I can find out if the compounds I have in a list belong to an organism using Keggrest.

library(keggrest)

find_organism <- function(compounds) {
  organism <- NULL
  for (i in compounds) {
    tryCatch({
      res <- kegg_search(i)$org
    }, warning = function(warn) {
      res <- NULL
    })
    organism <- append(organism, res)
  }
  organism <- unique(organism)
}