Senior Scientist
Environmental Microbiology (with special interest in High Altitude Bacteria)
+91 1894 233339, ext. 441


High Altitude Microbiology Laboratory (HAM_Lab): 

Our research focuses on exploring the microbial community from high altitude extreme environments of the Himalaya. One area has been exploring the extreme alpine regions like glacier ecosystem to understand the microbial succession and colonization patterns. Another important area has been to unravel the potential of extremophiles from Himalaya for bioprospection. Currently, with psychotropic efficient hydrolytic bacterial community we have been targeting to improve/accelerate organic waste degradation in alpine regions. Extremozymes for possible industrial applications has been another focus. Apart from bacterial community we have also been exploring the higher fungi (mushroom) of economic importance. We have begun with Lentinula edodes and currently we have developed its improved captive cultivations using local substrates and enriched it with Vitamin D.

The main focus of our lab can be summarized in the following broad themes

1. Study changes in community composition in different Himalayan glacier to understand its adaptational strategies and to reveal the response of microorganisms to environmental change.
2. Exploration of bacteria from alpine regions of Himalaya for bioprospection-organic waste management & industrial enzymes
3. Exploration of higher fungi its enrichment/fortification for value addition and analysis of its metabolites. 



Start-up Research Grant awarded byScience and Engineering Research Board (SERB) Department of Science and Technology, Government of India in November 2019

INSPIRE Faculty Award fromDepartment of Science & Technology, Government of India in July 2014

Dr. D S Kothari Postdoctoral Fellowship Award from University Grants Commission, Government of India in August 2013

DBT-Research Associateship in Biotechnology & Life Sciences from Department of Biotechnology, Ministry of Science and Technology, Government of India in May 2012



40. Khatri A, Thakur A, Lepcha A, Acharya V, Kumar R*. 2023. IHM-DB: a curated collection of metagenomics data from the Indian Himalayan Region, and an automated pipeline for 16S rRNA amplicon-based analysis (AutoQii2). Database, 2023 p.baad 039. DOI: 10.1093/database/baad039. (*Corresponding Author) [IF: 4.462]

39. Raj Y, Kumar A, Kumari S, Kumar R*, Kumar R. 2023. Comparative Genomics and Physiological Investigations Supported Multifaceted Plant Growth-Promoting Activities in Two Hypericum perforatum L.-Associated Plant Growth-Promoting Rhizobacteria for Microbe-Assisted Cultivation. Microbiology Spectrum. DOI: 10.1128/spectrum.00607-23. (*Corresponding Author) [IF: 9.03]

38. Dindhoria K, Jain R, Kumar R, Bhargava B, Kumar R*, Sanjay Kumar. 2023. Microbial community structure analysis of hypersaline niches and elucidation of their role in the biogeochemical cycling of nitrogen, sulphur, and methane. Ecological Informatics, 102023. DOI: 10.1016/j.ecoinf.2023.102023 (*Corresponding Author) [IF: 4.498]

37. Baliyan N, Maurya AK, Kumar A, Agnihotri VK, Kumar R*. 2023. Probiotics from the bovine raw milk of Lahaul valley showed cis-9, trans-11 conjugated linoleic acid isomer and antioxidant activity with food formulation ability. LWT-Food Science and Technology, 176:114553. DOI:10.1016/j.lwt.2023.114553. (*Corresponding Author) [IF: 6.056]

36. Mukhia S, Kumar A, Kumar R*. 2023. Antioxidant prodigiosin-producin cold- adapted Janthinobacterium sp. ERMR3: 09 from a glacier moraine: Genomic elucidation of cold adaptation and pigment biosynthesis. Gene, 857:147178. DOI:10.1016/j.gene.2023.147178. (*Corresponding Author) [IF: 3.913]

35. Dindhoria K, Manyapu V, Ali A, Kumar R*. 2023. Unveiling the role of emerging metagenomics for the examination of hypersaline environments. Biotechnology and Genetic Engineering Reviews. 6:1-39. DOI:10.1080/02648725.2023.2197717. (*Corresponding Author) [IF: 4.200]

