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

library(Keggrest)

compounds = c("C00159", "C00772", "C00678", "C00355", "C00022")

is_in_organism <- function(compound, organism)
{
  compound = toString(compound)
  organism = toString(organism)
  tryCatch(
    {
      resp <- kegg_compound_2_organism(compound)
      if (organism %in% resp)
      {
        return(TRUE)
      }
      else
      {
        return(FALSE)
      }
    },
    error = function(err)
    {
      return(FALSE)
    }
  )
}

is_in_organism("C00159", "eco")