Duplicate Species Entries with and without SGB Annotation

Microbial community profiling MetaPhlAn
1

Hi, I’m encountering duplicate entries for the same species (e.g., s__Megamonas_funiformis) in my MetaPhlAn output—some with SGB annotations (e.g., t__SGB6962) and others with NA for the SGB, both showing identical relative abundances.

Is this expected behavior?

For example: (psq_taxa is a phyloseq object)

psq_taxa %>%
subset_taxa(!is.na(Species)) %>%
psmelt2(sample.column = “sample”, feature.column = “taxa”) %>%
select(sample, Species, SGB, value) %>%
filter(str_detect(Species, “Megamonas_funiformis”)) %>%
arrange(desc(value))

sample Species SGB value

1 1 s__Megamonas_funiformis NA 16.7
2 1 s__Megamonas_funiformis t__SGB6962 16.7
3 2 s__Megamonas_funiformis NA 15.6
4 2 s__Megamonas_funiformis t__SGB6962 15.6
5 3 s__Megamonas_funiformis NA 13.2
6 3 s__Megamonas_funiformis t__SGB6962 13.2
7 4 s__Megamonas_funiformis NA 10.6