Excel spreadsheets of raw data.

The gut microbiota are critical for maintaining the health and physiological function of individuals. However, illness and treatment with antibiotics can disrupt bacterial community composition, the consequences of which are largely unknown in wild animals. In this study, we described and quantified the changes in bacterial community composition in response to illness and treatment with antibiotics in a native Australian rodent, the fawn-footed mosaic-tailed rat (Melomys cervinipes). We collected faecal samples during an undiagnosed illness outbreak in a captive colony of animals, and again at least one year later, and quantified the microbiome at each time point using 16s ribosomal rRNA gene sequencing. Gut bacterial composition was quantified at different taxonomic levels, up to family. Gut bacterial composition changed between time periods, indicating that illness, treatment with antibiotics, or a combination affects bacterial communities. While some bacterial groups increased in abundance, others decreased, suggesting differential effects and possible co-adapted and synergistic interactions. Our findings provide a greater understanding of the dynamic nature of the gut microbiome of a native Australian rodent species and provides insights into the management and ethical well-being of animals kept under captive conditions.肠道微生物群（gut microbiota）对维持个体健康与生理功能至关重要。然而，疾病与抗生素治疗会破坏细菌群落结构，但其对野生动物的影响目前仍知之甚少。本研究以澳大利亚本土啮齿类动物——褐足纹尾鼠（fawn-footed mosaic-tailed rat，Melomys cervinipes）为研究对象，对其因疾病与抗生素治疗引发的细菌群落结构变化进行了描述与定量分析。我们在该圈养种群暴发不明原因疾病期间收集了粪便样本，并在至少一年后再次采样，通过16S核糖体RNA基因（16s ribosomal rRNA gene）测序技术对两个时间点的微生物组进行定量分析。我们在包括科在内的不同分类学层级上对肠道细菌组成进行了定量表征。不同采样时段的肠道细菌组成存在显著差异，表明疾病、抗生素治疗或二者共同作用会对细菌群落产生影响。部分细菌类群的丰度升高，而另一些类群的丰度则出现下降，这提示不同细菌类群受到的影响存在差异，且可能存在协同适应与协同互作关系。本研究结果加深了我们对澳大利亚本土啮齿类物种肠道微生物组动态变化的认识，并为圈养条件下动物的管理与伦理福利保障提供了理论参考。