Taxonomy tree conflicts in Greengenes V 13.5

uloeber · 09-03-2019, 01:52 AM

Hi all,
I'm using the Lotus pipeline to investigate 16S stool samples. I assigned taxonomy with Greengenes, SILVA, HITdb , since greengenes was updated most recently, SILVA is the biggest database and the unassigned OTUs could then be classified by HITdb.
I was not surprised, that tree conflicts occurred, but what was surprising was that greengenes itself (V 13.5 05/2019) included conflicting information, or how would you judge this:
158718 k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Prevotellaceae; g__Prevotella; s__

186714 k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__[Paraprevotellaceae]; g__[Prevotella]; s__

What does the parenthesis mean? Anyways, unfortunately, this results in one genus on different nodes, retrieved from one database!

Looking much forward for a fruitful discussion with you.

Cheers,
Ulrike

asorbie · 09-09-2019, 12:31 AM

Greengenes hasn't actually been updated since 2013. Personally, I just wouldn't use it at all. Stick to Silva, RDP or GTDB if possible.

uloeber · 09-09-2019, 03:50 AM

Really? I used version 13-5 released this year 2019-05-01

asorbie · 09-09-2019, 03:53 AM

I think they may have changed some minor things this year but not the entire database. 13-5 is the May 2013 release.

uloeber · 09-10-2019, 04:17 AM

Thank you!

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09-03-2019, 01:52 AM	#1
uloeber Member Location: Germany Join Date: Mar 2013 Posts: 44	Taxonomy tree conflicts in Greengenes V 13.5 Hi all, I'm using the Lotus pipeline to investigate 16S stool samples. I assigned taxonomy with Greengenes, SILVA, HITdb , since greengenes was updated most recently, SILVA is the biggest database and the unassigned OTUs could then be classified by HITdb. I was not surprised, that tree conflicts occurred, but what was surprising was that greengenes itself (V 13.5 05/2019) included conflicting information, or how would you judge this: 158718 k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Prevotellaceae; g__Prevotella; s__ 186714 k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__[Paraprevotellaceae]; g__[Prevotella]; s__ What does the parenthesis mean? Anyways, unfortunately, this results in one genus on different nodes, retrieved from one database! Looking much forward for a fruitful discussion with you. Cheers, Ulrike

09-09-2019, 12:31 AM	#2
asorbie Junior Member Location: Munich Join Date: Jun 2017 Posts: 8	Greengenes hasn't actually been updated since 2013. Personally, I just wouldn't use it at all. Stick to Silva, RDP or GTDB if possible.

09-09-2019, 03:50 AM	#3
uloeber Member Location: Germany Join Date: Mar 2013 Posts: 44	Really? I used version 13-5 released this year 2019-05-01

09-09-2019, 03:53 AM	#4
asorbie Junior Member Location: Munich Join Date: Jun 2017 Posts: 8	I think they may have changed some minor things this year but not the entire database. 13-5 is the May 2013 release.

09-10-2019, 04:17 AM	#5
uloeber Member Location: Germany Join Date: Mar 2013 Posts: 44	Thank you!