Faculty Members

Research

The human microbiome is considered as the Second Genome and comprises of 50% of cells in the human body. The Human Microbiome Project (HMP) has unravelled the healthy human microbiome from different parts of the human body in Western populations. However, studies have clearly shown that there are significant differences in the composition and diversity of the healthy human microbiome in other world populations. The power of the human microbiome is recently being harnessed to understand its contribution in the maintenance of health and the changes that leads to the predisposition to various diseases in humans.

The main research goal of our human microbiome research (HMR) team in NIBMG is to characterize the genomic and metagenomic factors that contribute to the predisposition and progression of chronic, inflammatory conditions/diseases in humans with special reference to Indian populations. Besides this, we are also interested in studying the population genetics and molecular evolution of host-pathogen interacting genes, particularly the Innate Immune system to identify definite natural selection signatures acting on these genes across Human populations.

Broadly, our HMR team works on the following major research areas:

(A) Chronic Inflammatory Autoimmune Dry Skin Diseases and Antibiotic Resistant Wounds

Our laboratory is the first to characterize the Healthy Skin Microbiome in an Indian population of Dravidian descent which showed significant differences from Western Skin as well as Chinese Skin Microbiome. We also proved that change in quantitative levels of specific biophysical parameters in the Human skin can significantly predict the structure and composition of the Human Skin Microbiome. Based on our findings, we are involved in deciphering the host-microbiome interactions in inflammatory skin conditions like Psoriasis, Atopic Dermatitis etc.

Our research team is dedicated to unravel the viable but non culturable (VBNC) wound microbiome that leads to the development of antibiotic resistance in chronic, non healing diabetic foot ulcers (DFUs). DFUs are a dreaded complication of diabetes and comprise about 25% of the total number of diabetic patients worldwide.

(B) Maternal and Child Health: Preterm Birth and Childhood Growth Failure

Our laboratory is a part of a multi-institutional, multi-omics consortium on preterm birth using the GARBH-Ini cohort, the largest mother and child cohort in India. In this study, we aim to identify the significant changes in the vaginal microbiome in all the trimesters that leads to preterm birth in Indian women in collaboration with THSTI. We have jointly published the first paper on the dysbiotic vaginal microflora in Indian women associated with preterm birth. Currently, the results are being validated in a larger sample size and functional implications of the genomic findings are being tested in appropriate platforms.  

Our lab is also interested to study the host-microbiome interactions that leads to early child growth failures like stunting, wasting and malnutrition and the effect of interventions in ameliorating the same in well characterized child cohorts WINGS and ciKMC in collaboration with CHRD-SAS, a WHO collaborating centre for research, community based action and program development in child health in India. Currently, our HMR team is interested in characterizing the metagenomic biomarkers of early infancy growth failure in children in the first 1 year of life.

(C) Oncobiome: Characterizing Gut Microbiome-Metabolome Axis in Regulating Host Immunity in Colorectal Cancer

Our study aims to explore the differences in gut microbiome composition, function, and metabolomic profiles between chemotherapy-resistant and non-resistant colon cancer patients in India. By identifying microbiome-derived metabolite-induced host gene expression changes in colon tissue, we aim to uncover potential mechanisms driving chemoresistance. Furthermore, we will investigate the role of specific microbial metabolites in promoting chemoresistance using in vitro cell culture and animal models.

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For all our studies, we depend on affected individuals visiting hospital OPDs in and around Kolkata and Kalyani. Wet and dry Lab investigations are carried out in both NIBMG, Kalyani (Main Campus) and Biomedical Genomics Unit (BMGU) of NIBMG in P G Polyclinic Building, Kolkata. BMGU is in close proximity to several tertiary care hospitals in Kolkata which facilitates real-time sample collection and its processing that is crucial for metagenomic studies involving chronic diseases in Humans.

