Research
Publications
1. Athira Thulaseedharan Salaja, Karthika Suryaletha, Sabu Thomas, Abhirami Chithrakumari Raneshan, Deepthi Thankappan, Dijo Darjees,Sarika Ambika Rajendran. 2025. Acinetobacter baumannii: Insights into epidemiology, pathogenicity and drug resistance. The Microbe 9(2025) 100598. doi.org/10.1016/j.microb.2025.100598 2. Paul M, Sabu Thomas. 2025. Detection of morphological variants of colistin-resistant Klebsiella pneumoniae associated with sepsis in Kerala, India. Acta Microbiol Immunol Hung. 72(1):39-42. doi: 10.1556/030.2025.02515 3. Devika Das J, Vishnu SJ, Karthika Suryaletha, Merin Paul, Aparna Shankar, Swapna R Nath, Sabu Thomas. 2025. Probiotic Lacticasibacillus paracasei from human gut microbiome against colistin-resistant Klebsiella pneumoniae: in vitro, in vivo and probiogenomic approaches. Beneficial Microbes. 9:1–21. doi: 10.1163/18762891-bja00065. 4. Singh SK, Sudhir S, Menon V, Warrier AR, V AR, Edathadathil F, Sathyapalan DT, Sivaprasad PS, Thomas S (2025) Epidemiology and clinical outcomes of monomicrobial carbapenem-resistant Enterobacteriaceae (CRE) from a metropolitan area of Kerala, India. J Infect Dev Ctries 19:569–575. doi: 10.3855/jidc.18777 5. Vaikkathillam P, Sajeevan A, Mohan S, Solomon AP, Rajan PP, S M, Kumar P, Sabu Thomas. 2025. Genomic analysis of colistin and carbapenem resistant Klebsiella pneumoniae GC29. Microb Pathog. 199:107220. doi: 10.1016/j.micpath.2024.107220. 6. Aparna S, Devika DJ, Nayar S, Thomas S. 2023. Deciphering the effect of maternal postpartum antibiotic prophylaxis on the infant gut microbiome a whole metagenomic analysis. Future Microbiology. 18:427-441. 7. Betsy M, Karthika S, Amrutha ML, Alida S, Sabu Thomas, Jatish Kumar. 2022. Chiral Nanostructures Derived from Europium (III) Complexes for Enhanced Circularly Polarized Luminescence and Antibacterial Activity. Journal of Materials Chemistry C. 10, 13954-13963. 8. Karthika S, Sivakumar & Sabu Thomas. 2021. Comprehensive Genomics Depict Accessory Genes Encoding Pathogenicity and Biofilm Determinants in Enterococcus faecalis. Future Microbiology. 16:3. 9. Divya MP, Hardip R, Patel, Sivakumar Krishnankutty Chandrika, Sabu Thomas. 2021. Genomic attributes differ between Vibrio parahaemolyticus environmental and clinical isolates including pathotypes. Environmental Microbiology Reports. 14(3):365-375. 10. Lekshmi N, Sivakumar KC and Sabu Thomas. 2020. Adaptive laboratory evolution of Vibrio cholerae to doxycycline associated with spontaneous mutation. International Journal of Antimicrobial Agents. 56(2020). 11. Devika DJ, Shankar A, Johnson JB, Thomas S. 2020. Critical insights into antibiotic resistance transferability in probiotic Lactobacillus. Nutrition. 69:110567. 12. Lekshmi N, Vishnu S J, Sivakumar K C, Sabu Thomas. 220. Epidemiological and pathogenic characteristics of Haitian variant V. cholerae circulating in India over a decade (2000–2018). Microbial Pathogenesis. 149 (2020) 13. Divya M.P., Ramamurthy, T. & Sabu Thomas. 2020. Genetic and virulence characterisation of Vibrio parahaemolyticus isolated from Indian coast. BMC Microbiology 20, 62. 14. Wilson PA, Sajith R, Vipin G, Karthika S, Sabu Thomas. 2020. Deciphering the Cold Adaptive Mechanisms in Pseudomonas psychrophila MTCC12324 isolated from the Arctic at 79° N. Current Microbiology. 77, 2345–2355. 15. Aparna Shankar, Devika J, Megha PR, Merin Paul, Lekshmi N, Karthika S, Akhila VS, Sabu Thomas. 2020. Elucidation of health risks using metataxonomic and antibiotic resistance profiles of microbes in flood affected waterbodies, Kerala 2018. J Flood Risk Management. 2020:e12673. 16. Karthika S, Lekshmi N, Joby John, Megha PR, Sanil George & Sabu Thomas. 2019. Decoding the proteomic changes involved in the biofilm formation of Enterococcus faecalis SK460 to elucidate potential biofilm determinants. BMC Microbiology. 19:146. 17. Lekshmi N, Mary T Sivakumar KC and Sabu Thomas. 