Reviving diversity: cryoprotectants and culturing methods enhance recovery of mammalian gut microbes from field samples

Welcome!

Here you will find the codes used in the analysis we ran for our manuscript titled "Reviving diversity: cryoprotectants and culturing methods enhance recovery of mammalian gut microbes from field samples". We would be happy to help in way we can, so please do not hesitate to reach out if you have questions or suggestions.

In summary, we developed this study in response to challenges encountered in our own field research. Recent advancements in culturomics and microbiology are enabling us to further explore the realm of microbiome science. We aspire for this study to serve as a foundational step toward identifying preservation methods that can help protect the microbial communities of wild animals.

Our study aims are:

The primary objective of this study was to evaluate the effectiveness of various preservation solutions in maintaining microbial integrity of gut samples during collection and for a short duration, simulating transportation conditions, prior to long-term storage at -80°C. We cultivated the samples in three distinct culture media to maximize the recovery of microbial diversity.

The second objective was to compare the inventory of the preserved and cultured microbial community to that of the original uncultured samples, aiming to determine whether the preservation solutions retained unique taxa absent in the frozen original samples.

Notes to keep in mind:

We chose preservation solutions that have already been described for microbial culturing.

We chose culture media that have already been described for microbial culturing, especially gut microbiome samples.

As you go through the Rmd document included here, please make sure all documents have been properly downloaded. Additionally, please make sure to change the names of the alpha diversity metric files in the Rmd to that of the files here as they were modified for proper uploading methods here.