Checking for available genomes in MetaPhlAn Database

Microbial community profiling MetaPhlAn
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Hi Admin,

I am a first-year Ph.D. student and I intend to use MetaPhlAn and possibly StrainPhlAn for estimating the relative abundance of Lactobacillus plantarum ATCC 202195 (NCBI Accession numbers: CP063750.1, CP063751.1, and CP063752.1) (Lactiplantibacillus plantarum strain ATCC 202195 chromosome, complete - Nucleotide - NCBI)) in my stool samples.

How can I determine if my strain of interest is present in the MetaPhlAn and StrainPhlAn databases?

Kind regards,
Jennifer

2

Hi @jennychika
Using MetaPhlAn 3 you will be able to estimate the relative abundance of L. plantarum at the species level. Unfortunately, MetaPhlAn does not have the strain-level resolution.
For strain-level resolution, you can run StrainPhlAn after running MetaPhlAn. If you are interested in specific reference strains, you can add them to the tree with the parameter -r and then retrieve the SNPs between the strains in your samples and your references using the --mutation_rates parameter

1 Like
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Thank you for your response.

Please I am very new to metagenomic analysis and haven’t used these pipelines before. Apologies if my questions appear very naive.

I am wondering firstly if there is a way to check the StrainPhlAn database to know what strains are already uploaded as references (I have a list of strains that I am interested in), then I can know what extra strains to add.

Secondly, is there a link to a tutorial on how to add additional strains on StrainPhlAn that I access to gain a better understanding?

Finally, Do MetaPhlAn and StrainPhlAn accept abundance tables (not reads) for analysis?

Thanks again in anticipation of your response.
Jennifer

4

Thank you for your response. I thought I had previously replied but it appears that I didn’t reply directly to you.

Please I am very new to metagenomic analysis and haven’t used these pipelines before. Apologies if my questions appear very naive.

I am wondering firstly if there is a way to check the StrainPhlAn database to know what strains are already uploaded as references (I have a list of strains that I am interested in), then I can know what extra strains to add.

Secondly, is there a link to a tutorial on how to add additional strains on StrainPhlAn that I access to gain a better understanding?

Finally, Do MetaPhlAn and StrainPhlAn accept abundance tables (not reads) for analysis?

Thanks again in anticipation of your response.
Jennifer

5

Hi @jennychika
Unfortunately, there are no strains already uploaded as references in StrainPhlAn, any strain you want to add as reference genome in the tree should be manually added with the -r parameter. Please, have a look at this post: Identifying Strain Names
For your last question, no, MetaPhlAn should be run on the reads (or on the a sam/bowtie2out file produced already by MetaPhlAn) and StrainPhlAn should always start from the sam files from MetaPhlAn.

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Thanks for the clarification. Well appreciated.