Experiment 218
To extract DNA from fleas, we used a DNeasy Blood and Tissue Kit (QIAGEN, Valencia, CA) according to the QIAGEN “purification of total DNA from ticks” supplementary protocol for the detection of Borrelia DNA (Hawlena et al 2013). To extract DNA from rodent blood samples, we used a Bacteremia DNA isolation kit (MoBio Laboratories, Carlsbad, CA). We added 50 µl of blood to the Microbead tube and followed the manufacturer's instructions. We added a negative control to each extraction session by adding all reagents to phosphate-buffered saline instead of fleas or blood. We subjected the DNA extracts and nine negative controls to V1-V3 region 16S rRNA PCR, following Hawlena et al. (2013), and performed 454 pyrosequencing on a Roche/454 GS-FLX Titanium system.