Department of Agricultural, Food & Nutritional Science, Faculty of Agricultural, Life & Environmental Sciences, Edmonton, Alberta, Canada.
Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA.
Microbiol Spectr. 2024 Oct 3;12(10):e0084324. doi: 10.1128/spectrum.00843-24. Epub 2024 Aug 20.
The 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 ( < 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.
The microbiome of pigs plays a crucial role in shaping host physiology and health. This study sought to identify if domestication and current rearing practices have resulted in a loss of co-evolved bacterial species by comparing the microbiome of wild boar and conventionally raised pigs. It provides a comparison of domestic and wild pigs with the largest sample sizes and is the first to examine wild boars from multiple sites and continents. We were able to identify core microbiome members that were shared between wild and domestic populations, and on the contrary to expectation, few microbes were identified to be lost from wild boar. Nevertheless, the microbiome of wild boars had a lower abundance of important pathogenic genera and was distinct from domestic pigs. The differences in the microbial composition may identify an opportunity to shift the microbial community of domestic pigs towards that of wild boar with the intent to reduce pathogen load.
据信，野生动物的微生物组与宿主物种共同进化，这可能对宿主生理机能发挥着重要作用。人们推测，现代养猪业中严格的卫生实践、抗生素的使用以及简化配方的饮食可能会对肠道微生物组的建立和发展产生负面影响。在这项研究中，我们使用 16S rRNA 基因扩增子测序技术，评估了来自加拿大 9 个农场的 90 头家猪和来自两个大陆（北美洲和欧洲）的 3 个不同地点的 39 头野猪的粪便微生物组。令人惊讶的是，家猪的肠道微生物组的α多样性指数高于野猪（<0.0001）。与家猪相比，野猪的微生物组中厚壁菌门与拟杆菌门的比例较低，放线菌门、疣微菌门、蓝藻门和纤维杆菌门的存在更为丰富。在属水平上，野猪的微生物组富含已知的纤维降解和短链脂肪酸产生菌属。有趣的是，仅在家猪中观察到梭杆菌门。我们鉴定出 31 种在猪肠道微生物组中普遍存在的 ASV，无论宿主来源如何，它们都可以被认为是核心肠道微生物组的成员。有趣的是，我们发现有 5 种在野猪中常见但在家猪中缺失的 ASV，而家猪则存在 59 种完全不存在于野猪中的 ASV。本研究揭示了驯化对猪肠道微生物组的影响，包括新属的获得，这可能为识别操纵猪肠道微生物组以改善健康的新靶点提供依据。
猪的微生物组在塑造宿主生理机能和健康方面起着关键作用。本研究旨在通过比较野猪和传统饲养猪的微生物组，确定驯化和当前饲养方式是否导致了共同进化细菌物种的丧失。它比较了具有最大样本量的家猪和野猪，并首次研究了来自多个地点和大洲的野猪。我们能够确定在野生和家养群体中共享的核心微生物组成员，与预期相反，从野猪中鉴定出的丢失微生物较少。尽管如此，野猪的微生物组中重要的致病性属的丰度较低，并且与家猪不同。微生物组成的差异可能为将家猪的微生物群落向野猪的微生物群落转移提供机会，以期减少病原体负荷。
