Choudhury Raka, Kleerebezem Michiel
Host-Microbe Interactomics Group, Department of Animal Sciences, Wageningen University & Research, Wageningen, Netherlands.
Front Microbiol. 2022 Feb 22;13:804986. doi: 10.3389/fmicb.2022.804986. eCollection 2022.
Previously, we demonstrated that rectal swabs provide a legitimate alternative to faecal sampling for the assessment of the intestinal microbiota in young piglets. However, we also reported that mucosa-adhered microbial populations were more represented in rectal swabs compared to faecal samples, albeit to a degree that varied per swab-sample. Here, we explored the possibility to exploit this variable enrichment of adhered populations in the rectal swabs to assess the impact of diet on mucosa-adhered microbiota in pre-weaning piglets. Paired samples of rectal swabs and colon luminal contents were collected from piglets just before weaning during two independent but similarly designed animal experiments [ = 28 piglets (experiment 1); = 16 piglets (experiment 2)], with an early feeding treatment (EF) group that had access to customised fibrous feed in addition to sow's milk and a control (CON) group exclusively reared on sow's milk. The intestinal microbiome composition in rectal swabs and colon samples collected at 29 days of age were subjected to metataxonomic analysis. The results identified the genera , , and as discriminative taxa enriched in rectal swabs compared to colon. Apart from (10-11% average relative abundance), most of these mucosa-adhered microbial genera display relatively low abundance. Rectal swab microbiota was found to be more variable, which is likely due to variable enrichment of mucosa-adhered microbes. Although almost exclusively driven by one of the experiments, the post-weaning diarrhoea-associated taxa , was enriched in CON compared to the EF group, suggesting that early life feeding may suppress post-weaning-diarrhoea-related problems in piglets. Our findings demonstrate that rectal swabs allow the investigation of the mucosa-adhered microbial populations as a function of dietary treatment in piglets. This offers opportunities to further study dietary approaches that suppress the abundance of the post-weaning diarrhoea associated adherent microbes like . Furthermore, we demonstrate that the paired swab-colon microbiota information (obtained from a subset of animals) can predict the mucosa-adhered populations or "mucosity factor" in rectal swab samples, facilitating the analysis of the adhered microbiota in large animal cohort studies using readily obtainable rectal swabs.
此前，我们证明了直肠拭子可为评估仔猪肠道微生物群提供一种合理的粪便采样替代方法。然而，我们还报告称，与粪便样本相比，直肠拭子中黏膜附着的微生物种群占比更高，尽管每个拭子样本的差异程度有所不同。在此，我们探讨了利用直肠拭子中附着菌群的这种可变富集来评估日粮对断奶前仔猪黏膜附着微生物群影响的可能性。在两项独立但设计相似的动物实验中（实验1：28头仔猪；实验2：16头仔猪），在断奶前从仔猪采集直肠拭子和结肠腔内容物的配对样本，其中一个早期饲喂处理（EF）组除了母乳外还可获取定制的纤维饲料，另一个对照组（CON）仅以母乳饲养。对29日龄时采集的直肠拭子和结肠样本中的肠道微生物组组成进行宏分类分析。结果确定，与结肠相比，直肠拭子中 、 和 属为有鉴别力的富集分类群。除了 （平均相对丰度为10 - 11%），这些黏膜附着微生物属中的大多数丰度相对较低。发现直肠拭子微生物群变异性更大，这可能是由于黏膜附着微生物的可变富集所致。尽管几乎完全由其中一项实验驱动，但与EF组相比，断奶后腹泻相关分类群 在CON组中富集，这表明早期饲喂可能抑制仔猪断奶后腹泻相关问题。我们的研究结果表明，直肠拭子可用于研究仔猪日粮处理对黏膜附着微生物种群的影响。这为进一步研究抑制断奶后腹泻相关附着微生物（如 ）丰度的日粮方法提供了机会。此外，我们证明，配对的拭子 - 结肠微生物群信息（从一部分动物获得）可预测直肠拭子样本中的黏膜附着种群或“黏膜因子”，便于在大型动物队列研究中使用易于获取的直肠拭子分析附着微生物群。
