Long-Read Metagenomic Sequencing & Assembly

Metagenomic sequencing and analysis represent a groundbreaking approach in microbiology research, enabling the study of intricate microbial communities without the difficult task of isolating and cultivating individual organisms. Metagenomic assembly encompasses two key facets: wet-lab procedures, involving DNA extraction, library preparation, and sequencing, and dry-lab tasks, which include read quality enhancement, DNA sequence assembly, contig/scaffold binning, taxonomy annotation, gene prediction, and gene annotation. While assembly-independent pipelines offer avenues for taxonomy analysis without DNA sequence assembly, the assembly step becomes indispensable when the research goal extends beyond taxonomy analysis to encompass genome reconstruction, comprehensive gene retrieval, and organism-specific pathway exploration.

The objective of DNA sequence assembly is clear-cut: to attain extensive contigs/scaffolds while minimizing misassemblies and gaps, allowing for the reconstruction of complete genomes. In the context of pure bacterial culture genome assembly, the predominant challenge lies in repetitive sequences, e.g. multiple copies of ribosomal RNA sequences within a genome. However, in metagenomics, this process becomes exponentially challenging due to the varying sequencing depth/coverage of microbial genomes, the presence of closely related genomes (including multiple strains of a species), and horizontal gene transfers across phylogenetically distant genomes. Traditional short-read sequencing methods, such as Illumina sequencing, typically yield short contigs and require extensive computational resources, thereby limiting the advantages of DNA sequence assembly.

PacBio HiFi reads, generated through circular consensus sequencing (CCS) mode on PacBio long-read systems, have a size of up to 15-20 kb with an accuracy exceeding 99% (Q20 or better). By harnessing the potential of HiFi reads in conjunction with sophisticated bioinformatics pipelines, it is now feasible to directly derive hundreds of complete or high-quality genomes, known as metagenome-assembled genomes (MAGs), from complex metagenomic samples, such as human fecal specimens.

At the forefront of metagenomic analysis, Zymo Research offers a Certified PacBio Provider status, ensuring the meticulous handling of your samples. Our PacBio metagenomic sequencing and assembly service encompass the entire workflow, ranging from DNA extraction to metagenomic assembly and comprehensive analyses. We gladly accept high-molecular-weight DNA extracts, or alternatively, we can perform DNA extraction when provided with raw samples. Our use of ZymoBIOMICS DNA extraction kits guarantees impartial microbial lysis through mechanical bead beating while preserving high molecular weight (8-15kb). Our bioinformatics pipelines encompass adapter and quality trimming, DNA sequence assembly, binning, MAG taxonomy annotation, and taxonomy composition profiling. In the DNA sequence assembly phase, we employ state-of-the-art algorithms optimized for metagenomic assembly with HiFi reads, as recommended by PacBio. With us, you can have peace of mind, knowing that we will manage every aspect of your project with the utmost care and expertise.