Among many novel findings, he demonstrated that enrichment in rabbit intestine is an effective approach for isolating potentially virulent V. cholerae strains that were missed by conventional laboratory culture methods. He also significantly contributed in understanding the biology of bacteriophages. Dr. Chowdhury was awarded a prestigious Japanese Govt. fellowship to pursue his PhD study under supervision of Dr. Shinji Yamasaki. He examined the genetic diversity of superintegron (a large genetic island and reservoir of multi-drug resistance genes) and developed simple and rapid PCR-fingerprinting methods for epidemiological studies of V. cholerae. Dr. Chowdhury worked with Dr. Fidelma Boyd (University of Delaware) as a Postdoc-Researcher and   demonstrated the functions of two genetically diverse Tri-partite ATP independent Periplasmic (TRAP) transporters: one the SiaPQM being solely responsible for transporting sialic acid and the other DctPQM plays significant role in transporting C4-dicarboxylates, the intermediates of TCA cycle in V. cholerae. In another study, he demonstrated the sequence and expression divergence of an ancient duplication of the chaperonin groESEL operon in Vibrio species. Additionally, using adult mouse model he demonstrated that host sialic acid is an important nutrient that plays potential role in host-pathogen interaction and prolong persistence of V. cholerae.

     Before joining with Dr. Yilmaz research group, he worked as a Postdoc Scholar in the department of Chemical Engineering at the Pennsylvania State University with Dr. Thomas K. Wood where he studied the genetic basis of bacterial persistence (tolerance to antibiotics) and discovered that FDA approved anticancer drugs cisplatin and mitomycin C are more effective than other conventional antibiotics in killing of metabolically dormant persister cells. He also demonstrated that a bacterial toxin, part of toxin-antitoxin system that plays significant role in persisters formation, can cleave ssRNA irrespective of its 5ʹ-terminal group.  Moreover, he identified five new proteins through the screening of 4287 Escherichia coli proteins that increase persistence in the absence of ppGpp​ simply by reducing cell growth. So far, Dr. Chowdhury published 29 research articles in peer-reviewed high impact scientific journals including PNAS, Scientific Reports (Nature publishing group), Emerging Infectious disease, Molecular Microbiology, mBio, Applied and Environmental Microbiology, Biotechnology and Bioengineering, Environmental Microbiology, Microbiology etc.

     In Dr. Yilmaz’s lab, Dr. Chowdhury is investigating the functional genomics of a periodontal pathogen Porphyromonas gingivalis and the role of pathogen-encoded effector proteins in modulating the host response at the onset of infection in primary epithelial cells. His primary interest is to explore the role of danger molecules, ATP and adenosine in the context of host-pathogen persistence in vitro and in vivo.