Research

Why?

The purpose of our lab and the work we do is to make discoveries and solve problems that will benefit and / or be of value to all life in whatever small way possible. We work in a closely knit, inclusive team with undying passion for the science we pursue and a strong work ethic.

What do we do?

The Microbial Physiology Group has four major verticals:

Genomics to monitor virulence and antimicrobial resistance in Klebsiella pneumoniae 

We study the hospital-acquired pathogen Klebsiella pneumoniae (Kpn). Kpn was recently declared as a priority pathogen by the WHO and the Govt. of India due to increasing levels of virulence and antimicrobial resistance, which make it a formidable pathogen to treat. Some strains of Kpn have become hypervirulent due to the acquisition of virulence factors and can now cause infections in the community. Worryingly, genes responsible for hypervirulence and antimicrobial resistance can be readily transmitted and have started emerging together in some strains making them both hypervirulent and highly drug resistant. Such strains can quickly become serious threats to public health as they can infect healthy individuals in the community and are difficult to treat using existing antibiotics. In this context, our lab sequences and studies the genomes of hospital / ICU isolates of Kpn in collaboration with fantastic clinicians in the Department of Microbiology in AIIMS Jodhpur.

• We have showed that an Indian Kpn strain from Jodhpur, P34 can become hypermucoviscous (a type of virulence factor that enables cells to interact poorly with immunce cells, leading to their protection within the body) independent of rmpD, the only known genetic determinant of hypermucoviscosity.

• We used genomics to understand the mechanism by which a rare sequence type 16 strain of Kpn evolved resistance to the last-resort antibiotic colistin within the ICU of a tertiary care hospital in Jodhpur.

• We profiled the prevalence of virulence and antimicrobial resistance in a collection of 5300 global K. pneumoniae isolates, including several of outbreak isolates we obtained from AIIMS Jodhpur, to identify region-specific sequence, capsule and o-antigen types. In addition to showing what virulence factors and antimicrobial resistance factors are relevant in Indian settings, we also identified an endemic sequence type 231 isolate of K. pneumoniae, R65. Most model strains of K. pneumoniae pathogenesis studies use strains of sequence types that are prevalent in the global north . The strain R65 is currently being developed as a model to study the virulence and pathogenesis of K. pneumoniae so that the findings will be relevant to the Indian context.

Virulence regulation in Klebsiella pneumoniae and development of anti-virulence strategies

Klebsiella pneumoniae encodes several virulence factors that enable it to successfully cause disease. Some major virulence factors of K. pneumoniae that we are studying are:

• Hypermucoviscosity: decreases interaction with the host immune cells and prevent phagocytosis of the bacteria on detection. We created a library of around 21000 transposon insertion mutants of our non-rmpD, but hypermucoviscous strain P34. We have now identified some genetic loci in this strain, which we believe are contributing to this unique phenomenon. We are now performing genetic experiments to confirm the link between these loci and this virulence phenomenon.

• Capsular polysaccharides: conceals K. pneumoniae from the human immune system and offers protection from serum-mediated killing along with Lipopolysaccharides, which also protect the cell from antimicrobial peptides. In our collaborative genomic surveillance with AIIMS Jodhpur clinicians, we identified a strain of K. pneumoniae BC135, which does not produce sufficient capsular polysaccharides, but is still extremely resistant to the killing effects of human serum. We have profiled the transcriptome of this isolate on exposure to human serum and have identified differentially expressed small RNAs and protein-coding genes that are induced upon serum exposure. We are now performing genetic experiments to assess if the differentially expressed genes are necessary for serum tolerance in this unusual strain.

• Siderophores: scavenge the limiting nutrient iron from the host body for use by the bacteria. To simulate the iron-limiting conditions experienced by the bacteria during human infection, we profiled the transcriptional response of our India-endemic ST231 K. pneumoniae model under iron starvation conditions. We found several small RNAs and protein-coding genes that appear to be involved in iron starvation stress response. We are now interrogating differentially expressed loci to characterize their role in obtaining iron for the pathogen. 

