Complete, closed bacterial genomes from microbiomes using nanopore sequencing.

Area of Science:

• Microbiology
• Genomics
• Bioinformatics

Background:

• Short-read sequencing limits microbial genome assembly contiguity due to repeat elements.
• Accurate placement of repeats is vital for understanding genome structure and function.

Purpose of the Study:

• To develop and validate a workflow (Lathe) for assembling closed bacterial genomes from complex microbiomes using long-read sequencing and short-read error correction.
• To improve the contiguity of metagenome-assembled genomes (MAGs) for better analysis of microbial genome structure.

Main Methods:

• Application of Nanopore long-read sequencing combined with a novel workflow (Lathe) for assembly and error correction.
• Validation using a synthetic microbial community of 12 bacterial species.
• Analysis of metagenomic data from 13 human stool samples.

Main Results:

• Successfully assembled seven complete bacterial genomes into single contigs from a synthetic mixture.
• Achieved assembly of three additional genomes into four or fewer contigs.
• Assembled 20 circular genomes from human stool samples, including Prevotella copri.

Conclusions:

• The Lathe workflow enhances genome assembly contiguity for microbial communities, despite lower nucleotide accuracy compared to other methods.
• Improved contiguity enables the investigation of repeat elements' roles in microbial adaptation and function within complex environments.