Help with Microbiology Gut Microbiome IRP

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Hello,

Our group is planning to center our Independent Research Project (IRP) around the article Habitual coffee intake shapes the gut microbiome and modifies host physiology and cognition.

The article provides a Zenodo dataset that we are interested in analyzing using Galaxy tools.

We have a few questions regarding our project:

  1. Dataset suitability: Does the Zenodo dataset contain sufficient information for us to conduct our own analyses, such as alpha diversity, beta diversity, and taxonomic classification? Or would we need to use the raw sequencing data available through ENA?

  2. Galaxy analysis: We would appreciate guidance on how to import, process, and analyze these datasets in Galaxy, especially when combining microbiome data with information about participants’ coffee consumption, even an online guide link.

  3. Additional primary sources: We are also looking for at least one additional primary research article investigating the relationship between coffee or caffeine consumption and the gut microbiome, with publicly available Zenodo, SRA, or ENA data that we could independently analyze and compare with our initial study.

Our overall goal is to investigate how different levels of coffee or caffeine consumption are associated with changes in gut microbial diversity and bacterial composition.

We would greatly appreciate any guidance or recommendations on how to approach this project and determine whether our proposed analysis is feasible.

Thank you so much for your help!

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Hi Meera and friends,

I took just a cursory glance at this study.

It does have the taxonomic information, metadata, and a final count table available, however the way the data is organized is not very straightforward and I think would need a fair bit of wrangling. For example, we have 62 individuals’ metadata and 275 samples we would need to match and the naming scheme is not all that intuitive at first glance. The taxonomic data only contains the final two fields, which could make it difficult to look at the taxonomy at different levels (though my colleagues may know more about different tools or file formats that might make this easier). Not an impossible task, but not necessarily one that I would be drawn to at the beginning of a project especially with students.

Since we want to find some more studies to compare anyway, let’s see what else is out there. It seems like the effect of caffeine on human gut microbiota is surprisingly sparse, though it seems like some studies may be in the works.

If we cast a wider net we’ll have a better chance of finding multiple good public datasets. What do we think about expanding to other model organisms, beverages beyond caffeinated ones (milk? wine? fruit juice?), microbiomes besides the gut (oral?).

What is it about the caffeine and coffee angle that interests you, and what is adjacent but still appealing to your interests?