Long-Read Sequencing for Microbiome Research
Comprehensive long-read sequencing solutions for metagenomics, microbial genomics, and microbiome characterisation across human, animal, plant, and environmental samples.
CD Genomics provides comprehensive long-read sequencing solutions for microbiome research on PacBio HiFi and Oxford Nanopore platforms — covering metagenomics for complete MAG recovery, full-length 16S/18S/ITS amplicon sequencing for species and strain-level taxonomic profiling, microbial whole-genome de novo and resequencing, and antibiotic resistance gene analysis from human, animal, plant, and environmental microbiome samples.
CD Genomics provides comprehensive long-read sequencing solutions for microbiome research, leveraging both PacBio HiFi and Oxford Nanopore platforms to characterise microbial communities, assemble complete microbial genomes, and uncover functional potential across diverse microbiomes. Our services span the full workflow — from metagenomic community profiling and full-length amplicon sequencing through microbial whole-genome de novo assembly, resequencing, and antibiotic resistance gene analysis — supporting applications in human health, agriculture, industrial biotechnology, environmental monitoring, and public health surveillance.
How We Support Microbiome Research
- Complete microbial genomes from long reads. HiFi accuracy (>99.9%) and ONT ultralong reads (>100 kb) enable closed, circular bacterial genomes, complete plasmid reconstruction, and high-quality MAGs from metagenomes — without the fragmentation that limits short-read assemblies.
- Full-length amplicon resolution. Full-length 16S (1,500 bp), 18S, and ITS amplicon sequencing resolves taxonomy at species and strain level that short-read partial-amplicon approaches cannot distinguish, with accurate quantification of community composition.
- Functional potential and resistance profiling. Long-read metagenomics and ARG analysis capture the genomic context of antibiotic resistance genes, virulence factors, and mobile genetic elements, linking resistance determinants to their host genomes and mobile elements.
For Research Use Only. Not for use in diagnostic procedures, clinical decision-making, personal health assessment, or therapeutic decision-making.
Why Long-Read Sequencing for Microbiome Research?
Microbiome research aims to understand the composition, function, and dynamics of microbial communities. While short-read sequencing has been the dominant approach, it faces fundamental limitations: the fragmented assemblies it produces cannot resolve repetitive elements, plasmid structures, or genomic islands; its short amplicons (typically 250–450 bp of the 16S gene) provide limited taxonomic resolution; and it cannot reliably link antibiotic resistance genes to their host chromosomes or mobile elements.
Long-read sequencing addresses each of these limitations directly. PacBio HiFi sequencing delivers >99.9% accurate reads averaging 15–25 kb, enabling complete bacterial genome closure, full-length 16S/18S/ITS amplicon resolution at species and strain level, and accurate reconstruction of metagenome-assembled genomes (MAGs) from complex communities. Oxford Nanopore sequencing provides ultralong reads exceeding 100 kb that span entire repeat regions, resolve plasmid-host linkages, and close assembly gaps in even the most repetitive microbial genomes. When combined, these platforms produce comprehensive, contiguous assemblies that capture the full genetic repertoire of microbial communities — including the mobile elements, phages, and structural variants that drive functional adaptation and antibiotic resistance dissemination.
Our Long-Read Microbiome Service Portfolio Covers Metagenomics, Microbial WGS, and Application-Specific ARG Analysis
We offer a comprehensive portfolio of long-read sequencing services for microbiome research, organised into three categories. Each service page provides detailed information on methodology, bioinformatics analysis, sample requirements, and deliverables. Click on any service to learn more.
