Chava L. Weitzman, Dana M. Hawley, Bahman Rostama, Meghan May, Lisa K. Belden
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引用次数: 0
摘要
以 DNA 为基础的细菌分类群丰度和相对丰度测量方法可能会因死亡细菌或瞬时细菌的存在而产生偏差。因此,群落中活跃的功能性成员可能只是检测到的细菌群落的一小部分。这种不匹配会使推断群落在宿主健康中的作用变得困难,对于低丰度微生物群落(如结膜表面的微生物群落)尤其如此。在这项研究中,我们用一种抑菌抗生素处理鸟类结膜上的细菌群落,在保持活力的同时降低细菌活性,从而通过比较配对样本中的 16S 核糖体 DNA 和 RNA 来确定活的和活跃的结膜群落。与来自相同群落的 RNA 扩增片段相比,DNA 扩增片段包含更多的序列变异,因此多样性也存在差异。我们发现,DNA 样本中群落的变化大致代表了活体(RNA 扩增子)群落的变化,而 RNA 样本可以更好地描述群落功能,减少死亡细胞带来的背景噪音。我们进一步利用这些数据测试了 RNA 与 DNA 的比率,这种比率在其他微生物学环境中被用来检测抗生素破坏后细菌活性的变化,但这种方法无法检测到细菌活性的变化。
Characterizing living ocular bacterial communities and the effects of antibiotic perturbation in house finches
DNA-based methods to measure the abundance and relative abundance of bacterial taxa can be skewed by the presence of dead or transient bacteria. Consequently, the active, functional members of the community may be a small subset of the detected bacterial community. This mismatch can make inferences about the roles of communities in host health difficult and can be particularly problematic for low-abundance microbiomes, such as those on conjunctival surfaces. In this study, we manipulated bacterial communities on bird conjunctiva with a bacteriostatic antibiotic, reducing bacterial activity while preserving viability, to identify the living and active conjunctival communities using comparisons of 16S ribosomal DNA and RNA in paired samples. DNA amplicons included many more sequence variants than RNA amplicons from the same communities, with consequent differences in diversity. While we found that changes in communities in DNA samples broadly represent shifts in the living (RNA-amplicon) communities, assessments of community function may be better described by RNA samples, reducing background noise from dead cells. We further used these data to test RNA:DNA ratios, used in other microbiological contexts, to detect shifts in bacterial activity after antibiotic disruption but were unable to detect changes in bacterial activity with this method.
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