2019. Tryptanthrin, a potent biofilm inhibitor against toxigenic Vibrio cholerae, modulating the global quorum sensing regulator,LuxO. Biofouling. 35(10):1093–1103. 18. Merin.P, Lekshmi.N, Vasanthakumary A R, Iype Joseph, Sabu Thomas. 2019. Genome sequence of a multidrug-resistant Klebsiella pneumoniae ST78 with high colistin resistance isolated from a patient in India. Journal of Global Antimicrobial Resistance. 17: 187–188. 19. Karthika S, Joby John, Megha PR, S.George & Sabu Thomas. 2018. Metataxonomic approach to decipher the polymicrobial burden in diabetic foot ulcer and its biofilm mode of infection. International Wound Journal. 15:473–481. 20. Jose D, Lekshmi N, Goel AK, Kumar RA, Thomas S. 2017. Development of a Novel Herbal Formulation to Inhibit Biofilm Formation in Toxigenic Vibrio cholerae. J Food Prot. 80(11):1933-1940. 21. Dharmaprakash Akhilandeswarre, Mutt Eshita, Jaleel Abdul, Ramanathan Sowdhamini and Sabu Thomas. 2014. Proteome profile of pandemic Vibrio parahaemolyticus SC192 strain during planktonic and biofilm condition. Biofouling: The Journal of Bioadhesion and Biofilm 1Research. 30(6):7292-739. 22. Augustine N, Goel AK, Sivakumar KC, Kumar RA, Thomas S. 2014. Resveratrol–a potential inhibitor of biofilm formation in Vibrio cholerae. Phytomedicine. 21(3):286-9. 23. Praveen Kumar and Sabu Thomas. 2011. Presence of qnrVC3 gene cassette in SXT and class1 integrons of Vibrio cholerae. International Journal of Antimicrobial Agents. 37(3):280-1. 24. Nimmy Augustine, Praveen Kumar and Sabu Thomas. 2010. Inhibition of Vibrio cholerae biofilm by AiiA enzyme produced from Bacillus spp. Archives of Microbiology. 192 (12): 1019-1022. 25. Praveen Kumar and Sabu Thomas. 2009. Presence of dfr6 gene cassette in superintegron of non-O1/non-O139 strain of Vibrio cholerae. Antimicrob Agents Chemother. 53:4959–4960. Books Edited Human Microbiome: Clinical Implications and Therapeutic Interventions, 2022. Ed. Sabu Thomas. Springer Singapore. https://link.springer.com/book/10.1007/978-981-16-7672-7 Emerging Concepts in Bacterial Biofilms: Molecular Mechanisms and Control Strategies, 2020. ( Eds. Sabu Thomas). Cambridge Scholars Publisher, UK. https://books.google.co.in/books?id=hEbDywEACAAJ Antimicrobial Resistance: Global Challenges and Future Interventions, 2020. Ed.Sabu Thomas. Springer Nature Singapore Pte Ltd. https://www.springer.com/in/book/9789811536571
Dr.Sabu Thomas
Dr.Sabu Thomas Director director.coem@kerala.gov.in Dr. Sabu Thomas has 28 years of research experience in environmental/clinical bacteriology and molecular microbiology as Faculty Scientist and Principal Investigator in Rajiv Gandhi Centre for Biotechnology under the Dept. of Biotechnology, Government of India. The major research focuses are molecular biology of bacterial pathogens of gastrointestinal tract & chronic wound infections, antimicrobial resistance (AMR), biofilm and human microbiome. He has to his credit 95 research publications in national/international journals of repute, 15 book chapters, edited 3 academic books (Human Microbiome, Antimicrobial Resistance, Bacterial Biofilm) published by Springer Nature and Cambridge Scholars Publishing group, UK. Research includes strategies to control bacterial infections and AMR including biofilm inhibition, probiotic development, drug repurposing and combinatorial therapy. Another major focus is on human gut microbiome for the development of probiotics to control multi-drug-resistant bacterial infections and gut metagenome mining for human wellbeing. Dr.Thomas was a member in the Second Indian Arctic Expedition team to study Polar microbiome and bioprospecting potential of microbes in the Arctic at 79o North and contributed substantially to the Polar Science research in India. As a Member of Global Task Force of World Health Organization (WHO), was instrumental in preparing a road map to control cholera