34. Thakur M, Verma V, Chandel A, Kumar R, Sharma T, Kumar A, Bhardwaj S, Kumar R, Bhargava B. 2023. Lemon grass essential oil improves Gladiolus grandiflorus postharvest life by modulating water relations, microbial growth, biochemical activity, and gene expression. Scientific Reports. 14;13(1):2630. DOI:10.1038/s41598-023-28829-0.  [IF: 4.99]

33. Rathore S, Mukhia S, Kapoor S, Bhatt V, Kumar R, Kumar R. 2022. Seasonal variability in essential oil composition and biological activity of Rosmarinus officinalis L. accessions in the western Himalaya. Scientific Reports, 12.1: 3305. DOI:10.1038/s41598-022-07298. [IF: 4.99]

32. Lalthafamkimi, L, Bhau, B S, Kumar, S, Mukhia S, Kumar R., Banik D. Bhattacharyya P, 2022. Indirect organogenesis-mediated high frequency conversion of non-embryonic synthetic seeds, essential oil profiling and antibacterial activity in genetically stable plants of Patchouli. 3Biotech, 12.12: 349 (2022). DOI:10.1007/s13205-022-03302-3 [IF: 2.893]

31. Kumar A, Flèche-Matéos L, Kumar R*. Lomprez F, Fichenick F, Singh D, Grimont PA, Kumar S. 2022. Rahnella sikkimica sp. nov., a novel cold-tolerant bacterium isolated from the glacier of Sikkim Himalaya with plant growth-promoting properties. Extremophiles, 26.3:35. DOI:10.1007/s00792-022-01283-y (*Corresponding Author) [ IF: 3.035]

30. KumarA, Mukhia S. Kumar R*. 2022. Microbial community dynamics from a fast- receding glacier of Western Himalayas highlight the importance of microbes in primary succession, nutrient recycling, and xenobiotics degradation. Ecological Indicators, 144:109565. DOI:10.1016/j.ecolind.2022.109565 .(*Corresponding Author) [IF: 6.263].

29. Dindhoria, K., Kumar, S., Baliyan, N., Raphel, S., Halami, P.M. and Kumar, R*., 2022. Bacillus licheniformis MCC 2514 genome sequencing and functional annotation for providing genetic evidence for probiotic gut adhesion properties and its applicability as a bio-preservative agent. Gene, [Impact factor 3.913 ]

28. Kumari S, kumar A, Kumar R*. 2022. A cold active cellulase isolated from Exiguobacterium sibiricum K1 for the valorization of agro-residual resources. Biomass conversion and biorefinery. [Impact factor 4.05 ]

27. Borker SS, Thakur A, Khatri A and Kumar R*. 2022. Quality assessment, safety evaluation, and microbiome analysis of night-soil compost from Lahaul valley of northwestern Himalaya. Waste Management, 149, pp.42-52. [IF: 8.816]. See popular coverage on nature india and  The Indian Express  

26. Mukhia S, Kumar A, Kumari P and Kumar R*. 2022. Psychrotrophic plant beneficial bacteria from the glacial ecosystem of Sikkim Himalaya: Genomic evidence for the cold adaptation and plant growth promotion. Microbiological Research 260, p.127049. [IF: 5.07]. See popular coverage on nature india

25. Kumar A, Mukhia S, and Kumar R*. 2022. Production, characterisation, and application of exopolysaccharide extracted from a glacier bacterium Mucilaginibacter sp. ERMR7: 07. Process Biochemistry 113, 27–36. [IF: 4.88]

24. Mukhia S, Kumar A, Kumari P, Kumar R, and Kumar S. 2022. Multilocus sequence based systematics of Pseudomonas sp. from supraglacial site of Sikkim Himalaya and their adaptational strategies. Plos one. 17(1): e0261178 [IF: 3.75]

23. Rathore S, Mukhia S, Kapoor S, Bhatt V, Kumar R, and Kumar R*. (2022). Seasonal variability in essential oil composition and biological activity of Rosmarinusofficinalis L. accessions in the western Himalaya. Scientific Reports, 12(1), 1-13. [IF: 4.99]

