SILVA taxonomy naming conventions

silva
taxonomy
#1

Hi everyone,

Does anyone know why taxonomy in SILVA sometimes have square brackets?

Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Anaerotruncus;[Clostridium]_leptum

Why not just Clostridium leptum instead of [Clostridium] leptum? Does this have any significance, or is it just an error?

Secondly, it is my understanding that some taxa which lack formal classification are placed in groups (eg. Bacteroidales_S24_7_group). Does “S24_7” convey any information? What the naming convention?

(Justine) #2

Hi @SteveMcL,

I know that a lot of phylogenetic references use square brackets to indicate contested names. So, there may be some arguments about whether of not [Clostridium] leptum qualifies as a clostridia or should be re-named.

Best,
Justine

(Leo CA) #3

There is also the “Candidatus” genus which pops up very often. That is “A provisional name for well characterised but as-yet uncultured organisms”, as seen here https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1925548#note1