Santanu Chattopadhyay, PhD

GN Ramachandran Fellow (Scientist E1)


santanu chattopadhyay
santanu chattopadhyay

Santanu Chattopadhyay, PhD

GN Ramachandran Fellow (Scientist E1)


  • Profile

    • Ph.D. (2005) in Microbiology (National Institute of Cholera and Enteric Diseases, Calcutta, India).
    • M. Sc. (1998) in Physiology with Immunology and Microbiology as special paper (University of Calcutta, India).
    • B. Sc. (1996) in Physiology (City College, University of Calcutta, India).
    • 2015-till date: GN Ramachandran Fellow (Scientist E1), Rajiv Gandhi Centre for Biotechnology, Trivandrum, India.
    • 2014-2015: Visiting Lecturer, Prasanta Chandra Mahalanabis College, Kolkata, India.
    • 2012-2013: Post-doctoral Fellow, Albert Einstein College of Medicine, New York, USA.
    • 2010-2012: Post-doctoral Fellow, Cold Spring Harbor Laboratory, New York, USA.
    • 2010-2010: Post-doctoral Fellow, Vaccine and Gene Therapy Institute, Florida, USA.
    • 2005-2010: Post-doctoral Fellow, Lerner Research Institute, Cleveland Clinic, Ohio, USA. 
    • 2015: G. N. Ramachandran Fellowship.
    • 2001: Senior Research Fellowship (SRF) by ICMR.
    • 2000: National Eligibility Test (NET) by CSIR-UGC.
    • 1999: National Eligibility Test (NET) by CSIR-UGC.
    • 1996: National Scholarship.
  • Research

    Bacterial and Viral Diseases

    Project-1: Helicobacter pylori and the gastro-intestinal microbiome

    The bacterium and our work

    Helicobacter pylori chronically infects >50% of the world population and ~80% of the Indian population. A significant portion of the H. pylori infected population develops duodenal or gastric ulcer (10%–20%), distal gastric adenocarcinoma (1%–2%), and gastric mucosal-associated lymphoid tissue (MALT) lymphoma (<1%) and hence the bacterium is classified as type I carcinogen. Specific alleles of bacterial virulence genes like vacAs1 and the cagA were linked with diseases in Western and East-Asian countries. In stark contrast, our analyses, based on H. pylori strains isolated from gastric biopsies of West Bengal residents, revealed that the vacAs1 and the cagA are not associated with diseases, indicating other factors related to the pathogen and the host may contribute to disease progression. Our extensive analyses of the protein sequences revealed that the C-terminal ends of the CagAproteins have many discrete motifs that vary among strains and we have identified several unique CagA types. Moreover, by using the H. pylori multiplex PCR assay developed in our lab, RAPD DNA-fingerprinting and DNA sequence analyses, we have shown that one individual may become infected by multiple H. pylori strains.

    What Is Next?

    It is not clear why ~10-20% of the infected individuals develop H. pylori related diseases, while others don’t. Moreover, no virulence specific marker of H. pylori is identified for India. Finally, the information on the roles of co-existing other microorganisms (bacteria, virus etc) in disease progression is lacking. Advances in sequencing technology—so-called metagenomics (analyses of genomes without the need for culture)—now makes it possible to detect and analyze the genomes of all microbes collectively (microbiome) that inhabit in unusual locations (eg. gastric mucosa). Our present interest is to look into the roles of stomach and intestinal microbiomes using next-generation sequencing/ deep sequencing. These data and the results from the analyses of virulence associated genes, DNA-fingerprints, proteomics will give us insight to understand the factors that contribute to the progression of H. pylori related diseases.

    Project-2: Human virome

    Why Virome?

    The human virome is the viral component of the microbiome, which means it is the collection of all the viruses in human body.  Interestingly, information on human virome is significantly lesser in present literature as compared to the bacterial component. However, knowledge of human virome is of extreme importance since viruses are not only associated with many acute (eg. rotavirus) and chronic (eg. hepatitis B) illnesses, but also associated with cancers (eg. human papillomavirus), destruction of immune cells (eg. human immunodeficiency virus) and neuronal diseases (eg. rabies virus). Moreover, viruses are the most abundant infectious agents on our planet. They are capable of infecting every living creature (including human, animals, plants, fungi, protozoa, bacteria, etc) and altering the physiology of their hosts, which in turn is associated with human health. For example, only the CTX phage (a virus that does not infect human directly) infected Vibrio cholerae (a bacterium) strains can express the cholera toxin upon infection and are associated with pandemic spread of the human disease. 