In NIBMG, we have established a state of the art Human Microbiome Research (HMR) Laboratory equipped with BSL-2 cabinet, bead beater homogenizer and micro-centrifuge for microbiome DNA isolation from human specimens; thermal cycler (PCR machine), Gel electrophoresis and imaging systems (Gel Doc apparatus) for estimation of amplified products; Anaerobic Chamber for culturing the viable anaerobes from patient samples; human cell line-microbiome co-culture facility consisting of Phase Contrast Microscope, centrifuge micro-centrifuge, BSL-2 cabinet and CO2 incubators for both aerobic and anaerobic conditions. Our metagenomic data analysis is supported by Computer Workstations with parallel computing facility and high computational power.

CV

Education 

Professional Appointments

Assistant Professor, National Institute of Biomedical Genomics (2016-2023)

Assistant Professor, BioMedical Genomics Centre, Kolkata (2014-2016)

Postdoctoral Research Assistant, Indo-Spanish Immunity Project (2012-2014)

Professional Memberships

Life Member, Indian Society for Human Genetics (ISHG) 

Life Member, Calcutta Consortium of Human Genetics (CCHuGE) 

Technical Review Committee in ICMR Diarrhoeal Research (2019-2022)

Expert Committee on CSIR-Mission on Indian Microbiome Initiative (2020)

Awards/Honors

Year      Award

2026      1st Dr. Ananda Mohan Chakrabarty Memorial Award by Microbiologists Society of India

2018      India-EMBO Symposium Grant Award from Wellcome-DBT India Alliance & EMBO

2016      Genome Project Grant Award from SciGenom Research Foundation (SGRF)

2016      International Travel Award in “13th International Congress of Human Genetics (ICHG 2016)” held in Kyoto, Japan

2015       DST Young Scientist Grant Award

2014      Best Poster Award in “ICHG 2014 & 39th Annual Meeting of Indian Society of Human Genetics” held in BHU

2013      DST International Travel Award for “Joint Conference of HGM 2013 and 21st International Congress of Genetics” in Singapore

2005      CSIR-UGC Lectureship

2003      CSIR-JRF

2003      GATE-XL Life Science

Ongoing Projects

(A) Chronic Inflammatory Skin Diseases and Antibiotic Resistant Wounds

1. Influence of Host Genomic Alterations on Atopic Dermatitis and Involvement of Gut-Skin Metagenomic Axis [Funding Agency: DSTBT, Govt. of West Bengal; Sanctioned Amount: 29,00,000 INR]

(B) Maternal and Child Health: Preterm Birth and Childhood Growth Failure

1. Investigating the Gut Microbiome and Host Epigenomic Profiles in Preterm Stunted Infants at 6 months of Age in a Low to Mid Socioeconomic Neighborhood of North India [Funding Agency: ANRF (CRG), Govt. of India; Sanctioned Amount: 63,00,000 INR]
2. Impact of an integrated intervention package during preconception, pregnancy, and early childhood on biomarkers of infant growth in the first 6 months of life: A sub study in WINGS [Funding Agency: Wellcome Trust-DBT and Society for Applied Studies, New Delhi; Sanctioned Amount: 30,00,000 INR]
3. Effect of community-initiated Kangaroo mother care in low-birth-weight infants on infant breast milk intake and gut microbiome [Funding Agency: Wellcome Trust-DBT and Society for Applied Studies, New Delhi, Sanctioned Amount: 15,00,000 INR]

(C) Diabetes and Related Complications

1. Diabetic Retinopathy Microbiome Study-India (DRMS-India) [Funding Agencies: Hyderabad Eye Research Foundation and LVPEI, Hyderabad; Sanctioned Amount: 85,00,000 INR] 

(D) Genomic Surveillance for Novel Pathogens

1. Systems-level regulation of chemoresistance and immunity in MSI-defined colon cancer (A vUoE Project) [Department of Biotechnology, Govt. of India]
2. Role of Gut Microbiome-Metabolome Axis in the Development of Chemoresistance in Colorectal Cancer [Funding Agency: iBRIC PhD Program, Sanctioned Amount: 50,00,000 INR]

