The entire microbial repertoire of the human body, also called the microbiome, plays significant role in human health and disease and resides majorly in the human gut. I am interested in studying the perturbations of the microbiome (mainly in gut, but also in other body niches), both in human health and diseases, specifically using high-throughput omics data.
2018−2021 Postdoctoral Research Fellow, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA. Supervisor: Dr. Jaeyun Sung, Assistant Professor of Surgery, Mayo Clinic, Rochester, Minnesota, USA.
2012−2018 Doctor of Philosophy (Ph.D.), CSIR-NET fellow, CSIR- Indian Institute of Chemical Biology (CSIR-IICB), Kolkata, India. Supervisor: Dr. Snehasikta Swarnakar [Senior Principal Scientist & Head of the Department, Infectious Diseases and Immunology, CSIR-IICB]. Co-Supervisor: Dr. Chitra Dutta [Chief scientist (Retired), Structural Biology & Bioinformatics, CSIR-IICB].
2009−2011 Master of Technology (M.Tech) in Bioinformatics. West Bengal University of Technology (WBUT), Kolkata, West Bengal, India.
My doctoral research focused on understanding the complex relationships of the symbiotic and pathogenic microbes in human gut microbiota through comparative genomics and bioinformatics analyses. During my postdoctoral research, I was mainly trained in tracking microbiome perturbations in different clinical outcomes to correlate with disease activity and microbial resistance to therapy. Identification of such microbiome biomarkers is an extremely exciting and promising area for the generation of new diagnostics, prognostics, and therapeutics. The area of microbiome-based biomarker detection is much more compelling among Indian population, owing to the high diversity of dietary habits, lifestyles, and overall genetic diversity.
The broad research areas of our lab are:
Microbiome-based pan-Indian biomarker discovery: Here, we will try to define microbiome-based healthy biomarkers and measure their variation in different pathophysiological conditions and with other related variables such as food and lifestyle. Next, we will target the features that are responsible for these variations so that we can decide whether to test the information with machine learning models for generating an early detection system for various metabolic diseases.
Personalized microbiome-profiling for managing healthy gut: Here, we want to use the microbiome-based biomarkers as a clinical tool to monitor gut health. The long-term plan of this project is to develop a personalized microbiome profiling method where individuals can check their microbiome-based gut health status. The health status will be highly personalized, as the effect of lifestyle, diet, and other physiological parameters of an individual needs to be considered while designing such status. This kind of personalized medicine approach of the microbiome-based health-monitoring system may become a highly useful field for health maintenance in the coming days.
Research / Administrative Experience+
Postdoctoral fellow at Mayo Clinic, Rochester, USA (2018-2021)
Assistant Professor at Institute of Advanced Research, Gandhinagar, Gujarat, India (2021- 2022)
Teaching / Other Experience+
Bioinformatics, Functional Genomics, Multi-omics Data Mining, Statistical Programming with R
Post Graduate Supervision+
The American Society for Microbiology
The International Society of Computational Biology
Bakshi, U., Gupta, V.K., Lee, A.R., Davis, J.M., Yong-Su, J., Freeman, M.F. and Sung, J., TaxiBGC: a Taxonomy-guided Approach for the Identification of Experimentally Verified Microbial Biosynthetic Gene Clusters in Shotgun Metagenomic Data. [Preprint at bioRxiv]
Mukherji, S., Bakshi, U. & Ghosh, A., 2022. Draft genome sequences of hydrocarbon degrading Haloferax sp. AB510, Haladaptatus sp. AB618 and Haladaptatus sp. AB643 isolated from the estuarine sediments of Sundarban mangrove forests, India. 3 Biotech, 12, 204.
Gupta, V. K., Cunningham, K. Y., Hur, B., Bakshi, U., Huang, H., Warrington, K. J., Taneja, V., Myasoedova, E., Davis, J. M., and Sung, J., 2021. Gut microbial determinants of clinically important improvement in patients with rheumatoid arthritis. Genome medicine, 13(1), 149.
Gupta, V.K., Kim, M., Bakshi, U., Cunningham, K.Y., Davis, J.M., Lazaridis, K.N., Nelson, H., Chia, N. and Sung, J., 2020. A predictive index for health status using species-level gut microbiome profiling. Nature Communications, 11(1):4635.
Roy, C., Rameez, M.J., Haldar, P.K., Peketi, A., Mondal, N., Bakshi, U., Mapder, T., Pyne, P., Fernandes, S., Bhattacharya, S. and Roy, R., 2020. Microbiome and ecology of a hot spring-microbialite system on the Trans-Himalayan Plateau. Scientific reports, 10(1), pp.1-22.
Roy, C., Bakshi, U., Rameez, M.J., Mandal, S., Haldar, P.K., Pyne, P. and Ghosh, W., 2019. Phylogenomics of an uncultivated, aerobic and thermophilic, photoheterotrophic member of Chlorobia sheds light into the evolution of the phylum Chlorobi. Computational biology and chemistry, 80, pp.206-216.
Bhattacharyya, C., Bakshi, U., Mallick, I., Mukherji, S., Bera, B. and Ghosh, A., 2017. Genome-guided insights into the plant growth promotion capabilities of the physiologically versatile Bacillus aryabhattai strain AB211. Frontiers in microbiology, 8, p.411.
Bakshi, U., Sarkar, M., Paul, S. and Dutta, C., 2016. Assessment of virulence potential of uncharacterized Enterococcus faecalis strains using pan genomic approach–Identification of pathogen–specific and habitat-specific genes. Scientific reports, 6, p.38648.
Chowdhury, A.R. and Bakshi, U., 2014. Pathophysiological responses from human gut microbiome. World Journal of Translational Medicine, 3(3), pp.133-140.
86/1 College Street, Kolkata - 700073,
West Bengal, India
Email: utpal.ihs at presiuniv.ac.in
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