A discrepancy in the identification of Actinomyces sp. oral taxon 181 between Metaphlan3 and Metaphlan4

Microbial community profiling MetaPhlAn
1

Hi Developers,

I am currently using Metaphlan, a valuable tool for taxonomic profiling of microbial communities, and I have encountered a discrepancy in the identification of Actinomyces sp. oral taxon 181 between Metaphlan3 and Metaphlan4.

using the same metagenomic sequencing data, I can find Actinomyces sp. oral taxon 181 in Metaphlan3 and the prevalence and relative abundance is quite high, but but cann’t find it in the metaphlan4 analysis results.

I try to find another name for Actinomyces sp. oral taxon 181, and I find the annotation for SGB17137_group is
k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces_sp_ph3,

k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Trueperella|s__Trueperella_pyogenes,

k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces_sp_oral_taxon_181

I think Actinomyces sp. oral taxon 181 may be re-named as Trueperella_pyogenes or Actinomyces_sp_ph3. But the prevalence and relative abundance are quite low for these two bacteria from metaphlan4 results.

I would greatly appreciate your assistance in understanding the reasons behind this difference. Could you kindly provide some insights into the updates made in the reference databases or changes in the taxonomic classification system that might have led to the exclusion of Actinomyces sp. oral taxon 181 in Metaphlan4?

Thank you very much for your time and attention.

2

Hi @WooJenny27
Indeed, SGB17137_group contains the only reference genome in our database labelled as s__Actinomyces_sp_oral_taxon_181 (the same used to build in the metaphlan3 database GCA_000318335). The discrepancy in the identification might be a FP result in metaphlan 3 due to the lack of reference information to build the marker genes database (some genes that were detected as markers back then might not really be species-specific markers genes after assessing a larger panel of species). But it is really complicated to assess

3

Thanks for your explanation.

Does it mean the gene markers for Actinomyces_sp_oral_taxon_181 in metaphlan3 may not be correct? but these gene markers were indeed detected in metaphlan3. what are these sequences belong to? :joy:

4

Hi @WooJenny27
It is an hypothesis that requires further investigation: The markers genes of mpa3 for Actinomyces_sp_oral_taxon_181 are still core gene sequences of Actinomyces_sp_oral_taxon_181 but probably are also present in other species we did not account for in mpa3, and thus, not marker genes (i.e. core genes not present in any other species) anymore in metaphlan 4.