Santosh Lamichhane
 Academy Research fellow


santosh.lamichhane@utu.fi



Medicina, D7 Institute of Biomedicine






Areas of expertise
Lipidomics/Metabolomics- Gut microbial metabolism- Multivariate data analysis
Reverse Metabolomics- Molecular networking


Research community or research topic
Functional Gut Microbiomics-The focus of our group is to explore microbial derived small molecules in the gut and their influence on human health.

Biography

Santosh Lamichhane is a Research Council of Finland Academy Research Fellow. He holds the title of Docent, equivalent to Associate Professor, in Metabolomics at the Department of Life Technologies, University of Turku. As part of his research fellowship, Lamichhane will investigate the relationship between gut microbiota, lipids, and their clinical effects in early childhood.

Lamichhane was a Visiting Researcher at The Dorrestein Lab, University of California, San Diego, where he gained expertise in reverse and repository-scale metabolomics to better understand microbial chemistry and its influence on human metabolism.





Research

Lamichhane's research interest lies in the interface of human health, diet and gut microbial activity. He heads a research group (Functional Gut Microbiomics) at Intitute of Biomedicine, Faculty of Medicine. The focus of his group is to explore microbial derived small molecules in the gut and their influence on human health. By integrating advanced laboratory techniques such as metabolomics, gut organoids, and microbial cultures with computational analysis, we investigate the chemical interactions between gut microbes and their impact on the host.



Teaching

Metabolomics lecture in Systems biology (SYS21012), Modern biotechnologies and bioinformatics course (BIOT1524), Bioanalytical Techniques (CHEMI6429) at University of Turku.




Publications
  
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  • A guide to reverse metabolomics—a framework for big data discovery strategy  (2025)  
    • Nature Protocols
     Charron-Lamoureux, Vincent; Mannochio-Russo, Helena; Lamichhane, Santosh; Xing, Shipei; Patan, Abubaker; Gomes, Paulo Wender Portal; Rajkumar, Prajit; Deleray, Victoria; Caraballo-Rodriguez, Andres Mauricio; Chua, Kee Voon; Lee, Lye Siang; Liu, Zhao; Ching, Jianhong; Wang, Mingxun; Dorrestein, Pieter C.

    (
    A2 Refereed review article in a scientific journal )


  • Intra- and inter-individual variation of the human lipidome  (2025)  
    • Trends in Analytical Chemistry
     Anh, Nguyen Hoang; Beyene, Habtamu B.; Mocciaro, Gabriele; Hahnefeld, Lisa; Lamichhane, Santosh; Fabritius, Mikael; Avela, Henri; Wang, Yuqin; Dickens, Alex M.; Gurke, Robert; Yang, Baoru; Griffiths, William J.; Hyötyläinen, Tuulia; Meikle, Peter J.; Orešič, Matej
    (
    A2 Refereed review article in a scientific journal )


  • The microbiome diversifies long- to short-chain fatty acid-derived N-acyl lipids  (2025)  
    • Cell
     Mannochio-Russo, Helena; Charron-Lamoureux, Vincent; van Faassen, Martijn; Lamichhane, Santosh; Gonçalves, Nunes Wilhan D.; Deleray, Victoria; Ayala, Adriana V.; Tanaka, Yuichiro; Patan, Abubaker; Vittali, Kyle; Rajkumar, Prajit; El Abiead, Yasin; Zhao, Haoqi Nina; Gomes, Paulo Wender Portal; Mohanty, Ipsita; Lee, Carlynda; Sund, Aidan; Sharma, Meera; Liu, Yuanhao; Pattynama, David; Walker, Gregory T.; Norton, Grant J.; Khatib, Lora; Andalibi, Mohammadsobhan S.; Wang, Crystal X.; Ellis, Ronald J.; Moore, David J.; Iudicello, Jennifer E.; Franklin, Donald; Letendre, Scott; Chin, Loryn; Walker, Corinn; Renwick, Simone; Zemlin, Jasmine; Meehan, Michael J.; Song, Xinyang; Kasper, Dennis; Burcham, Zachary; Kim, Jane J.; Kadakia, Sejal; Raffatellu, Manuela; Bode, Lars; Chu, Hiutung; Zengler, Karsten; Wang, Mingxun; Siegel, Dionicio; Knight, Rob; Dorrestein, Pieter C.
    (
    A1 Refereed original research article in a scientific journal)


