Lamichhane Group- Gut Microbiomics

We want to understand what gut microbes do inside our bodies, and we use metabolomics to study them.

Microbial metabolomics

The focus of our group is to explore microbially derived small molecules (metabolites) in the gut and their influence on human health. By integrating advanced laboratory techniques such as metabolomics, 3D cell culture, and microbial monocultures with computational analysis, we investigate the chemical interactions between gut microbes and their impact on the host.

Ongoing projects 

    1. Cataloging lipidomic profiles from cultured human gut microbes to build shared knowledge on human gut microbiome associated lipids.
    2. Characterizing novel microbiome linked lipids in human fecal samples and examining their dynamics throughout early life.
    3. Elucidating the influence of microbiome derived lipids on the progression of islet autoimmunity.
    4. Assessing the impact of gut microbe derived lipids on cellular dysfunction using intestinal cell culture model (Caco-2 and HT-29 cell lines).

Selected publications 

Google Scholar link to other publication by  Lamichhanes Team.

Anna-Katariina Aatsinki, Matilda Kråkström, Katja Salonen, Heidi Isokääntä, Abhijit Paul, Thomaz Bastiaanssen, Leo Lahti, Minna Lukkarinen, Eveliina Munukka, Tiina Paunio, Katri Kantojärvi, Pieter C. Dorrestein, Hasse Karlsson, Linnea Karlsson, Matej Oresic, Alex M. Dickens, Santosh Lamichhane,
Early life gut microbial and metabolic shifts reflected in stool consistency-a gut transit time proxy, Gut Microbiology, Volume 3, 2026, 100013, ISSN 3051-1720, https://doi.org/10.1016/j.gutmic.2026.100013.

Lamichhane, Santosh, Dickens, Alex M. Buchacher, Tanja Lou, Tianai Charron-Lamoureux, Vincent Kattelus, Roosa Karmacharya, Pragya da Silva, Lucas Pinto Kråkström, Matilda Rasool, Omid Sen, Partho Walker, Corinn Patan, Abubaker Gentry, Emily C. Zuffa, Simone Arzoomand, Aron Lakshmikanth, Tadepally Mikeš, Jaromir Mebrahtu, Aman Vatanen, Tommi Raffatellu, Manuela Zengler, Karsten Hyötyläinen, Tuulia Xavier, Ramnik J. Brodin, Petter Lahesmaa, Riitta Dorrestein, Pieter C. Knip, Mikael Orešič, Matej. Microbiome-derived bile acid signatures in early life and their association with islet autoimmunity. Nature Communications (2025). https://doi.org/10.1038/s41467-025-66619-6

Mannochio-Russo, H., V. Charron-Lamoureux, M. van Faassen, S. Lamichhane, W. D. Gonçalves Nunes, V. Deleray, A. V. Ayala, Y. Tanaka, A. Patan, K. Vittali, P. Rajkumar, Y. El Abiead, H. N. Zhao, P. W. P. Gomes, I. Mohanty, C. Lee, A. Sund, M. Sharma, Y. Liu, D. Pattynama, G. T. Walker, G. J. Norton, L. Khatib, M. S. Andalibi, C. X. Wang, R. J. Ellis, D. J. Moore, J. E. Iudicello, D. Franklin, Jr., S. Letendre, L. Chin, C. Walker, S. Renwick, J. Zemlin, M. J. Meehan, X. Song, D. Kasper, Z. Burcham, J. J. Kim, S. Kadakia, M. Raffatellu, L. Bode, H. Chu, K. Zengler, M. Wang, D. Siegel, R. Knight and P. C. Dorrestein “The microbiome diversifies long- to short-chain fatty acid-derived N-acyl lipids.” Cell. Volume 188, Issue 15, 4154 – 4169.e19

Isokääntä, H.; Pinto da Silva, L.; Karu, N.; Kallonen, T.; Aatsinki, A. K.; Hankemeier, T.; Schimmel, L.; Diaz, E.; Hyötyläinen, T.; Dorrestein, P. C.; Knight, R.; Orešič, M.; Kaddurah-Daouk, R.; Dickens, A. M.; Lamichhane, S., Comparative Metabolomics and Microbiome Analysis of Ethanol versus OMNImet/gene•GUT Fecal Stabilization. Analytical Chemistry 2024, 96 (22), 8893-8904

Lamichhane, S., P. Sen, A. M. Dickens, M. A. Alves, T. Härkönen, J. Honkanen, T. Vatanen, R. J. Xavier, T. Hyötyläinen, M. Knip and M. Orešič (2022). “Dysregulation of secondary bile acid metabolism precedes islet autoimmunity and type 1 diabetes.” Cell Reports Medicine 3(10):

Lamichhane, S., Kemppainen, E., Trošt, K., Siljander, H., Hyöty, H., Ilonen, J., Toppari, J., Veijola, R., Hyötyläinen, T., Knip, M., & Orešič, M. (2019). Circulating metabolites in progression to islet autoimmunity and type 1 diabetes. Diabetologia, 62(12), 2287–2297.

