To mark the twentieth anniversary of Nature Reviews Gastroenterology & Hepatology, we asked three experts to comment on how the gut microbiome has transformed our understanding of biology and the strengths and limitations of microbiome research today as well as to look ahead at what the next 20 years of microbiome research and clinical applications might look like.
This is a preview of subscription content, access via your institution
Access options
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$32.99 / 30 days
cancel any time
Subscribe to this journal
Receive 12 print issues and online access
$189.00 per year
only $15.75 per issue
Buy this article
- Purchase on SpringerLink
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
References
Kennedy, K. M. et al. Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature 613, 639–649 (2023).
Pronovost, G. N. et al. The maternal microbiome promotes placental development in mice. Sci. Adv. 9, eadk1887 (2023).
Lopez-Tello, J. et al. Maternal gut microbiota Bifidobacterium promotes placental morphogenesis, nutrient transport and fetal growth in mice. Cell Mol. Life Sci. 79, 386 (2022).
Kaisanlahti, A. et al. Maternal microbiota communicates with the fetus through microbiota-derived extracellular vesicles. Microbiome 11, 249 (2023).
Li, Y. et al. In utero human intestine harbors unique metabolome, including bacterial metabolites. JCI Insight 5, e138751 (2020).
Dominguez-Bello, M. G. et al. Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. Nat. Med. 22, 250–253 (2016).
Korpela, K. et al. Maternal fecal microbiota transplantation in cesarean-born infants rapidly restores normal gut microbial development: a proof-of-concept study. Cell 183, 324–334.e5 (2020).
Levan, S. R. et al. Elevated faecal 12,13-diHOME concentration in neonates at high risk for asthma is produced by gut bacteria and impedes immune tolerance. Nat. Microbiol. 4, 1851–1861 (2019).
Fujimura, K. E. et al. Neonatal gut microbiota associates with childhood multisensitized atopy and T cell differentiation. Nat. Med. 22, 1187–1191 (2016).
Sender, R., Fuchs, S. & Milo, R. Are we really vastly outnumbered? Revisiting the ratio of bacterial to host cells in humans. Cell 164, 337–340 (2016).
Qin, J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59–65 (2010).
Ghosh, T. S. & Valdes, A. M. Evidence for clinical interventions targeting the gut microbiome in cardiometabolic disease. BMJ 383, e075180 (2023).
Raygoza Garay, J. A. et al. Gut microbiome composition is associated with future onset of Crohn’s disease in healthy first-degree relatives. Gastroenterology 165, 670–681 (2023).
Sharvin, B. L., Aburto, M. R. & Cryan, J. F. Decoding the neurocircuitry of gut feelings: region-specific microbiome-mediated brain alterations. Neurobiol. Dis. 179, 106033 (2023).
Ghosh, T. S. et al. Mediterranean diet intervention alters the gut microbiome in older people reducing frailty and improving health status: the NU-AGE 1-year dietary intervention across five European countries. Gut 69, 1218–1228 (2020).
Routy, B. et al. Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors. Science 359, 91–97 (2018).
Santos-Júnior, C. D. et al. Discovery of antimicrobial peptides in the global microbiome with machine learning. Cell 187, 3761–3778.e16 (2024).
Swanson, K. et al. Generative AI for designing and validating easily synthesizable and structurally novel antibiotics. Nat. Mach. Intell. 6, 338–353 (2024).
Turjeman, S. & Koren, O. Using the microbiome in clinical practice. Micro. Biotechnol. 15, 129–134 (2022).
Cai, X. et al. Atomic structures of a bacteriocin targeting Gram-positive bacteria. Nat. Commun. 15, 7057 (2024).
Acknowledgements
M.C.C. would like to acknowledge support from H2020-ERC Starting Grant (MAMI-639226 project), Spanish Ministry of Science and Innovation (MCIN) research grant (ref. PID2022-139475OB-I00), and an award from the Spanish Government MCIN/Agencia Estatal de Investigación (AEI) to the Institute of Agrochemistry and Food Technology – National Research Council as Centre of Excellence Severo Ochoa (CEX2021-001189-S MCIN/AEI/10.13039/ 501100011033). T.S.G. acknowledges the Department of Biotechnology, Ministry of Science & Technology, Government of India for the Ramalingaswami Re-entry Fellowship (BT/HRD/35/02/2006) and Indraprastha Institute of Information Technology-Delhi for a Research Initiation Grant.
Author information
Authors and Affiliations
Contributions
Maria Carmen Collado is a Full Research Professor at the Institute of Agrochemistry and Food Technology – National Research Council (IATA-CSIC), Valencia, Spain, and Docent (adjunct professor) of the University of Turku, Finland. Her research work is multidisciplinary and includes microbiology, food science and nutrition areas, and her research interests are focused on the effect of diet and microbiota interactions on maternal and infant health during the early-life period as well as across the lifespan of women. Twitter/X: @mcarmen_collado
Suzanne Devkota is an Associate Professor in the Division of Gastroenterology and Director of the Human Microbiome Research Institute at Cedars-Sinai Medical Center, Los Angeles, CA, USA. Her lab studies microbial mechanisms underlying the pathogenesis of inflammatory bowel diseases and dietary modulation of the gut microbiome.
Tarini Shankar Ghosh is an Assistant Professor in the Department of Computational Biology at the Indraprastha Institute of Information Technology, Delhi, India. His lab uses a combination of statistical, machine learning and artificial intelligence tools to understand microbiome assembly and stability, the generic markers of health and disease, and their correlation with environment and lifestyle. Twitter/X: @tarini_ghosh
Corresponding authors
Ethics declarations
Competing interests
The authors declare no competing interests.
Additional information
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Collado, M.C., Devkota, S. & Ghosh, T.S. Gut microbiome: a biomedical revolution. Nat Rev Gastroenterol Hepatol 21, 830–833 (2024). https://doi.org/10.1038/s41575-024-01001-3
Accepted:
Published:
Issue date:
DOI: https://doi.org/10.1038/s41575-024-01001-3
This article is cited by
-
Is precision microbiome medicine just around the corner?
Nature Reviews Gastroenterology & Hepatology (2025)