Carole Belliardo, post-doc, INRAE, Institut Sophia Agrobiotech, Sophia Antipolis, France
Keywords: Metagenomics, Soil Microbiome, Genome assembly, HiFi sequencing, method benchmark
The soil microbiome remains poorly understood, but unraveling its genetic diversity is essential, given the pivotal functions primarily mediated through their protein arsenal [1]. Although short-read (SR) shotgun metagenomics provided interesting insights into microbiome gene diversity, it fell short in delivering comprehensive microbial genome reconstructions. Metagenome-assembled genomes (MAGs) obtained from SR often yield fragmented assemblies and incomplete gene sets (over 90% contigs <1kb and thus unusable for gene prediction) [2].
Using PacBio HiFi sequencing, we previously obtained long-reads (N50: 6kb) from tunnel culture soil metagenomes, surpassing the contig length of publicly available short-read metagenomes (N50: 1kb) [2]. Even if a substantial part of the reads remain unassembled, we succeeded in reconstructing dozens of MAGs, which further enhanced reads contiguity encompassing bacterial, archaeal, and viral genomes from terrestrial environments. To compare more comprehensively LR and SR approaches, we generated ultra-high depth short-read sequencing on the same soil sample. Although with SR technology contigs were substantially shorter, ultra-high depth sequencing seem to have captured a higher diversity of taxa than LR. However, this impression needs to be confirmed by an independent metabarcoding method.
HiFi LR sequencing exhibits significant potential in elucidating the complexity of microbial genome reconstruction. Nevertheless, several critical considerations remain to be addressed such as the sequencing depth required to capture and reconstruct a significant representation of the real biodiversity of soil microbiomes.
Full text: Belliardo et al. (2024) Exploring and quantifying the soil genetic diversity captured by long and short-read shotgun metagenomic sequencing, hal-04423917
References:
- Fierer, N., 2017. Nat Rev Microbiol
- Belliardo, C., et al., 2022, Scientific Data 9, 311
