Sharma, H., Ira, R., Sood, D., Kumar, R., Devi, S., Prakash, T. (2026). Comparative analysis using 16S rRNA metagenomics to explore the microbial diversity of plant based fermented foods. Springer Nature: Food safety and Risk. 

P Patidar, T Prakash (2026). An integrative analysis of genetic factors reveals dysregulation of cytokines, immune signaling, and T cell activity as the underlying immune mechanisms in autoimmune immune thrombocytopenia. Thrombosis Journal. 

AO Krishnan, R Shrivastava, MA Jamal, D Pundhir, T Prakash (2026). A Genomic Investigation into the Probiotic Attributes Among Members of the Lactobacillaceae family. Current Microbiology 83 (1), 81. 

Orkkatteri Krishnan, A.#, Mudgal, L. N.#, Soni, V., & Prakash, T. (2025). ProbML: A Machine Learning‐Based Genome Classifier for Identifying Probiotic Organisms. Molecular Nutrition & Food Research, e70025. #: Authors contributed equally

Prabhu, P. S., Kalita, R., Sharma, V., & Prakash, T. (2025). Understanding Inflammatory Bowel Disease: An Integrative Framework of Microbiome, Metabolome, and Immunological Biomarkers. Journal of Translational Gastroenterology, 3(1), 24-38.

Patidar, P., Jain, A., & Prakash, T. (2025). Deciphering the role of molecular mimicry in the etiopathogenesis of Autoimmune Hemolytic Anemia using an immunoinformatics approach. ImmunoInformatics, 100047. 

Ira, R., Deswal, S., & Prakash, T. (2024). Role of the Microbial Community in Energy Recovery via Wastewater Treatment. In Application of Microbial Technology in Wastewater Treatment and Bioenergy Recovery (pp. 213-249). Springer. 

Understanding Aging through the Lense of Gut Microbiome. R Ira, J Adwani, AO Krishnan, G Subramanian, S Yadav, S Shukla, S Rao, ...T Prakash* Exploratory Research and Hypothesis in Medicine, 0-0, 2024

Production of biohythane from cow dung using novel microbial synthetic consortia designed by heat-treated and acclimatized combined wastes. R Ira, V Sharma, S Kumar, M Koul, L Sharma, A Halder, T Prakash*, Environmental Science: Advances 3 (9), 1289-1308 2024.

Arjun, O. K., Sethi, M., Parida, D., Dash, J., Das, S. K., Prakash, T., & Senapati, S. (2024). Comprehensive physiological and genomic characterization of a potential probiotic strain, Lactiplantibacillus plantarum ILSF15, isolated from the gut of tribes of Odisha, India. Gene, 931, 148882.  

Prakash, T., Yadav, S. R., Bürger, M., & Jendrossek, D. (2024). Cleavage of natural rubber by rubber oxygenases in Gram-negative bacteria. Applied Microbiology and Biotechnology, 108(1), 191.

Sethi, M., Ok, A., Dash, J., Parida, D., Kar, S., Mishra, S., ... & Senapati, S. (2024). Whole Genome Mining and Characterization of a New Probiotic Strain Levilactobacillus brevis ILSH3 from Handia: An Ethnic Fermented Beverage of Odisha, India. Probiotics and Antimicrobial Proteins, 1-19. 

Anaerobic co-digestion of food waste, bio-flocculated sewage sludge, and cow dung in CSTR using E (C2) Tx synthetic consortia. Thakur, H., Ira, R., Verma, N. K., Sharma, V., Kumar, S., Dhar, A., Prakash, T., & Powar, S.  Environmental Technology & Innovation 2023 , 32, 103263.

Arjun, O. K., & Prakash, T. (2023). Identification of conserved genomic signatures specific to Bifidobacterium species colonising the human gut. 3 Biotech, 13(3), 97.

Patidar, P., & Srivastava, T. P. (2023). Metagenomics for the Identification of Microbial Enzymes for Nutraceutical Production. In Microbial Enzymes in Production of Functional Foods and Nutraceuticals (pp. 263-282). CRC Press.

Patidar, P., & Prakash, T. (2022). Decoding the roles of extremophilic microbes in the anaerobic environments: Past, Present, and Future. Current Research in Microbial Sciences, 3, 100146.

Gut microbiota alternation under the intestinal epithelium-specific knockout of mouse Piga gene. Aditi Jangid, Shinji Fukuda, Yutaka Suzuki, Todd D Taylor, Hiroshi Ohno, Tulika Prakash*. Scientific Reports 2022 12:10812.

