Metagenomic Insights into the Gut Microbiota of Eudrilus eugeniae (Kinberg) and Its Potential Roles in Agroecosystem

Gut microbiomes, a consortium of microorganisms that live in the animal gut, are highly engineered microbial communities. It makes a major contribution to digestive health, metabolism management, and the development of a strong immune system in the host. The present study was taken up to answer the long-running question about the existence of truly indigenous microflora of the epigeic earthworm gut. This is due to the general difficulties of culturing many of the microorganisms found in soil or earthworms’ gut. Keeping this fact in a view, the metagenomics approach using 16S rRNA marker gene incorporated with amplicon-based sequencing was used to explore microbiota of commercially overriding, diversely fed epigeic earthworm Eudrilus eugeniae (Kinberg) in three varied habitats viz., artificial soil (AS), organic agricultural farm soil (OAFS) and conventional agriculture farm soil (CAFS). There are predominant bacteria that belong to different phyla such as Proteobacteria (29.72–76.81%), Actinobacteria (11.06–34.42%), Firmicutes (6.02–19.81%), and Bacteroidetes (2.40–9.22%) present in the gut of E. eugeniae. The alpha diversity (Observed species, Chao1, ACE, Shannon, Simpson, and Fisher alpha) indices showed that OAFS had significantly higher alpha diversity than AS and CAFS groups. The core microbiota analysis showed that OAFS and AS groups had a relatively similar bacterial panel in comparison to the CAFS group. Various statistical tools i.e. MetagenomeSeq, LEfSe, and Random Forest analysis were performed and the findings demonstrated prevalence of the most significant bacterial genera; Aeromonas, Gaiella, and Burkholderia in CAFS group. Nonetheless, in AS and OAFS groups, the common existence of Anaerosporobacter and Aquihabitans were found respectively. Metagenomic functional prediction revealed that earthworms' gut microbial communities were actively involved in multiple organic and xenobiotics compound degradation-related pathways. This is the first research to use high-throughput 16S rRNA gene amplicon sequencing to show the gut microbiota of E. eugeniae in diverse agricultural systems. The findings suggest the configuration of the gut microbiota of earthworms and its potential role in the soil ecosystem depends on the microbial communities of the soil.