Metagenomics-guided bioprospecting of products and processes

IIT Jodhpur is located in the colorful state of Rajasthan and on the frontiers of great Indian Thar desert. Life in the desert is difficult due to extreme aridity, heat, salt stress, UV radiation etc. Microbes in such environments are adapted for survival in such harsh conditions. However, wherever resources are abundant, microbes need to compete with each other to grow and proliferate. Biological soil crusts / biocrusts are unique microbial communities that act as ecological engineers in the desert, transforming the sandy, loose, nutrient-poor soils into crusted, relatively nutrient-rich soils that are more suitable for other life forms to grow. As part of the Thar DESIGNS (Desert EcoSystem Innovations Guided by Nature and Selection) initiative of  the Jodhpur City Knowledge and Innovation Cluster, we have:

• Applied Oxford Nanopore sequencing-based metagenomic methods to profile the microbes inhabiting a few of the biocrusts of the Thar desert. This survey have provided us with key insights into the assembly of microbes in biocrusts of the Thar region and the functions these microbes perform within such elegant communities that thrive under the harshest conditions.

• Identified major inhabitants of the Thar biocrusts. We then used our metagenomic dataset as a guide to direct bioprospecting efforts for relevant bioactive compounds from these microbial communities. Currently our efforts have led to the identification of several leads with antimicrobial activity against extensively drug-resistant bacteria. We are currently characterizing the mechanism of action of these lead molecules and their suitability as potential therapeutics.

Understanding the response of the human gut microbial community to exposures

The human gut microbiota is a fascinating organ that performs various key functions for the host, not limited to nutrient metabolism, immunomodulation, providing resistance to pathogens, vitamin synthesis etc. Naturally, it's dysbiosis has been implicated in various states of disease. As the gut microbiota is exposed to our diet and anything else that we consume, it can also be easily influenced by these exposures. For example, any changes to our diet or medication we consume on a short or long term can impact the gut microbiota by changing its composition and thereby altering its functions. We are currently pursuing two interesting problems in this domain:

• Response of the India gut microbiome to the antidiabetic Metformin: India was home to over 79 million diabetics in 2021 and the number is projected to increase to around 124 million in 2045. Naturally, Indians also consume a wide variety of antidiabetic medication, the most preferred, firstline therapeutic among them being metformin. Metformin is also prescribed for obesity, PCOD and is sometimes also considered an anti-ageing agent. We asked the question if exposure of a person's gut microbiome to metformin could influence the gut microbiota composition and functions. Most of what is known in this area is known from western subjects, who have very different gut microbiota compared to Indians.

  • • In partnership with our collaborators from AIIMS Jodhpur, we have comprehensively profiled the gut microbiota composition, its functions and its metabolites before and after exposure to metformin in a small group of treatment-naive Indian subjects. We are currently elucidating the personalized response of the gut microbiota of these individuals to metformin by integrating these data layers.

    • As part of this pilot project, we generated shotgun metagenomic data for a subset of our subjects from where we have recovered and are characterizing several metagenome assembled genomes of resident microbes of the Indian gut.

• Urbanization and food system-driven changes in the gut microbiota of Indian tribal populations: India is home to around 700 indigenous tribal communities. These communities are the perhaps the last remaining  traditional ecological knowledge banks and have access to rich and diverse food systems. The gut microbiota of various tribal communities across the world, including a few in India have been investigated to ascertain microbes associated with their nature-aligned lifestyle. As would be expected,  the non-urbanized gut microbiota of indigenous communities was highly diverse and starkly different in comparison with urban-dwelling, industrialized communities, which were poor in diversity and enriched for microbes associated with metabolic diseases. The rich and diverse food systems of Indian tribal communities are facing continuous threats from factors like climate, socioeconomic changes and demographic changes etc. The CARISMMA food systems study is aimed at ChAracterizing, RevIving, Supporting, Monitoring and MAnaging Sustainable Food Systems to address malnutrition in indigenous tribal communities of India.

  • • As part of this multi-institutional and multi-national team science study, our group will temporally profile the gut microbiota of selected Indian tribal communities in Madhya Pradesh, Meghalaya and Odisha to find signatures in the gut microbiota, which may be associated with changes in the dietary patterns and by extension with specific drivers of food system changes