Single-Cell Genomics for Unculturable Microbes

While shotgun metagenomics is excellent for profiling whole communities, it often struggles to correctly assemble genomes for low-abundance species or correctly link mobile genetic elements (like plasmids carrying AMR or virulence genes) to their specific bacterial hosts. Single-cell genomics physically isolates a single microbe before sequencing, guaranteeing that all resulting genomic data belongs to that specific individual cell. This provides unequivocal strain-level resolution and high-confidence functional predictions for microbes that cannot be cultured in vitro.

Multiple Displacement Amplification (MDA) is highly efficient but known to cause uneven read coverage across the genome. We mitigate this through a combination of optimized reaction chemistries during the wet-lab phase to maximize uniformity, and specialized bioinformatics pipelines during data analysis. Our algorithms employ sequence normalization and specialized single-cell assemblers (like SPAdes optimized for single-cell data) that are specifically designed to handle uneven depth profiles, maximizing genome recovery and contig lengths.

Yes. One of the most valuable outputs of a Single Amplified Genome (SAG) is the metabolic pathway reconstruction. By identifying which essential biosynthetic pathways (such as specific amino acid or vitamin synthesis pathways) are missing from the genome, we can pinpoint the organism's auxotrophies. This provides you with targeted clues on what specific nutrients, co-factors, or cross-feeding metabolites need to be supplemented into your media to successfully cultivate the microbe in vitro.

Our protocols are adaptable to a wide variety of sample matrices. We commonly process fecal samples, mucosal swabs, tissue biopsies (ex vivo), and diverse environmental samples. The key to success is prompt and proper sample preservation to maintain cell wall integrity. During project scoping, our experts will provide detailed protocols on sample collection, buffer storage, and shipping requirements to ensure optimal viable cell recovery for FACS isolation.