Research

One of the integral sources of micronutrients for human has been the gut microbiota, known to produce some of those essential micronutrients. However, behaviour of native gut microbiota in case of malnutrition has not been thoroughly investigated. So our hypothesis is whether altered abundance/composition of microbes contribute to the prevalence of deficiency of essential micronutrients? Several gut microbes may have metabolic capability for biosynthesis of some of the essential micronutrients, but they fail to do so due to lack of either one or a few genes. Such microbes can potentially be engineered or complemented in the form of pairs for in vivo or in vitro micronutrient production.

Funding: UoH-IoE

UoH researchers: Nisha; Priyansh; Amit;  Dr Pramod Rajaram (Dept of Systems Biol) 

Collaborators: Dr Anil Verma and Dr Suyash Srivastave (ICMR-NIRTH)

Relevant Publications:

• Chandel N, Patel P, Somvanshi PR, Verma AK, Thakur V. Inverse Association between Serum Vitamin B12 Level and Abundance of Potential B12-Producing Gut Microbes in Indian Children. J Nutr. 2025 Oct 13:S0022-3166(25)00640-6. https://doi.org/10.1016/j.tjnut.2025.10.021  

• Chandel N, Maile A, Shrivastava S, Verma AK, Thakur V. Establishment and perturbation of human gut microbiome: common trends and variations between Indian and global populations. Gut Microbiome. 2024;5:e8. https://doi.org/10.1017/gmb.2024.6   

• Chandel, N.,Gorremuchu, J.P., & Thakur, V. (2024). Antimicrobial resistance burden, and mechanisms of its emergence in gut microbiomes of Indian Population. Front. Microbiomes Sec. Omics Approaches Volume 3 - 2024 | https://doi.org/10.3389/frmbi.2024.1432646   

• Chandel N, Somvanshi PR, Thakur V. Characterisation of Indian gut microbiome for B-vitamin production and its comparison with Chinese cohort. British Journal of Nutrition. 2024;131(4):686-697. https://doi.org/10.1017/S0007114523002179   

Driven by the challenge of food insecurity, some global projects are already underway to develop future crops by modifying the C 3 photosynthetic pathway to C 4 type, as the latter provides higher yield/biomass with reduced inputs. The major hurdle to these efforts has been incomplete knowledge of the genomic changes needed to operate the C 4 pathway. Attempts based on gene expression studies limit only to the genes and thus miss the regulatory elements involved, and also provide list of genes too long to be implementable.

In order to discover the missing genetic components as well as to address the limitations of current approach, We would like to take an alternate approach:

 Discover genome-wide changes in the genomes of C 4 species that associate with C4 phenotype.  Obtain a comprehensive set of genetic components (regulatory elements, genes, etc.) that were recruited during establishment of C 4 features from their ancestral counterparts (C3 ).  Discover trajectory of changes in the origin of C4 trait.  Propose a module for the development of future crops with higher yields despite limited resources.

Funding: DBT-Ramalingaswami Re-entry grant; CSIR research fellowship

Researchers: Angeo Saji, Gopikrishnan

Relevant publications:

1. Saji A, Bijukumar G, Thakur V. Adaptive evolutionary changes in regulatory genes and cis-elements associated with Kranz development in monocots. BioRxiv 2024.02.22.581542; doi: https://doi.org/10.1101/2024.02.22.581542 

2. Chatterjee J, Coe RA, Acebron K, Thakur V, [….], Quick WP. Identification of a low CO2 responsive mutant from chemical mutagenesis of Setaria viridis shows that reduced carbonic anhydrase severely limits C4 photosynthesis. Journal of Experimental Botany, Volume 72, Issue 8, 2 April 2021, Pages 3122–3136 (2021), https://doi.org/10.1093/jxb/erab039

3. Danila F, Thakur V, et al. “Bundle sheath suberisation is required for C4 photosynthesis in a Setaria viridis mutant" Communications Biology 4, 254 (2021) https://doi.org/10.1038/s42003-021-01772-4 

4. Karki S, Lin H.S., Danila FR, Abu-Jamous B, Giuliani R, Emms DM, Coe RA, Covshoff S, Woodfield H, Bagunu E, Thakur V, Wanchana S, Slamet-Loedin I, Cousins AB, Hibberd JM, Kelly S, Quick WP. A role for neutral variation in the evolution of C4 photosynthesis. BioRxiv (2020) https://doi.org/10.1101/2020.05.19.104299          

5. Kelly S, Covshoff S, Thakur V, Wanchana S, Quick WP, Zhu X, Ludwig M, Bruskievich R, Sage R, Wong G, Hibberd JM (2017) Wide sampling of natural diversity identifies conserved molecular signatures of the highly  complex trait C4 photosynthesis. BioRxiv; https://doi.org/10.1101/163097 

6. Rizal G, Karki S, Thakur V, Wanchana S , Alonso-Cantabrana H,  Dionora J, Sheehy JE, Furbank R, Von Caemmerer S, Quick WP (2017) A Sorghum (Sorghum bicolor) Mutant with Altered Carbon Isotope Ratio. PLoS One 12(6): e0179567. https://doi.org/10.1371/journal.pone.0179567

7. Chatterjee J, Dionora J, Mabilangan AE, Wanchana S, Thakur V, Bandopadhyaya A, Brar DS, Quick WP (2016) The Evolutionary Context of Naturally Diverse Rice Leaf Anatomy. PLoS One 11(10): e0164532.

