Symbiotic microbiota vary with breeding group membership in a highly social joint-nesting bird

Symbiotic microbes affect the health, fitness, and behavior of their animal hosts, and can even affect the behavior of non-hosts. Living in groups presents numerous benefits and challenges to social animals, including exposure to symbiotic microbes, which can mediate both cooperation and competition. In social mammals, individuals from the same social group tend to share more similar microbes, and this social microbiome, the microbial community of all hosts in the same social group, can shape the benefits and costs of group living. In contrast, little is known about the social microbiome of group-living birds. We tested the predictions that communally breeding smooth-billed anis (Crotophaga ani) belonging to the same breeding group share more similar microbes and that microbial community composition differs between body regions. To test this, we used 16S rRNA gene sequencing to characterize the preen gland and body feather microbiota of adult birds from 16 breeding groups at a long-term..., See main text for details.
Summary from main text: We extracted bacterial DNA from preen gland swabs and feathers using Norgen soil DNA isolation plus kits and amplified the V4 region of the bacterial 16S rRNA gene using the universal primers F518 (Lane et al. 1985) and R806 (Caporaso et al. 2011). We pooled PCR amplified products of the expected band size (approx. 300 nt) into a library and sequenced with 250 nt paired-end reads on an Illumina MiSeq at the London Regional Genomics Centre. We used the R package dada2 (Callahan et al. 2016) to overlap reads, remove ambiguous reads, chimeras, and singleton sequences, and assign reads to samples. Sequences rarer than 0.1% in any sample were removed as they contain little information and removing them has no impact on downstream analyses (Bian et al. 2017). The workflow and parameters used are available at github.com/ggloor/miseq_bin/. After performing these steps, we obtained an initial dataset of 12,532 unique sequences (i.e., amplicon se..., R
Microsoft Excel