Background Microorganisms living in insect gut plays a crucial role in the adaptation, growth and development of the insect hosts. The identification and molecular analysis of insect gut microbes will enable us to develop novel strategies for industrial product development, effective utilization of by products and facilitate us with the best pest management practices. In our present study, we employed a culture independent metagenomic approach in conjunction with metaproteomic profiling to enumerate the gut microbes in pure races and cross breeds of silkworm, Bombyx mori L.Results The phylogenetic analysis showed that the gut microflora was majorly grouped into four bacterial classes: Gamma Proteobacteria, Actinobacteria, Cocci and Bacilli. Two novel proteins in both silkworm races were identified and an additional three proteins were found to be differentially expressed between the races.Conclusions Silkworm undergoes radical morphological variations upon metamorphosis and a key challenge in studying gut microflora is the ability to access different genomes and the corresponding protein profiles. The results presented in this study may help to bridge the gap between the unknowns of silkworm gut microbiota and their importance in the silkworm gut ecosystem.

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