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.