Add bacterial and archaeal strain phenotypes (BacDive)

Joins per-species microbial phenotype and growth-condition traits from BacDive, the Bacterial Diversity Metadatabase (DSMZ), to a taxify() result by looking up accepted_name. Strain-level records are aggregated to one row per species (categorical traits by mode, numeric by median); temperature and pH prefer the optimum measurement, falling back to the growth measurement.

Usage

add_bacdive(x, cols = NULL, verbose = TRUE)

Arguments

x

A data.frame returned by taxify().

cols

Which columns to attach: NULL (default) the curated set, "all" every column the source carries, or a character vector of names. See enrichment_cols.

verbose

Logical. Default TRUE.

Value

The same data.frame with additional columns:

gram_stain

Gram reaction (positive / negative / variable).

cell_shape

Cell morphology (rod, coccus, ...).

motility

motile / non-motile.

oxygen_metabolism

Oxygen tolerance (aerobe, anaerobe, facultative anaerobe, microaerophile, ...).

cell_length_um, cell_width_um

Cell dimensions in micrometres.

optimal_growth_temp_c

Optimal (or reported growth) temperature, C.

optimal_growth_ph

Optimal (or reported growth) pH.

Details

Source: BacDive (Reimer et al.), DSMZ, CC BY 4.0. ~18.6k bacterial and archaeal species with at least one phenotypic trait.

References

Reimer LC et al. (2022) BacDive in 2022: the knowledge base for standardized bacterial and archaeal data. Nucleic Acids Research 50:D741-D746. doi:10.1093/nar/gkab961

Examples

if (FALSE) { # \dontrun{
taxify("Escherichia coli", backbone = "gbif") |>
  add_bacdive()
} # }