Lamichhane, S., T. Härkönen, T. Vatanen, T. Hyötyläinen, M. Knip and M. Orešič (2023). “Impact of exposure to per-and polyfluoroalkyl substances on fecal microbiota composition in mother-infant dyads.” Environment International176: 107965.

Charron-Lamoureux, V., H. Mannochio-Russo, S. Lamichhane, S. Xing, A. Patan, P. W. Portal Gomes, P. Rajkumar, V. Deleray, A. M. Caraballo-Rodríguez, K. V. Chua, L. S. Lee, Z. Liu, J. Ching, M. Wang and P. C. Dorrestein (2025). “A guide to reverse metabolomics-a framework for big data discovery strategy.” Nature Protocol.

Zhao HN, Kvitne KE, Brungs C, Mohan S, Charron-Lamoureux V, Bittremieux W, Tang R, Schmid R, Lamichhane S, El Abiead Y, Andalibi MS, Mannochio-Russo H, Ambre M, Avalon NE, Bryant M, Caraballo-Rodríguez AM, Maya MC, Chin L, Ellis RJ, Franklin D, Girod S, Gomes PWP, Hansen L, Heaton R, Iudicello JE, Jarmusch AK, Khatib L,Letendre S, Magyari S, McDonald D, Mohanty I, Cumsille A, Moore DJ, Rajkumar P, Ross DH, Sapre H, Shahneh MRZ, Thomas SP, Tribelhorn C, Tubb HM, Walker C, Wang CX, Xing S, Zemlin J, Zuffa S, Wishart DS, Kaddurah-Daouk R, Wang M, Raffatellu M, Zengler K, Pluskal T, Xu L, Knight R, Tsunoda SM, Dorrestein PC. A resource to empirically establish drug exposure records directly from untargeted metabolomics data. Nature communications.

Zhang, P., J. Liu, A. Lee, I. Tsaur, M. Ohira, V. Duong, N. Vo, K. Watari, H. Su, J. Y. Kim, L. Gu, M. Zhu, S. Shalapour, M. Hosseini, G. Bandyopadhyay, S. Zeng, C. Llorente, H. N. Zhao, S. Lamichhane, S. Mohan, P. C. Dorrestein, J. M. Olefsky, B. Schnabl, P. Soroosh and M. Karin (2024). “IL-22 resolves MASLD via enterocyte STAT3 restoration of diet-perturbed intestinal homeostasis.” Cell Metabolism 36(10): 2341-2354.e2346.

Aatsinki, A.-K., S. Lamichhane, H. Isokääntä, P. Sen, M. Kråkström, M. A. Alves, A. Keskitalo, E. Munukka, H. Karlsson, L. Perasto, M. Lukkarinen, M. Oresic, H.-M. Kailanto, L. Karlsson, L. Lahti and A. M. Dickens “Dynamics of Gut Metabolome and Microbiota Maturation during Early Life.” Science. 2025 Sep 25;28(11):113596. doi: 10.1016/j.isci.2025.113596. PMID: 41280675; PMCID: PMC12636393

Lamichhane, S., Ahonen, L., Dyrlund, T. S., Kemppainen, E., Siljander, H., Hyöty, H., Ilonen, J., Toppari, J., Veijola, R., Hyötyläinen, T., Knip, M., & Oresic, M. (2018). Dynamics of Plasma Lipidome in Progression to Islet Autoimmunity and Type 1 Diabetes – Type 1 Diabetes Prediction and Prevention Study (DIPP). Scientific reports, 8(1), 10635.

Lamichhane, S., Siljander, H., Duberg, D., Honkanen, J., Virtanen, S. M., Orešič, M., Knip, M., & Hyötyläinen, T. (2021). Exposure to per- and polyfluoroalkyl substances associates with an altered lipid composition of breast milk. Environment international, 157, 106855.

Lamichhane, S., Sen, P., Dickens, A. M., Orešič, M., & Bertram, H. C. (2018). Gut metabolome meets microbiome: A methodological perspective to understand the relationship between host and microbe. Methods, 149, 3–12.