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Long-read Metagenomics

Unlock deeper insights into microbial communities with our specialized Long-Read Metagenomics services. Utilizing long-read sequencing with Oxford Nanopore Technologies (ONT), we provide highly contiguous assemblies and high-quality metagenome-assembled genomes (MAGs) from complex samples such as soil, wastewater, and gastrointestinal systems.

Long-read Metagenomics

Unlock deeper insights into microbial communities with our specialized Long-Read Metagenomics services. Utilizing long-read sequencing with Oxford Nanopore Technologies (ONT), we provide highly contiguous assemblies and high-quality metagenome-assembled genomes (MAGs) from complex samples such as soil, wastewater, and gastrointestinal systems.

What is Long-Read Metagenomics?

Long-read metagenomics focuses on retrieving complete genomes from samples containing diverse mixtures of microorganisms. This genome-centric approach allows researchers to study the structure and function of microbes in their natural environments or in association with hosts (microbiomics). By assembling genomes directly from metagenomic data, we create detailed blueprints of microbial metabolic potentials, essential for downstream analyses like metatranscriptomics and proteomics.
 

Advantages of Long-Read Sequencing

  • Highly Contiguous Assemblies: Long-read sequencing produces longer DNA fragments, resulting in more complete genome assemblies and higher-quality MAGs compared to short-read methods.
  • Bias Reduction: Eliminates common biases associated with short-read sequencing, such as GC-content bias and amplification bias, leading to more accurate abundance estimates.
  • Enhanced Genome Recovery: Improved ability to reconstruct genomes from complex communities, including rare or previously uncharacterized organisms.
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Our Workflow

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Sample Processing and DNA Extraction

  • Customized DNA Extraction Protocols: Optimized for a wide range of sample types to minimize biases and maximize yield and purity, including high-molecular-weight (HMW) DNA.

  • Versatile Sample Handling: Capable of processing both low- and high-biomass samples using manual and automated methods.

Library Preparation and Sequencing

  • Long-Read Sequencing: Preparation of native DNA sequencing libraries for use on the Oxford Nanopore Technologies platform.

  • Hybrid Sequencing Options: Integration of short-read data (e.g., from Element Biosciences) for projects requiring enhanced genome polishing, particularly for eukaryotic organisms.

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Data Analysis and Bioinformatics

  • Quality Control: Rigorous pre- and post-sequencing quality assessments to ensure data integrity.

  • De Novo Assembly: Generation of highly contiguous metagenome assemblies using advanced algorithms.

  • Genome Binning: Isolation of individual MAGs using machine learning models and experimental variables such as time points and treatments.

  • Taxonomic Classification and Annotation:

    • Classification against genome and rRNA taxonomy databases.

    • Gene annotation to identify metabolic pathways and functional potentials.

  • Abundance Estimation: Estimation of MAG relative abundances within your samples.

  • Advanced Bioinformatics Analyses: High-quality MAGs enable further analyses, including metabolic pathway reconstruction, functional characterization, and potential for metatranscriptomic profiling.

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Sample Types We Handle

Our DNA extraction expertise allows us to process a diverse array of sample matrices, including but not limited to:

  • Environmental Samples: Soil, wastewater, oil spills, marine and freshwater samples, sediments.
  • Biological Samples: Prokaryotes, invertebrates, fungi, aquaculture organisms, animal gut contents (e.g., pigs, chickens, fish), plant materials.
  • Clinical Samples: Biopsies (lung, colon, liver), swabs (skin, oral), feces, environmental DNA (eDNA).
  • Industrial Samples: Bioreactors, microbial-induced corrosion samples, mining/drill site samples.
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Service Packages 

Standard Package Includes:

  • Consultation: Optional pre- and post-project meetings with our specialists to tailor the analysis strategy.

  • DNA Extraction: High-quality extraction optimized for your sample type.

  • Library Preparation and Sequencing: Preparation of sequencing libraries and execution of sequencing runs.

  • Quality Control: QC before and after sequencing.

  • Data Analysis:

    • De novo assembly of metagenomes.

    • Genome binning to retrieve MAGs.

    • Taxonomic profiling and gene annotation.

  • Results Delivery: Access to raw data files, detailed result files, and a tailored scientific report.

Add-On Services:

  • Customized DNA Extraction and Purification: Tailored protocols for challenging sample types.

  • Manual Genome Binning: Expert curation of MAGs for improved accuracy.

  • Advanced Functional Annotation:

    • Annotation using custom databases.

    • Functional enrichment analysis and metabolic pathway reconstruction.

  • Custom Analyses:

    • Gene mining and custom annotation based on your specific research questions.

    • Data submission assistance for public repositories.

Why Choose Cmbio for Long-Read Metagenomics?

  • Expertise: Our team has extensive experience in metagenomics and stays at the forefront of technological advancements.

  • State-of-the-Art Technologies: Access to the latest sequencing platforms and bioinformatics tools.

  • Customized Solutions: We tailor our workflows to meet the unique requirements of your project.

  • Quality Assurance: Commitment to delivering high-quality data with thorough quality control measures.

  • Collaborative Support: We work closely with you from experimental design through data interpretation to ensure the success of your project.