Viral Communities in Millipede Guts: Insights into Diversity and the Potential Role in Modulating the Microbiome

Abstract Millipedes are important detritivores harbouring a diverse microbiome. Previous research focused on the microbiome, while the virome remains neglected. We elucidated the viral diversity in the hindguts of two millipede model species with distinct microbiomes: the tropical Epibolus pulchripes and the temperate Glomeris connexa. Based on metagenomic and metatranscriptomic assembled viral genomes (MAVGs), the viral communities differed markedly and preferentially infected the most abundant prokaryotic taxa. The majority of DNA viruses were Caudoviricetes (dsDNA), Cirlivirales (ssDNA), and Microviridae (ssDNA), while RNA viruses consisted of Leviviricetes (ssRNA), Potyviridae (ssRNA) and Eukaryotic viruses. A high abundance of subtypes I-C, I-B and II-C CRISPR-Cas systems was found, primarily from Pseudomonadota, Bacteroidota and Bacillota. In addition, auxiliary metabolic genes (AMGs) that modulate chitin degradation, vitamins and amino acid biosynthesis, and sulfur metabolism were also detected. Lastly, we found low virus-to-microbe-ratios (mVMR) and a prevalence of lysogenic viruses, supporting a Piggyback-the-Winner dynamic in both hosts.