Introduction. Red squirrel populations have declined in the UK since the introduction of the grey squirrel, due to resource competition and grey squirrels carrying a squirrelpox virus that is fatal to red squirrels. Hypothesis/Gap Statement. It is not known if the gut microbiota of the two species is similar and if this could impact the survival of red squirrels. Aim. The aim of this study was to profile the caecal microbiota of red and grey squirrels obtained opportunistically from a conservation programme in North Wales. Methodology. Bacterial DNA was extracted from ten red and ten grey squirrels and sent for 16S rRNA sequencing. Three samples from red squirrels returned less than 5000 reads, and so were not carried forward for further analyses. Results. Samples taken from the caeca of red squirrels had significantly lower bacterial diversity and a higher percentage of Bacilli bacteria when compared to samples from grey squirrels. When the abundance of bacterial groups across all levels of phylogenetic classifications was compared between the two groups of squirrels, grey squirrels had a higher abundance of bacteria belonging to the families S24-7, RF39 and Rikenellaceae. Escherichia coli with resistance to amoxicillin/clavulanic acid was identified in all samples. Cefotaxime resistance was identified in two samples from grey squirrels along with sulfamethoxazole/trimethoprim in one of these samples. Conclusion. Clear differences between the caecal microbiota of the two species of squirrel were identified, which could potentially impact their overall health and ability to compete for resources.

中文翻译：

---

英国红松鼠和灰松鼠的盲肠细菌微生物群存在显着差异

介绍。自灰松鼠引入以来，由于资源竞争以及灰松鼠携带对红松鼠致命的松鼠痘病毒，英国红松鼠的数量有所下降。假设/差距陈述。目前尚不清楚这两个物种的肠道微生物群是否相似，以及这是否会影响红松鼠的生存。目的。本研究的目的是对从北威尔士的一项保护计划中机会获得的红松鼠和灰松鼠的盲肠微生物群进行分析。方法。从 10 只红松鼠和 10 只灰松鼠中提取细菌 DNA 并送去进行 16S rRNA 测序。来自红松鼠的三个样本返回的读数少于 5000 个，因此没有进行进一步分析。结果。与灰松鼠的样本相比，从红松鼠盲肠中获取的样本的细菌多样性明显较低，而杆菌的比例较高。当比较两组松鼠之间各个系统发育分类水平的细菌群丰度时，发现灰松鼠具有更高丰度的属于 S24-7、RF39 和 Rikenellaceae 科的细菌。所有样品中均鉴定出对阿莫西林/克拉维酸具有抗性的大肠杆菌。灰松鼠的两个样品中发现了头孢噻肟耐药性，其中一个样品中发现了磺胺甲恶唑/甲氧苄啶耐药性。结论。两种松鼠的盲肠微生物群之间存在明显差异，这可能会影响它们的整体健康和争夺资源的能力。