After searching around a bit for resources, I came across a YouTube playlist called “Microbiome Discovery” by Dan Knights. It’s dated 2016, so it’s not that old (although he’s using QIIME and not QIIME2), and so most of the information should be fairly up-to-date. At least the big picture concepts should mostly be there, which is the important thing. I’m fairly certain I can work out the code part as I go.

Introduction to the Microbiome

This is just a quick introductory video. He does work in gut microbiome. The project that I’m trying to get involved with is soil microbiome, but the concepts should be similar.

He lists a few challenges of analyzing the gut microbiome, which includes the problem of gut microbes not living very well outside of the gut. So he talks about extracting the DNA from the microbiome. There are also computational challenges.

• Given a data file of DNA sequences, can you identify what’s actually there and what they do?
• Can you use that information to identify what a healthy microbiome looks like? This is challenging because “healthy” can come in many forms. Also, an individual’s microbiome changes.
• Can you use the information to identify specific diseases in people?

He then provides a slide that outlines the topics that will be covered. I can see some machine learning things in there, which gives me comfort (since those are things I know a little about), and so at this point the only concern is whether his intended audience is going to be people who are already fairly comfortable with biology (in which case I may still have knowledge gaps), or if this is meant for a slightly more general audience.