How can I reveal the name of species ?

Hi,

When I analyzed the differential abundance testing with ANCOM,
The results were as follows.

k__Bacteria;p__Fusobacteria;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium;s__

I want to know what name is s_ .
So how can I get the information of feature ?

I chosed 99% OTU sequences and 99% OTU taxonomy.

If I chose 97% or more lower% OTU sequences and OTU taxonomy, can I reveal the name of species ?

Please tell me.

Hi @yoshikisuzu,

The joy of many microbiome databases (greengenes in particular) is that there often isn’t a specific species name. This is one example. My suggestion here is that you use the OTU/ASV identifier and describe that. It gets away from the problem of uncultured (and therefore unnamed) species; the fact that species are a messy concept in microbiology; and makes your results more externally valid if you’re using ASVs.

Best,
Justine

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Dear, jwdebelius,
Thank you for your reply !
Does this mean that what you mean is this?

Hi @yoshikisuzu,

Yes, those are your ASV IDs. They tell you what’s happeninhg at the species level. You can describe them as something like "An ASV belonging to genus Fusobacterium and not have to worry about species names.

I usually provide my sequences as supplementary information in my manuscript (if you have more than 1 sample, its deidentified aggregate data which is no different from providing quartiles for sample characteristics).

Best,
Justine

Dear Justine,

Yes. Your advice is very helpful.
Thank you very much !
I learned a lot.

yoshiki

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