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ORIGINAL RESEARCH article

Front. Vet. Sci.

Sec. Animal Nutrition and Metabolism

Volume 12 - 2025 | doi: 10.3389/fvets.2025.1582122

This article is part of the Research Topic Advancements in Synthetic Microbiomes for Enhancing Animal Health View all 9 articles

Characterization of the diversity, genomic features, host bacteria, and distribution of crAss-like phages in the pig gut microbiome

Provisionally accepted
  • Jiangxi Agricultural University, Nanchang, China

The final, formatted version of the article will be published soon.

    Phages play an important role in shaping the gut microbiome. CrAss-like phages, which are key members of the gut virome, show high abundance in the human gut and have attracted increasing interest. However, few studies have been found in pigs, and the distribution of crAss-like phages across broader pig populations remains unknown.Here, we obtained 1,251 pig crAss-like phage genomes from 403 metagenomes publicly available and a pig gut virome dataset constructed by ourselves. These crAsslike phage genomes were further clustered into 533 virus operational taxonomic units (vOTUs). Phylogenetic analysis revealed that crAss-like phages in pig guts were distributed across four well-known family-level clusters (Alpha, Beta, Zeta, and Delta) but were absent in the Gamma and Epsilon clusters. Genomic structure analysis identified 149 pig crAss-like phage vOTUs that utilize alternative genetic codes. Gene blocks encoding replication and assembly proteins varied across crAss-like phage clusters. Approximately 64.73% of crAss-like phage genes lacked functional annotations, highlighting a gap in understanding their functional potential. Numerous anti-CRISPR protein genes were identified in crAss-like phage genomes, and CAZymes encoded by these phages were primarily lysozymes. Host prediction indicated that bacterial hosts of pig crAss-like phages primarily belonged to Prevotella, Parabacteroides, and UBA4372. We observed that interactions between crAss-like phages and Prevotella copri might have a possible effect on fat deposition in pigs.Finally, all detected vOTUs exhibited low prevalence across pig populations, suggesting heterogeneity in crAss-like phage compositions. This study provides key resources and novel insights for investigating crAss-like phage-bacteria interactions and benefits research on the effects of crAss-like phages on pig health and production traits.

    Keywords: crAss-like phage, pig, gut, Genomic features, Host bacteria, Prevotella copri

    Received: 24 Feb 2025; Accepted: 02 Apr 2025.

    Copyright: © 2025 Wang, Wei, Chen, Zhou, Huang and Chen. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence:
    Lusheng Huang, Jiangxi Agricultural University, Nanchang, China
    Congying Chen, Jiangxi Agricultural University, Nanchang, China

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.

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