Classification - given names

Dear Mothur/microbiome experts, I was wondering about the classification results. I used SILVA 132 which resulted e.g. in Family_XIII_unclassified and Family_XIII_ge (names given at the genus level). What are the differences between these two taxa? For me they look the same, taxa that were not able to be classified at the genus level; therefore, their names were changed to the higher-order name in this case Family_XIII (family name). Am I right? And if yes, then why they are called differently? I would be grateful for your help, Joanna

bacterial taxonomy is a mess. if you look at that group, does family xiii mean anything? if not, I’ll just use “unclassified whatever Order” when talking about it.

Despite the fact that the name (Family XIII) is meaningless, do you know what might be a reason that I got two names Family_XIII_unclassified and Family_XIII_ge. And what are the differences between them that Family_XIII_ge is not called Family_XIII_unclassified? I wonder if I am missing some point by which mothur determines if something should be called xxx_unclassified or xxx_ge.

On Mac/Linux, if you do the following…

$ cut -f 2 | grep "XIII" | sort | uniq -c

You will get…

  82 Bacteria;Firmicutes;Clostridia;Clostridiales;Family_XIII;Anaerovorax;
  81 Bacteria;Firmicutes;Clostridia;Clostridiales;Family_XIII;Family_XIII_AD3011_group;
  18 Bacteria;Firmicutes;Clostridia;Clostridiales;Family_XIII;Family_XIII_UCG-001;
 133 Bacteria;Firmicutes;Clostridia;Clostridiales;Family_XIII;Family_XIII_ge;
 149 Bacteria;Firmicutes;Clostridia;Clostridiales;Family_XIII;Mogibacterium;
  10 Bacteria;Firmicutes;Clostridia;Clostridiales;Family_XIII;S5-A14a;
  54 Bacteria;Firmicutes;Clostridia;Clostridiales;Family_XIII;uncultured;

As Kendra says, taxonomy, (especially Clostridia!) is a mess. Family_XIII is the family name and there appear to be some genera within it that are not validly named. If you have a sequence that only classifies to the family level within this group, then you’ll get “Family_XIII_unclassified” for the genus name. Alternatively, if you have a sequence that returns “Family_XIII_ge”, then that means that your sequence is most closely affiliated with that genus within Family_XIII.

Thank you! Now, I see that Family_XIII_ge is just a given (strange) name. This raises another question when I run the code on tax_slv_ssu_132.txt, I noticed that it doesn’t have Family_XIII_ge instead it has [Eubacterium] brachy group and [Eubacterium] nodatum group and [Eubacterium] saphenum group. Do you know why this is the case? In the end, this is the same version (132) of SILVA db.

I suspect full length sequences from those groups didn’t make it into the sequences in the nr version of the database.

Is it possible to use directly e.g. SILVA_132_SSURef_tax_silva.fasta.gz in mothur instead of NR version? Or do I have to make it mothur-compatible? And if so, I would appreciate a tip on how to do it.

Our code for generating the reference files we provide is available on the blog at

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