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.

中文翻译：

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马陆肠道中的病毒群落：深入了解多样性和调节微生物组的潜在作用

千足虫是重要的食腐动物，拥有多样化的微生物组。之前的研究主要集中在细菌和古菌的多样性上，而病毒组仍然被忽视。我们阐明了两种具有不同微生物组的模式千足虫后肠中的 DNA 和 RNA 病毒多样性：热带Epibolus pulchripes（产甲烷，以芽孢杆菌为主）和温带Glomeris connexa（非产甲烷，以假单胞菌为主）。基于宏基因组和宏转录组组装的病毒基因组，病毒群落存在显着差异，并优先感染最丰富的原核类群。 DNA病毒主要是有尾病毒目(dsDNA)、环病毒目(ssDNA)和微病毒科(ssDNA)，而RNA病毒包括短尾病毒目(ssRNA)、马铃薯病毒科(ssRNA)和真核病毒。发现了大量的亚型 IC、IB 和 II-C CRISPR-Cas 系统，主要来自假单胞菌门、拟杆菌门和芽孢杆菌门。此外，还检测到调节几丁质降解、维生素和氨基酸生物合成以及硫代谢的辅助代谢基因。最后，我们发现病毒与微生物的比率较低，并且溶原性病毒普遍存在，这支持了两种宿主中“胜者为王”的动态。