Metagenomics & Community Analysis
| Service | Description |
| Long-Read Metagenomics Sequencing | Shotgun metagenomic sequencing using PacBio HiFi and/or ONT long reads for comprehensive microbial community characterisation, MAG reconstruction, and functional profiling of complex microbiomes from gut, soil, water, and other environmental samples. |
| Full-Length 16S/18S/ITS Amplicon Sequencing | Full-length 16S rRNA (~1,500 bp), 18S rRNA, and ITS region sequencing on PacBio and ONT platforms for high-resolution taxonomic profiling at species and strain level, capturing diversity that partial-amplicon approaches systematically miss. |
| Full-Length Plasmid Sequencing | Complete plasmid reconstruction from isolated plasmids or metagenomic DNA using long reads, resolving plasmid structure, replicon types, and the genomic context of accessory genes including resistance determinants and virulence factors. |
Microbial Whole Genome Sequencing
| Service | Description |
| Microbial WGS — De Novo Sequencing | De novo whole-genome assembly of bacterial, fungal, and viral genomes using long-read sequencing, producing complete, circular chromosomes and plasmids without the fragmentation inherent to short-read assembly. |
| Bacterial WGS — De Novo Sequencing | Dedicated bacterial genome de novo assembly service using PacBio HiFi and ONT platforms for complete, closed bacterial genomes including plasmids, with QV >40 accuracy. |
| Fungal WGS — De Novo Sequencing | Fungal genome de novo assembly optimised for the larger, more repetitive genomes of yeasts, moulds, and filamentous fungi, with HiFi accuracy resolving repeat-rich regions and mating-type loci. |
| Viral Genome De Novo Sequencing | Complete viral genome assembly from isolated virus cultures or enriched viral preparations, including RNA virus genome reconstruction via ONT direct RNA or cDNA sequencing. |
| Microbial WGS — Resequencing | Long-read resequencing of microbial strains for variant discovery (SNP, SV, CNV), strain-level comparison, and population genomics across bacterial, fungal, and viral isolates. |
| Bacterial WGS — Resequencing | Bacterial strain resequencing using long reads for high-confidence variant calling, AMR gene profiling, phylogenetic analysis, and comparative genomics across closely related isolates. |
| Fungal WGS — Resequencing | Fungal genome resequencing for population-level variant discovery, including structural variant detection in repeat-rich regions that short-read approaches cannot resolve. |
| Viral WGS — Resequencing | Viral genome resequencing for mutation tracking, quasispecies analysis, and evolutionary monitoring using long-read platforms capable of spanning entire viral genomes in single reads. |
Application-Specific Microbiome Services
| Service | Description |
| Human Microbiome | Long-read sequencing solutions for human gut, oral, skin, and other microbiome studies, enabling strain-level resolution of commensal and pathogenic microbial communities and their impact on health and disease. |
| Plant and Animal Microbiome | Microbiome analysis of plant rhizosphere, phyllosphere, and animal gastrointestinal/respiratory microbiomes using long-read sequencing to understand host-microbe interactions, crop productivity, and livestock health. |
| Industrial Microbiome | Long-read characterisation of microbial communities in industrial environments — wastewater treatment, biogas production, food fermentation, and bioremediation — for process optimisation and monitoring. |
| Antibiotic Resistance Gene (ARG) Analysis | Comprehensive ARG profiling using long-read sequencing to identify resistance genes, determine their genomic context (chromosomal vs. plasmid-borne), and track horizontal gene transfer in clinical and environmental samples. |
| Microbial Genomics with Long-Read Sequencing | Integrated microbial genomics services combining de novo assembly, resequencing, comparative genomics, and pangenome analysis for bacterial, fungal, and viral research projects. |
Long-Read Sequencing Supports Microbiome Applications from Public Health Surveillance to Industrial Bioprocessing
Beyond the major application areas described below, long-read microbiome sequencing is increasingly applied in multi-kingdom microbiome studies that simultaneously profile bacterial, fungal, and viral communities from the same samples — where long-read metagenomic assemblies capture complete genomes across kingdoms, and long-read metatranscriptomics provides functional activity data for all three domains. The gut-brain axis, vaginal microbiome in preterm birth, and built-environment microbiome surveillance represent additional emerging applications where the strain-level resolution and functional completeness of long-read data provide biological insights that short-read community profiling alone cannot deliver.
Long-read sequencing supports a wide spectrum of microbiome research applications. Below we highlight the major application areas and the services most relevant to each.
Public Health Surveillance
Long-read genomics enables real-time tracking of pathogens, antimicrobial resistance determinants, and outbreak strains at nucleotide resolution. Complete genome closure and plasmid reconstruction provide the linkage data needed to distinguish vertical transmission from horizontal gene transfer in epidemiological investigations.
Relevant services: Bacterial WGS, ARG Analysis, Metagenomics
Human Gut & Oral Microbiome
The human gut and oral microbiomes harbour hundreds of co-existing species whose interactions modulate host metabolism, immunity, and disease susceptibility. Long-read metagenomics and full-length 16S sequencing provide the strain-level resolution needed to track microbial dynamics in longitudinal and interventional studies.
Relevant services: Human Microbiome, Metagenomics, 16S/18S/ITS
Plant & Agricultural Microbiome
The rhizosphere, phyllosphere, and endosphere microbiomes influence crop yield, nutrient uptake, disease resistance, and stress tolerance. Long-read sequencing enables comprehensive characterisation of plant-associated microbial communities and the identification of beneficial strains for biocontrol and biofertiliser development.