Shotgun metagenomic sequencing revealed the prebiotic potential of a grain-based diet in mice. Aditi Jangid, Shinji Fukuda, Yutaka Suzuki, Todd D Taylor, Hiroshi Ohno, Tulika Prakash*. Scientific Reports 2022 12:6748.

Impact of dietary Fructooligosaccharides (FOS) on murine gut microbiota and intestinal IgA secretion Running Title: FOS affects gut microbiota and IgA secretion. Aditi Jangid, Shinji Fukuda, Tamotsu Kato, Masahide Seki, Yutaka Suzuki, Todd D Taylor, Hiroshi Ohno, Tulika Prakash*. 3Biotech (BITC) 2022 Feb;12(2):56.

Comparative Human Gut Microbiome Analysis of Prakriti and Sasang Systems Reveals Functional Level Similarities in the Constitutionally Similar Classes. Fauzul Mobeen, Vikas Sharma, Tulika Prakash*. 3Biotech (BITC) 2020, Sep; 10(9): 379. 

In Silico Functional and Evolutionary Analyses of Rubber Oxygenases (RoxA and RoxB). 
Vikas Sharma, Fauzul Mobeen, Tulika Prakash*. 3Biotech (BITC) 2020, Sep; 10(9): 376. 

Association of colitis with gut-microbiota dysbiosis in clathrin adapter AP-1B knockout mice. Aditi Jangid, Shinji Fukuda, Masahide Seki, Terumi Horiuchi, Yutaka Suzuki, Todd D Taylor, Hiroshi, Ohno, Tulika Prakash*. PLoS One 2020, Mar 24; 15(3) e0228358. 

The Entner-Doudoroff and Nonoxidative Pentose Phosphate Pathways Bypass Glycolysis and the Oxidative Pentose Phosphate Pathway in Ralstonia solanacearum. Poonam Jyoti, Manu Shree, Chandrakant Joshi, Tulika Prakash, Suvendra Kumar Ray, Siddhartha Sankar Satapathy, Shyam Kumar Masakapalli. MSystems 2020 Vol. 5, No. 2, e00091-20.


Microbial Networking to Divulge Targets for Microbiome Therapeutics, Comprehensive Gut Microbiota. Arjun OK and Tulika Prakash* Book chapter in Elsevier "Microbiome, therapeutics application and Epigenetics.” 2020. 

Functional Signature Analysis of Extreme Prakriti Endophenotypes in Gut Microbiome of Western Indian Rural Population. Fauzul Mobeen, Vikas Sharma, Tulika Prakash*. Bioinformation. 2019; 15(7): 490-505. 

Microbial Genomics in Carbon Management and Energy Production. Shatabisha Bhattacharjee and Tulika Prakash* Book titled Springer “Microbial Genomics in Sustainable Agroecosystems.” 2019.

Microbial Genome Diversity and Microbial Genome Sequencing. Aditi Jangid and Tulika Prakash* Book titled Springer “Microbial Genomics in Sustainable Agroecosystems.” 2019.

Enterotype Variations of the Healthy Human Gut Microbiome in Different Geographical Regions. Fauzul Mobeen, Vikas Sharma, Tulika Prakash*. Bioinformation. 2018;14(9):560-73. 

Exploration of survival traits, probiotic determinants, host interactions, and functional evolution of bifidobacterial genomes using comparative genomics. Vikas Sharma, Fauzul Mobeen, Tulika Prakash*. Genes. 2018 Oct;9(10):477. 


Metabolic and taxonomic insights into the Gram-negative natural rubber degrading bacterium Steroidobacter cummioxidans sp. nov., strain 35Y. Vikas Sharma, Gabriele Siedenburg, Jakob Birke, Fauzul Mobeen, Dieter Jendrossek, Tulika Prakash* PLoS One. 2018 May 31;13(5):e0197448. 

Western Indian rural gut microbial diversity in extreme Prakriti endo-phenotypes reveals signature species. Nar Singh Chuahan, Rajesh Pandey, Anupam Kumar Mondal, Shashank Gupta, Jitendra Kumar, Rutuja Patil, Dhiraj Agarwal, Bhushan Girase, Ankita Shrivastava, Fauzul Mobeen, Vikas Sharma, Tulika Prakash, Sanjay Juvekar, Bhavana Prasher, Mitali Mukerji, Debasis Dash. Front Microbiol. 2018 Feb 13;9:118. 

Lactobacilli combat hypercholesterolemia via alteration of gut microbiota. Huey-Shi Lye, Hiroshi Ohno, Wai-Yee Low, Todd Taylor, Tulika Prakash, Tamotsu Kato, Lee-Ching Lew, Min-Tze Liong. J Biotechnol. 2017 Nov 20;262:75-83.

