Taxonomy of OTUs using phylotype

Theory behind mothur
1

Hi,

I’m currently writing a paper and I have a small question about how to refer to the taxonomic identifications of OTUs after you have used the phylotype command.

I have been referring to OTUs as, for example, Bradyrhizobium sp. However, I’m not sure this is how I should be referring to them because, if I understand correctly, an OTU which is assigned the phylotype Bradyrhizobium sp. might actually be made up of several species of Bradyrhizobium. Would it be more accurate to refer to the OTU as Bradyrhizobium spp. ?

I don’t particularly want to have to go down the very long winded route of having to say something like ‘this OTU, which was assigned to the phylotype Bradyrhizobium’, mainly because I don’t know how I would put that in a table…

Thanks for your help,

Laura

2

Hi Laura,

We generally refer to things as “OTU X, which is affiliated with the Bradyrhizobium”. Admittedly, this gets long winded and tedious. I’d probably also just say “Bradyrhizobium OTUs were associated with phenotypes X, Y, and Z”. We don’t mess with the sp and spp stuff.

pat