Accurate MAG reconstruction from a complex soil microbiome through combined short- and HiFi long-reads metagenomics
Abstract
Advances in high-fidelity long-read (HiFi-LR) sequencing technologies have opened new opportunities to explore the microbial genomic diversity of complex environments, such as soils. While short-read (SR) sequencing has enabled broad insights at the gene level, the limited read length constrains the reconstruction of complete metagenome-assembled genomes (MAGs). HiFi-LR, in contrast, improves assembly continuity and completeness, supporting higher-resolution taxonomic and functional annotation. However, the cost and relatively low throughput of HiFi-LR sequencing can limit genome recovery, particularly at the binning stage, where coverage depth is critical. In this study, we assess the benefit of combining HiFi-LR and SR sequencing for genome-resolved characterization of a soil microbiome. Results We generated metagenomic data for a tunnel-cultivated soil sample using high-coverage Illumina SRs as well as a combination of two HiFi-LR sequencing platforms (PacBio Sequel II and PacBio Revio). We found that assemblies generated from pooled HiFi-LRs data alone exhibited higher completeness than those generated from ultra-deep SR data. Incorporating SR-derived coverage information into the binning of HiFi-LR contigs increased MAG recovery by 24% (313 vs. 252) while reducing contamination (116 vs. 132 contaminated bins; mean contamination 7.09% vs. 8.07%). Importantly, 67% of the newly recovered MAGs belonged to low-abundance and taxonomically diverse lineages representing 36 novel lineages, including Archaea. Conclusion Our results demonstrate that the integration of HiFi-LR and SR sequencing markedly enhances genome recovery and binning accuracy in a highly diverse environment such as soil. The hybrid approach used leverages the strengths of both technologies, leading to more contiguous assemblies and enabling the recovery of a broader range of genomes, including low-abundance and taxonomically diverse taxa. Although factors such as sequencing depth, cost, and DNA quality remain important considerations, our study provides practical guidance for designing future soil metagenomics projects. It underscores the value of adopting long-read technologies for more comprehensive characterization of complex microbial communities.
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BibTeX
@article{belliardo2026accurate,
title = {{Accurate MAG reconstruction from a complex soil microbiome through combined short- and HiFi long-reads metagenomics}},
author = {Carole Belliardo and Nicolas Maurice and Arthur Pere and Samuel Mondy and Alain Franc and Marc Bailly-Bechet and Claire Lemaitre and Riccardo Vicedomini and Jean-Marc Frigerio and Franck Salin and Élodie Belmonte and Marie Gislard and David James Sherman and Pierre Abad and Clémence Frioux and Étienne Danchin},
journal = {Environmental Microbiome},
year = {2026},
month = sep,
doi = {10.1186/s40793-026-00952-1},
url = {https://hal.science/hal-05789444v1},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Accurate MAG reconstruction from a complex soil microbiome through combined short- and HiFi long-reads metagenomics
AU - Carole Belliardo
AU - Nicolas Maurice
AU - Arthur Pere
AU - Samuel Mondy
AU - Alain Franc
AU - Marc Bailly-Bechet
AU - Claire Lemaitre
AU - Riccardo Vicedomini
AU - Jean-Marc Frigerio
AU - Franck Salin
AU - Élodie Belmonte
AU - Marie Gislard
AU - David James Sherman
AU - Pierre Abad
AU - Clémence Frioux
AU - Étienne Danchin
PY - 2026
DA - 2026/09/02
JO - Environmental Microbiome
DO - 10.1186/s40793-026-00952-1
UR - https://hal.science/hal-05789444v1
AB - Advances in high-fidelity long-read (HiFi-LR) sequencing technologies have opened new opportunities to explore the microbial genomic diversity of complex environments, such as soils. While short-read (SR) sequencing has enabled broad insights at the gene level, the limited read length constrains the reconstruction of complete metagenome-assembled genomes (MAGs). HiFi-LR, in contrast, improves assembly continuity and completeness, supporting higher-resolution taxonomic and functional annotation. However, the cost and relatively low throughput of HiFi-LR sequencing can limit genome recovery, particularly at the binning stage, where coverage depth is critical. In this study, we assess the benefit of combining HiFi-LR and SR sequencing for genome-resolved characterization of a soil microbiome. Results We generated metagenomic data for a tunnel-cultivated soil sample using high-coverage Illumina SRs as well as a combination of two HiFi-LR sequencing platforms (PacBio Sequel II and PacBio Revio). We found that assemblies generated from pooled HiFi-LRs data alone exhibited higher completeness than those generated from ultra-deep SR data. Incorporating SR-derived coverage information into the binning of HiFi-LR contigs increased MAG recovery by 24% (313 vs. 252) while reducing contamination (116 vs. 132 contaminated bins; mean contamination 7.09% vs. 8.07%). Importantly, 67% of the newly recovered MAGs belonged to low-abundance and taxonomically diverse lineages representing 36 novel lineages, including Archaea. Conclusion Our results demonstrate that the integration of HiFi-LR and SR sequencing markedly enhances genome recovery and binning accuracy in a highly diverse environment such as soil. The hybrid approach used leverages the strengths of both technologies, leading to more contiguous assemblies and enabling the recovery of a broader range of genomes, including low-abundance and taxonomically diverse taxa. Although factors such as sequencing depth, cost, and DNA quality remain important considerations, our study provides practical guidance for designing future soil metagenomics projects. It underscores the value of adopting long-read technologies for more comprehensive characterization of complex microbial communities.
SN - 2524-6372
SN - 2524-6372
ER -