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).

Recent pre-print

  •  Ifrat  Tamanna ,  Katja  Salonen ,  Helena  Mannochio-Russo ,  Matilda  Kråkström ,  Paulo Wender P.  Gomes ,  Vincent Charron  Lamoureux ,  Ipsita  Mohanty ,  Sofia D.  Forssten ,  Arthur C.  Ouwehand ,  Tuulia  Hyötyläinen ,  Alex M  Dickens ,  Pieter C  Dorrestein ,  Matej  Orešič ,  Santosh  Lamichhane. Microbial lipid shifts in a multi-stage simulated gut. 
  • Lamichhane S, Dickens AM, Buchacher T, Lou ET, Charron-Lamoureux V, Kattelus R, Karmacharya P, Pinto da Silva L, Kråkström M, Rasool O, Sen P, Walker C, Patan A, Gentry EC, Arzoomand A, Lakshmikanth T, Mikeš J, Mebrahtu A, Vatanen T, Raffatellu M, Zengler K, Hyötyläinen T, Xavier RJ, Brodin P, Lahesmaa R, Dorrestein PC, Knip M, Orešič M. Trajectories of microbiome-derived bile acids in early life – insights into the progression to islet autoimmunity. medRxiv [Preprint]. 2025 Feb 24:2025.02.18.25322275. doi: 10.1101/2025.02.18.25322275. PMID: 40061321; PMCID: PMC11888530. 

Selected publications 

Google Scholar link to other publication by Santosh Lamichhane.

  1. 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
  2. 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
  3. 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 (Accepted in press).
  4. 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.
  5. 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.
  6. 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):
  7. 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.” iScience. (#Share first authors)
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.

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