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