Analyzing whole-metagenomic shotgun sequencing data with V4 amplicon sequence data

[jwdebelius (Justine Debelius)]

Hi @turtle,

You may find these papers relevant:

• Usyk et al, 2024: Comprehensive evaluation of shotgun metagenomics, amplicon sequencing, and harmonization of these platforms for epidemiological studies
• McDonald et al, 2024, Greengenes2 unifies microbial data in a single reference tree

There's a Greengenes2 plug-in for QIIME 2, you can learn more here:

Introducing Greengenes2 2022.10

Introduction We are excited to announce a new release of the Greengenes database, full redesigned from the ground up, backed by whole genomes, with a focus on harmonizing 16S rRNA and shotgun metagenomic datasets. We're calling the new database Greengenes2 due to substantial changes in the design. However, like the original Greengenes, it relies on a de novo phylogeny, and expresses a taxonomy that is derived from the phylogeny. The focus of this forum post is on how to use the new Greengenes2 …

I personally haven't used it (yet!) but it might be starting place.

Best,
Justine