  • The microbiome diversifies long-to short-chain fatty acid-derived N-acyl lipids  (2025)  
    • Cell
     Mannochio-Russo, Helena; Charron-Lamoureux, Vincent; van Faassen, Martijn; Lamichhane, Santosh; Nunes, Wilhan D. Goncalves; Deleray, Victoria; Ayala, Adriana, V; Tanaka, Yuichiro; Patan, Abubaker; Vittali, Kyle; Rajkumar, Prajit; El Abiead, Yasin; Zhao, Haoqi Nina; Gomes, Paulo Wender Portal; Mohanty, Ipsita; Lee, Carlynda; Sund, Aidan; Sharma, Meera; Liu, Yuanhao; Pattynama, David; Walker, Gregory T.; Norton, Grant J.; Khatib, Lora; Andalibi, Mohammadsobhan S.; Wang, Crystal X.; Ellis, Ronald J.; Moore, David J.; Iudicello, Jennifer E.; Franklin Jr, Donald; Letendre, Scott; Chin, Loryn; Walker, Corinn; Renwick, Simone; Zemlin, Jasmine; Meehan, Michael J.; Song, Xinyang; Kasper, Dennis; Burcham, Zachary; Kim, Jane J.; Kadakia, Sejal; Raffatellu, Manuela; Bode, Lars; Chu, Hiutung; Zengler, Karsten; Wang, Mingxun; Siegel, Dionicio; Knight, Rob; Dorrestein, Pieter C.
    (
    A1 Refereed original research article in a scientific journal)


  • Comparative Metabolomics and Microbiome Analysis of Ethanol versus OMNImet/gene•GUT Fecal Stabilization  (2024)  
    • Analytical Chemistry
     Isokääntä Heidi, Pinto da Silva Lucas, Karu Naama, Kallonen Teemu, Aatsinki Anna-Katariina, Hankemeier Thomas, Schimmel Leyla, Diaz Edgar, Hyötyläinen Tuulia, Dorrestein Pieter C., Knight Rob, Orešič Matej, Kaddurah-Daouk Rima, Dickens Alex M., Lamichhane Santosh
    (
    A1 Refereed original research article in a scientific journal)


  • IL-22 resolves MASLD via enterocyte STAT3 restoration of diet-perturbed intestinal homeostasis  (2024)  
    • Cell Metabolism
     Zhang P., Liu J., Lee A., Tsaur I., Ohira M., Duong V., Vo N., Watari K., Su H., Kim J.Y., Gu L., Zhu M., Shalapour S., Hosseini M., Bandyopadhyay G., Zeng S., Llorente C., Zhao H.N., Lamichhane S., Mohan S., Dorrestein P.C., Olefsky J.M., Schnabl B., Soroosh P., Karin M.
    (
    A1 Refereed original research article in a scientific journal)


  • Infant gut microbiota and negative and fear reactivity  (2024)  
    • Development and Psychopathology
     Huovinen Venla, Aatsinki Anna-Katariina, Kataja Eeva-Leena, Munukka Eveliina, Keskitalo Anniina, Lamichhane Santosh, Raunioniemi Peppi, Bridgett David J., Lahti Leo, O’Mahony Siobhain M., Dickens Alex, Korja Riikka, Karlsson Hasse, Nolvi Saara, Karlsson Linnea
    (
    A1 Refereed original research article in a scientific journal)


  • Multiplatform metabolomic interlaboratory study of a whole human stool candidate reference material from omnivore and vegan donors  (2024)  
    • Metabolomics
     Cruz, Abraham Kuri; Alves, Marina Amaral; Andresson, Thorkell; Bayless, Amanda L.; Bloodsworth, Kent J.; Bowden, John A.; Bullock, Kevin; Burnet, Meagan C.; Carnevale Neto, Fausto; Choy, Angelina; Clish, Clary B.; Couvillion, Sneha P.; Cumeras, Raquel; Dailey, Lucas; Dallmann, Guido; Davis, W. Clay; Deik, Amy A.; Dickens, Alex M.; Djukovic, Danijel; Dorrestein, Pieter C.; Eder, Josie G.; Fiehn, Oliver; Flores, Roberto; Gika, Helen; Hagiwara, Kehau A.; Pham, Tuan Hai; Harynuk, James J.; Aristizabal-Henao, Juan J.; Hoyt, David W.; Jean-Francois, Focant; Krakstroem, Matilda; Kumar, Amit; Kyle, Jennifer E.; Lamichhane, Santosh; Li, Yuan; Nam, Seo Lin; Mandal, Rupasri; de la Mata, A. Paulina; Meehan, Michael J.; Meikopoulos, Thomas; Metz, Thomas O.; Mouskeftara, Thomai; Munoz, Nathalie; Gowda, G. A. Nagana; Orešic, Matej; Panitchpakdi, Morgan; Pierre-Hugues, Stefanuto; Raftery, Daniel; Rushing, Blake; Schock, Tracey; Seifried, Harold; Servetas, Stephanie; Shen, Tong; Sumner, Susan; Carrillo, Kieran S. Tarazona; Thibaut, Dejong; Trejo, Jesse B.; Van Meulebroek, Lieven; Vanhaecke, Lynn; Virgiliou, Christina; Weldon, Kelly C.; Wishart, David S.; Zhang, Lu; Zheng, Jiamin; Da Silva, Sandra
    (
    A1 Refereed original research article in a scientific journal)


