When should a DDH experiment be mandatory in microbial taxonomy?

Area of Science:

• Microbiology
• Taxonomy
• Bioinformatics

Background:

• 16S rRNA gene sequence similarity is a primary tool for microbial species delineation.
• DNA-DNA hybridizations (DDH) are crucial for differentiating species when 16S rRNA similarity exceeds 97%.
• The current 97% threshold for 16S rRNA gene sequence similarity may be overly conservative.

Purpose of the Study:

• To re-evaluate the 16S rRNA gene sequence similarity threshold for microbial species discrimination.
• To determine if and when the 97% threshold is too conservative.
• To assess the impact of different 16S rRNA gene similarity inference methods and DDH techniques.

Main Methods:

• Analysis of real-world 16S rRNA gene sequences and DNA-DNA hybridization (DDH) data.
• Statistical estimation of similarity thresholds, both generally and for specific phyla.
• Comparison of various methods for inferring 16S rRNA gene sequence similarities.

Main Results:

• Most routinely applied 16S rRNA gene similarity inference methods are suitable for microbial taxonomy.
• Different DDH methods have insignificant effects on species discrimination outcomes.
• A revised threshold between 98.2% and 99.0% is proposed as reasonable for many taxonomic groups.

Conclusions:

• Increasing the 16S rRNA gene sequence similarity threshold can significantly reduce the need for DDH experiments.
• Up to 50% of DDH experiments could be omitted without compromising accurate species differentiation.
• This revised threshold offers a more efficient approach to microbial species delineation.