Difference between unclassified and unknown clade in metaphlan3

Microbial community profiling MetaPhlAn
1

Hi!

I am using metaphlan3 for metagenomics analysis on colorectal samples. Some samples result in a lot of taxa and some don’t. At the moment I am reading online about how the ‘unclassified’ and ‘unknown’ clades are generated. I was wondering if there are any differences of the meaning ‘unclassified’ and ‘unknown’.

Kind regards,

Moelong Yu

2

Hi @Moellie
The difference between metaphlan 3 “unknown” and metaphlan 4 “unclassified” is just terminology. Since we introduce the concept of unknown species (uSGBs) in metaphlan 4, keep calling that fraction “unknown” could be misleading. To avoid that, we decide to change the term to “unclassified” fraction.