Synchronized shift of oral, faecal and urinary microbiotas in bats and natural infection dynamics during seasonal reproduction

Dietrich, Muriel; Kearney, Teresa; Seamark, Ernest C. J.; Paweska, Janusz T.; Markotter, Wanda

DNA extraction and sample preparation were performed as detailed previously [21] (electronic supplementary material, texts S1, S2, S3) after which the eluted DNA was split in two separated tubes. The first part was used for Illumina sequencing of 16S amplicons, as described previously [21] . The inclusion of negative controls during DNA extraction and library preparation was used to further identify and remove potential exogenous bacterial phylotypes following the approach of Dietrich et al. [21] (electronic supplementary material, text S2). The second part of samples was used for the screening of Leptospira bacteria based on a probe-specific real-time polymerase chain reaction [28] (later 'RT-PCR'), and the screening of herpes-and adenoviruses using previously published nested-PCR protocols [29, 30] (electronic supplementary material, text S3). The Ct of Leptospira-positive samples was noted to infer the relative bacterial load. Phylogenetic trees for bacterial and viral agents were constructed using BEAST [31] (electronic supplementary material, text S4).