The School of Biological Sciences, The University of Queensland, St Lucia, QLD, Australia.
School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia.
BMC Genomics. 2023 Jul 31;24(1):427. doi: 10.1186/s12864-023-09520-0.
The study of the host-microbiome by the collection of non-invasive samples has the potential to become a powerful tool for conservation monitoring and surveillance of wildlife. However, multiple factors can bias the quality of data recovered from scats, particularly when field-collected samples are used given that the time of defecation is unknown. Previous studies using scats have shown that the impact of aerobic exposure on the microbial composition is species-specific, leading to different rates of change in microbial communities. However, the impact that this aging process has on the relationship between the bacterial and fungal composition has yet to be explored. In this study, we measured the effects of time post-defecation on bacterial and fungal compositions in a controlled experiment using scat samples from the endangered koala (Phascolarctos cinereus).
We found that the bacterial composition remained stable through the scat aging process, while the fungal composition did not. The absence of an increase in facultative anaerobes and the stable population of obligate anaerobic bacteria were likely due to our sampling from the inner portion of the scat. We report a cluster of fungal taxa that colonises scats after defecation which can dilute the genetic material from the autochthonous mycoflora and inhibit recovery.
We emphasize the need to preserve the integrity of scat samples collected in the wild and combat the effects of time and provide strategies for doing so.
通过收集非侵入性样本来研究宿主-微生物组，有可能成为保护监测和野生动物监测的有力工具。然而，多种因素会影响从粪便中回收数据的质量，特别是当使用野外收集的样本时，因为不知道排便的时间。先前使用粪便的研究表明，好氧暴露对微生物组成的影响是具有物种特异性的，导致微生物群落的变化率不同。然而，这种老化过程对细菌和真菌组成之间关系的影响尚未得到探索。在这项研究中，我们使用濒危考拉（Phascolarctos cinereus）的粪便样本在受控实验中测量了粪便老化后对细菌和真菌组成的影响。
我们发现，细菌组成在粪便老化过程中保持稳定，而真菌组成则没有。兼性厌氧菌数量没有增加，而专性厌氧菌的稳定种群可能是由于我们从粪便的内部进行了采样。我们报告了一组在粪便中定殖的真菌类群，这些真菌类群在排便后会定殖，可以稀释土著真菌群落的遗传物质并抑制其回收。
我们强调需要保护在野外收集的粪便样本的完整性，并应对时间的影响，并提供了一些应对策略。
