Gut microbial composition in Hipposideros caffer D

The samples originate from an extensive sampling campaign to uncover virus diversity in Ghanaian bats in line with research (A04957) and ethic (CHRPE49/09/CITES) permits granted by the Wildlife Division of the Forestry Commission of the Ministry of Lands, Forestry and Mines. In brief, fecal samples were collected from H. caffer D captured at five different cave sites in Central Ghana, stored in RNAlater and subsequently frozen to -80C for subsequent virus and microbiome screening. For the virus screening real-time reverse transcription-PCR assay were designed to detect several alpha- and beta-CoVs, as described in Meyer et al. (2024) Nat Comms. Bacterial DNA was extracted following standardized protocols for wildlife samples, the V4 region of the 16s rRNA gene was amplified using the 515f and 806r primers, and sequenced as paired-end run on an Illumina MiSeq platform. The bioinformatic processing was completed in Qiime2 and the statistical analysis in the Rstudio environment (https://github.com/DominikWSchmid/GhanaHippos_CoV_microbiome)