I have been troubled about the taxa annotation recently. I adopted
metaphlan3 to profile the taxa previously, about April 8, but last week I used the latest
metaphlan3 to profile the taxa again with the same command, but the taxa profile was totally different. Then I adopted
kraken2+bracken to profile the taxa, then I got another different result. I am really really really confounded. I understand there might be some differences between different software, but I cannot accept they are completely distinct. Which one should I believe? If the result would totally be changed if the software or database has been updated, how can we trust the previously published work? How can we make our results reproducible?