Are fecal samples an appropriate proxy for amphibian intestinal microbiota?

The intestinal microbiota, an invisible organ supporting a host’s survival, has essential roles in metabolism, immunity, growth, and development. Since intestinal microbiota influences a host’s biology, application of such data to wildlife conservation has gained interest. There are standard protocols for studying the human intestinal microbiota, but no equivalent for wildlife. A major challenge is sampling the intestinal microbiota in an effective, unbiased way. Fecal samples are a popular proxy for intestinal microbiota because collection is non-invasive, convenient, and allows for longitudinal sampling. Yet, it is unclear whether the fecal microbiota is representative of the intestinal microbiota. In amphibians, research on sampling methodology is limited. In this study, we characterize and compare microbiota (small intestine, large intestine, feces) of two Hong Kong stream-dwelling frog species: Lesser Spiny Frog (Quasipaa exilispinosa), and Hong Kong Cascade Frog (Amolops hongkonge..., Frog surveys
Night surveys were conducted within three hours after sunset, from June to August 2021. Each survey included 3–4 surveyors experienced in herpetological field work. Surveyors walked along the stream looking for the two target species using headlamps and flashlights. Individuals were captured with gloved hands, with gloves changed between individuals to prevent cross contamination. After sampling skin microbiota for another study, each individual was stored in separate air-filled plastic bags for transport to laboratory within two hours.
Fecal microbiota
All equipment was sterilized with a 10% bleach solution beforehand to avoid contamination. Upon arrival to the laboratory, each individual was kept separately in sterile plastic boxes for 12–24 hours waiting for defecation. The boxes have a wire mesh floor that allows the feces to fall and avoid contamination by the individual. Each box was humidified by spraying sterile water, and kept in dark to minimize disturbance. Appr..., Bioinformatics work was performed using Quantitative Insights into Microbial Ecology 2 (QIIME 2, version 2022.11) (Bolyen et al., 2019) and R (R Core Team 2021). Raw sequence data were demultiplexed by Macrogen (Seoul, South Korea). We evaluated the quality of demultiplexed reads and trimmed to remove poor-quality bases. Sequence quality control and denoising were performed with DADA2 (Callahan et al., 2016) to generate amplicon sequence variants (ASVs) using q2-dada2. Representative sequences were aligned with MAFFT (Katoh and Standley, 2013) using q2-alignment. To maximize taxonomic classification accuracy, we assigned taxonomy to ASVs using a weighted Bayes classifier that incorporates information on environment-specific taxonomic abundance (Kaehler et al. 2019), pre-trained on the 16S 515F/806R region in SILVA 138 (Quast et al., 2013) (MD5: b9476399080d189b4c9917d1246e7c69) (Bokulich et al., 2018; Robeson II et al., 2021) using q2-feature-classifier (Bokulich et al., 2018). Sequence..., # Are fecal samples an appropriate proxy for amphibian intestinal microbiota?

This study compared the bacterial community of three sample types (feces, small intestine, large intestine) on two stream-dwelling amphibian species (*Amolops hongkongensis*, and *Quasipaa exilispinosa*) sampled in Hong Kong. The dataset is based on metabarcoding of the 16SV4 region on the Illumina MiSeq PE300 platform. We showed that feces is not an approxiate proxy of both intestine sections, and identified a set of microbial taxa significantly differs between sample types.

## Description of the Data and file structure

This dataset contains compressed text-based format in .fastq.gz format to store nucleotide sequence and its corresponding quality scores in both sequencing directions. Please refer to the metadata file for more details.

The file name contains information as follows:

Take \"AMHO-LR-LI01_1.fastq.gz\" as an example,

1. The first section \"AMHO\" indicates species.
Two available options:
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