Long-Read Metagenomic Sequencing & Assembly

Assembling Complete Genomes from Metagenomes

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Comprehensive Metagenomic Assembly Analysis

Sequence assembly, binning, taxonomy assignment, composition profiling, etc.

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Unbiased High Molecular Weight DNA Extraction

HMW DNA from DNA extraction with mechanical microbial lysis

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Simplify Metagenome Assembly

Let Us Handle the Complexity of Metagenomic Analyses

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Navigating the metagenomic assembly bioinformatic process can be intimidating, but our service transforms it into a seamless experience. Fueled by the expertise of Zymo Research Microbiome Sequencing specialists, we integrate comprehensive and sophisticated bioinformatic analyses. This ensures that you can effortlessly dive into scientific discovery with confidence and ease.

Streamline Data Interpretation with User-Friendly Report

Comprehensive bioinformatic analysis with a publication-ready report

Zymo Research reports

The Metagenomic Assembly sequencing service report provides assembly contigs, binning results, taxonomy profile, and more . Our team of expert bioinformaticians are here to help you get the most out of your data.

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Achieve Both Long-Read Sequencing and Unbiased Profiling

Enabled by High Molecular Weight DNA Extraction with Unbiased Mechanical Lysis

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Fragment size distribution of fecal DNA extracted using ZymoBIOMICS 96 DNA MagBead Kit or Miniprep Kit.

One Hundred High-Quality MAGs from Fecal Sample Assembled by PacBio Sequencing

genome sizes depths
HiFi Reads >Q20 Mean Read Length High-quality MAGs
1,792,146 reads 10,318 bp 100 MAGs

In this study, DNA from ZymoBIOMICS Fecal Reference (D6323) was extracted and sequenced using PacBio HiFi Sequencing. The assembly of this dataset produced 100 high-quality metagenome assembled genomes (MAGs) using our bioinformatics pipeline.

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How Our Microbiome Analysis Service Works

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Metagenomic Assembly Technical Specifications

Sequencing Platform PacBio Sequel Ile
Sequencing Kit SMRT Cell 8M
Accepted Sample Types Extracted genomic DNA, or raw samples
DNA Extraction

ZymoBIOMICS 96 Magbead DNA (D4308)

ZymoBIOMICS DNA Miniprep (D4300)

Library Prep

SMRTbell® Prep Kit 3.0 (with SMRTbell cleanup beads) (PacBio)

SMRTbell Barcoded Adapter Plate 3.0 (PacBio)

Quality Control A positive control for DNA extraction (ZymoBIOMICS Microbial Community Standard, D6300) is included in each project as a quality control.
Sequencing Analysis First, the PacBio HiFi reads are assembled into contigs using hifiasm-meta. The contigs are binned into bins or metagenome assembled genomes (MAGs) with MetaBAT 2 and SemiBin2 respectively. The binning results from these two tools are merged DASTool. The quality of the bins/MAGs is assessed using CheckM2. High quality MAGs (with CheckM2 completeness >60% and contamination <10%) are selected and annotated with GTDBtk. Additionally, PacBio HiFi reads are classified to obtain taxonomy composition using sourmash.
Reference Database For taxonomy profiling with sourmash, the full GTDB database (R07-RS207) is used for bacterial and archaea identification. Pre-formated GenBank databases (v. 2022.03) provided by sourmash are also used for virus, protozoa and fungi identification (https://sourmash.readthedocs.io/en/latest/databases.html).
Data Visualization Alpha and beta diversity plots and microbial composition barplots are created with functions from QIIME. Taxonomy heatmaps are created using internal scripts.
Statistical Analysis Given group information, statistical analysis for taxonomy biomarker discovery will be performed using LEfSe.

Advancing Microbiome Research: Unlocking Complete Genomes from Metagenomes with PacBio HiFi Sequencing

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.

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