Isolation, identification, and genomic analysis of Gilliamella sp. G0441 from gut microbiota of Apis cerana cerana

The gut microbiota of honey bees consists of a specialized group of bacteria that are essential for host nutrition metabolism, immune regulation, and detoxification. In this study, a bacterial strain designated G0441 was isolated from the intestinal tract of worker bees of Apis cerana cerana. This strain was subsequently identified and its genome was analyzed. The colonies of G0441 exhibited a circular morphology, measuring approximately 1 mm in diameter, with a smooth and translucent surface. The G0441 grew under strict anaerobic conditions. The result by 16S rRNA gene sequence analysis showed that G0441 strain belonged to γ-Proteobacteria, the family Orbaceae with the closest relatives being members of the Gilliamella genus. The genome of G0441 was 2.6 Mb in size and had a total GC content ratio of 35%. It encoded a total of 2350 genes, including 2299 protein-coding genes, which accounted for 85% of the genome's total length. Function clarified annotation of the protein-coding genes using the Cluster of Orthologous Groups (COG) database showed that the following function clarifications were enriched significantly, including amino acid transport and metabolism, carbohydrate transport and metabolism, translation-ribosomal structure and biogenesis, transcription, replication-recombination-repair, and cell wall/membrane/envelope biogenesis. Additionally, genome annotation of G0441 identified 159 virulence factors, 77 antibiotic resistance genes, 22 carbohydrate-active enzymes, 255 transporter proteins, 565 transmembrane protein genes, 201 signal peptide protein genes, and multiple lipoproteins genes. Pan-genome analysis showed that among six closely related strains, there were 145 core genes and 7190 strain-specific genes, with G0441 containing 221 specific genes. Phylogenetic analysis, based on both core single-copy genes and whole-genome SNPs, consistently demonstrated that G0441 was most closely related to the Gilliamella sp. ESL0441 strain. This study successfully isolated and identified a strain of Gilliamella bacteria, designated as Gilliamella sp. G0441, from gut microbiota of A. cerana. The genomic data obtained in this study provide a foundation for further investigation of Gilliamella sp. G0441 related functions.