Relevant services: Plant & Animal Microbiome, 16S/18S/ITS, Microbial WGS
Industrial & Environmental Microbiome
Microbial communities drive critical processes in wastewater treatment, biogas production, bioremediation, and industrial fermentation. Long-read sequencing provides the genomic resolution needed to optimise microbial consortia performance, monitor community stability, and discover novel enzymes and metabolic pathways.
Relevant services: Industrial Microbiome, Metagenomics, Plasmid Sequencing
Our End-to-End Microbiome Workflow Spans Sample Preparation Through Multi-Omics Bioinformatics and Biological Interpretation
1. Sample Preparation & QC
HMW DNA extraction from microbiome samples (stool, soil, water, tissue, swabs, or cultured isolates). Sample quality assessed by PFE and fluorometric quantification. For metagenomics: minimum 1–5 µg input depending on community complexity. For isolate WGS: standard HMW DNA extraction protocols.
2. Library Construction & Sequencing
PacBio HiFi library (SMRTbell) for high-accuracy long reads, or ONT library (ultralong protocol, R10.4.1 flow cells) for maximum read length. Full-length 16S/18S/ITS amplicon libraries for targeted community profiling. Multiplexing available for cost-effective population-scale studies.
Overview of the long-read microbiome analysis workflow — from HMW DNA extraction and library preparation through sequencing, bioinformatics, and biological interpretation.
3. Bioinformatics Analysis
Tailored bioinformatics pipelines depending on service type: metagenomic assembly and binning (Flye, metaFlye, Hifiasm-meta, SemiBin, DASTool), MAG QC and taxonomy assignment (GTDB-Tk, CheckM2), full-length amplicon analysis (DADA2, LACA), microbial genome assembly and annotation (Flye, hifiasm, Bakta, Prokka), ARG and mobile element profiling (CARD, ResFinder, MobileElementFinder, geNomad), and comparative genomics (panX, Roary, pangenome analysis).
4. Interpretation & Delivery
Comprehensive project report including assembly and binning statistics, community composition profiles, MAG completeness and contamination metrics, ARG and virulence gene inventories, comparative genomics results, and publication-ready figures. Data delivered on secure storage with full archiving.
Long-Read Sequencing Delivers Complete Closed Genomes, Strain-Level Resolution, and ARG Genomic Context for Microbiome Research
- Complete, closed microbial genomes. Long reads span repetitive elements and plasmid junctions, enabling single-contig circular chromosomes and complete plasmid reconstruction without gaps or ambiguity.
- Strain-level taxonomic resolution. Full-length 16S/18S/ITS amplicons and metagenomic long reads resolve species and strains that short partial-amplicon approaches collapse into operational taxonomic units.
- AMR gene genomic context. Long reads determine whether resistance genes are chromosomal or plasmid-borne, identify the mobile genetic elements responsible for horizontal transfer, and resolve multi-gene resistance cassettes.
- High-quality MAGs from metagenomes. HiFi accuracy combined with long-read contiguity produces near-complete to complete MAGs from complex communities, including low-abundance members that short-read binning cannot recover.
- Phasing and haplotype resolution. Long reads span heterozygous sites in microbial genomes and metagenomes, enabling strain phasing and allele-specific expression analysis in community transcriptomics.
- Direct RNA and epigenetic detection. ONT direct RNA sequencing enables transcriptome profiling of active microbial communities without amplification bias, and HiFi kinetic signatures detect DNA base modifications (methylation) in microbial genomes.
