# Core microbiome species

**URL:** https://forum.biobakery.org/t/core-microbiome-species/2927
**Category:** MetaPhlAn
**Created:** [December 20, 2021, 11:52am UTC](https://forum.biobakery.org/t/core-microbiome-species/2927 "2021-12-20T11:52:47Z")
**Posts on this page:** 4
**Page:** 1

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### Author: ![saras22](https://avatars.discourse-cdn.com/v4/letter/s/59ef9b/32.png) [@saras22](https://forum.biobakery.org/u/saras22)
#### Post date: [December 20, 2021, 11:52am UTC](https://forum.biobakery.org/t/core-microbiome-species/2927/1 "2021-12-20T11:52:47Z")

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Hi @fbeghini  
I want to find out the core microbial species from the 7 groups of the samples that I have. How do I make venn diagramm from the metaphlan3 merged abundance table? Thera are tools but for that I need biom format table which I am not able to make.

Saraswati Awasthi

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### Author: ![fbeghini](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fbeghini/32/81_2.png) [@fbeghini](https://forum.biobakery.org/u/fbeghini)
#### Post date: [January 6, 2022, 4:02pm UTC](https://forum.biobakery.org/t/core-microbiome-species/2927/2 "2022-01-06T16:02:10Z")

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There are plenty of packages for creating venn diagrams from vectors (e.g. R VennDiagram). If you are using a package that requires a BIOM file as input, MetaPhlAn can produce a BIOM output by using `--biom_output_file`

![](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/1X/2daeaa8b5f19f0bc209d976c02bd6acb51b00b0a.gif)ᐧ

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### Author: ![saras22](https://avatars.discourse-cdn.com/v4/letter/s/59ef9b/32.png) [@saras22](https://forum.biobakery.org/u/saras22)
#### Post date: [January 11, 2022, 6:11am UTC](https://forum.biobakery.org/t/core-microbiome-species/2927/3 "2022-01-11T06:11:32Z")

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@fbeghini  
Do I have to run the whole analysis again to obtain the biom format or I can obtain it from the bowtie 2 output files?

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### Author: ![fbeghini](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fbeghini/32/81_2.png) [@fbeghini](https://forum.biobakery.org/u/fbeghini)
#### Post date: [January 11, 2022, 1:12pm UTC](https://forum.biobakery.org/t/core-microbiome-species/2927/4 "2022-01-11T13:12:07Z")

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No need to re run everything, you can use the bowtie2out as input to generate the BIOM file.