Characterization of Phormidium lacuna strains from the North Sea 1 and the Mediterranean Sea for biotechnological applications. Fabian Nies, Sybille Wörner, Nadja Wunsch, Olivier Armant, Vikas Sharma, Anne Hesselschwerdt, Fabian Falk, Nora Weber, Julia Weiß, Andreas Trautmann, Clemens Posten, Tulika Prakash, Tilman Lamparter. Process Biochemistry. 2017 Aug 1;59:194-206. 

Comparative Genomics of Herpesviridae Family to look for Potential Signatures of Human Infecting Strains. Vikas Sharma, Fauzul Mobeen, Tulika Prakash*. Int J Genomics 2016, 9543274. 

Genome Sequence of the Tsetse Fly (Glossina morsitans): Vector of African Trypanosomiasis. International Glossina Genome Initiative. Science 2014 344(6182): 380- 6. 

Human Intestinal Microbiome. Tulika Prakash and Masahira Hattori. Encyclopedia of Metagenomics. Article ID: 357742, Chapter ID: 776.* Invited Review. 

Functional Assignment of metagenomic data: Insights for the Microbial Nitrogen Cycle. Vikas Sharma, Gaurav Chetal, Todd D. Taylor, Tulika Prakash, Horizon Press, Book titled Microbial Nitrogen Cycle: Theory, Methods and Applications. 2014.

Functional assignment of metagenomic data: challenges and applications. Prakash T, Taylor TD. Brief Bioinform. 2012 13(6):711-27. 

Fast and accurate taxonomic assignments of metagenomic sequences using MetaBin. 
Sharma VK, Kumar N, Prakash T, Taylor TD. PLoS ONE 2012 7(3):e34030. 

Complete genome sequences of rat and mouse segmented filamentous bacteria, a potent inducer of Th17 cell differentiation. Prakash T, Oshima K, Morita H, Fukuda S, Imaoka A, Kumar N, Sharma VK, Takahashi M, Saitou N, Taylor TD, Ohno H, Umesaki Y, Hattori M. Cell Host Microbe 2011 10(3):273-84. (Cover page)

Expression of conjoined genes: another mechanism for gene regulation in eukaryotes. 
Prakash T, Sharma VK, Adati N, Ozawa R, Kumar N, Nishida Y, Fujikake T, Takeda T, Taylor TD. PLoS One 2010 5(10):e13284. 

MetaBioME: a database to explore commercially useful enzymes in metagenomic datasets. Sharma VK, Kumar N, Prakash T, Taylor TD. Nucleic Acids Res. 2009 38 (Database):D468-D472. 

Genome of an endosymbiont coupling N2 fixation to cellulolysis within protist cells in termite gut. Hongoh Y*, Sharma VK*, Prakash T, Noda S, Toh H, Taylor TD, Kudo T, Sakaki Y, Toyoda A, Hattori M, Ohkuma M. Science 2008 322(5904):1108-1109. 


Complete genome of the uncultured Termite Group 1 bacteria in a single host protist cell. Hongoh Y*, Sharma VK*, Prakash T, Noda S, Taylor TD, Kudo T, Sakaki T, Toyoda A, Hattori M, Ohkuma M. Proc Natl Acad Sci USA 2008 105(14):5555-5560. 

Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. Kurokawa K, Itoh T, Kuwahara T, Oshima K, Toh H, Toyoda A, Takami H, Morita H, Sharma VK, Srivastava TP, Taylor TD, Noguchi H, Mori H, Ogura Y, Ehrlich DS, Itoh K, Takagi T, Sakaki Y, Hayashi T, Hattori M. DNA Res., 2007, 14(4), 169-181. 

Conformational Analysis of Invariant Peptide Sequences in Bacterial Genomes. Prakash T, Ramakrishnan C, Dash D, Brahmachari SK. J. Mol. Biol. 2005, 345, 937-955.

CoPS: comprehensive peptide signature database. Prakash T, Khandelwal M, Dasgupta D, Dash D, Brahmachari SK. Bioinformatics, 2004, 20(16), 2886-2888.

In silico characterization of the INO80 subfamily of SWI2/SNF2 chromatin remodeling proteins. Bakshi R, Prakash T, Dash D, Brahmachari V. Biochem Biophys Res Commun. 2004, 320(1), 197-204.

Recognition and analysis of protein-coding genes in severe acute respiratory syndrome associated coronavirus. Sharma R, Maheshwari JK, Prakash T, Dash D, Brahmachari SK. Bioinformatics, 2004, 20(7), 1074-1080.