A data set containing the microbial taxonomy of six kingdoms from the Catalogue of Life. MO codes can be looked up using
A data.frame with 67,151 observations and 16 variables:
ID of microorganism as used by this package
Full name, like
Taxonomic rank of the microorganism
Text of the taxonomic rank of the microorganism, like
Author(s) and year of concerning scientific publication
ID of the species as used by the Catalogue of Life
Either "CoL", "DSMZ" (see Source) or "manually added"
Prevalence of the microorganism, see
Parte, A.C. (2018). LPSN — List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; doi: 10.1099/ijsem.0.002786
Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany, Prokaryotic Nomenclature Up-to-Date, https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date and https://lpsn.dsmz.de (check included version with
Manually added were:
11 entries of Streptococcus (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)
2 entries of Staphylococcus (coagulase-negative (CoNS) and coagulase-positive (CoPS))
3 entries of Trichomonas (Trichomonas vaginalis, and its family and genus)
1 entry of Candida (Candida krusei), that is not (yet) in the Catalogue of Life
1 entry of Blastocystis (Blastocystis hominis), although it officially does not exist (Noel et al. 2005, PMID 15634993)
5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)
6 families under the Enterobacterales order, according to Adeolu et al. (2016, PMID 27620848), that are not (yet) in the Catalogue of Life
7,411 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications
This data set is available as 'flat file' for use even without R - you can find the file here:
The file in R format (with preserved data structure) can be found here:
Names of prokaryotes are defined as being validly published by the International Code of Nomenclature of Bacteria. Validly published are all names which are included in the Approved Lists of Bacterial Names and the names subsequently published in the International Journal of Systematic Bacteriology (IJSB) and, from January 2000, in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) as original articles or in the validation lists. (from https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date)
In February 2020, the DSMZ records were merged with the List of Prokaryotic names with Standing in Nomenclature (LPSN).
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (http://www.catalogueoflife.org). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this
AMR package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find all download links on our website, which is automatically updated with every code change.
On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey!