State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.
Institute of Animal Husbandry and Veterinary Medicine, Jinhua Academy of Agricultural Sciences, Jinhua, China.
Microbiol Spectr. 2023 Jun 15;11(3):e0002323. doi: 10.1128/spectrum.00023-23. Epub 2023 May 11.
To date, studies on the swine gut microbiome have focused almost exclusively on bacteria. Despite recent advances in the understanding of the swine gut bacteriome at different growth stages, a comprehensive longitudinal study of the lifetime dynamics of the swine gut virome is lacking. Here, we used metagenomic sequencing combined with bioinformatic analysis techniques to characterize the gut viromes of parental-generation and offspring pigs at different biological classification levels. We collected 54 fecal samples from 36 parental-generation pigs (18 breeding boars [Duroc] and 18 pregnant/lactating sows [Landrace]) and 108 fecal samples from 18 offspring pigs during the lactation (day 3), nursery (days 26, 35, and 49), growing (day 120), and finishing (day 180) stages. Alpha diversity, including community richness (richness index) and diversity (Shannon index), showed an overall increasing trend in offspring pigs. Distinct shifts (beta diversity) in the microbiome structure along different growth stages were observed. The linear discriminant analysis effect size (LEfSe) algorithm revealed 53 viral genus that are stage specific. Host prediction results showed that enteric viruses are probably correlated with carbohydrate decomposition. We identified abundant auxiliary carbohydrate-active enzyme (CAZyme) genes from enteric viruses, most of which are glycoside hydrolase genes and participate in the biolysis of complex polysaccharides. This study shows that distinct stage-associated swine gut viromes may be determined by age and/or gut physiology at different growth stages, and enteric viruses probably manipulate carbohydrate decomposition by abundant glycoside hydrolases. These findings fill a gap in the longitudinal pattern of the swine gut virome and lay the foundation for research on the function of swine enteric viruses.
迄今为止，有关猪肠道微生物组的研究几乎完全集中在细菌上。尽管在不同生长阶段对猪肠道细菌组的理解有了最近的进展，但缺乏对猪肠道病毒组一生动态的综合纵向研究。在这里，我们使用宏基因组测序结合生物信息学分析技术，在不同的生物学分类水平上描述了亲代和后代猪的肠道病毒组。我们收集了 36 头亲代猪（18 头繁殖公猪[杜洛克]和 18 头怀孕/哺乳期母猪[长白])的 54 个粪便样本和 18 头后代猪在哺乳期（第 3 天）、保育期（第 26、35 和 49 天）、生长期（第 120 天）和育肥期（第 180 天）的 108 个粪便样本。包括群落丰富度（丰富度指数）和多样性（香农指数）在内的 α 多样性在后代猪中表现出总体上增加的趋势。在不同的生长阶段，微生物组结构发生了明显的（β 多样性）变化。线性判别分析效应量（LEfSe）算法显示 53 个病毒属具有特定的阶段特异性。宿主预测结果表明，肠道病毒可能与碳水化合物分解有关。我们从肠道病毒中鉴定出丰富的辅助碳水化合物活性酶（CAZyme）基因，其中大多数是糖苷水解酶基因，参与复杂多糖的裂解。这项研究表明，不同阶段相关的猪肠道病毒组可能由不同生长阶段的年龄和/或肠道生理学决定，肠道病毒可能通过丰富的糖苷水解酶来操纵碳水化合物分解。这些发现填补了猪肠道病毒组纵向模式的空白，为研究猪肠道病毒的功能奠定了基础。
