The major research goal of our lab is to characterize the genomic and metagenomic factors that contribute to the predisposition and progression of chronic, inflammatory diseases in Humans. 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. Recently we have characterized 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.
Another focus of our lab is to unravel the importance of viable but non-culturable (VBNCs) microorganisms in the development of antibiotic resistance in chronic wounds and other contributing factors responsible for delayed wound healing. 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 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. BMGU maintains a state of the art molecular biology lab with Thermal Cyclers (PCR machines), Gel Electrophoresis and Imaging Systems (Gel Doc) along with Microbial culture and Microbiome DNA isolation facilities using Biosafety Level 2 and Laminar airflow cabinets respectively. BMGU also harbours a Genome Wide Genotyping (iSCAN) platform for GWAS, Transcriptomic and Epigenetic studies and a Genetic Analyser for performing Sanger Sequencing. Data analysis in BMGU is supported by Workstations with parallel computing facility and high computational power.
Genomic characterisation of Skin surface Microbiome across different skin types in Humans
(Extramurally Funded by Unilever Research R&D)
The skin is a natural habitat for trillions of micro-organisms collectively termed as the skin microbiome. Potential challenges in skin microbiome research are mostly related to its impact in skin health and disease. In this study our major objective is to assess the importance of the skin microbiome with respect to skin health and integrity by evaluating the temporal variation and change in oilyness and dryness across different skin types in humans. In this regard, we are studying the skin metagenomics of both the healthy individuals and those affected by a common dry skin disorder, Atopic Dermatitis, in India.
Metagenomic Characterisation of the Cutaneous Microbiome Associated with Major Immunogenetic Subtypes of Psoriasis in India
(Extramurally funded by DST Fast Track Young Scientist Scheme)
The project aims to identify specific microbiome signatures in the skin of Psoriasis affected patients with and without genetic predisposition, differential disease severity and other clinical factors. The microbiome patterns thus identified will serve as an important addition to the already known factors for Psoriasis susceptibility. This will serve as the basis for undertaking a longitudinal study to evaluate the therapeutic efficacy and episodic relapses that are the major hurdles in the treatment of Psoriasis.
Diabetic Foot Ulcer Microbiome: Contribution in Biofilm formation, Antibiotic Resistance and Wound healing
(Extramurally funded by West Bengal-DBT)
Diabetes mellitus is a major and rapidly increasing health problem worldwide. Foot disorders, including Diabetic Foot Ulcers (DFU) are a major source of morbidity and a leading cause of hospitalization for persons with diabetes. Targeting microbial populations to promote healing and deter infection-related complications might be a novel treatment option. In this study our major objective is to determine the microbiome profiles in both superficial and chronic DFUs associated with biofilm formation, antibiotic resistance and wound healing and comparison between culturable and non-culturable bacterial populations.
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 7, 44742; doi: 10.1038/srep44742.
Mukherjee S*, Mitra R, Maitra A, Gupta S, Kumaran S, Chakrabortty A & Majumder PP. (2016) Sebum and Hydration Levels in Specific Regions of Human Face Significantly Predict the Nature and Diversity of Facial Skin Microbiome. Scientific Reports 6, 36062;doi 10.1038/srep36062.
Mukherjee S*, Ganguli D and Majumder PP. (2014) Global Footprints of Purifying Selection on Toll-Like Receptor Genes Primarily Associated with Response to Bacterial Infections in Humans. Genome Biology and Evolution. 6:551–558.
Mukherjee S*, Ganguli D and Majumder PP. (2013) Discovery of High Frequencies of the Gly-Ile Haplotype of TLR4 in Indian Populations Requires Reformulation of the Evolutionary Model of its Maintenance. Infection Genetics and Evolution 19:223-225.
India Project Team of International Cancer Genome Consortiuma. (2013) Mutational landscape of gingivo-buccal oral squamous cell carcinoma reveals new recurrently-mutated genes and molecular subgroups. Nature Communications 4:2873. doi: 10.1038/ncomms3873.
[aCollaborators: Maitra A, Biswas NK, Amin K, Kowtal P, Kumar S, Das S, Sarin R, Majumder PP, Bagchi I, Bairagya BB, Basu A, Bhan MK, Chaturvedi P, Das D, D'Cruz A, Dhar R, Dutta D, Ganguli D, Gera P, Gupta T, Mahapatra S, Mujawar MH, Mukherjee S, Nair S, Nikam S, Nobre M, Patil A, Patra S, Rama-Gowtham M, Rao TS, Roy B, Roychowdhury B, Sarkar D, Sarkar S, Sarkar-Roy N, Sutradhar D]
Mukherjee S, Sarkar-Roy N, Wagener DK, Majumder PP. (2009) Signatures of natural selection are not uniform across genes of innate immune system, but purifying selection is the dominant signature. Proceedings of the National Academy of Sciences, USA 106:7073-7078.