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, creating a gap for microbial studies.

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 atlases for human and environmental microbiomes using single cell data.

Main Methods:

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

Main Results:

• EASi-seq allows thousands of microbes to be sequenced per run, generating large shotgun genome datasets.
• The bioinformatic pipeline improved whole genome assembly, strain identification, taxonomic classification, and gene annotation.
• Integration with metagenomic data successfully reduced capture bias and increased genome coverage.

Conclusions:

• EASi-seq provides a high-quality, accessible workflow for single cell genomic data from microbiome samples.
• This method opens new avenues for discovering and analyzing microbial species subpopulations.
• EASi-seq leverages commercially available platforms, facilitating widespread adoption in microbiome research.