by 2030. Currently, he is a Task Force Member in Indian Council of Medical Research, Govt. of India, Kerala State Nodal Officer in intersectoral AMR research, Expert Member in Kerala Biotechnology Commission and Member of several scientific committees of the prestigious institutes and Subject Expert in selection committees, Syllabus modification of Universities/R&D Institutes. He has received the Fellow Award in Medical Biotechnology of Society for Applied Biotechnology, Fellow Award (FAS) of the Kerala Academy of Sciences and Royal Society of Biology, London. He was honoured with the Best Scientist Catholicate award in 2022. Currently Dr. Thomas is the Director of the Centre of Excellence in Microbiome (CoEM), a new initiative of the Govt. of Kerala.
Research
Startup Support
Centre of Excellence in Microbiome (CoEM), a premier institution working in the field of microbiome, is initiated by the Govt. of Kerala under the aegis of KSCSTE. The major focus of CoEM is to create a strong knowledge base in the area of microbiome and to disseminate the knowledge for the development of products, technologies and measurable outcomes for the benefit of society.Alongside its scientific mandate, CoEM plays a catalytic role in fostering a vibrant startup ecosystem in the microbiome sector.Our vision is to support innovators, student teams, and early-stage companies in developing impactful, market-ready microbiome-based solutions. To foster the vision, Centre of Excellence in Microbiome has envisaged multiple programs that ultimately handhold aspiring innovators to accomplish their goals. MICROBIOME STARTUP SUPPORTING PROGRAM PURPOSE AND PROCESS CoEM extends structured incubation support to selected microbiome-based startups, with a focus on transforming innovative concepts into market-ready products. Startups at the Proof-of-Concept stage may apply by submitting an application as per format, outlining their profile, required support, and a basic workplan with achievable milestones in a 11-month period. To safeguard intellectual property, applicants are advised to sign a Non-Disclosure Agreement (NDA). Applications will undergo committee evaluation, following which selected firms will be invited for a discussion. Inducted teams may start with a three-month pre-incubation program upon payment of a nominal bench fee (see payment options below). Performance during this phase will be closely monitored and evaluated by CoEM. Subsequent extension of support will be contingent on evaluation report. Startups inducted to CoEM will also benefit from industry-connect initiatives, enabling direct interaction with leading industrial partners. This provides them with valuable exposure to current industrial challenges, emerging opportunities, and sector-specific requirements in the microbiome domain, thereby aligning their product development with market relevance. WHAT WE OFFER FULL FLEDGED LAB FACILITIES IN PLUG AND PLAY MODE ADVANCED EQUIPMENT FACILITY AMBIENT CO-WORKING SPACE EXPERT SCIENTIFIC MENTORING, IF REQUIRED AUDIO-VISUALLY EQUIPPED MINI SEMINAR HALL WIFI CONNECTIVITY CONDUCIVE ENVIRONMENT FOR MICROBOIME BASED STARTUPS PAYMENT PACKAGES MONTHLY RENT FOR SITTING SPACE: Rs. 2000/- PACKAGE FOR BASIC LAB FACILITY: Rs. 8000/- pm Basic lab package includes the usage* of: Microbial culture facility Basic lab equipments Minimum storage space in -20 and -80 deep freezers Seminar hall of 25 pax capacity (3 meetings per month) Scientific mentoring support** (one meeting per month) Entry cards Wifi access THREE-MONTHS PRE-INCUBATION PACKAGE: Rs. 6000/- per month. This include Rs. 2000 as sitting space rent and Rs. 4000 as basic lab package. *Shared facility; Pre-booking is mandatory ** If required and subjected to NDA ACCESS TO ADVANCED EQUIPMENTS* This includes the usage of: PCR Animal cell culture facility Phase Contrast microscope Gel documentation unit Inverted microscope