HiFi-Based Metagenomic Assembly Strategy Provides Accuracy Near Isolated Genome Resolution in MAGs Assembly

High-quality genomes of bacteria were significantly resource for exploring the diversity, function of different environments, including gut microbiome. The limitation of short reads and higher error rate of previous technologies make it difficult to get high quality genomes without isolation. Pacbio HiFi sequencing technology may overcome these limitations in genome assembly from metagenomic sequencing data. However, there is not comprehensive comparison between different sequencing technologies for metagenomic assembled genomes (MAGs). In this study, a total number of 31 high-quality MAGs assembled using Pacbio HiFi metagenomic sequencing data, including 10 complete MAGs with genomic circularity. The quality comparison of MAGs by illumina, ONT, and HiFi based methods suggesting that HiFi-based method provided higher completeness, continuity, and lower contamination than ONT and illumina based methods (p<0.05). Compared with the isolate genomes from the NCBI database, the HiFi-based MAGs were closer to the isolate genomes at both of gene and single nucleotide level (SNP) level. Further validates the assembly accuracy of these strategies by isolating and sequencing bacterial strains from the same samples. Phylogenetic and Principal Coordinates Analysis (PCoA) based on gene presence/absence affirmed that HiFi-based MAGs closely match isolated strains at the SNP and gene level. In conclusion, this study provided a benchmark for recovering MAGs, and suggesting HiFi-based MAGs could approach the completeness genomes of isolated strains. This research offers invaluable insights into the practical utility of Pacbio HiFi on the MAGs assembly and guides future endeavors requiring accurate microbial genomic information.