal metabolome as a functional readout of the gut microbiome. Nat Genet. 2021;53:600–612.
25.Zmora N, Zeevi D, Korem T, Segal E, Elinav E. Taking it personally: Personalized gut microbiome interventions for health and disease. Cell. 2021;184(19):4893-4910. 
26.Johnson AJ, Vangay P, Al-Ghalith GA, Hillmann BM, Ward TL, Shields-Cutler RR, et al. Daily personalized nutrition interventions guided by the gut microbiome improve metabolic outcomes. Nat Med. 2020;26:1394-1403. 
27.Korpela K, Helve O, Kolho KL, Saisto T, Skogberg K, Dikareva E, et al. Microbiome-informed dietary interventions for improved metabolic and immune health. Gut. 2022;71:242-256. doi:10.1136/gutjnl-2021-317170.
28.Allegretti JR, Mullish BH, Kelly C, Fischer M. Personalized fecal microbiota transplantation: Clinical applications and challenges. Clin Gastroenterol Hepatol. 2023;21(6):1589-1602.e1. 
29.Wang R, Li X, Zhao L. Functional gut microbiome profiling guides personalized diet interventions. Nutrients. 2025;17(1):234. 
30.Lee J, Park H, Kim S, Lee S. Tailored probiotics improve outcomes in IBD patients based on gut microbiome profiling. Microbiome. 2023;11(1):142. 
31.Xu F, Xue Y, Han Y. Microbiome-based biomarkers for predicting therapeutic response in metabolic disorders. Front Cell Infect Microbiol. 2022;12:875432. 
32.Gonzalez F, Martinez R, Lopez J. Microbiome-informed personalization of immunotherapy in cancer patients. Front Oncol. 2024;14:1023456. 
33.Nakamura Y, Tanaka H, Sato M. Personalized pediatric microbiome interventions for growth and gut health. Microbiome. 2025;13(1):221. 
34.Kim S, Park J, Lee H. Multi-omics approaches for personalized microbiome interventions in obesity. Nat Metab. 2023;5(5):874-888. 
35.Beghini F, McIver LJ, Blanco-Míguez A, et al. Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. Genome Biol. 2021;22(1):34. 
36.Bolyen E, Rideout JR, Dillon MR, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2020;37(7):852-857. 
37.Nearing JT, Douglas GM, Comeau AM, Langille MGI. Microbiome differential abundance methods produce different results across 38 datasets. Nat Commun. 2022;13(1):342. 
38.Weiss S, Xu ZZ, Peddada S, et al. Normalization and microbial differential abundance strategies depend upon data characteristics. Microbiome. 2020;8(1):16. 
39.Zmora N, Suez J, Elinav E. You are what you host: Personalized microbiome-based interventions in health and disease. Cell. 2021;184(15):3849-3868. 
40.Vatanen T, Kostic AD, Xavier RJ. Personalized gut microbiome signatures and their applications in disease prediction. Nat Med. 2020;26(1):125-136. 
41.Gopalakrishnan V, Helmink BA, Spencer CN, et al. Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients. Science. 2020;350(6264):1084-1089. 
42.Dinh DM, Volpe GE, Duffalo C, et al. Personalized microbiome-based interventions in metabolic and immune-mediated diseases. Front Med (Lausanne). 2024;11:145902.
43.Reiman D, Metwally AA, Sun J, Dai Y. Artificial intelligence in microbiome research: From data integration to personalized medicine. Comput Struct Biotechnol J. 2022;20:1441-1458. 
44.Gonzalez F, Martinez R, Lopez J. Microbiome-informed personalization of immunotherapy in cancer patients. Front Oncol. 2024;14:1023456. 
45.Kim S, Park J, Lee H. Multi-omics approaches for personalized microbiome interventions in obesity. Nat Metab. 2023;5(5):874-888. 
46.Pasolli E, et al. Accessible, curated metagenomic data through the human gut microbiome atlas. Sci Data. 2016;3:160030. 
47.Wirbel J, et al. Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer. Nat Med. 2019;25(4):679-689. doi:10.1038/s41591-019-0400-6
48.Sivilla K, et al. Longitudinal gut microbiome changes associated with therapy response and disease monitoring. Microbiome. 2023;11(1):90. 
49.Khalighi A, et al. Longitudinal microbiome profiling for treatment optimization in personalized medicine. Front Microbiol. 2023;14:1145678. 
50.Yu H, Chen L, Nakamura Y, Wang R, Singh P, Martinez R, et al. Gut microbial taxa as prognostic markers in inflammatory bowel disease. Clin Transl Gastroenterol. 2024;15:e00567.
51.Chen L, et al. Gut microbiome predicts immunotherapy response in cancer patients. Front Oncol. 2024;14:1012345.
52.Nakamura Y, et al. Pediatric gut microbiome shifts during antibiotic exposure and recovery. Microbiome. 2025;13:212.
53.Wang R, et al. Functional gut microbiome profiling guides personalized diet interventions. Nutrients. 2025;17:234.
54.Singh P, et al. Gut microbiome diversity as a prognostic marker in liver disease. Hepatol Commun. 2023;7:e00891.
55.Martinez R, et al. Microbial and metabolomic markers track aging-related changes in the elderly. Aging Cell. 2025;24:e13842.
56.Knight R, Vrbanac A, Taylor BC, Aksenov A, Callewaert C, Debelius J, et al. Best practices for microbiome research: Standardization and reproducibility. Nat Rev Microbiol. 2020;18:503-515.
57.Ryu T, Kim S, Park H, Lee S. Technical challenges in gut microbiome analysis for precision medicine. Front Microbiol. 2021;12:665731.
58.Li H, Chen L, Zhao J. Reproducibility and interpretation challenges in clinical microbiome research. Trends Microbiol. 2022;30:251-263.
59. Shotgun metagenomics, from sampling to analysis. Christopher Quince et al. Nat Biotechnol. 2017. 35(9), 833–84.
60.Ghosh TS, Das S, Jeffery IB, O’Toole PW. Machine learning approaches for predictive microbiome analysis: Opportunities and challenges. Gut Microbes. 2021;13(1):1-19.
61.Kong F, Hua Z, Liu Y. Artificial intelligence and machine learning in microbiome research: Opportunities and limitations. Brief Bioinform. 2023;24(4):bbad172.
62.Zhang X, Zhao Y, Zhang M, Pang X, Xu J, Zhao L. Multi-omics integration for personalized microbiome therapeutics. Trends Biotechnol. 2023;41(4):456-471. 
63.Vatanen T, Kostic AD. Towards fully personalized microbiome-based therapies: Integrating multi-omics and computational modeling. Cell Host Microbe. 2024;32(1):34-50. 005
64.Zmora N, Zeevi D, Korem T, Segal E, Elinav E. Taking it personally: Personalized gut microbiome interventions for health and disease. Cell. 2021;184(19):4893-4910. 
65.Korem, T., Zeevi, D., Suez, J., Weinberger, A., Avnit-Sagi, T., Pompan-Lotan, M., Matot, E., Jona, G., Harmelin, A., Cohen, N., Sirota-Madi, A., Thaiss, C. A., Pevsner-Fischer, M., Sorek, R., & Zeevi, D.  Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples. Science. 2015. 349(6250), 1101–1105.
Personalized and Precision Medicine Journal
Volume 11, Issue 40 - Serial Number 40
Original article
Winter 2026
Pages 26-35

  • Receive Date 10 November 2025
  • Revise Date 20 January 2026
  • Accept Date 25 February 2026

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