How Does One Decide Which Bacterial Taxonomic Classification To Use: Rdp, Silva Or Greengenes?

Question

[ARich]

Hello Biostar,

Can anyone tells me whats the major differences between silva, RDP and green genes taxonomy files except their implementation. And which classify better and why?

Thanks ARich

[cts]

what do you mean by "taxonomy files except their implementation"? are you talking about the structure of the files themselves or how the databases define their taxonomy?

[ARich]

Hello Thanks for the reply. The question is simple why the preference for one over other. Is the structure varies means one classify in better way over other. if yes which one? and why? Actually I have just started working on Microbiome and I'm confused which one to use for Classification.

[Istvan Albert]

I have edited the title, you may also want to edit the body - your sentence "except their implementation" is very confusing. Just keep it simple.

[Michael]

I think this question requires a little more care from you, ARich, given that an answer might take a considerable amount of work.

Answer 1

[satanicodr]

RDP uses the Bergeys taxonomy, which is more conservative and standard. Silva and Greengenes use their own taxonomies which are developed by their own teams and collaborators. For some groups, collaborations have improved the taxonomy and may help you if you are working with a specific groups of organisms. E.g. Silva has a nice eukaryotic taxonomy. Another key difference is that with RDP the lowest taxonomy level is genus whereas you can go to species and strain. Having said that, I will not have a lot of confidence working at strain level if I have a 100 bp read. If you are working with the human microbiome, the thee of them will do a good work since the human-related microorganism are better studied that some rare phyla.

[crespialba]

It is possible to map the silva entries to the standard taxonomic classification/ids used by NCBI and EBI. In the archive section, for each release there is a directory called "taxonomy". In here you can find a file that contains the name "taxmap_embl". This file tells you for each silva id the corresponding taxid according to NCBI/EBI.

[Leonardo]

HI crespialba, Would you mind to clarify where that taxmap_embl file is? I couldn't find it in both Silva and NCBI databaases.

Answer 2

[cts]

Just to add to satanicodr's answer, one of the main differences between Greengenes and Silva is the way in which the tree is built. Greengenes construct a de novo tree; Silva use a seed tree and add extra sequences into it parsimoniously. There is a tradeoff between these two methods in that a de novo tree should give the most accurate topology of the sequence data however it is more sensitive to poor quality sequences or chimeras.

Differences in taxonomy arise due to differences in the topology of the tree causing sequences to be grouped differently into monophyletic groups. This is also compounded by regions of the tree that are only known by environmental sequences where the names are up to whoever is curating the tree and naming these groups. I known that the people behind both Greengenes and Silva are working on trying to standardise the naming in these instances.

Greengenes or Sliva will serve you well but I use greengenes because I prefer the de novo tree construction (and because one of my PhD advisors is the curator).

Answer 3

[-_-]

I have found many error records with wrong taxonomy in SILVA database, and I don't feel they're of very high quality in any sense. The author also told there is no way to systematically remove those entries yet. The library location is http://www.arb-silva.de/fileadmin/silva_databases/release_119_1/Exports/SILVA_119.1_SSURef_Nr99_tax_silva.fasta.gz.

>EU661378.1.1449 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Klebsiella pneumoniae
>EU693565.1.1364 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Enterobacter sp. 2V5B
>EU693571.1.1348 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Enterobacter sp. 2B5C
>HM587332.1.1358 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Enterobacter sp. IBP-VN5
>KF835768.1.1391 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Enterobacter aerogenes
>KF835769.1.1392 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Enterobacter aerogenes
>FJ025770.1.1396 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Enterobacter sp. 12-1
>JQ396392.1.1408 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Enterobacter sp. PXG15
>HQ670758.1.1517 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Klebsiella pneumoniae
>AB680212.1.1465 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Klebsiella pneumoniae
>AB680226.1.1465 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Klebsiella pneumoniae
>AB680392.1.1465 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Klebsiella pneumoniae
>EF185903.1.1234 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Enterobacter cloacae
>FJ608708.1.1457 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Serratia marcescens
>EF185902.1.1234 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Enterobacter cloacae
>EU231611.1.1533 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Klebsiella pneumoniae
>EU301778.1.1265 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Klebsiella pneumoniae
>ATRO01000398.8366.9885 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Klebsiella pneumoniae LCT-KP289
>KF475833.1.1481 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Enterobacter asburiae
>JF772061.1.1504 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Klebsiella pneumoniae
>AJHE02000449.2162.3681 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Klebsiella pneumoniae subsp. pneumoniae LCT-KP214
>AJHE02000454.164.1683 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Klebsiella pneumoniae subsp. pneumoniae LCT-KP214
>AJHE02000044.64686.66205 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Klebsiella pneumoniae subsp. pneumoniae LCT-KP214
>AJJI01000015.278576.280108 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Klebsiella pneumoniae subsp. pneumoniae DSM 30104
>AJJI01000014.612023.613555 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Klebsiella pneumoniae subsp. pneumoniae DSM 30104
>JQ912515.1.1261 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Enterobacter sp. DL4.6
>JQ912519.1.1290 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Enterobacter sp. HD4.3
>JN644624.1.1541 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Klebsiella pneumoniae
>KC342873.1.1376 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Enterobacter sp. 1FTM7
>AYIL01000018.41808.43335 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Klebsiella pneumoniae UCICRE 4
>AYJB01000001.521310.522837 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Klebsiella pneumoniae MGH 32
>AYJB01000018.59517.61044 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Klebsiella pneumoniae MGH 32
>AYIB01000001.237286.238813 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Klebsiella pneumoniae BIDMC 21
>AYJL01000017.211699.213226 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Klebsiella pneumoniae MGH 19
>AYJB01000001.1270191.1271718 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Klebsiella pneumoniae MGH 32
>AYIJ01000014.367298.368825 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Klebsiella pneumoniae UCICRE 6
>AYIQ01000014.486.2013 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Klebsiella pneumoniae BWH 30
>AYIQ01000015.99655.101182 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Klebsiella pneumoniae BWH 30
>HF968745.1.1324 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Enterobacter sp. TN468
>HM461212.1.1460 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Enterobacter sp. enrichment culture clone HSL83A
>HM461153.1.1464 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Enterobacter sp. enrichment culture clone HSL30