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Data Set with 78 678 Taxonomic Records of Microorganisms

Source: R/data.R
microorganisms.Rd

A data set containing the full microbial taxonomy (last updated: June 24th, 2024) of six kingdoms. This data set is the backbone of this AMR package. MO codes can be looked up using as.mo() and microorganism properties can be looked up using any of the mo_* functions.

This data set is carefully crafted, yet made 100% reproducible from public and authoritative taxonomic sources (using this script), namely: List of Prokaryotic names with Standing in Nomenclature (LPSN) for bacteria, MycoBank for fungi, and Global Biodiversity Information Facility (GBIF) for all others taxons.

Usage

microorganisms

Format

A tibble with 78 678 observations and 26 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", "not validly published", "synonym", or "unknown"

  • kingdom, phylum, class, order, family, genus, species, subspecies
    Taxonomic rank of the microorganism. Note that for fungi, phylum is equal to their taxonomic division. Also, for fungi, subkingdom and subdivision were left out since they do not occur in the bacterial taxonomy.

  • 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.

  • 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 68.3% of all ~39 000 bacteria in the data set contain an oxygen tolerance.

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

  • lpsn
    Identifier ('Record number') of 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. This is a unique identifier, though available for only ~33 000 records.

  • lpsn_parent
    LPSN identifier of the parent taxon

  • lpsn_renamed_to
    LPSN identifier of the currently valid taxon

  • mycobank
    Identifier ('MycoBank #') of MycoBank. This is a unique identifier, though available for only ~18 000 records.

  • mycobank_parent
    MycoBank identifier of the parent taxon

  • mycobank_renamed_to
    MycoBank identifier of the currently valid taxon

  • gbif
    Identifier ('taxonID') of Global Biodiversity Information Facility (GBIF). This is a unique identifier, though available for only ~49 000 records.

  • gbif_parent
    GBIF identifier of the parent taxon

  • gbif_renamed_to
    GBIF identifier of the currently valid taxon

  • prevalence
    Prevalence of the microorganism based on 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 16th, 2024 (see Source). Use mo_snomed() to retrieve it quickly, see mo_property().

Source

Taxonomic entries were imported in this order of importance:

  1. List of Prokaryotic names with Standing in Nomenclature (LPSN):

    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 June 24th, 2024.

  2. MycoBank:

    Vincent, R et al (2013). MycoBank gearing up for new horizons. IMA Fungus, 4(2), 371-9; doi:10.5598/imafungus.2013.04.02.16 . Accessed from https://www.mycobank.org on June 24th, 2024.

  3. Global Biodiversity Information Facility (GBIF):

    GBIF Secretariat (2023). GBIF Backbone Taxonomy. Checklist dataset doi:10.15468/39omei . Accessed from https://www.gbif.org on June 24th, 2024.

Furthermore, these sources were used for additional details:

  • BacDive:

    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 July 16th, 2024.

  • Systematized Nomenclature of Medicine - Clinical Terms (SNOMED-CT):

    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). Accessed from https://phinvads.cdc.gov on July 16th, 2024.

  • 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

Details

Please note that entries are only based on LPSN, MycoBank, and 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 until 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 from LPSN, MycoBank, and GBIF are:

  • All ~39 000 (sub)species from the kingdoms of Archaea and Bacteria

  • ~28 000 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).

  • ~8 100 (sub)species from the kingdom of Protozoa

  • ~1 600 (sub)species from 39 other relevant genera from the kingdom of Animalia (such as Strongyloides and Taenia)

  • All ~22 000 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.

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, and Stata. Please visit our website for the download links. The actual files are of course available on our GitHub repository.

See also

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

Examples

microorganisms
#> # A tibble: 78,678 × 26
#>    mo          fullname   status kingdom phylum class order family genus species
#>    <mo>        <chr>      <chr>  <chr>   <chr>  <chr> <chr> <chr>  <chr> <chr>  
#>  1 B_GRAMN     (unknown … unkno… Bacter… (unkn… (unk… (unk… "(unk… (unk… "(unkn…
#>  2 B_GRAMP     (unknown … unkno… Bacter… (unkn… (unk… (unk… "(unk… (unk… "(unkn…
#>  3 B_ANAER-NEG (unknown … unkno… Bacter… (unkn… (unk… (unk… "(unk… (unk… "(unkn…
#>  4 B_ANAER-POS (unknown … unkno… Bacter… (unkn… (unk… (unk… "(unk… (unk… "(unkn…
#>  5 B_ANAER     (unknown … unkno… Bacter… (unkn… (unk… (unk… "(unk… (unk… "(unkn…
#>  6 F_FUNGUS    (unknown … unkno… Fungi   (unkn… (unk… (unk… "(unk… (unk… "(unkn…
#>  7   UNKNOWN   (unknown … unkno… (unkno… (unkn… (unk… (unk… "(unk… (unk… "(unkn…
#>  8 P_PROTOZOAN (unknown … unkno… Protoz… (unkn… (unk… (unk… "(unk… (unk… "(unkn…
#>  9 F_YEAST     (unknown … unkno… Fungi   (unkn… (unk… (unk… "(unk… (unk… "(unkn…
#> 10 F_AABRN     Aabaarnia  unkno… Fungi   Ascom… Leca… Ostr… ""     Aaba… ""     
#> # ℹ 78,668 more rows
#> # ℹ 16 more variables: subspecies <chr>, rank <chr>, ref <chr>,
#> #   oxygen_tolerance <chr>, source <chr>, lpsn <chr>, lpsn_parent <chr>,
#> #   lpsn_renamed_to <chr>, mycobank <chr>, mycobank_parent <chr>,
#> #   mycobank_renamed_to <chr>, gbif <chr>, gbif_parent <chr>,
#> #   gbif_renamed_to <chr>, prevalence <dbl>, snomed <list>