Bacterial 16s rDNA diversity in the gut of Eisenia fetida revealed by metagenomics and high-throughput sequencing technology

Earthworms and microorganisms vermicompost organic waste. The microbial community inhabiting the gut of earthworms is a key factor affecting vermicomposting. In this study, the structural and functional genes of the microbial population in various functional areas of the earthworm gut were investigated by high-throughput sequencing and metagenomic sequencing. Eisenia fetida, which is often cultured by dewatered sludge, was selected as the test worm species. The results of high-throughput sequencing showed that both the Shannon index and Simpson index of the bacterial population were the highest in the stomach and the lowest in the gizzard of E. fetida. The beta diversity index of bacteria in the gizzard, stomach, and hindgut of earthworms was significantly different. Metagenomic analysis revealed that Actinobacteria (22.10%), Proteobacteria (13.60%), and Chloroflexi (7.58%) were dominant in the hindgut of earthworms. For the dominant bacteria genus, the genera Candidatus Microthrix had the highest abundance in the hindgut of earthworms, followed by Caldilinea and Candidatus Nephrothrix. In addition, denitrification module genes were enriched in the hindgut of earthworm, whereas the abundance of nitrification genes was extremely low. Compared with high-throughput sequencing, metagenomic sequencing is more suitable for analyzing the gut microorganisms of earthworms.