While running MetaPhlAn3 with the latest marker-database and my zebrafish gut microbiome data, I received an incredibly low alignment-rate of 0.86% from Bowtie2.
I came across a post on the forum from April 2020 where a response mentioned that the MetaPhlAn database (then) included human, murine and some soil associated species (100 Unknown raw reads).
My question: Is MetaPhlAn3 able to handle zebrafish gut microbiome data (nowadays)? I reckon zebrafish gut data would be more similar to murine and human then lichen data from the earlier mentioned forum post, however it could explain the low alignment rate if the database would not include zebrafish associated species.
Thank you very much,
P.S. There is always the possibility that my data is… not great. Kraken2 and MG-RAST both found somewhat differing results.