Diverse bacterial communities are found on every surface of macro-organisms, and they play important roles in maintaining normal physiological functions in their hosts. While the study of microbiomes has expanded with the influx of data enabled by recent technological advances, microbiome research in reptiles lags behind other organisms. We sequenced the nasal microbiomes in a sample of four North American tortoise species, and we found differing community compositions among tortoise species and sampling sites, with higher richness and diversity in Texas and Sonoran desert tortoises. Using these data, we investigated the prevalence and operational taxonomic unit (OTU) diversity of the potential pathogen Pasteurella testudinis, and found it to be common, abundant, and highly diverse. However, the presence of this bacterium was not associated with differences in bacterial community composition within host species. We also found that the presence of nasal discharge from tortoises at the time of sampling was associated with a decline in diversity and a change in microbiome composition, which we posit is due to the harsh epithelial environment associated with immune responses. Repeated sampling across seasons, and at different points of pathogen colonisation, should contribute to our understanding of the causes and consequences of different bacterial communities in these long-lived hosts.

OTU biom tableOTU biom table of bacteria in the upper respiratory tracts of 146 North American tortoises. Biom table includes only bacterial OTUs and excludes OTUs represented by only one sequence.otu_bacteriaonly.biomTortoise sample data fileData file including information on each tortoise sampled, presence or absence of pathogens in the samples, and barcode sequences for pyrosequencing. Includes sheet of column descriptions.WeitzmanTortoise454mapping.xlsxTortoise Nasal Bacterial SequencesSequences from 454-pyrosequencing of nasal flush samples from North American tortoises. Sequences are demultiplexed. Mapping file provides information on host species, site, and sex; sampling year; presence of mucus at sampling time; presence of two Mycoplasma spp. in the samples from quantitative PCR; and sequencing information such as barcode sequences.tortoise_nasal_seqs.fna