22. Manyapu V, Kumar A, Kumar R*. 2021. Psychrophilic biomethanation for enhanced bioenergy production in cold regions. Clean Technologies and Environmental Policy 20:1-6.1. [IF: 4.7]

21. Chander R, Maurya AK, Kumar K, kumari S, kumar R and Agnihotri VK. 2022. In vitro antidiabetic and antimicrobial activity of Dracocephalum heterophyllum Benth. essential oil from different sites of North-western Himalayas India. Natural Product Research. [Impact factor 2.488]

20. Maurya AK, Baliyan N, Kumar R, Agnihotri VK, 2022. Synthesis of Sulfur Containing Analogues of Hedychenone, a Labdane Diterpenoid from Hedychium spicatum. Journal of Natural Products. [Impact factor 4.803]

19. Maurya AK, Sharma A, Mukhia S, Rani D, Kumar A, Kumar D, Kumar R, Padwad, YS and Agnihotri VK. 2022. Essential Oil Composition, In Vitro Biological Activities and Safety Evaluation of Cultivated Hedychium spicatum Seeds. Indian Journal of Pharmaceutical Sciences, DOI: 10.36468/pharmaceutical-sciences.973 84(3), pp.783-790.[IF: 0.664]

18. Dindhoria K, Kumar S, Kumar R*. 2021. Taxonomic and functional analysis of proglacial water bodies of Triloknath glacier ecosystem from North-Western Himalayas. Ecological Informatics, p.101365. [IF: 4.49] 

17. Kumar A, Mukhia S, Kumar R*. 2021. Industrial applications of cold-adapted enzymes- challenges, innovations and future perspective. 3 Biotech. 11(10), pp.1-18. doi.ogr/10.1007/s13205-021-02929-y. [IF: 2.8]

16. Kumar R, Borker SS, Thakur A, Thapa P, Kumar S, Mukhia S, Kumari A, Bhattacharya A, Kumar S. 2021. Physiological and genomic evidence supports the role of Serratiaquinivorans PKL:12 as a potential biopriming agent for the biohardening of micropropagatedPicrorhizakurroa plantlets in cold regions. Genomics. 113(3):1448-1457. [IF: 4.3]. See popular coverage on ThePrint

15. Baliyan N, Dindhoria K, Kumar A, Thakur A, Kumar R*. 2021. Comprehensive substrate-based exploration of probiotics from undistilled traditional fermented alcoholic beverage ‘Lugri’. Frontiers in Microbiology. 12: 626964. doi./10.3389/fmicb.2021.626964. [IF: 6.06]

14. Suyal DC, Joshi D, Kumar S, Bhatt P, Narayan A, Giri K, Singh M, Soni R, Kumar R, Yadav A. 2021. Himalayan Microbiomes for Agro-environmental Sustainability: Current Perspectives and Future Challenges. Microbial Ecology, pp.1-33.[IF: 4.19]

13. Thakur A, Kumari S, Borker SS, Prashant SP, Kumar R*. 2021. Solid waste management in Indian Himalayan Region: Current scenario, resource recovery, and way forward for sustainable development”. Frontiers in Energy Research. 9:609229. [IF: 3.85]

12. Mukhia S, Kumar A, Kumar R*. 2021.Generation of antioxidant peptides from soy protein isolate through psychrotrophic Chryseobacterium sp. derived alkaline broad temperature active protease. LWT-Food Science and Technology. 143:111152. doi/.org/10.1016/j.lwt.2021.111152. [IF: 6.05]

11. Mukhia S, Khatri A, Acharya V, Kumar R*. 2021. Comparative genomics and molecular adaptational analysis of Arthrobacter from Sikkim Himalaya provided insights into its survivability under multiple high-altitude stress. Genomics. 113(1) ,151-158. [IF: 4.3]

10. Kumar A, Mukhia S, Kumar N, Acharya V, Kumar S, Kumar R*. 2020. A broad temperature active lipase purified from a psychrotrophic bacterium of Sikkim Himalaya with potential application in detergent formulation. Frontiers in Bioengineering and Biotechnology. 8, p.642.[IF: 6.06]

