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A comparison of wild boar and domestic pig microbiota does not reveal a loss of microbial species but an increase in alpha diversity and opportunistic genera in domestic pigs

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dc.contributor.authorRahman, Rajibur
dc.contributor.authorFouhse, Janelle
dc.contributor.authorJu, Tingting
dc.contributor.authorFan, Yi
dc.contributor.authorSchultz Marcolla, Camila
dc.contributor.authorPieper, Robert
dc.contributor.authorBrook, Ryan K.
dc.contributor.authorWilling, Benjamin Peter
dc.date.accessioned2024-12-02T20:22:33Z
dc.date.available2024-12-02T20:22:33Z
dc.date.issued2024-08-20
dc.descriptionThe version of record of this article, first published in Microbiology Spectrum, is available online at Publisher’s website: https://doi.org/10.1128/spectrum.00843-24
dc.description.abstractThe microbiome of wild animals is believed to be co-evolved with host species, which may play an important role in host physiology. It has been hypothesized that the rigorous hygienic practices in combination with antibiotics and diets with simplified formulas used in the modern swine industry may negatively affect the establishment and development of the gut microbiome. In this study, we evaluated the fecal microbiome of 90 domestic pigs sampled from nine farms in Canada and 39 wild pigs sampled from three different locations on two continents (North America and Europe) using 16S rRNA gene amplicon sequencing. Surprisingly, the gut microbiome in domestic pigs exhibited higher alpha-diversity indices than wild pigs (P < 0.0001). The wild pig microbiome showed a lower Firmicutes-to-Bacteroidetes ratio and a higher presence of bacterial phyla Elusimicrobiota, Verrucomicrobiota, Cyanobacteria, and Fibrobacterota when compared to their domestic counterparts. At the genus level, the wild pig microbiome had enriched genera that were known for fiber degradation and short-chain fatty acid production. Interestingly, the phylum Fusobacteriota was only observed in domestic pigs. We identified 31 ASVs that were commonly found in the pig gut microbiome, regardless of host sources, which could be recognized as members of the core gut microbiome. Interestingly, we found five ASVs missing in domestic pigs that were prevalent in wild ones, whereas domestic pigs harbored 59 ASVs that were completely absent in wild pigs. The present study sheds light on the impact of domestication on the pig gut microbiome, including the gain of new genera, which might provide the basis to identify novel targets to manipulate the pig gut microbiome for improved health.
dc.description.sponsorshipAlberta Livestock and Meat Agency (ALMA), Natural Sciences and Engineering Research Council of Canada (NSERC)
dc.description.versionPeer Reviewed
dc.identifier.citationRahman R, Fouhse JM, Ju T, Fan Y, S Marcolla C, Pieper R, Brook RK, Willing BP. A comparison of wild boar and domestic pig microbiota does not reveal a loss of microbial species but an increase in alpha diversity and opportunistic genera in domestic pigs. Microbiol Spectr. 2024 Oct 3;12(10):e0084324. doi: 10.1128/spectrum.00843-24. Epub 2024 Aug 20. PMID: 39162552; PMCID: PMC11448168.en
dc.identifier.doihttps://doi.org/10.1128/spectrum.00843-24
dc.identifier.urihttps://hdl.handle.net/10388/16294
dc.language.isoen
dc.publisherAmerican Society for Microbiology
dc.rightsAttribution 2.5 Canadaen
dc.rights.urihttp://creativecommons.org/licenses/by/2.5/ca/
dc.subjectswine
dc.subjectwild boar
dc.subjectdomestic
dc.subjectmicrobiota
dc.subjectporcine
dc.titleA comparison of wild boar and domestic pig microbiota does not reveal a loss of microbial species but an increase in alpha diversity and opportunistic genera in domestic pigs
dc.typeArticle

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