Bacterial and Phage Genetics

The Molecular
Arms Race
Never Ends

Decoding the ancient conflict between bacteria and bacteriophages — a battle billions of years in the making. We uncover the molecular weapons and defenses that shape microbial life, translating discoveries into tools for biotechnology and medicine.

Lab Objective

Our lab explores the fascinating molecular conflict between bacteria and bacteriophages — a never-ending evolutionary arms race that has been ongoing for billions of years. Our aim is to uncover fundamental mechanisms of microbial warfare: how phages take over their bacterial hosts and how bacteria defend themselves against phage attack.

Using a combination of microbial genetics, molecular biology, and biochemistry, we investigate these interactions and translate our discoveries into innovative tools for biotechnology and medicine.

    LYTIC PHAGE LIFE CYCLE
  

Research Focus

What We Study

Discovery of Novel Bacterial Immune Systems

We explore pathogenic bacterial genomic DNA — mobile genomic island and environmental — metagenome to discover new bacterial immune systems. Understanding these systems may reveal evolutionary parallels to human immune pathways.

Unravelling Phage Counter-Defense Strategies

Phages have evolved remarkable strategies to overcome bacterial defenses, including direct inhibitors that neutralize immune systems. We study these counter-defense mechanisms to understand how phages disarm host immunity and harness these molecular tools for therapeutic applications.

Exploring Phage-Encoded Antimicrobials

Phages encode a vast repertoire of proteins targeting diverse bacterial metabolic processes. We identify phage-encoded proteins with antimicrobial activity, elucidate their mechanisms of action, and explore their potential to combat multidrug-resistant bacteria.

Ongoing Work

Research

Research Details Coming Soon

Detailed descriptions of our ongoing projects, methodologies, and findings will be added here. In the meantime, explore our publications or contact us directly.

View Publications

Research Output

Publications

2025

Phage-encoded homing endonucleases attenuate bacterial immunity Preprint

Mahata T, Kanarek K, Goren MG, Ragavan RM, Haldar A, Shur G, Yehia R, Burstein D, Haitin Y, Qimron U, Salomon D.

BioRxiv, 2025

2024

Gamma-Mobile-Trio systems are mobile elements rich in bacterial defensive and offensive tools

Mahata T, Kanarek K, Goren MG, Ragavan RM, Bosis E, Qimron U, Salomon D.

Nature Microbiology 2024, 9, 3268–3283

2023

Engineering mice for female-biased progeny without impacting genetic integrity and litter size Preprint

Yosef I, Mahata T, Chen Y, Bar-joseph H, Shalgi R, Munitz A, Gerlic M, Qimron U.

BioRxiv, 2023

An efficient, scarless, selection-free technology for phage engineering

Goren MG, Mahata T, Qimron U.

RNA Biology 2023, 20(1), 830–835

Inhibition of Host Cell Division by T5 protein 008 (Hdi)

Mahata T, Molshanski-Mor S, Goren MG, Kohen-Manor M, Yosef I, Avram O, Salomon D, Qimron U.

Microbiology Spectrum 2023, 11(6), e01697-23

Highly active CRISPR adaptation proteins revealed by a robust enrichment technology

Yosef I,† Mahata T,† Goren MG, Degany OJ, Ben-Shem A, Qimron U.

Nucleic Acids Research 2023, 51(14), 7552–7562

† Equal contributions

2022

Thou shalt not cleave DNA — only repress transcription: A compact Cas protein representing a new CRISPR-Cas subtype

Mahata T, Qimron U.

Molecular Cell 2022, 82(23), 4403–4404

Cleavage of Abasic Sites in DNA by an Aminoquinoxaline Compound. Augmented Cytotoxicity and DNA Damage in Combination with Chlorambucil in Human Colorectal Carcinoma Cells

Mandi CS, Mahata T, Patra D, Chakraborty J, Bora A, Pal R, Dutta S.

ACS Omega 2022, 7(8), 6488–6504

2021

A phage mechanism for selective nicking of dUMP-containing DNA

Mahata T, Molshanski-Mor S, Goren MG, Jana B, Kohen-Manor M, Yosef I, Avram O, Pupko T, Salomon D, Qimron U.

PNAS 2021, 118(23), e2026354118

Interaction of a Triantennary Quinoline Glycoconjugate with the Asialoglycoprotein Receptor

Palit S,† Banerjee S,† Mahata T,† Niyogi S, Das T, Mandi CS, Chakrabarty P, Dutta S.

ChemMedChem 2021, 16(14), 2211–2216

† Equal contributions

2019

Quinoxaline derivatives disrupt the base stacking of hepatitis C virus-internal ribosome entry site RNA: Reduce translation and replication

Chakraborty J, Kanungo A, Mahata T, Kumar K, Sharma G, Pal R, Ahammed SK, Patra D, Majhi B, Chakrabarti S, Das S, Dutta S.

Chem. Commun. 2019, 55, 14027–14030

2018

Intercalator induced DNA superstructure formation: Doxorubicin and a synthetic quinoxaline derivative

Mahata T, Chakraborty J, Kanungo A, Patra D, Basu G, Dutta S.

Biochemistry 2018, 57(38), 5557–5563

2016

The Benzyl Moiety in a Quinoxaline-Based Scaffold Acts as a DNA Intercalation Switch

Mahata T, Kanungo A, Ganguly S, Modugula EK, Choudhury S, Pal SK, Basu G, Dutta S.

Angewandte Chemie 2016, 55(27), 7733–7736

2015

Synthesis of a visibly emissive 9-nitro-2,3-dihydro-1H-pyrimido[1,2-a]quinoxalin-5-amine scaffold with large Stokes shift and live cell imaging

Kanungo A, Patra D, Mukherjee S, Mahata T, Maulik PR, Dutta S.

RSC Advances 2015, 5(87), 70958–70967

Our People

The Team

Principal Investigator

Tridib Mahata, Ph.D.

Assistant Professor

School of Biological Sciences, NISER Bhubaneswar

tridibmahata@niser.ac.in

[ Biography and research interests of Prof. Mahata — add text here ]

PhD Students

Photo
Soon

Samchita Sarangi

( Sammy )

M.Sc.

PhD Student

[ Short bio or research focus for Samchita — add text here ]

Photo
Soon

Lalitmohan Kar

( Lalit )

M.Sc.

PhD Student

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Get In Touch

Mahata Lab

Phage–Bacteria Interaction Lab

Principal Investigator

Prof. Tridib Mahata

Laboratory

Phage Bacteria Interaction Lab
School of Biological Sciences

Location

Rooms 422 and 423
National Institute of Science Education and Research
Bhubaneswar, Jatni, Khordha
Odisha, India — 752050

tridibmahata@niser.ac.in

Join the Lab

We welcome motivated students and researchers interested in phage–bacteria interactions, microbial genetics, and molecular biology. Reach out via email with your CV and a brief statement of interest.