9. Walia S, Mukhia S, Bhatt V, Kumar R, Kumar R*. 2020. Variability in chemical composition and antimicrobial activity of Tagetesminuta L. essential oil collected from different locations of Himalaya. Industrial Crops and Products. 1; 150:112449. [IF: 6.44]

8. Kumari M, Kumar R, Singh D, Bhatt S, Gupta M. 2020. Physiological and genomic characterization of an exopolysaccharide-producing Weissellacibaria CH2 from cheese of the western Himalayas. Food Bioscience. 21:100570. [IF: 5.31]

7. Khare D, Kumar R, Acharya C. 2020. Genomic and functional insights into the adaptation and survival of Chryseobacterium sp. strain PMSZPI in uranium enriched environment. Ecotoxicology and Environmental Safety. 15; 191:110217. [IF: 7.12]

6. Kumar V, Thakur V, Kumar V, Kumar R, Singh D. 2020. Genomic insights revealed physiological diversity and industrial potential for Glaciimonas sp. PCH181 isolated from Satrundi glacier in Pangi-Chamba Himalaya. Genomics. 112(1), 637-646. [IF: 4.3]

5. Kumar R, Acharya V, Mukhia S, Singh D, Kumar S. 2019. Complete genome sequence of Pseudomonas frederiksbergensis ERDD5: 01 revealed genetic bases for survivability at high altitude ecosystem and bioprospection potential. Genomics. 111(3), 492-499. [IF: 4.3]

4. Kumar R, Acharya V, Singh D, Kumar S. 2018. Strategies for high-altitude adaptation revealed from high quality draft genome of non-violacein producing Janthinobacteriumlividum ERGS5:01. Environmental Microbiome. 13(1), 1. [IF:6.36]

3. Maurya AK, Devi R, Kumar A, Koundal R, Thakur S, Sharma A, Kumar D, Kumar R, Padwad YS, Chand G and Singh B. 2018. Chemical Composition, Cytotoxic and Antibacterial Activities of Essential Oils of Cultivated Clones of Juniperuscommunis and Wild Juniperus Species. Chemistry & Biodiversity. 15(9): e180018. [IF: 2.74]

2. Borker S S, Thakur A, Kumar S, Kumari S, Kumar R, and Kumar S. 2021. Comparative genomics and physiological investigation supported safety, cold adaptation, efficient hydrolytic and plant growth-promoting potential of psychrotrophic Glutamicibacterarilaitensis LJH19, isolated from night-soil compost. BMC genomics, 22(1), 1-17. [IF: 4.547] [Citation : 6] . See popular coverage on: ThePrint

1. Singh J, Prashant S P, Kumari S, Borker S S, and Kumar R*. (2020). Conservation of the night soil composting and the importance of organic farming in high altitude regions: A review BharatiyaVaigyanikevam Audyogik Anusandhan Patrika (BVAAP). 28(2), 132-139. [CSIR Journal]


 Detailed publications with citations





PhD Students:

Srijana Mukhia (ICMR-SRF)

Shruti Sinai Borker (UGC-SRF)

Anil Kumar (DBT-SRF)

Neha Baliyan (ICMR-SRF)

Kiran Dindhoria (CSIR-SRF)

Aman Thakur (ICMR-SRF)

Aman Kumar (ICMR-SRF)

Sareeka Kumari (CSIR-SRF)

Ayush Lepcha (UGC-JRF)

Sanjeev Kumar Sharma (DST-INSPIRE Fellow)



Project Staff: Ashif Ali, Krishna Kanta Pandey, Abhishek Khatri, Avika Subba and Ritu Kaachra

Field-Assistant: Kishan Kharka and Abhishek Bhatt

Field Investigator: Jagdeep Singh

Lab Attendant: Bhunesh Kumar, Kalyan Yadev, Ramesh Dogra, Rakesh Kumar



Candidate with experience in Bioiformatics analysis of bacterial genome and metagenome may contact to join our group




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