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Genome Taxonomy Database (GTDB) for prokaryotes #202
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About 2/3 of GTDB are non Linnean names like phyla I wonder how much of these names are stable over time to be of any relevance for users. |
@thomasstjerne do you know how these non Linnean names are generated? |
There is some info on placeholder names and stability here. |
For COL to include GTDB it would require the name parser to detect OTU names reliably. |
thanks for the FAQ links, @pragermh ! |
COL is considering to use the List of Prokaryotic names with Standing in Nomenclature LPSN. It is a different taxonomy, but would at least be an up to date one. |
LPSN is probably mostly (only?) suitable for formally described taxa (= a cultured type specimen exist). The major part of prokaryotic data in GBIF origins from metabarcoding studies based on the 16S region. These data types will have taxonomy assigned through some classification pipeline using a reference database such as GTDB or SILVA. GTDB states that
So LPSN probably more or less makes up the subset of formally described taxa in GTDB. |
@dhobern @olafbanki @yroskov for your attention |
Can't we use the football LPSN for the core COL content and the rest of GTDB to extend it? |
I believe LPSN is nomenclature, whereas GTDB is a full Taxonomy (Phylogeny based on assembled genomes). Therefore GTDB might re-organise the classification of names in LPSN quite heavily in some cases. There might therefore be quite some conflicts. |
LPSN has been reorganised to reflect consensus classification in a way that matches what we need for a full COL/GBIF species list based on published names. I am sure there will be some mismatches with molecular phylogeny, but surely that is no different from all other parts of the list. |
Indeed that seems like a plausible and consistent way forward to me. Not much different to the situation with UNITE and BOLD really. |
Neither a taxonomist nor prokaryote expert myself, but perhaps @erikrikarddaniel or @andand has something to add? |
GTDB is quite different than BOLD or UNITE. The latter two uses a short fragment (COI and ITS) to cluster into "species-like" taxa (BINs, SHs). These BINs or SHs are then placed into a consensus classification that in most cases will be much like COL / GBIF. Here is an example: Classification in GTDB: The Phylum It might be safe to conclude that the GTDB phylum |
Yes, the merging procedure we consider will prevent splitting genera into different classifications, even if far apart. By extending LPSN we would therefore use the Binatota placement for all Binatus species coming from GTDB. This is obviously problematic, but that problem is true for all the "extended" sources. I suppose the difference in Bacteria taxonomy is just much larger than anywhere else in the tree, so it has a bigger impact and is more visible. |
Will they move to the other phylum along with Binatus? |
Not if we do it as in the GBIF builds. But it might be a good idea if we can work out how to do this. |
Here are some metrics from the latest data we have in CLB: |
I have created a first version of an ColDP LPSN dataset using their API here: https://www.dev.checklistbank.org/dataset/284997 The main problem with that is that I cannot find a way to access the classification they do show on their site (parent link on top). I have contacted them and asked how to do that, lets see. Also they made LPSN CC BY SA! |
I have opened a dedicated issue for adding LPSN: #632 |
@DianRHR @camiplata I have discussed with @thomasstjerne and @tobiasgf how to best integrate GTDB into the XCOL. |
Dataset title
Genome Taxonomy Database (GTDB)
Dataset contact & access
https://gtdb.ecogenomic.org/
https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/ar122_taxonomy.tsv
https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/bac120_taxonomy.tsv
Taxonomic group & CoL sector
Prokaryotes: Archaea & Bacteria
Dataset description
The Genome taxonomy database (GTDB) is a standardised microbial taxonomy based on genome phylogeny, primarily funded by the Australian Research Council. GTDB currently includes ca. 30,000 prokaryote species clusters based on 195,000 genomes from isolates, metagenomes and single-cells from RefSeq and GenBank.
References:
Parks, D.H., et al. (2020). "A complete domain-to-species taxonomy for Bacteria and Archaea." Nature Biotechnology, https://doi.org/10.1038/s41587-020-0501-8.
Parks, D.H., et al. (2018). "A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life." Nature Biotechnology, 36: 996-1004, https://doi.org/10.1038/nbt.4229.
Motivation for changing/adding
GTDB is a well-defined and fast-growing taxonomy of prokaryotes: Between release 89 (Aug 2019) and 95 (Jul 2020), included genomes and species clusters both increased with ca. 30%, while 99,77% of existing genomes were still assigned to the same species clusters. When publishing a dataset of ca. 3000 Amplicon Sequence Variants (ASVs) of Baltic Sea microbes to the Swedish GBIF node (SBDI), we furthermore found that merging GTDB into the GBIF taxonomy backbone substantially increased the taxonomic resolution for our occurrences: The share of ASVs identified at genus and family level increased from 32 to 62% and 55 to 77%, respectively. Since the database is based on draft genomes rather than a single taxonomic marker gene, it gives a lot of flexibility in terms of usage. For example, shotgun metagenome data can be annotated as well as 16S rRNA gene data.
Suggested by
Anders Andersson (KTH), Daniel Lundin (LnU) and Maria Prager (SU/KI), all associated with the Swedish Biodiversity Data Infrastructure (SBDI).
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