Vibrio Clade 3.0: New Vibrionaceae Evolutionary Units Using Genome-Based Approach

Area of Science:

• Microbial Phylogenetics
• Bacterial Taxonomy
• Genomics

Background:

• The family Vibrionaceae comprises over 190 species across nine genera, with rapid expansion in described species.
• Previous molecular phylogenetic updates, like Vibrio Clade 2.0, have been crucial for understanding Vibrionaceae evolution.
• The classification of Vibrionaceae, including uncultured taxa, requires robust molecular phylogenetic frameworks.

Purpose of the Study:

• To perform an updated molecular phylogenetic analysis of the Vibrionaceae family, termed "Vibrio Clade 3.0."
• To evaluate the efficacy of different gene sets for classifying Vibrionaceae, including novel and uncultured species.
• To enhance the taxonomic resolution and evolutionary understanding of the Vibrionaceae family.

Main Methods:

• Phylogenetic analysis based on nucleotide sequences of eight housekeeping genes (8-HKGs) from 22 newly sequenced genomes.
• Evaluation of delineation power using nucleotide sequences of 34 single-copy genes and 11 ribosomal protein genes (11-RPGs) from core-genome sequences.
• Comparative analysis of gene set performance for classifying cultured and uncultured Vibrionaceae taxa.

Main Results:

• Identification of 51 distinct clades within Vibrionaceae, with 21 clades newly described in this update.
• Confirmation that the eight housekeeping genes (8-HKGs) set maintains high delineation power for Vibrionaceae classification and identification.
• Demonstration that 11 ribosomal protein genes (11-RPGs) are effective for identifying uncultured species within metagenome-assembled genomes (MAGs) and single-cell genomes (SAGs).

Conclusions:

• The "Vibrio Clade 3.0" analysis significantly expands the understanding of Vibrionaceae diversity and evolutionary history.
• The eight housekeeping genes (8-HKGs) remain a reliable marker set for routine classification and identification of Vibrionaceae.
• The 11 ribosomal protein genes (11-RPGs) offer a valuable tool for the taxonomic classification of uncultured bacteria from complex genomic datasets.