How to deal with the trailing number in taxa table?

General Discussion
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#1

Below are several observations that are filtered from my taxa table. I have one question regarding the training results, some features are labeled as Prevotella, but some of them end with numbers “Prevotella 6”, “Prevotella 7”. Do these represent the same genus? Should I remove the number and treat just as Prevotella or leave the original assignments unchanged?

D_0__Bacteria;D_1__Bacteroidetes;D_2__Bacteroidia;D_3__Bacteroidales;D_4__Prevotellaceae;D_5__Prevotella;D_6__Prevotella amnii DSM 23384 = JCM 14753
D_0__Bacteria;D_1__Bacteroidetes;D_2__Bacteroidia;D_3__Bacteroidales;D_4__Prevotellaceae;D_5__Prevotella 6;D_6__Prevotella colorans
D_0__Bacteria;D_1__Bacteroidetes;D_2__Bacteroidia;D_3__Bacteroidales;D_4__Prevotellaceae;D_5__Prevotella;D_6__Prevotella amnii DSM 23384 = JCM 14753
D_0__Bacteria;D_1__Bacteroidetes;D_2__Bacteroidia;D_3__Bacteroidales;D_4__Prevotellaceae;D_5__Prevotella 7
D_0__Bacteria;D_1__Bacteroidetes;D_2__Bacteroidia;D_3__Bacteroidales;D_4__Prevotellaceae;D_5__Prevotella;D_6__Prevotella disiens JCM 6334 = ATCC 29426
D_0__Bacteria;D_1__Actinobacteria;D_2__Actinobacteria;D_3__Corynebacteriales;D_4__Corynebacteriaceae;D_5__Corynebacterium 1

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#2

Welcome back to the forums!

I googled the text after D_6__ and they seems to be different strains!
https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1122979
https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?lvl=0&id=1235811

D_5__Prevotella is the genus
D_6__Prevotella amnii is the species (well, the genus-species I guess).*

And D_6__Prevotella amnii DSM 23384 = JCM 14753 is genus-species-strain.

All good options. I think it’s cool that you got strain level resolution! But if you wanted to make a bar graph at the genus level or the genus-species level, you could trim those off then merge the features together.

Colin

*Are there any microbes known by just their species? :thinking:
Why don’t viruses go by their genus-species? :face_with_monocle:

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#3

Many thanks for your answers! :grinning:

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