8. Campen JV, Yaapar M, Narawatthana S, Lehmeier C, Wanchana S, Thakur V, Kelly S, Rolfe S, Quick W, and Fleming A (2016) Combined Chlorophyll Fluorescence and Transcriptomic Analysis Identifies the P3/P4 Transition as a Key stage in Rice Leaf Photosynthetic Development. Plant Physiology 170(3): 1655. 

9. Rizal G*, Thakur V*, Dionora J*, Karki S, Wanchana S, Acebron K, Larazo N, Garcia R, Mabilangan A, Montecillo F, Danila F, Mogul R, Pablico P, Leung H, Langdale JA, Sheehy J, Kelly S, Quick, WP (2015) Two forward genetic screens for vein density mutants in sorghum converge on a cytochrome P450 gene in the brassinosteroid pathway. The Plant Journal 84(2):257. (Cover article)  (*: equal author)

10. Rizal G, Karki S, Thakur V, Chatterjee J, Coe RA, Wanchana S, Quick WP (2012) Towards a C4 rice. Asian Journal of Cell Biology 7: 13-31. (Invited review)

Book Chapter:

11. Biswal AK, Singh AK, Thakur V, Mangrauthia SK, and Ponnuswamy R (2017) Breeding Strategies to Convert C3 into C4 Plants. In Advanced Molecular Plant Breeding, ed by DN Bhardwaj, Apple Acad. Press, USA.

Given the decline in populations of several vulture species in the Indian subcontinent due to factors such as Diclofenac toxicity, habitat loss, and food scarcity, conservation efforts are now being initiated. To support policymakers in developing effective conservation plans, insight into this species' genetic diversity will be immensely useful. Research works on various aspects of Indian vultures have earlier been reported mainly by researchers from the Bombay Natural History Society (India) and the Wildlife Institute of India, often in close collaboration with Prof. Rhys Green from Cambridge University, which also included a population genetic study done a decade back involving only 9 microsatellite markers (Ishtiaq et al., 2015).

Our research so far uniquely captures the genomic landscape of a few threatened vulture taxa by employing SNP-based marker analysis for the first time, attempting to uncover the patterns of genetic diversity and population dynamics. It was an outcome of a collaborative effort with a Vulture Breeding Center and a vulture conservation reserve for sample collection; and to avoid any threat to the birds, instead of using the blood samples, we explored a non-invasive alternative of using molted feathers as a DNA source, though it came at a cost of losing over two-thirds of the samples due to poor yield/quality.  

Funding: UoH-IoE-iPDF

UoH Researchers: Manas Shukla; Dr Shashi Kiran (Dept of Biochemistry)

Collaborators: Nehru Zoological Park, Hyderabad; Dr Daulal Bohra, Podar College, Jhunjhunu, Rajasthan

Relevant publications:

1. Shukla M, Bohra DL, Rao B, Narayan L, Kiran S, Thakur V. Genomic Footprints of Bottlenecks, Isolation, and Inbreeding: A Case Study of Two Vulture Cohorts in India. BioRxiv 2026.04.30.721611; https://doi.org/10.64898/2026.04.30.721611

The gut microbiome is not just a bystander—it may be an early trigger, propagator, and modulator of PD pathology. Understanding its role opens promising avenues for early diagnosis, risk stratification, and even microbiome-targeted therapies for PD.

Clinical collaborators: Dr Vishnu Vardhan Reddy & Dr Lalitha (Renova Hospital)

UoH Researchers: Shayamolima Gogai; Dr NV Prasuja and Dr Pramod Rajaram (Dept of Systems Biol)

Antimicrobial resistance (AMR) is a mounting global concern, driven not only by the misuse of antibiotics but also by complex environmental pressures. This study conducted in 2024 presents a comprehensive genomic surveillance of AMR genes across eight lakes in Hyderabad, India, four each were categorized as less polluted and polluted. Using the AMR++ pipeline for metagenomic analysis, a total of 579 AMR genes were identified, spanning 39 resistance classes. This marks a substantial increase from previous studies in the region, including a 2019 study that reported 388 AMR genes across 25 classes from four lakes.

Funding: UoH-IoE-iPDF

UoH Researchers: Sura Suma

Several microbial strains or isolates, which were characterized for having a few plant growth-promoting features, have been further examined for the underlying genes or pathways, which include a couple of studies by us on multiple isolates from Streptomyces and Amycolatopsis genera.

Funding: DBT-Ramalingaswami Re-entry grant

UoH researchers: Sachidanand; Angeo

Collaborators: Dr Gopalakrishnan, Dr Abhishek Rathore and Dr Rachit Saxena (ICRISAT) 

Relevant publications:

1. Nayak,  S., Gandham,  P., Rani,  T. S., Vadlamudi,  S., Ruperao,  P., Saxena,  R., Rathore,  A., Thakur,  V., & Gopalakrishnan,  S. (2026). Genome Sequencing, In Vitro Assays, and Metabolomics Reveals Biocontrol and PGP Traits of a Rhizobacterium, Streptomyces cavourensis SAI-25. Preprints. https://doi.org/10.20944/preprints202504.2632.v4

2. Gandham, P., Vadla, N., Saji, A., …, Thakur V. Genome assembly, comparative genomics, and identification of genes/pathways underlying plant growth-promoting traits of an actinobacterial strain, Amycolatopsis sp. (BCA-696). Sci Rep 14, 15934 (2024). https://doi.org/10.1038/s41598-024-66835-y  

3. Subramaniam, G., Thakur, V., Saxena, R.K. et al. Complete genome sequence of sixteen plant growth promoting Streptomyces strains. Sci Rep 10, 10294 (2020). https://doi.org/10.1038/s41598-020-67153-9