When to Choose Long-Read Sequencing for Microbiome Research — and When Alternative Methods May Be More Suitable
Choose long-read sequencing for microbiome research when:
- Complete, closed microbial genomes are required — If your research demands finished genomes rather than fragmented bins — for accurate functional annotation, plasmid reconstruction, or strain-level pangenomics — long-read sequencing is the only approach that routinely produces complete, circular chromosomes from microbial isolates and metagenomes
- Species-level or strain-level taxonomic resolution is essential — Full-length 16S/18S/ITS amplicon sequencing (~1,500 bp) provides species-level resolution that short partial-amplicon approaches (V3–V4, ~250–450 bp) systematically miss. For strain-level resolution in metagenomes, long reads provide complete genome context that distinguishes near-identical strains
- Determining the genomic context of antibiotic resistance genes is a project goal — Only long reads provide the contiguous sequence needed to determine whether ARGs are chromosomal or plasmid-borne, identify flanking mobile genetic elements, and resolve multi-gene resistance cassettes — critical information for understanding horizontal gene transfer and resistance dissemination
- You need high-quality MAGs from low-biomass or complex communities — Long-read metagenomics recovers 44–64× more complete MAGs per Gbp than Illumina, making it the superior choice for samples where sequencing depth is limited or community complexity is high (soil, sediment, clinical samples)
Consider alternative methods when:
- Broad community profiling at the lowest per-sample cost is sufficient — For large-scale screening where genus-level taxonomic profiles are adequate, short-read amplicon sequencing (V3–V4 16S rRNA) provides the most cost-effective approach per sample. We offer both short-read and long-read options and can advise on the best strategy for your study scale
- You need to compare results with large existing short-read microbiome datasets — While cross-platform concordance is generally high, long-read and short-read metagenomic profiles differ systematically in community composition estimates due to differences in assembly completeness and taxonomic resolution. Projects that must integrate directly with large existing short-read datasets should consider generating a bridging dataset or budgeting for cross-platform normalization analysis
- RNA-level community activity (metatranscriptomics) is the sole research focus — For projects centered on gene expression rather than genomic potential, RNA-seq (with rRNA depletion) provides direct functional activity data without the expense of metagenomic sequencing and genome assembly. We offer both RNA-seq and DNA-seq services for integrated studies
CD Genomics provides free project consultation to help determine the optimal microbiome research strategy for your specific research questions and sample types. Contact our scientists to discuss your project requirements.
FAQs
Q: What sequencing depth is recommended for microbial genome assembly?
For bacterial genome de novo assembly, we recommend 50–100× HiFi coverage (or 50–100× ONT + polishing) to produce a complete, circular chromosome. For fungal genomes (larger and more repetitive), 50–100× HiFi or a combination of ONT ultralong + HiFi polishing is recommended. For viral genomes, 100–500× coverage depending on genome size and complexity. Our project scientists can help determine the optimal coverage for your specific organism.
Q: What is the minimum DNA input for long-read microbiome sequencing?
Minimum input requirements depend on the library type and platform. For PacBio HiFi microbial WGS, we recommend >1 µg HMW gDNA. For ONT ultralong sequencing, >5 µg is recommended for maximum read lengths. For metagenomic libraries (where community DNA is limited), we have protocols optimised for low-input samples (>100 ng). For full-length 16S/18S/ITS amplicon sequencing, as little as 10 ng of community DNA is sufficient.
Q: Can you process samples with mixed microbial communities (metagenomes)?
Yes. Our long-read metagenomics service is specifically designed for complex microbial communities. We accept DNA extracted from stool, soil, water, sediment, biofilm, and other environmental samples. For metagenomic sequencing, we recommend >1 µg of community DNA. Our bioinformatics pipeline includes metagenomic assembly (metaFlye, Hifiasm-meta), binning (SemiBin, MetaBAT2, DASTool), MAG QC (CheckM2, GTDB-Tk), and functional annotation. We can also perform full-length 16S/18S/ITS amplicon sequencing on the same community DNA for complementary taxonomic profiling.
Q: How do you determine whether ARG genes are chromosomal or plasmid-borne?
Long-read sequencing is uniquely suited to this question because reads spanning 10–100+ kb can bridge ARGs and their surrounding genomic context. Our ARG analysis pipeline maps long reads to a comprehensive resistance gene database (CARD, ResFinder, MEGARes) and classifies each ARG hit by its genomic neighbourhood: chromosomal (flanked by housekeeping genes and core genome), plasmid-borne (flanked by plasmid replicons, relaxases, and conjugation machinery), or phage-associated. Only long reads provide the contiguous sequence data needed for this classification with high confidence.
Inquiries & References
CD Genomics is committed to advancing microbiome research through comprehensive long-read sequencing solutions. Whether you are characterising a single bacterial isolate, profiling a complex environmental metagenome, or tracking antimicrobial resistance in a clinical surveillance programme, our platform flexibility and bioinformatics expertise ensure you receive high-quality, publication-ready results.
To discuss your microbiome project requirements, sample types, or to request a detailed quotation, please contact our scientific team.
References
- Moss EL, Maghini DG, Bhatt AS. Complete, closed bacterial genomes from microbiomes using nanopore sequencing. Nature Biotechnology. 2020;38:701–707. doi:10.1038/s41587-020-00746-x (reference only)
- For additional references and case studies specific to each service, please see the individual service pages linked in the services section above.