Why might older papers report very different diversity figures than contemporary ones using the same raw data?
Answer
The underlying analysis tool itself was updated
A crucial factor in comparing microbiome studies across different time points is recognizing the rapid evolution of analytical software. Since the development of analysis tools constantly iterates, using a different version of the software—even on the exact same raw sequencing data—can lead to variations in reported metrics, including diversity figures. An updated algorithm, a change in the statistical model used (like rarefaction methods), or an updated reference database version can all cause shifts in relative abundance numbers, meaning the difference observed is often an artifact of the analytic pipeline rather than a true biological distinction.
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