Would qiime 2 support Mycobacterium data analysis ?

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Hello,

Can you confirm if QIIME 2 platform support mycobacterium data analysis ? can we also used it for Mycobacterium species discrimination (eg Mycobacterium tuberculosis versus Mycobacterium bovis ) ?

Thanks

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Hello Meriem,

It's good to hear from you!

species discrimination

This will depend mostly on the gene region you decide to target with PCR. Qiime2 and other bioinformatics software will only be able to resolve differences captured during sequencing.

Have you found primers that reliably differentiate these taxa? You can share the citations for these PCR primers if you would like!

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Thanks for the reply @colinbrislawn.

We are searching for a specific gene target that enables us to discriminate between mycobacterium species. Do you think that 16 S would be a good candidate for mycobacterial discrimination ?

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Maybe not... I like using the 16S v4 gene because it detects many different microbes down to family and genus levels. If I really cared about species or strain level, I would probably also care about the expression of specific transcripts using RNA seq.

How do you currently detect differences between mycobacterium species?

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