    Challenges bring opportunities

    We know less about viruses because the viruses offer many challenges to the microbiome researchers, like—they do not have a genetic marker to look for, like the 16S rDNA in bacteria; they have either DNA or RNA as genetic material (for RNA, it can be single or double stranded and for the single stranded ones, it can be either positive or negative stranded, and even segmented or non-segmented); the genetic material can become integrated into the host chromosome etc., which collectively makes the genome analyses tricky. But these challenges are actually our opportunities to develop newer and better methods to understand the role of known and unknown viral infections in various human diseases (viral and bacterial infections, cancer etc.). Our present aim is to utilize our expertise in molecular and biochemical techniques of virology for establishing methodology for metagenomic analyses of virome and recognize their role in modulating different microflora (eg. skin, gut, blood, vagina etc.) and their combined significance in human health.  

    • ECR grant from SERB/DST
  • Publications

    1. Mydhily R. B. Nair, Deepak Chouhan, Sourav Sen Gupta and Santanu Chattopadhyay. (2016). Fermented Foods: Are They Tasty Medicines for Helicobacter pylori Associated Peptic Ulcer and Gastric Cancer? Front. Microbiol. 2016;7:1148.
    2. Patra R, Chattopadhyay S, De R, Ghosh P, Ganguly M, Chowdhury A, Ramamurthy T, Nair GB, Mukhopadhyay AK. Multiple infection and microdiversity among Helicobacter pylori isolates in a single host in India. PLoS One. 2012;7(8):e43370.
    3. Chattopadhyay S, Patra R, Chatterjee R, De R, Alam J, Ramamurthy T, Chowdhury A, Nair GB, Berg DE, Mukhopadhyay AK. Distinct repeat motifs at the C-terminal region of CagA of Helicobacter pylori strains isolated from diseased patients and asymptomatic individuals in West Bengal, India. Gut Pathog. 2012. 25;4(1):4.
    4. Patra R, Chattopadhyay S, De R, Datta S, Chowdhury A, Ramamurthy T, Nair GB, Berg DE, Mukhopadhyay AK. Intact cag pathogenicity island of Helicobacter pylori without disease association in Kolkata, India. Int J Med Microbiol. 2011 Apr;301(4):293-302.
    5. Mao H, Chattopadhyay S, Banerjee AK. Domain within the C protein of human parainfluenza virus type 3 that regulates interferon signaling. Gene Expr. 2010;15(1):43-50.
    6. Sarkar A*, Chattopadhyay S*, Ming Luo and Amiya K. Banerjee. Structural and functional properties of the vesicular stomatitis virus nucleoprotein-RNA complex as revealed by proteolytic digestion. Virology. 2010. 401: 61-69.
    7. Mao H, Chattopadhyay S, Banerjee AK. N-terminally truncated C protein, CNDelta25, of human parainfluenza virus type 3 is a potent inhibitor of viral replication. Virology. 2009. 10;394(1):143-8.
    8. Chattopadhyay S, Banerjee AK. Phosphoprotein, P of human parainfluenza virus type 3 prevents self-association of RNA-dependent RNA polymerase, L. Virology. 2009. 383:226-236.
    9. Saha DR, Datta S, Chattopadhyay S, Patra R, De R, Rajendran K, Chowdhury A, Ramamurthy T, Mukhopadhyay AK. Indistinguishable cellular changes in gastric mucosa between Helicobacter pylori infected asymptomatic tribal and duodenal ulcer patients. World J Gastroenterol. 2009. 15(9):1105-12.
    10. Mao H, Thakur CS, Chattopadhyay S, Silverman RH, Gudkov A, Banerjee AK. Inhibition of human parainfluenza virus type 3 infection by novel small molecules. Antiviral Res. 2008. 77(2):83-94.
    11. Malur AG, Chattopadhyay S, Maitra RK, Banerjee AK. Inhibition of STAT 1 phosphorylation by human parainfluenza virus type 3 C protein. J Virol. 2005. 79(12):7877-7882.
