Help with Understanding Microbial Community Analysis Tools

Microbial community profiling HUMAnN
1

Hi everyone,

I am new to microbial community analysis and would really appreciate some guidance. I have recently started working with microbiome data and came across several tools like MetaPhlAn HUMAnN and others…

However I am feeling a bit overwhelmed by all the different software options and their purposes. Could someone help me understand the basic differences between these tools. For example when would you choose MetaPhlAn over other approaches and how does HUMAnN fit into the analysis pipeline.

Also any suggestions for beginner friendly resources or tutorials that could help me get started would be amazing. I am looking to learn the best practices for analyzing microbial communities especially with respect to metagenomic data.
I also read this topic on this site https://www.frontiersin.org/journals/microbiology/articles-sap-analytics/ However unable to find any relevant information.

Thanks in advance for your help

Best,
[Smith]

2

This is a broad question. I can say that the purpose of running HUMAnN is to quantity functions from your community (e.g. metabolic enzymes/pathways) and to, where possible, assign those pathways to specific contributing species. This is called “functional profiling” and is different from the more frequently discussed problem of “taxonomic profiling.” To get a better handle on these methods and their inputs and outputs, I’d refer you to the bioBakery demo pages here:

Or some of our recent review articles on these topics.