Lyophiliser Multi-mode reader Anaerobic Culture Facility Support firms to utilise facilities such as Genomics, Metagenomics and advanced analysis, Proteomics, Metabolomics and advanced imaging services through outsourcing. The Microbiome Commercialisation Programme by the Centre of Excellence in Microbiome is a PhD-led translational initiative designed to support researchers in transforming microbiome-based doctoral research into commercially viable products and technologies. The programme focuses on bridging academia and entrepreneurship by providing structured mentorship, startup incubation support, networking opportunities, and exposure to intellectual property and market readiness pathways. It encourages innovative, application-driven projects across human, agricultural, environmental, aquatic, and veterinary microbiome domains with strong translational potential. Through this initiative, researchers are empowered to take their work beyond publications toward scalable, industry-relevant microbiome solutions. For more details, contact us *On payment basis; Pre-booking is mandatory; Use of advanced equipments will be supported/supervised by staff of CoEM Connect us at Ph. 8138999099 Email: coemkscste@gmail.com
Services
Training
As part of its commitment to human resource development, the Centre of Excellence in Microbiome (CoEM) offers structured mentoring and training opportunities for students at the MSc, BSc, B.Tech, M.Phil, and M.Tech levels across diverse life science disciplines. Our Skill Development Training Programmes include dissertation work, short- and long-term project assignments, and guided initiations into lab-scale microbiome-based product development. These programmes span areas such as Microbiology, Molecular Biology, Microbiome Analysis, and allied domains. While these trainings meet the academic requirements of many postgraduate students, CoEM’s broader objective is to provide participants with meaningful exposure to scalable microbiome-based solutions for real-world challenges. Trainees benefit from hands-on sessions, expert interactions, access to research facilities, and visits to relevant industries. Programme Duration: Projects and dissertation work may range from 1 to 6 months, depending on the nature of the assignment and availability. Fee Structure: A service fee is collected from trainees to cover training and facility usage costs. The fee may be paid in full or in two instalments. Sl. No Duration of Project Fee (INR) 1 1 Month 10 000/- 2 3 Months 20 000/- 3 4 Months 25 000/- 4 5 Months 30 000/- 5 6 Months 35 000/- Application Window: Applications are accepted throughout the year. However, admission to the programme is subject to the availability of slots in the respective laboratories. Important Note: Short-term trainees typically contribute to ongoing research activities in the host laboratory. They will not be eligible for Intellectual Property Rights (IPR), authorship in publications, or participation in conferences/seminars/presentations arising from the laboratory’s research outputs. Any violation of these guidelines will be dealt with strictly. For further information, please contact the Academic Affairs Department at:coemkscste@gmail.com
Services
Consultancy
As part of its industrial connectivity and translational research initiatives, the Centre of Excellence in Microbiome (CoEM) has established industry-linked consultancy programmes to support microbiome-based product and process development. Interested industries can submit an Expression of Interest (EoI), which is evaluated by internal and external expert committees. Following the necessary documentation and approvals, a detailed project report and budget are prepared for mutual agreement. This initiative has generated significant interest among industries within and outside the state, with several collaborative projects currently in the pipeline.
