# Discrepancies in analysis

**URL:** <https://forum.biobakery.org/t/discrepancies-in-analysis/1590>\
**Category:** MetaPhlAn\
**Created:** [January 21, 2021, 4:34pm UTC](https://forum.biobakery.org/t/discrepancies-in-analysis/1590 "2021-01-21T16:34:39Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Chandrima-04](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/chandrima-04/32/596_2.png) [@Chandrima-04](https://forum.biobakery.org/u/Chandrima-04)\
**Post date:** [January 21, 2021, 4:34pm UTC](https://forum.biobakery.org/t/discrepancies-in-analysis/1590/1 "2021-01-21T16:34:40Z")

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While analyzing the same dataset with Metaphlan2 and Metaphlan3, there are huge discrepancies in the microbiome profile with less than 50% similarity between any 2 samples. How is the change supposed to be interpreted?

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**Author:** ![Dario](https://avatars.discourse-cdn.com/v4/letter/d/bc79bd/32.png) [@Dario](https://forum.biobakery.org/u/Dario)\
**Post date:** [April 27, 2021, 3:00am UTC](https://forum.biobakery.org/t/discrepancies-in-analysis/1590/2 "2021-04-27T03:00:05Z")

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I would say it is mainly because of the greatly expanded database of bacterial genomes used. The pre-print in bioRxiv states “MetaPhlAn 3 incorporates 13500 species (more than twice than  
MetaPhlAn 2) with a completely new set of 1.1 million marker genes.” If the marker genes changed a lot, I expect that results would change a lot, too.