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Biosketch

Dr. Yogesh Shouche is currently working as Director at SKAN ResearchTrust Bengluru. He started his career as scientist National Centre for Cell Science (NCCS) in Pune, India. After working on different aspect of microbial, especially bacterial diversity of various ecological niches, his thrust area of research is now to understand succession of microbial communities in human gut during development and their role in health and diseases. He is working since 25 years in the field of microbial ecology, microbial molecular taxonomy and biodiversity; published more than 400 publications in journals of relevant area; reviewed publications in International journals like FEMS Ecology, International Journal of Systematic and Evolutionary Microbiology and Microbial Ecology. He is also on Editorial board of prestigious journals like Current Science, PlosOne etc. He is fellow of Maharashtra Academy of Sciences, Indian National Science Academy and National Academy of Sciences India.

During his tenure at NCCS he established Microbial Culture Collection (MCC), now known as National Center for Microbial Resource. It holds more than 150,000 bacteria and fungi in its collection recognized by WFCC (World Federation of Culture Collection). MCC is also recognized as International Depositary Authority (IDA) and is Designated Repository by Ministry of Environment, Forests & Climate Change, Government of India under the Biological Diversity Act 2002. In September 2018, Department of Biotechnology extended the mandate of this repository to include Anti Microbial Resistant microbes. He also initiated ambitious project on mapping of human microbiome of Indian population across diverse biogeographic regions.

After successful career at NCCS for 32 years, he joined Azim Premji University from 1st March 2022 and from August 2023 he took over as Director of SKAN Research Trust. He was also on the member of the Executive Boards of International Society for Systematics of Prokaryotes till August 2023 and presently on Executive Board of World Federation of Culture Collections. As a recognition of his contributions, recently a genus has been named in his honor Shouchella. Interestingly, after recent re classification this genus now contains well known probiotic species. Bacillus clausii is now renamed as Shouchella clausii.

Research Focus

  • Human gut microbiome diversity in Indian populations
    Dr Shouche’s research seeks to understand how India’s exceptional dietary, geographical, ethnic and socioeconomic diversity shapes the human gut microbiome. A major component of this work has been the development of India-specific microbiome reference data, including the initiation of a pan-India human microbiome mapping programme and studies of rural, urban and tribal communities that are underrepresented in international datasets.
  • Microbiome contributions to health, disease and therapeutic response
    A central interest is the relationship between microbial community structure and human diseases, particularly diabetes, obesity, coeliac disease, non-coeliac gluten sensitivity, inflammatory bowel disease, kidney-stone disease, cardiovascular disorders and neurological conditions. This work combines clinical phenotyping with metagenomics, metabolomics, multi-omics and intervention studies to identify microbiome-associated mechanisms, biomarkers and potential therapeutic targets.
  • Microbial cultivation, functional microbiology and microbiome-derived bioactives
    Dr Shouche’s programme extends beyond community profiling to the cultivation and functional characterisation of microorganisms. His interests include culturomics, anaerobic gut microorganisms, microbial metabolic functions, intermicrobial antagonism and the discovery of microbiome-derived compounds with anti-infective, anti-inflammatory, antidiabetic and other therapeutic properties. His leadership in establishing the National Centre for Microbial Resource provides an important infrastructure for this work.
  • Microbial systematics, genomics and biological-resource development
    Dr Shouche has made foundational contributions to molecular microbial taxonomy in India. His work encompasses phylogenetics, whole-genome analysis, identification and description of novel microbial taxa, microbial preservation and the development of nationally important culture collections. He established a major microbial repository that became an International Depositary Authority under the Budapest Treaty and a national repository under India’s Biological Diversity Act.
  • Environmental microbiomes, antimicrobial resistance and host–microbe interactions
    Another major interest is the movement of microorganisms and antimicrobial-resistance determinants across humans, animals and the environment. This includes studies of sewage, pharmaceutical-manufacturing wastewater, environmental resistomes and public-health surveillance, as well as pioneering investigations of mosquito-associated microorganisms and their influence on the transmission of dengue and Japanese encephalitis viruses.

Team Members

Publications

  1. Foundational perspective on the Indian gut microbiome
    Shetty SA, Marathe NP, Shouche YS.
    “Opportunities and challenges for gut microbiome studies in the Indian population.”
    Microbiome. 2013;1:24.
    DOI: 10.1186/2049-2618-1-24.
  2. Identification of distinctive features of the Indian gut microbiome
    Bhute S, Pande P, Shetty SA, et al.; Shouche YS.
    “Molecular Characterization and Meta-Analysis of Gut Microbial Communities Illustrate Enrichment of Prevotella and Megasphaera in Indian Subjects.”
    Frontiers in Microbiology. 2016;7:660.
    DOI: 10.3389/fmicb.2016.00660.
  3. Diet-associated gut-microbiome variation in Indian tribal populations
    Ebel ER, Kulkarni AS, Mongad DS, et al.; Shouche YS, Sonnenburg JL, Dhotre DP.
    “Gut microbiomes of tribal communities in India vary with dairy and grain consumption.”
    Gut Microbes. 2026;18(1):2694242.
    DOI: 10.1080/19490976.2026.2694242.
  4. Environmental reservoirs of multidrug resistance
    Marathe NP, Regina VR, Walujkar SA, Charan SS, Moore ER, Larsson DG, Shouche YS.
    “A treatment plant receiving waste water from multiple bulk drug manufacturers is a reservoir for highly multidrug-resistant integron-bearing bacteria.”
    PLOS ONE. 2013;8(10):e77310.
    DOI: 10.1371/journal.pone.0077310.
  5. Genomics of an important malaria vector
    Jiang X, Peery A, Hall AB, et al.; Shouche Y, Tu Z.
    “Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi.”
    Genome Biology. 2014;15:459.

Additional Information

He has secured grants worth over 200 Cr in his tenure at NCCS and given several talks across India and written popular science articles in English and Marathi. He enjoys interacting with students and motivating them.

Grants

Press Releases

Professional Profiles

Collaborations

As a Director of SKAN, he is instrumental in fostering several national and international collaborations including those with NIMHANS, St John Hospital, Quadram Institute Bioscience and Cambridge University.