Microbiome single cell atlases generated with a commercial instrument.

Area of Science:

• Microbiology
• Genomics
• Bioinformatics

Background:

• Single cell sequencing is crucial for analyzing complex biological systems but lacks accessible tools for microbes.
• Commercial instruments are widely available for mammalian single cell analysis, highlighting a gap for microbial applications.

Purpose of the Study:

• To introduce EASi-seq (Easily Accessible Single microbe sequencing), a novel method for efficient individual microbe genome sequencing.
• To enable the generation of detailed genomic atlases for human and environmental microbiomes using single cell analysis.

Main Methods:

• Adapted the commercial Mission Bio Tapestri instrument's single cell workflow for microbial applications.
• Developed a companion bioinformatic pipeline for clustering microbes, improving genome assembly, strain identification, taxonomic classification, and gene annotation.
• Integrated metagenomic contigs with EASi-seq data to mitigate capture bias and enhance genome coverage.

Main Results:

• EASi-seq allows thousands of microbes to be sequenced per run, generating large shotgun genome datasets.
• Demonstrated the generation of detailed atlases for human and environmental microbiomes.
• Showcased improved whole genome assembly, strain identification, taxonomic classification, and gene annotation through the bioinformatic pipeline and data integration.

Conclusions:

• EASi-seq provides a high-quality, accessible single cell genomic data solution for microbiome research.
• The method opens new avenues for discovering and analyzing microbial species subpopulations.
• Facilitates comprehensive genomic analysis of individual microbes on a commercially available platform.