Hi Colin,
Thanks for drawing the recent fix (October 2024) to my attention. My post was meant to light a fire to draw attention to a substantive problem. I'm sorry if you found the tone off. I wish the Greengenes2 team well, and am grateful for their work. My criticism is not intended to be personal.
But, let's not skirt around accountability. The issue was flagged 11 months ago and it was obviously a major concern given the number of host-associated microbiome projects and the profile of your article (published in Nature Biotechnology). This error will require many projects to be reanalyzed (it has in my research group) and this will only occur when the microbiome community becomes aware of the issue. I hope the Greengenes2 team might speak to their efforts to notify users of the flaws in the first version of their database (Greengenes 2; 2022.10)? This would go a long way to rebuild trust in their work. My group and I missed the news, which has left us scratching our head about how something like this could have gone on for so long!