(E) Genomic Surveillance for Emerging Pathogens and AMR Genes

1. Expansion of INSACOG: Wastewater Surveillance of SARS-CoV-2, Emerging Pathogens and Antimicrobial Resistance through Genomics-Based Methods (INSACOG-III) [Funding Agencies: Grand Challenges Program of BIRAC and Gates Foundation; Sanctioned Amount: 2,40,00,000 INR]

Past Major Projects

As PI/Co-PI

(A) Chronic Inflammatory Skin Diseases and Antibiotic Resistant Wounds

1. Metagenomic Characterization of the Cutaneous Microbiome Associated with Major Immunogenetic Subtypes of Psoriasis in India (Duration: 2015-2018) [Funding Agency: DST Young Scientist Grant, Govt. of India, Amount Sanctioned: 22,25,000 INR]
2. Diabetic Foot Ulcer Microbiome: Contribution to Biofilm Formation, Antibiotic Resistance and Wound Healing (Duration: 2016-2020) [Funding Agency: WBDBT, Govt. of West Bengal, Amount Sanctioned: 40,00,000 INR]
3. Probiotic Approach to Control Dry Skin: Host Genomic Alterations and Metagenomic Profiles of Skin Microbiome Associated with Atopic Dermatitis (Duraton: 2017-2021) [Funding Agency: Unilever R&D, India, Amount Sanctioned: 60,00,000 INR]
4. Genomic characterization of Skin Surface Microbiome across different skin types in humans (Duration: 2014-2017) [Funding Agency: Unilever R&D, India, Amount Sanctioned: 25,00,000 INR]  
5. Wastewater Surveillance of SARS-CoV-2 in India: Indian SARS-CoV-2 Genomics Consortium (INSACOG-II) (Duration: 2021-2023) [Funding Agency: DBT, Govt. of India, Amount Sanctioned: 1,00,00,000 INR]
6. Inter Institutional Program for Maternal, Neonatal and Infant Sciences-A translational approach to studying preterm birth- Garbh-Ini Phase 2 (Duration: 2019-2024) [Funding Agency: DBT, Govt. of India, Amount Sanctioned: 50,00,000 INR]
7. Multi-Omics Signatures of Human Placenta: Real time assessment of placental functions for development and birth outcomes (Duration: 2020-2024)  [Funding Agency: DBT, Govt. of India, Amount Sanctioned: 15,00,000 INR]

As Doctoral and Post Doctoral Researcher

Population genetic and functional analyses of maintenance of DNA sequence variability in response to infectious agents

Genomic alterations in Gingivobuccal cancer: The International Cancer Genome Consortium-India Project

Population Genetics Analysis Program---Immunity to Vaccines/Infections                

Invited/Special lectures

Publications

​As Co-Author:

• Chowdhury R, Maiti U, Devi S, Pasanna RM, Taneja S, Majumder PP, Strand TA, Pandey RM, Kurpad AV, MUKHERJEE S, Bhandari N (2025). Impact of an integrated intervention package during preconception, pregnancy, and early childhood on inflammation, IGF-1, IGFBP3 during first 6 months of life: Findings from the WINGS randomized controlled trial. PLOS Glob Public Health. 2025 Dec 15;5(12):e0005118. doi: 10.1371/journal.pgph.0005118. PMID: 41396889

• Talukdar, D., Raju, Y. J., Jana, P., Sharma, K., Babele, P., Kothidar, A., Ahrodia, T., Narendrakumar, L., Shyam, K. R., Singh, U., Tanwar, S., Harle, S., Chaudhuri, S., Raghavan, S., Wadhwa, N., MUKHERJEE S., Bhatnagar, S., Das, B., & GARBH-Ini study group (2025). Genomic insights into the potency and functional roles of Lactobacillus species in term and preterm births. Genomics 2025 Jul;117(4):111063. https://doi.org/10.1016/j.ygeno.2025.111063 PMID: 40456421

