what is the difference between"f__Ruminococcaceae" AND "f__Lachnospiraceae"

[Ming Liao]

OTU_ID	Sample1	Sample2
k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae;g__Prevotella	0.001138146	0.016509101
k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__[Paraprevotellaceae];g__[Prevotella]	0.002782134	0.040567236

k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Ruminococcus	0.023774597
k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__[Ruminococcus]	0.001441651

There were similar answers to this question: 

https://groups.google.com/forum/#!newtopic/qiime-forum/qiime-forum/WnhQiB5q9Hc

https://groups.google.com/forum/#!newtopic/qiime-forum/qiime-forum/Vc4PWSTwSrE

But I am still confused about "f__Ruminococcaceae;g__Ruminococcus" and "f__Lachnospiraceae;g__[Ruminococcus]"

Since the g__[Ruminococcus] is the recommended one, why its phylum level is NOT the same as g__Ruminococcus?

Does that mean the "g__Ruminococcus" can belong to either "f__Ruminococcaceae" or "f__Lachnospiraceae"?

By the way, there were "g__Clostridium"s  in four different levels: 

k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Clostridium

k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Peptostreptococcaceae;g__Clostridium

k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium

k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Clostridium There as similar question here as well:

https://groups.google.com/forum/#!searchin/qiime-forum/g__Clostridium/qiime-forum/uJ89GGM6C8E/u_lI3aQn-KMJ

But the topic is so old than not open for reply again. I tried to connect with the former replier but failed.

As said by the replier, some of the older taxonomic naming conventions based on morphology/biochemistry don't always match with phylogeny.

Can anyone tell in the case of "g__Clostridium", which phylum name is the latest one? 

I am curious about why the old phylum name is not updated since it do not math with phylogeny. I am really confused.

Thanks

[Colin Brislawn]

Hello there,

I think Danial says it really well in that thread:

The reason these are recommended changes, 
and that they get special annotation, is because they are not 
officially recognized groupings by Bergeys (which is based on 
physiochemical and morphological traits) but are groupings Greengenes 
has observed to be supported by whole genome phylogeny. 

Taxonomy levels [inside brackets] are suggested corrections or candidate levels which are not "official."  

Categorizing living things into discrete groups is challenging! Defining the groups is hard because you have to decide which characteristics are important to you (morphological traits, functional potential, evolutionary history, etc). Dividing up the organisms into the groups is hard because there may be conflicting evidence or confusing information about the organisms. 

Colin Brislawn

[Ming Liao]

Thanks, Colin Brislawn. 

Actually, I am trying to make a published heat map, but I am wondering whether it is fine to show the brackets [ ] with the genus name in the plots. I have not found out any papers presenting the results in this way. Maybe I have not read enough papers to find it out. Could you please give me some suggestion in this case? 

Let me show my questions in details:

case 1:

OTU_ID	Sample1	Sample2
k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae;g__Prevotella	0.001138146	0.016509101
k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__[Paraprevotellaceae];g__[Prevotella]	0.002782134	0.040567236

Is it fine to show "g__Prevotella_in_Prevotellaceae", "g__[Prevotella]_in_[Paraprevotellaceae]" or just "g__Prevotella","g__[Prevotella]"?

case 2:

k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Clostridium

k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Peptostreptococcaceae;g__Clostridium

k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium

k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Clostridium

Since these four are "g__Clostridium" officially recognized by Bergeys, i it  fine to sum up as one "g__Clostridium"? I knew little about how to categorize the living things into discrete groups. Please help. I really appreciate it.

Ming

[Colin Brislawn]

Hello Ming,

I think this is good:
"g__Prevotella","g__[Prevotella]"


This is also good:
f__Prevotellaceae;g__Prevotella
f__[Paraprevotellaceae];g__[Prevotella]

Then in the figure caption, you say "candidate taxonomy shown in square brackets" or "brackets indicate candidate taxonomy."

Colin Brislawn

[Colin Brislawn]

Hello Ming,

Since these four are "g__Clostridium" officially recognized by Bergeys, i it fine to sum up as one "g__Clostridium"?

I think I would keep them separate because they are different at the family level.

Colin Brislawn

[Ming Liao]

OK. Thanks Colin Brislawn. I would like to chose this way:

f__Prevotellaceae;g__Prevotella

f__[Paraprevotellaceae];g__[Prevotella]

 and I am going to keep  "g__Clostridium" separately. 

Sincerely,

Ming