microorganisms {AMR}

Data Set with 52 171 Microorganisms

Description

A data set containing the full microbial taxonomy (last updated: December 11th, 2022) of five kingdoms from the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF). This data set is the backbone of this AMR package. MO codes can be looked up using as.mo().

Usage

microorganisms

Format

A tibble with 52 171 observations and 23 variables:

• mo
  ID of microorganism as used by this package. This is a unique identifier.

• fullname
  Full name, like "Escherichia coli". For the taxonomic ranks genus, species and subspecies, this is the 'pasted' text of genus, species, and subspecies. For all taxonomic ranks higher than genus, this is the name of the taxon. This is a unique identifier.

• status
  Status of the taxon, either "accepted" or "synonym"

• kingdom, phylum, class, order, family, genus, species, subspecies
  Taxonomic rank of the microorganism

• rank
  Text of the taxonomic rank of the microorganism, such as "species" or "genus"

• ref
  Author(s) and year of related scientific publication. This contains only the first surname and year of the latest authors, e.g. "Wallis et al. 2006 emend. Smith and Jones 2018" becomes "Smith et al., 2018". This field is directly retrieved from the source specified in the column source. Moreover, accents were removed to comply with CRAN that only allows ASCII characters.

• lpsn
  Identifier ('Record number') of the List of Prokaryotic names with Standing in Nomenclature (LPSN). This will be the first/highest LPSN identifier to keep one identifier per row. For example, Acetobacter ascendens has LPSN Record number 7864 and 11011. Only the first is available in the microorganisms data set.

• oxygen_tolerance
  Oxygen tolerance, either "aerobe", "anaerobe", "anaerobe/microaerophile", "facultative anaerobe", "likely facultative anaerobe", or "microaerophile". These data were retrieved from BacDive (see Source). Items that contain "likely" are missing from BacDive and were extrapolated from other species within the same genus to guess the oxygen tolerance. Currently 73.4% of all ~37 000 bacteria in the data set contain an oxygen tolerance.

• lpsn_parent
  LPSN identifier of the parent taxon

• lpsn_renamed_to
  LPSN identifier of the currently valid taxon

• gbif
  Identifier ('taxonID') of the Global Biodiversity Information Facility (GBIF)

• gbif_parent
  GBIF identifier of the parent taxon

• gbif_renamed_to
  GBIF identifier of the currently valid taxon

• source
  Either "GBIF", "LPSN", or "manually added" (see Source)

• prevalence
  Prevalence of the microorganism according to Bartlett et al. (2022, doi:10.1099/mic.0.001269), see mo_matching_score() for the full explanation

• snomed
  Systematized Nomenclature of Medicine (SNOMED) code of the microorganism, version of July 1st, 2021 (see Source). Use mo_snomed() to retrieve it quickly, see mo_property().

Details

Please note that entries are only based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF) (see below). Since these sources incorporate entries based on (recent) publications in the International Journal of Systematic and Evolutionary Microbiology (IJSEM), it can happen that the year of publication is sometimes later than one might expect.

For example, Staphylococcus pettenkoferi was described for the first time in Diagnostic Microbiology and Infectious Disease in 2002 (doi:10.1016/s0732-8893(02)00399-1), but it was not before 2007 that a publication in IJSEM followed (doi:10.1099/ijs.0.64381-0). Consequently, the AMR package returns 2007 for mo_year("S. pettenkoferi").

Included Taxa

Included taxonomic data are:

• All ~37 000 (sub)species from the kingdoms of Archaea and Bacteria

• ~7 900 (sub)species from the kingdom of Fungi. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package. Only relevant fungi are covered (such as all species of Aspergillus, Candida, Cryptococcus, Histoplasma, Pneumocystis, Saccharomyces and Trichophyton).

• ~5 100 (sub)species from the kingdom of Protozoa

• ~1 400 (sub)species from 43 other relevant genera from the kingdom of Animalia (such as Strongyloides and Taenia)

• All ~9 800 previously accepted names of all included (sub)species (these were taxonomically renamed)

• The complete taxonomic tree of all included (sub)species: from kingdom to subspecies

• The identifier of the parent taxons

• The year and first author of the related scientific publication

Manual additions

For convenience, some entries were added manually:

• ~1 500 entries of Salmonella, such as the city-like serovars and groups A to H

• 36 species groups (such as the beta-haemolytic Streptococcus groups A to K, coagulase-negative Staphylococcus (CoNS), Mycobacterium tuberculosis complex, etc.), of which the group compositions are stored in the microorganisms.groups data set

• 1 entry of Blastocystis (B. hominis), although it officially does not exist (Noel et al. 2005, PMID 15634993)

• 1 entry of Moraxella (M. catarrhalis), which was formally named Branhamella catarrhalis (Catlin, 1970) though this change was never accepted within the field of clinical microbiology

• 8 other 'undefined' entries (unknown, unknown Gram-negatives, unknown Gram-positives, unknown yeast, unknown fungus, and unknown anaerobic Gram-pos/Gram-neg bacteria)

The syntax used to transform the original data to a cleansed R format, can be found here: https://github.com/msberends/AMR/blob/main/data-raw/reproduction_of_microorganisms.R.

Direct download

Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit our website for the download links. The actual files are of course available on our GitHub repository.

About the Records from LPSN (see Source)

LPSN is the main source for bacteriological taxonomy of this AMR package.

The List of Prokaryotic names with Standing in Nomenclature (LPSN) provides comprehensive information on the nomenclature of prokaryotes. LPSN is a free to use service founded by Jean P. Euzeby in 1997 and later on maintained by Aidan C. Parte.

Source

• Parte, AC et al. (2020). List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; doi:10.1099/ijsem.0.004332. Accessed from https://lpsn.dsmz.de on December 11th, 2022.

• GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset doi:10.15468/39omei. Accessed from https://www.gbif.org on December 11th, 2022.

• Reimer, LC et al. (2022). BacDive in 2022: the knowledge base for standardized bacterial and archaeal data. Nucleic Acids Res., 50(D1):D741-D74; doi:10.1093/nar/gkab961. Accessed from https://bacdive.dsmz.de on May 12th, 2023.

• Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microorganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: https://phinvads.cdc.gov

• Grimont et al. (2007). Antigenic Formulae of the Salmonella Serovars, 9th Edition. WHO Collaborating Centre for Reference and Research on Salmonella (WHOCC-SALM).

• Bartlett et al. (2022). A comprehensive list of bacterial pathogens infecting humans Microbiology 168:001269; doi:10.1099/mic.0.001269

See Also

as.mo(), mo_property(), microorganisms.groups, microorganisms.codes, intrinsic_resistant

Examples

microorganisms