    12. Datta S, Chattopadhyay S, Chowdhury A, Santra A, Saha DR, Ramamurthy T, Bhattacharya SK, Berg DE, Nair GB, Mukhopadhyay AK. Diagnosis and genotyping of Helicobacter pylori by polymerase chain reaction of bacterial DNA from gastric juice. J Gastroenterol Hepatol. 2005. 20(8):1253-1259.
    13. Datta S, Chattopadhyay S, Patra R, De R, Ramamurthy T, Hembram J, Chowdhury A, Bhattacharya SK, Berg DE, Nair GB, Mukhopadhyay AK. Most Helicobacter pylori strains of Kolkata in India are resistant to metronidazole but susceptible to other drugs commonly used for eradication and ulcer therapy. Aliment Pharmacol Ther. 2005. 22(1):51-57.
    14. Nahar S, Mukhopadhyay AK, Khan R, Ahmad MM, Datta S, Chattopadhyay S, Dhar SC, Sarker SA, Engstrand L, Berg DE, Nair GB, Rahman M. Antimicrobial susceptibility of Helicobacter pylori strains isolated in Bangladesh. J Clin Microbiol. 2004. 42(10):4856-4858.
    15. Chattopadhyay S, Patra R, Ramamurthy T, Chowdhury A, Santra A, Dhali GK, Bhattacharya SK, Berg DE, Nair GB, Mukhopadhyay AK. Multiplex PCR assay for rapid detection and genotyping of Helicobacter pylori directly from biopsy specimens. J Clin Microbiol. 2004. 42(6):2821-2824.
    16. Pandey M, Khan A, Das SC, Sarkar B, Kahali S, Chakraborty S, Chattopadhyay S, Yamasaki S, Takeda Y, Nair GB, Ramamurthy T. Association of cytolethal distending toxin locus cdtB with enteropathogenic Escherichia coli isolated from patients with acute diarrhea in Calcutta, India. J Clin Microbiol. 2003. 41:5277-5281.
    17. Datta S, Chattopadhyay S, Balakrish Nair G, Mukhopadhyay AK, Hembram J, Berg DE, Rani Saha D, Khan A, Santra A, Bhattacharya SK, Chowdhury A. Virulence genes and neutral DNA markers of Helicobacter pylori isolates from different ethnic communities of West Bengal, India. J Clin Microbiol. 2003. 41(8):3737-3743.
    18. Datta S, Khan A, Nandy RK, Rehman M, Sinha S, Chattopadhyay S, Das SC, Nair GB. Environmental isolates of Aeromonas spp. harboring the cagA-like gene of Helicobacter pylori. Appl Environ Microbiol. 2003. 69(7):4291-4295.
    19. Chaudhuri S, Chowdhury A, Datta S, Mukhopadhyay AK, Chattopadhyay S, Saha DR, Dhali G, Santra A, Nair GB, Bhattacharya S, Berg DE. Anti-Helicobacter pylori therapy in India: differences in eradication efficiency associated with particular alleles of vacuolating cytotoxin (vacA) gene. J Gastroenterol Hepatol. 2003. 18(2):190-195.
    20. Bhattacharyya A, Pathak S, Datta S, Chattopadhyay S, Basu J, Kundu M. Mitogen-activated protein kinases and nuclear factor-kappaB regulate Helicobacter pylori-mediated interleukin-8 release from macrophages. Biochem J. 2002. 368(Pt 1):121-129.
    21. Chattopadhyay S, Datta S, Chowdhury A, Chowdhury S, Mukhopadhyay AK, Rajendran K, Bhattacharya SK, Berg DE, Nair GB. Virulence genes in Helicobacter pylori strains from West Bengal residents with overt H. pylori-associated disease and healthy volunteers. J Clin Microbiol. 2002. 40(7):2622-2625.
    22. Datta S, Kurazono H, Chattopadhyay S, Chowdhury A, Chaudhuri, S. Estimation of vacuolating cytotoxin secreted by different strains of Helicobacter pylori using bead enzyme-linked immunosorbent assay & its correlation with bacterial genotype. Indian J Med Res. 2001. 114:192-198.

    *Co-first author.

    1. Sen Gupta S, Chattopadhyay S and Nair GB. Undernourished Children and the gut microbiome. In Probiotics from Bench to Community. Ed. Ramakrishna BS, Nair GB and Takeda Y. Elsevier. 2016.
    2. Chattopadhyay S, Esper F, Banerjee, A. K. Respirovirus. Springer Index of Viruses. Tidona C and Darai G (Eds.) 2nd ed. Springer. Heidelberg. Germany. 2011. 243.
    3. Chattopadhyay S, Esper F, Banerjee AK. Parainfluenza viruses. In The Biology of Paramyxoviruses. Samal SK (Eds). Caister Academic Press, Norfolk, UK. Page 175-209
  • Team

  • Alumni