Midi-metagenomics: A novel approach for cultivation independent microbial genome reconstruction from environmental samples

Abstract

Since the majority of microbial organisms still evade cultivation attempts, genomic insights into many taxa are limited to cultivation-independent approaches. However, current methods of metagenomics and single cell genome sequencing have individual drawbacks, which can limit the quality as well as completeness of the reconstructed genomes. Current attempts to combine both approaches still use amplification techniques which are prone to bias. Here, we propose a novel approach for the purpose of genome reconstructions, that utilizes the potential of cell sorting for targeted enrichment and depletion of different cell types to create distinct cell fractions of sufficient size, circumventing amplification. By distributing sequencing efforts over these fractions as well as the original sample, co-assemblies become highly optimized for co-abundance variation based binning approaches. "Midi-metagenomics" enables accurate metagenome assembled genome (MAG) reconstruction from individual sorted samples with higher quality than co-assembly of multiple distinct samples and has potential for the targeted enrichment and sequencing of microbial dark matter.