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
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.