• Banerjee, D.#, Paul, S.#, Selvan, C., Pai, S., Nandakumar, B. S., MUKHERJEE S., & Raghavendra, P. B. (2025). Uncovering the Role of Tertiary Lymphoid Organs in the Inflammatory Landscape: A Novel Immunophenotype of Diabetic Foot Ulcers. Journal of cellular and molecular medicine 2025 Apr;29(7):e70479. https://doi.org/10.1111/jcmm.70479 PMID: 40159626

• Pratap Singh R, Kumari N, Gupta S, Jaiswal R, Mehrotra D, Singh S, MUKHERJEE S, Kumar R. (2023) Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma. Microbiology Spectrum 2023 Aug 17;11(4):e0459622. https://doi.org/10.1128/spectrum.04596-22 PMID: 37409975

• Roy S., Roy M., Nath S., Chaudhuri S. J., Ghosh M. K., MUKHERJEE S., & Chatterjee M. (2023). Role of molecular approaches to distinguish post kala-azar dermal leishmaniasis from leprosy: A case study. Indian journal of dermatology, venereology and leprology 2023 Jan-Mar;89(2):298-300 doi.org/10.25259/IJDVL_415_2022 3 PMID: 36461804

• Gupta N, Chhibber-Goel J, Gupta Y, MUKHERJEE S, Maitra A, Sharma A, Tandon R. (2023) Ocular conjunctival microbiome profiling in dry eye disease: A case control pilot study. Indian Journal of Ophthalmology 2023 Apr;71(4):1574-1581. doi: 10.4103/ijo.IJO_1756_22 PMID: 37026304

• Sehgal S, Vyawhare S, Bhatnagar S, Kshetrapal P; GARBH-Ini study group (2022) Longitudinal profile of sHLA-G during pregnancy and its association with small for gestational age births in North Indian pregnant females: A nested case-control study. Am J Reprod Immunol. 2022 Jan;87(1):e13504. https://doi.org/10.1111/aji.13504 PMID: 34657322.

• Kaushal K, Ayushi, Sharma N, Wadhwa N, Misra S, Bhatnagar S, Desiraju BK, Thiruvengadam R, Sopory S; GARBH-Ini study group (2022) Longitudinal changes in serum immune markers during normal pregnancy in a North-Indian population. Am J Reprod Immunol. 2022 May;87(5):e13531 https://doi.org/10.1111/aji.13531 PMID: 35312132

• Bhattacharyya C, Das C, Ghosh A, Singh AK, MUKHERJEE S, Majumder PP, Basu A and Biswas NK (2021) SARS CoV-2 mutation 614G creates an elastase cleavage site enhancing its spread in high AAT deficient regions. Infection Genetics and Evolution 2021 Jun;90:104760. https://doi.org/10.1016/j.meegid.2021.104760 PMID: 33556558

• Vijayram R, Damaraju N, Xavier A, Desiraju BK, Thiruvengadam R, Misra S, Chopra S, Khurana A, Wadhwa N; GARBH-Ini Study Group, Rengaswamy R, Sinha H, Bhatnagar S. (2021) Comparison of first trimester dating methods for gestational age estimation and their implication on preterm birth classification in a North Indian cohort. BMC Pregnancy and Childbirth 2021 Apr 30;21(1):343. https://doi.org/10.1186/s12884-021- 03807-4 PMID: 33931016

• Yadav, P., Banerjee, A., Boruah, N. Singh CS, Chatterjee P, MUKHERJEE S Dakhar H, Nongrum HB, Bhattacharjee A, Chatterjee A (2020) Glutathione S-transferasesP1 AA (105Ile) allele increases oral cancer risk, interacts strongly with c-Jun Kinase and weakly detoxifies areca-nut metabolites. Scientific Reports 2020 Apr 7;10(1):6032. https://doi.org/10.1038/s41598-020-63034-3 PMID: 32265484

