Sar11 clade and Pelagibacteraceae classification in gg

[sln (selin küçükavşar)]

Dear All,

It might not be suitable topic to discuss here but I need your kind help and understanding.

I am working with marine samples and analysed my data using q2. What we observed is the most dominant taxa is classified as k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Pelagibacteraceae;g__
I realized that this is the SAR11 clade proposed to be considered a distinct family, as Pelagibacteraceae, fam. nov by Thrash et al., 2011. I would like to discuss my results with previous studies but I cannot be sure that these are referring to the same. I checked gg_13_5 otus files’ taxonomy file if there is any taxa classified as SAR11 clade but I could not find. The paper published after 2011 has considered Pelagibacteraceae as SAR11 clade (Spatial and temporal patterns in the Pelagibacteraceae across an estuarine gradient by Ortmann and Santos, 2016.)
My question is if gg database considers the SAR11 clade as Pelagibacteraceae. Or is there a way that I can confirm that they are the same or not.

Sorry for this really specific question.

Selin

[wasade (Daniel McDonald)]

Hi @sln,

I would guess that the de novo phylogeny in the 13_5 release did not support a distinct clade, or the input taxonomy combined with a phylogeny was unable to reconcile a placement for SAR11. If you have the Genbank accessions for SAR11 organisms then you may be able to cross reference them with the records in Greengenes with the accession map.

SILVA may be worth using here too as it has a marine specific focus.

Best,
Daniel

[sln (selin küçükavşar)]

Dear Daniel,

Thanks a lot for the information. I will try checking accession numbers and also SILVA for taxonomy.

Bests,

Selin