Taxonomy Problem about Greengene 13.8

The question is how can we deal with the taxonomy like k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Clostridium;s__colinum?
It indeed exists in 99%taxonomy file in Greengene 13.8 database.
But we can only find that Clostridium(genus level) belongs to Clostridiaceae( family level ) in NCBI Toxonomy NCBI Taxonomy.

l would appreciate if someone could tell me something about it.

Good morning @cxf514,

This is probably a simple difference in taxonomy naming levels. Take a look at the second paper published on the greengenes database and their discussion of how their uniform 7 levels differes from NCBI. Especially this part:

Changes in sequence classifications between NCBI and Greengenes at each rank are summarized in Figure 2b. Most changes were from uninformative (domain/kingdom name only) in NCBI to informative in Greengenes again reflecting the classification of the large fraction of unclassified environmental sequence in NCBI. The percentage of changes to informative NCBI classifications were relatively low (<7% for all ranks), indicating the degree of congruence between NCBI and Greengenes classifications achieved in part by accommodating polyphyletic groups (see below).

Looks like you found one of those 7% of differing levels. :woman_shrugging:

It’s also possible that the taxonomy of this microbe has been updated in NCBI but not in greengenes, which has not been updated since 2013.

If a ref mentioned this in review, you can change it to whatever family they like best. Which family do YOU think Clostridium belongs to?

Colin

Thanks for your detailed reply.

l think it make sense.

l decide to divide Clostridium into Clostridiaceae which just follows the Taxonomy.
Thanks again

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