Paired viromics resolves the modular ecological architecture of the swine nasopharyngeal phageome

Abstract

BackgroundBacteriophages are recognized modulators of microbiome composition and function, yet their role in the porcine upper respiratory tract, a primary gateway for pathogen colonization in the post-weaning period, remains unexplored. Unlike the porcine gut, no reference framework is available for respiratory sites. Furthermore, the low-biomass nature of nasopharyngeal specimens makes virome recovery highly sensitive to extraction strategy, but the extent to which workflow choice shapes ecological inference in this niche has not been evaluated. ResultsWe profiled the nasopharyngeal phageome of post-weaning piglets across ten commercial farms (30 pen-level pools) using paired DNA-microbiome (DNA-m) and virus-like particle-enriched (VLP-e) short-read metagenomics (n = 60 libraries). Protocol choice strongly reshaped viral recovery (PERMANOVA R{superscript 2} = 0.448, p < 0.0001), with a contig overlap between workflows of <1%. DNA-m favored assembly contiguity, while VLP-e maximized viral detection. By integrating both approaches, we constructed a curated catalogue of 2,501 non-redundant viral operational taxonomic units (vOTUs), with only 5.2% showing similarity to known phages, underscoring the extensive novelty of this niche. Ecologically, within the integrated community dataset (n = 4,357), predicted replication strategy emerged as a dominant organizing axis: lifestyle explained up to 40.6% of compositional variation at family level. Host prediction linked phages to dominant upper-airway colonizers, including Streptococcaceae, Moraxellaceae, Pasteurellaceae, with a marked lifestyle-host polarization: virulent phages were preferentially linked to Bacteroidota (particularly Prevotella), whereas temperate phages were enriched in Streptococcaceae and Moraxellaceae. Integration of viral taxonomy and host affiliation resolved a modular architecture in which a few recurrent phage-host couplings (e.g., Suoliviridae-Bacteroidota, Peduoviridae-Pasteurellaceae, Aliceevansviridae-Streptococcaceae) were conserved but differentially weighted between virulent and temperate fractions. ConclusionsThis study establishes the first phageome catalogue and ecological framework for a respiratory site in livestock. The nasopharyngeal phageome is organized into recurrent, host-linked taxonomic modules jointly constrained by viral lineage, host affiliation and replication strategy, with lifestyle-dependent connections to key colonizers implicated in the porcine respiratory disease complex. This catalogue and its modular architecture provide a foundation for investigating phage-mediated modulation of bacterial dynamics during the post-weaning transition and for the selection of lytic phage candidates targeting respiratory pathogens.