For a study, it was determined that although the human gut microbiome had yielded many microbial genomes, understanding the relevance of low-abundance species at the individual level remains difficult, owing to the very shallow sequencing depth utilized in most research. A HiSeq-PacBio hybrid ultra-deep metagenomic sequencing technique was used to reconstruct metagenomic-assembled genomes (MAGs) from 12 fecal samples to increase genome assembly performance. To increase the sequencing coverage of the low-abundance subpopulation in the gut microbiome, researchers coupled third-generation sequencing with ultra-deep second-generation sequencing. The research produced 44 megabase-scale scaffolds, including 4 single-scaffolds of complete (circularised, no gaps) MAGs (CMAGs), which were their species’ first circular genomes. Furthermore, across all samples, 475 high-quality MAGs were assembled. There were 234 MAGs that had never been cultivated before, including 24 MAGs that had never been detected in any public genome database. In addition, in each individual, 287 and 77 MAGs were identified as low-abundance (0.1–1%) and extra-low-abundance (<0.1%) gastrointestinal species, respectively. Individual-specific genomic traits in MAG profiles, such as microbial genome development rate, selective pressure, and chromosomal mobile genetic elements frequency, were also discovered. Finally, the metagenomic data revealed thousands of extrachromosomal mobile genetic factors, including 5,097 bacteriophages and 79 new plasmid genomes. Overall, the approach marked a significant step towards the human gut microbiota’s individual-level genetic and functional characterization.