Which version of the Metaphlan2 marker database was used to generate the marker and bug abundance data in curatedMetagenomicData? I am looking for some species that are represented in v20 of the Metaphlan2 marker database, but can't find them in the curatedMetagenomicData package. If an earlier marker database was used, are there plans to rerun the analyses using a more complete database?

We used MetaPhlAn 2.0, with ~17,000 reference genomes (~13,500 bacterial and archaeal, ~3,500 viral, and ~110 eukaryotic). Note that each dataset shows only clades that were present in at least one specimen - are you sure that the species you are looking for is not present in any dataset in curatedMetagenomicData? All species in the phylogeny are available as follows:

suppressPackageStartupMessages(library(curatedMetagenomicData))
suppressPackageStartupMessages(library(ape))
tree <- getMetaphlanTree()
length(tree$tip.label)
#> [1] 4088
head(tree$tip.label)
#> [1] "s__Methanopyrus_kandleri"                 
#> [2] "s__Methanothermus_fervidus"               
#> [3] "s__Methanothermobacter_thermautotrophicus"
#> [4] "s__Methanothermobacter_marburgensis"      
#> [5] "s__Methanobacterium_formicicum"           
#> [6] "s__Methanobacterium_sp_Maddingley_MBC34"

Or the complete list of rownames directly from the datasets, including all levels of taxonomy. This list may be missing anything from the above tree that was not present in any dataset.

suppressPackageStartupMessages(library(curatedMetagenomicData))
suppressPackageStartupMessages(library(magrittr))
suppressMessages(res <- curatedMetagenomicData("*metaphlan*", dryrun = FALSE))
all <- lapply(res, rownames) %>%
  unlist() %>%
  unique()
length(all)
#> [1] 4690
head(all)
#> [1] "k__Bacteria"                   "k__Viruses"                   
#> [3] "k__Bacteria|p__Proteobacteria" "k__Bacteria|p__Actinobacteria"
#> [5] "k__Bacteria|p__Firmicutes"     "k__Viruses|p__Viruses_noname"