Faecal pathogens and ectoparasites associated with small mammals in forest fringes around Sydney, Australia

This dataset contains curated and Hellinger-tranformed sequencing data obtained from DNA extracted from small mammal scats collected in Ku-ring-gai Chase National Park, and surrounding urban reserves. We present the csv files neccesary to obtained the published results of our study, in which we aimed to analyse the influence of host species identity and traits (i.e. sex, body mass index; BMI), and seasonality on the presence of faecal pathogenic fungi and bacteria as well as the ectoparasites associated with small mammals inhabiting forest reserves near urban areas in the Sydney region, New South Wales (NSW), Australia. Across samples, we identified 12 pathogenic fungi, nine bacterial pathogens, and 15 ectoparasite taxa. The most abundant representatives of each group were Malassezia japonica (fungi), Escherichia coli (bacteria), and Siphonaptera (fleas). Host traits influenced pathogen and ectoparasite occurrence in distinct ways. Host sex affected flea prevalence, with males..., We live-trapped small mammals at five sites in Ku-ring-gai Chase National Park, each paired with one surrounding urban reserve. The urban reserves were located at least 100 m outside the KNP boundary and separated from one another by at least 1.5 km. At each site, we installed 50 Elliot traps in a sampling grid spaced at 10 m intervals. At the forest sites, the sampling grids were 5 × 10 trap rectangles. At the urban reserves, this grid arrangement was not always feasible due to the irregular shape of some sites. We sampled a pair of sites simultaneously. Each trap was baited with a mixture of peanut butter, vanilla essence, and oats. We sampled the sites during both spring (September 2023) and autumn (April 2024). Upon capture, any small mammals showing signs of stress (16% of captures) were immediately released. The remaining individuals were taxonomically identified. After processing the captured individuals, any fresh scats present were collected in 1.5 ml E..., # Faecal pathogens and ectoparasites associated with small mammals in forest fringes around Sydney, Australia

Dataset DOI: [10.5061/dryad.8sf7m0d2g](10.5061/dryad.8sf7m0d2g)

## Description of the data and file structure

The provided data were retrieved from sequencing data of DNA extracted from live-trapped small mammal scats using the primers ITS1F-ITS2R and 16S V3-V4 primers 341F and 806R. The DADA2 pipeline was used to curate this data, where the taxonomic assignment was done using the reference database SILVA taxonomic training data version 138.2. The data on ectoparasite counts were obtained by direct inspection of small mammals and morphological identification.

### Files and variables

#### File: 20241123_sp80_40r_hellinger.csv

**Description:** Taxonomical identification of fungi with a bootstrap confidence above 80 % found in small mammal scat samples, and those fungal species with more than 50 reads. The sequencing depth was rarefied to 40,000 reads. The resulting sequencin...,