Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities

Abstract

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Long-read-resolved, ecosystem-wide exploration of nucleotide and structural microdiversity of lake bacterioplankton genomes

“…Alternative possible approaches include genome-free metagenomics, which directly handles pan-metagenomic graphs without the prerequisite of a linear genomic assembly (90). The ultimate approach will be a strain-resolved assembly, which usually requires an isolated culture or single cell but was recently accomplished in a metagenomic assembly using highly accurate long reads (i.e., PacBio HiFi reads) (20), although it is still too costly for common application.…”

“…We targeted freshwater bacterioplankton assemblages sampled spatiotemporally (2 depths × 12 months) at a pelagic station on Lake Biwa, a monomictic lake with an oxygenated hypolimnion that harbors one of the best-studied freshwater microbial ecosystems (12)(13)(14)(15)(16). The second step was long-read metagenomic assembly, which can overcome the problem of fragmented assembly using reads longer than a repeat or hypervariable region (17)(18)(19)(20).…”

HiFi Metagenomic Sequencing Enables Assembly of Accurate and Complete Genomes from Human Gut Microbiota

“…HiFi sequencing offers substantial advantages in terms of base accuracy and read length 20 . In addition, HiFi metagenomic sequencing improves the quantity and quality of MAG assembly 9 . In the present study, we successfully retrieved complete circularized prokaryotic genomes of human gut microbiota through HiFi metagenomic sequencing without any binning process.…”

“…Long-read metagenomic sequencing using Oxford nanopore technology (ONT) has enabled the assembly of 20 circularized complete MAGs (cMAGs) from 13 human stool samples, albeit with low nucleotide accuracy 6 . More recently, PacBio high-accuracy long-read (HiFi) sequencing, which has become popular for the assembly of reference animal and plant genomes 7,8 , has been applied for the analysis of complex microbiomes, such as sheep fecal samples 9 and chicken cecum samples 10 . HiFi repetitive sequencing of a circularized SMRTbell library calls reads by consensus, substantially improving nucleotide accuracy while maintaining long read length.…”

Hi-C Metagenomics in the ICU: Exploring Clinically Relevant Features of Gut Microbiome in Chronically Critically Ill Patients

“…Recently, conventional metagenomics have been combined with chromosome conformation capture techniques like Hi-C and 3C-seq to enable a deeper exploration of complex microbial communities. Besides the environmental microbiome (Baudry et al, 2019;Stalder et al, 2019), such techniques have been applied to mammal host-associated communities (Marbouty et al, 2017;Stewart et al, 2018;Bickhart et al, 2022). In the human microbiome field, all but one Hi-C metagenomic survey (Kent et al, 2020) performed to date investigated the gut community of healthy subjects (Press et al, 2017; Abbreviations: ARG, antibiotic resistance gene; CCI, chronically critically ill; HGT, horizontal gene transfer; ICU, intensive care unit; MAG, metagenomeassembled genome; SCG, single-copy core genes; UTIs, urogenital tract infections; VF, virulence factors.…”