Microfungi are essential components of the gut microbiome in vertebrates, forming what is known as the gut mycobiome. The gut mycobiome has a significant contribution to the phenotype of vertebrate holobionts, but knowledge about the composition of the gut mycobiome in wild-living vertebrates remains limited.

Two radiations of murid rodents from the tropical island of New Guinea (NG) present a unique system for studying the vertebrate gut mycobiome within various phylogenetic and ecological contexts. This project will focus on analyzing the gut mycobiome of NG rodents using DNA metabarcoding data.

The student will undertake the following tasks:

1. Study existing literature on the composition of the gut mycobiome in both model and non-model vertebrates, including humans.
2. Participate in generating ITS2 metabarcoding data using available DNA samples from the cecum of NG rodents. This involves preparing a database of samples, indexes, and metadata.
3. Analyze raw sequencing data, including demultiplexing, filtering, trimming, correlating technical duplicates, and defining fungal ASVs/OTUs.
4. Select an appropriate classifier and database for identifying fungal variants.
5. Design or adapt an approach to distinguish diet-derived fungi from the endogenous mycobiome.
6. Analyze differences in the gut mycobiome composition between the two radiations of NG rodents and between the two sampled mountain ranges.
7. Interpret the results in light of the current scientific knowledge.

Literature:

Tedersoo et al. 2022, Best practices in metabarcoding of fungi: From experimental design to results. Molecular Ecology, https://doi.org/10.1111/mec.16460

Lavrinientko et al. 2021, Defining gut mycobiota for wild animals: a need for caution in assigning authentic resident fungal taxa. Animal Microbiome, https://doi.org/10.1186/s42523-021-00134-z.

Roycroft et al. 2022, New Guinea uplift opens ecological opportunity across a continent. Current Biology, https://doi.org/10.1016/j.cub.2022.08.021.