Amplicon library preparation and sequencing
Samples of 190 Polyplax serrata , 14 Hoplopleura acanthopus, and 2 Hoplopleura edentula were collected from different rodent species and populations from 2014-2018. Details on sample origin, including the sampling locations, GPS coordinates, and rodent host species, are provided in SupplementaryData2. DNA templates were extracted from each individual using QIAamp DNA Micro Kit (Qiagen, Hilden, Germany). Two independent multiplexed 16S rRNA gene amplicon libraries were built for each of the louse genera. Detailed description of the library designs and MiSeq sequencing is provided in SupplementaryInformation/SupplementaryText. Amplicon data for the lice microbiomes (demultiplexed, quality filtered and merged) are available at https://www.ebi.ac.uk/ena/data/view/PRJEB35541.