• Banerjee P, Chakraborty A, Mondal RK, Khatun M, Datta S, Das K, Pandit P, MUKHERJEE S, Banerjee S, Ghosh S, Chakrabarti S, Chowdhury A, Datta S. (2017) HBV quasispecies composition in Lamivudine-failed chronic hepatitis B patients and its influence on virological response to Tenofovir-based rescue therapy. Scientific Reports 2017 Mar 17;7:44742. https://doi.org/10.1038/srep44742 PMID: 28303969

• India Project Team of International Cancer Genome Consortium (2013) Mutational landscape of gingivo-buccal oral squamous cell carcinoma reveals new recurrently- mutated genes and molecular subgroups. Nature Communications 2013;4:2873. https://doi.org/10.1038/ncomms3873 PMID: 24292195

• ​Bairagya BB, Bhattacharya P, Bhattacharya SK, Dey B, Dey U, Ghosh T, Maiti S, Majumder PP, Mishra K, Mukherjee S, MUKHERJEE S, Narayanasamy K, Poddar S, Sarkar-Roy N, Sengupta P, Sharma S, Sur D, Sutradhar D, Wagener DK. (2008) Genetic Variation and Haplotype Structures of Innate Immunity Genes in Eastern India. Infection Genetics and Evolution 2008 May;8(3):360-6. https://doi.org/10.1016/j.meegid.2008.02.009  PMID: 18396467

 Book Chapters

• Mukherjee S (2019) The Microbiome in Skin Health and Disease. Edited by: Nair G.B., Kurpad A.V. and Takeda Y. Probiotics in Health- Emerging Opportunities. Wiley India Pvt. Ltd.

• Chowdhury A, Mukherjee S (2015) Importance of Gut Microbiome in the Pathogenesis of NAFLD and NASH. Edited by: Kumar A, Anand A.C., Duseja A, Wadhawan M. Monograph on Non-Alcoholic Steatohepatitis (NASH), Academic Wing of the Association of Physicians of India, Indian College of Physicians (Published in the ISGCON 2015 Conference)

Lab members

Human Microbiome Research (HMR) Laboratory

PhD Students

Mr. Shankha Nath, ICMR-SRF

Ms. Ankita Maddheshiya, CSIR-SRF

Mr. Shouvik Paul, DBT-SRF

Mr. Aditya Agarwal, UGC-SRF

Ms. Laxmi Devi, iBRIC PhD Student

Mr. Sayantan Daripa, iPhD student

Mr. Anand Jha, CSIR-JRF

Project Linked Persons

Dr. Naina Kumari, Project Scientist-I (Dry Lab) [INSACOG-III Project]

Mr. Shreesh Mukherjee, Project Associate-II (Wet lab) [INSACOG-III Project]

Ms. Hazel Anna Sebastian, Project Associate-I (Dry lab) [LVPEI DRMS Project]

Mr. Golam Kabir, Lab Assistant (Wet lab) [INSACOG-III Project]

Mr. Srijan Pal, Lab Assistant (Wet lab) [INSACOG-III Project]

Mr. Ayanabha Samaddar, Admin Assistant [INSACOG-III Project]

Past Lab Members

Dr. Mousumi Sarkar (PhD Degree Awarded 2025)

Dr. Debjit De, Project Associate (Dry-lab)

Dr. Vani A, Senior Project Associate (Dry-lab)

Dr. Pieu Adhikary, Senior Project Associate (Wet-lab)

Ms. Naina Kumari, Data Analyst

Ms. Samiha T Ghori, Project Associate (Wet-lab)

Ms. Navdeep Kaur, Data Analyst

Ms Vemiya M, Project Associate-I (Wet lab)

Mr. Debadri Dey, Project Associate-I (Wet lab)