Classification of the Bacteroidetes family Muribaculaceae: application of Nanopore long read sequencing to link 16S rRNA gene amplicon and metagenome assembled genome-derived taxonomies

The Bacteroidales family Muribaculaceae, previously known as S24-7 or Homeothermaceae, is a predominate member of the mouse gut microbiome and common microbe in other mammalian gut environments.
Most of what we know about Muribaculaceae has come from 16S rRNA gene studies or short read metagenomic studies.
Muribaculaceae is large family with ~3000 16S rRNA gene representatives in the non-redundant SILVA REF 132 16S rRNA gene database.
~250 metagenomic assembled genome (MAG), representing 13 genera, in the Genome Taxonomy Database (GTDB).
Muribaculaceae is difficult to culture and isolate in laboratory conditions and only six isolates, representing three genera, have been published.
Short read shotgun sequencing techniques, such as Illumina, produce reads too small to associate 16S rRNA genes to MAGs when sequencing environmental samples.
The result is poor taxonomic linking between metagenomic genome taxonomy and 16S rRNA gene taxonomy.
To address this poor taxonomic connectivity, we proposed two methods.
- Direct linking via single cell approach
- Improve MAG quality via long read sequencing