Highly host-linked viromes in the built environment possess habitat-dependent diversity and functions for potential virus-host coevolution

Abstract

Viruses in built environments (BEs) raise public health concerns, yet they are generally less studied than bacteria. To better understand viral dynamics in BEs, this study assessed viromes from 11 habitats across four types of BEs with low to high occupancy. The diversity, composition, metabolic functions, and lifestyles of the viromes were found to be habitat dependent. Caudovirales species were ubiquitous on surface habitats in the BEs, and some of them were distinct from those present in other environments. Antimicrobial resistance genes were identified in viruses inhabiting surfaces frequently touched by occupants and in viruses inhabiting occupants’ skin. Diverse CRISPR-Cas immunity systems and anti-CRISPR proteins were found in bacterial hosts and viruses, respectively, consistent with the strongly coupled virus–host links. Evidence of viruses potentially aiding host adaptation in a specific-habitat manner was identified through a unique gene insertion. This work illustrates that virus–host interactions occur frequently in BEs and that viruses are integral members of BE microbiomes.

Chronic exposure to polycyclic aromatic hydrocarbons is associated with alterations in skin virome composition and increased virus–host coevolution

“…Bacteriophages can insert AMGs into their hosts that help them adapt to their environment 22,48 . In the present study, we found evidence that an AMG encoding an arylalcohol dehydrogenase 49 was inserted into a bacterium in cutotype 2 under high-PAH exposure conditions, suggesting that this enzyme may help the bacterium to biodegrade xenobiotics.…”

“…Three complementary in silico methods were adopted to improve the accuracy of host prediction, namely methods that find exact or close matches of CRISPR spacers and integrated viral fragments in host genomes and a method that finds consistent k-mer signatures, as described previously 48 . Briefly, CRISPR spacers in the rMAGs were identified using CRT (v.1.2) 91 and PILER-CR (v.1.0.6) 92 .…”

“…Viral contigs were detected using VirSorter2 64 and DeepVirFinder 65 , as previously described 48 . Variational autoencoders were employed for metagenomic binning: microbial species were binned using VAMB (v.3.1), 66 and bacteriophages were binned using PHAMB (v.1.0.1) 67 .…”

“…Genomic regions shared between vOTUs and rMAGs were detected using BLASTn with an identity ≥ 90%, a hit length ≥ 1,000 bp, and an E-value ≤ 0.001. The k-mer frequencies of sequences from rMAGs and vOTUs were estimated using WIsH (v.1.1) 93 , as previously described 48 . The host predicted by WIsH that had the lowest p-value (≤ 10 −5 ) was retained for each vOTU.…”