Viral communities in millipede guts: Insights into the diversity and potential role in modulating the microbiome

Millipedes are important detritivores harbouring a diverse microbiome. Previous research focused on bacterial and archaeal diversity, while the virome remained neglected. We elucidated the DNA and RNA viral diversity in the hindguts of two model millipede species with distinct microbiomes: the tropi...

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Bibliographic Details
Published in:Environmental microbiology 2024-02, Vol.26 (2), p.e16586-n/a
Main Authors: Nweze, Julius Eyiuche, Schweichhart, Johannes Sergej, Angel, Roey
Format: Article
Language:English
Subjects:
Amino acids
Biosynthesis
Chitin
CRISPR
Deoxyribonucleic acid
Detritivores
DNA
DNA viruses
DNA Viruses - genetics
Gastrointestinal Microbiome - genetics
Gene editing
Genes
Genomes
Metabolism
Metagenomics
Microbiomes
Microbiota - genetics
Plant viruses
Ribonucleic acid
RNA
RNA viruses
RNA Viruses - genetics
Sulphur
Viruses
Viruses - genetics
Vitamins
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Summary:Millipedes are important detritivores harbouring a diverse microbiome. Previous research focused on bacterial and archaeal diversity, while the virome remained neglected. We elucidated the DNA and RNA viral diversity in the hindguts of two model millipede species with distinct microbiomes: the tropical Epibolus pulchripes (methanogenic, dominated by Bacillota) and the temperate Glomeris connexa (non‐methanogenic, dominated by Pseudomonadota). Based on metagenomic and metatranscriptomic assembled viral genomes, 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 that modulate chitin degradation, vitamins and amino acid biosynthesis and sulphur metabolism were also detected. Lastly, we found low virus‐to‐microbe‐ratios and a prevalence of lysogenic viruses, supporting a Piggyback‐the‐Winner dynamic in both hosts. Relative abundance of the metagenome‐assembled viral genomes (bottom arch) identified in the hindgut metagenomes and metatranscriptomes of Epibolus pulchripes and Glomeris connexa. The top arch shows the coverage of each viral phylum mapped to the identified metagenome‐assembled viral genomes in transcripts per million.
ISSN:1462-2912
1462-2920
DOI:10.1111/1462-2920.16586