Research page Shantanu Shukla MRDG IISc
Our latest research
We characterize the microbiome of the Indian lac insect Kerria lacca, identifying two major endosymbionts of the insect.
Using 16S rRNA and 18S rRNA amplicon sequencing, we identify a Wolbachia and a novel yeast-like symbiont (YLS) related to the Ophiocordyceps fungus in the insect. Using a combination of approaches involving whole genome sequencing, metatranscriptomics and fluorescence microscopy, the study shows that the tyrosine side chain and the polyketide backbone of the lac pigment are encoded only in the genome of the YLS, not in the genomes of the host insect or the Wolbachia bacterium. Genomic and transcriptomic analysis show that the YLS genome also codes for essential amino acids and vitamins missing from the insects diet, thus allowing it to adapt to diet consisting exclusively of plant sap.
. The yeast-like symbiont in the insect hemolymph and oocyte.
We use long read Oxford Nanopore Technology for whole-genome sequencing of the host and the endosymbionts.
Genomes of the following organisms have now been submitted at NCBI
1. The lac insect Kerria lacca (GCA_051170995.1)
2. The Yeast-like symbiont “KLYLS” (GCA_051170975.1)
3. The Wolbachia endosymbiont of K. lacca
The full publication and all details can be accessed here.
Research
We use a multidisciplinary approach to elucidate the molecular and cellular nuts-and-bolts of insect-microbiome long term associations in order to gain a better understanding of how and why the interacting organisms show the traits that we observe. The lab asks questions at multiple levels ranging from molecules to organisms and communities.
The research primarily uses methods in
1. Bioinformatics (whole genome sequence analysis, metagenomics, amplicon sequencing, metatranscriptomics) for studying insect microbiome interactions
2. Microscopy: Epifluorescence and confocal microscopy to visualize microbial transmission and tissue-specific localization of microbes.
3. Molecular biology to characterize gene density and expression using PCR, qPCR and RT-PCR as well as droplet digital PCR.
4. Microbial ecology to characterize microbial communities using culture dependent and culture independent methods.
5. Insect physiology and ecology to study the role of microbial symbionts in digestion, detoxification, nutritional supplementation and production of primary and secondary metabolites.
We aim to use our understanding of fundamental aspects of insect-microbiome associations to develop applications in health and agriculture.

Illustration showing potential applications of studying insect-microbe associations. For more details see the original paper in Applied Microbial Biotechnology.
Why insects?
Insects are an extraordinarily successful group of animals that can feed on a wide range of diets. From feeding on fungi, detritus, leaves, plant sap and pollen, animal blood and feathers, to carcasses – insects can successfuly exploit challenging and potentially noxious diets. Despite the widespread recognition of their ecological success, our understanding of the molecular basis of their dietary triumphs is poor. Understanding the mechanistic basis of how insects achieve this extraordinary task is itself a major motivation.
Insects are also incredibly important. EO Wilson describes insects (and invertebrates) as “the little things that run the world”. They get very little credit for keeping alive food webs, for engineering important ecological processes, for shaping terrestrial biomass dynamics, and for pollinating plants which ensures the success of many of our crops. Thus, understanding insect nutritional physiology and ecology has both fundamental and applied significance.
Insects show highly complex and intricate associations with microorganisms. In some species, these associations are obligatory – insects cannot survive without their symbionts and the microbes have lost their free living ability outside their insect hosts. Such interdependence has ramifications on the biology of both the interacting partners at the genomic, morphological, behavioral and ecological levels. Insect-microbe interactions thus offer a fascinating chance to study the ancient phenomenon of symbiosis that has altered the very way life has evolved on the planet.
Their dietary specializations across life stages, their growth in microbe-rich habitats, their diverse adaptations to abiotic factors and their remarkable diversity makes insects an excellent model system to ask interesting questions in physiology and ecology.