I’m planning to select a mock microbial community to validate our DNA extraction and bioinformatics pipeline. Since our work focuses on the gut microbiome, the ZymoBIOMICS Gut Microbiome Standard seems like a relevant choice. However, it appears to be more challenging due to its higher strain-level diversity compared to alternatives like the ATCC MSA-2006 or the ZymoBIOMICS Microbial Community Standard.
I would greatly appreciate hearing about your experience with taxonomic profiling of short-read sequencing data using MetaPhlAn, HUMAnN, or other classifier(e.g., mOTUs, Kraken/Bracken) or even appraoches i.e., MAGs binning.
In my opinion, if you want to validate DNA extractions and bioinformatics with a reference material, I would go with the ZymoBIOMICS Fecal Reference with TruMatrix™ Technology. This is a well-characterized “standard” community on which you can benchmark your results; it reflects true gut richness and evenness, both of which will impact MAG generation and other analyses. When sequenced at the same read depth as samples, we have found this to be a helpful inclusion in our gut community short-read runs.
The first rows are the community standard with evenly distributed or log distributed abundances, while the second is the gut standard. In both case we compare the species identified in MetaPhlAn (vJan25) with the Gold Standard (GS).
We haven’t tested the other communities you mentioned.
