ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences

Area of Science:

• Microbiology
• Bioinformatics
• Genomics

Background:

• Advancements in DNA sequencing have reduced prokaryotic genome sequencing costs and time.
• High-throughput sequencing is susceptible to contamination due to high coverage depth.
• Existing bioinformatics tools for contamination detection have limitations, primarily using protein-coding genes.

Purpose of the Study:

• To introduce ContEst16S, a novel algorithm for detecting contamination in prokaryotic genome assemblies.
• To utilize 16S rRNA genes for more comprehensive contamination identification.

Main Methods:

• Development of the ContEst16S algorithm.
• Screening of 69,745 prokaryotic genomes from the NCBI Assembly Database.
• Comparison of ContEst16S results with existing protein-coding gene-based tools.

Main Results:

• ContEst16S identified 594 contaminated prokaryotic genomes.
• Contamination sources included bacteria, human, and plants.
• 8% of contaminated genomes identified by ContEst16S were missed by protein-coding gene-based tools.

Conclusions:

• ContEst16S is an effective tool for detecting genome contamination using 16S rRNA genes.
• ContEst16S complements existing methods, improving the accuracy of genome data.
• The algorithm is available as a web service for broader accessibility.