Comparative shotgun metagenomic data of the silkworm Bombyx mori gut microbiome

Abstract

Lepidoptera (butterflies and moths) is a major insect order including important pollinators and agricultural pests, however their microbiomes are little studied. Here, using next-generation sequencing (NGS)-based shotgun metagenomics, we characterize both the biodiversity and functional potential of gut microbiota of a lepidopteran model insect, the silkworm Bombyx mori. Two metagenomes, including the standard inbred strain Dazao (P50) and an improved hybrid strain Qiufeng × Baiyu (QB) widely used in commercial silk production, were generated, containing 45,505,084 and 69,127,002 raw reads, respectively. Taxonomic analysis revealed that a total of 663 bacterial species were identified in P50 silkworms, while 322 unique species in QB silkworms. Notably, Enterobacter, Acinetobacter and Enterococcus were dominated in both strains. The further functional annotation was performed by both BlastP and MG-RAST against various databases including Nr, COG, KEGG, CAZy and SignalP, which revealed >5 × 10⁶ protein-coding genes. These datasets not only provide first insights into all bacterial genes in silkworm guts, but also help to generate hypotheses for subsequently testing functional traits of gut microbiota in an important insect group.

Figure 1. Silkworm (Bombyx mori) strains used for this study and overview of the experimental design.

(a) The hybrid QB silkworm has a higher growth rate than P50. (b) Cocoon size and shape of P50 (yellow) and QB (white). (c) Workflow used to process silkworm gut samples to generate metagenomes. (d) Length distributions of filtered metagenome sequencing reads. (e) The functional gene rarefaction curve for each strain. (f) The taxonomical diversity rarefaction curve for each strain.

Figure 2. Composition of metabolism category in COG.

BlastP (denoted with circle symbols) and MG-RAST (denoted with triangle symbols) methods are used respectively to query against COG database. Best hits of two strains are shown in the bar plot in the upper right panel.

Figure 3. Species abundance and phylogenetic relationship of gut bacteria between P50 and QB.

The phylogenetic tree is shown at the genus level, colored by the phylum. Bacterial abundance is indicated in outer ring with shape plot (P50, blue circle; QB, red circle). The size of circle represents sequence log10 reads per genus.