  • Serum proteomics of mother-infant dyads carrying HLA-conferred type 1 diabetes risk  (2024)  
    • iScience
     Bhosale, Santosh D.; Moulder, Robert; Suomi, Tomi; Ruohtula, Terhi; Honkanen, Jarno; Virtanen, Suvi M.; Ilonen, Jorma; Elo, Laura L.; Knip, Mikael; Lahesmaa, Riitta
    (
    A1 Refereed original research article in a scientific journal)


  • Changes in lipids and inflammation in adults with super-refractory status epilepticus on a ketogenic diet  (2023)  
    • Frontiers in Molecular Biosciences
     Dickens Alex M, Johnson Tory P, Lamichhane Santosh, Kumar Anupama, Pardo Carlos A, Gutierrez Erie G, Haughey Norman, Cervenka Mackenzie C
    (
    A1 Refereed original research article in a scientific journal)


  • Circulating metabolic signatures of rapid and slow progression to type 1 diabetes in islet autoantibody-positive children  (2023)  
    • Frontiers in Endocrinology
     Lamichhane Santosh, Sen Partho, Dickens Alex M, Kråkström Matilda, Ilonen Jorma, Lempainen Johanna, Hyöty Heikki, Lahesmaa Riitta, Veijola Riitta, Toppari Jorma, Hyötyläinen Tuulia, Knip Mikael, Orešič Matej

    (
    A1 Refereed original research article in a scientific journal)


  • Classification of Common Food Lipid Sources Regarding Healthiness Using Advanced Lipidomics: A Four-Arm Crossover Study  (2023)  
    • International Journal of Molecular Sciences
     Monfort-Pires Milena, Lamichhane Santosh, Alonso Cristina, Egelandsdal Bjørg, Oresic Matej, Jordahl Vilde Overrein, Skjolsvold Oda, Perez-Ruiz Irantzu, Blanco Maria Encarnación, Skeie Siv, Martins Catia, Haug Anna
    (
    A1 Refereed original research article in a scientific journal)


  • Deep learning facilitates multi-data type analysis and predictive biomarker discovery in cancer precision medicine  (2023)  
    • Computational and Structural Biotechnology Journal
     Mathema Vivek Bhakta, Sen Partho, Lamichhane Santosh, Orešič Matej, Khoomrung Sakda
    (
    A2 Refereed review article in a scientific journal )


  • Dynamics of the Lipidome in a Colon Simulator  (2023)  
    • Metabolites
     Kråkström Matilda, Dickens Alex M, Amaral Alves Marina, Forssten Sofia D, Ouwehand Arthur C, Hyötyläinen Tuulia, Orešič Matej, Lamichhane Santosh
    (
    A1 Refereed original research article in a scientific journal)


  • Impact of exposure to per- and polyfluoroalkyl substances on fecal microbiota composition in mother-infant dyads  (2023)  
    • Environment International
     Lamichhane Santosh, Härkönen Taina, Vatanen Tommi, Hyötyläinen Tuulia, Knip Mikael, Orešič Matej
    (
    A1 Refereed original research article in a scientific journal)


  • Recent advances towards mass spectrometry-based clinical lipidomics  (2023)  
    • Current Opinion in Chemical Biology
     Salihovic Samira, Lamichane Santosh, Hyötyläinen Tuulia, Orešič Matej
    (
    A2 Refereed review article in a scientific journal )


  • Dysregulation of secondary bile acid metabolism precedes islet autoimmunity and type 1 diabetes  (2022)  
    • Cell Reports Medicine
     Lamichhane Santosh, Sen Partho, Dickens Alex M., Alves Marina Amaral, Härkönen Taina, Honkanen Jarno, Vatanen Tommi, Xavier Ramnik J., Hyötyläinen Tuulia, Knip Mikael, Oresic Matej
    (
    A1 Refereed original research article in a scientific journal)


  • Impact of Extensively Hydrolyzed Infant Formula on Circulating Lipids During Early Life  (2022)  
    • Frontiers in Nutrition
     Lamichhane Santosh, Siljander Heli, Salonen Marja, Ruohtula Terhi, Virtanen Suvi M., Ilonen Jorma, Hyötyläinen Tuulia, Knip Mikael, Orešič Matej
    (
    A1 Refereed original research article in a scientific journal)


  • Association Between Circulating Lipids and Future Weight Gain in Individuals With an At-Risk Mental State and in First-Episode Psychosis  (2021)  
    • Schizophrenia Bulletin
     Lamichhane Santosh, Dickens Alex M, Sen Partho, Laurikainen Heikki, Borgan Faith, Suvisaari Jaana, Hyötyläinen Tuulia, Howes Oliver, Hietala Jarmo, Orešič Matej
    (
    A1 Refereed original research article in a scientific journal)


  • Deep learning meets metabolomics: a methodological perspective  (2021)  
    • Briefings in Bioinformatics
     Partho Sen, Santosh Lamichhane, Vivek B Mathema, Aidan McGlinchey, Alex M Dickens, Sakda Khoomrung, Matej Orešič
    (
    A2 Refereed review article in a scientific journal )



Last updated on 2025-09-09 at 15:07