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, e.g. "Váňová" becomes "Vanova".
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 ~36 000 bacteria in the data set contain an oxygen tolerance.
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)
Included Taxa
-Included taxonomic data are:
All ~36 000 (sub)species from the kingdoms of Archaea and Bacteria
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)
For convenience, some entries were added manually:
~1 500 entries of Salmonella, such as the city-like serovars and groups A to H
34 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
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)