What specific diligence should a researcher perform regarding taxonomy assignment validation?

Answer

Check the specific version of the reference database used

When critically evaluating published microbiome research, especially findings related to species identification, diligence regarding analytical starting points is essential. If an article reports results, the reader should verify not only the software version but critically check the specific version of the reference database utilized for taxonomic assignment. Even minor updates or revisions to databases like Greengenes or SILVA can subtly alter how sequences are matched, potentially leading to slight variations in calculated relative abundances between two analyses performed months apart, thus preventing spurious conclusions about biological differences.

What specific diligence should a researcher perform regarding taxonomy assignment validation?

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