# Unclassified at the phylum level **URL:** https://forum.qiime2.org/t/unclassified-at-the-phylum-level/31260 **Category:** General Discussion **Tags:** taxonomy, feature-classifier, greengenes2 **Created:** [August 28, 2024, 11:01am UTC](https://forum.qiime2.org/t/unclassified-at-the-phylum-level/31260 "2024-08-28T11:01:26Z") **Posts on this page:** 1 **Showing post:** 5
### Author: ![salias](https://forum.qiime2.org/user_avatar/forum.qiime2.org/salias/32/18594_2.png) [@salias](https://forum.qiime2.org/u/salias) #### Post date: [August 28, 2024, 4:28pm UTC](https://forum.qiime2.org/t/unclassified-at-the-phylum-level/31260/5 "2024-08-28T16:28:01Z")
Hello! > [@microbiome\_25](#): > > They seem to be treated as different phyla in the classification Functionally, they are the same (lack of) phylum. The difference is that, for `d __Bacteria;__ ` the classifier couldn't assign any taxonomy beyond the domain level; whereas for `d __Bacteria;p__ ` the classifier found a match but that match is not annotated at phylum level. So, long story short: yes, they can be understood as the same on a practical level. [This post](https://forum.qiime2.org/t/what-is-the-differences-between-k-bacteria-and-k-bacteria-p/10572) addresses the same issue. > [@microbiome\_25](#): > > should I merge them into one phylum category (unclassified bacteria) > [@microbiome\_25](#): > > I have seen discussions in this forum that it is better to discard bacteria that are not classified at the phylum level Yes you could merge them into one "Unclassified" phylum, although I personally prefer to get rid off these too general taxonomic annotations. I came to this conclusion when I asked [this question](https://forum.qiime2.org/t/taxa-collapse-shows-too-general-taxonomic-assignations/30526) a couple of months ago. > [@microbiome\_25](#): > > I could not find published papers mentioning this in their method sections. Sadly there are a lot of bioinformatic work out there with a Methods section that does not allow replication due to too shallow explanations (not to mention those with no shared code at all...). I suppose this is because a lot of people still think of bioinformatic tools as a black box, and they follow default steps with default variables that they assume they don't need to mention in Methods. Anyway, if you want an example of a Methods section where this filtering is stated, [here you have one](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10269740/). From its Methods section: > _The table and sequences were filtered to exclude any ASV without phylum-level annotation or which could not be inserted into the phylogenetic tree._ I hope this is useful for you. Best wishes! Sergio --- _[View the full topic](https://forum.qiime2.org/t/unclassified-at-the-phylum-level/31260)._