# I only detected a few bacteria

**URL:** <https://forum.biobakery.org/t/i-only-detected-a-few-bacteria/2542>\
**Category:** HUMAnN\
**Created:** [September 1, 2021, 7:35am UTC](https://forum.biobakery.org/t/i-only-detected-a-few-bacteria/2542 "2021-09-01T07:35:52Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![CK\_zhu](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/ck_zhu/32/151_2.png) [@CK\_zhu](https://forum.biobakery.org/u/CK_zhu)\
**Post date:** [September 1, 2021, 7:35am UTC](https://forum.biobakery.org/t/i-only-detected-a-few-bacteria/2542/1 "2021-09-01T07:35:52Z")

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Hi I use humann3 but find only 38 species in metaphaln\_bugs\_list， but the results from kraken and motus have 6199 and 91 each, humann2 have 52 ?  
why humann3 less than huamnn2?

```auto
# humann3
$ grep "s__" 10WK-D54_humann_temp/10WK-D54_metaphlan_bugs_list.tsv |wc -l
38

# kraken2
[$ grep "s__" 10WK-D54.report |awk -F" " '$2 !=0 {print $2}'|wc -l
6199

# motus2
grep -v "#" 10WK-D54_taxonomy.txt |awk -F " " '$2!=0 {print $2}'|wc -l
91

# humann2
cat 10WK-D54_metaphlan_bugs_list.tsv |grep "s__"|wc -l
52

```

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<div class="post-metadata">

**Author:** ![franzosa](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/franzosa/32/3511_2.png) [@franzosa](https://forum.biobakery.org/u/franzosa)\
**Post date:** [September 3, 2021, 9:35pm UTC](https://forum.biobakery.org/t/i-only-detected-a-few-bacteria/2542/2 "2021-09-03T21:35:40Z")

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I can think of a few reasons - MetaPhlAn 3 makes more effort to group together very very closely related species as “species groups.” In addition, MetaPhlAn 2 will list “Genus\_X\_unclassified” and subpecies-level (`t__`) clades which are not found in MetaPhlAn 3. If you look at which rows are different between the v2 and v3 output it may provide some additional clues.