See metagenomes in high resolution
Generating new insights into how microbial communities function and interact with their environments requires improved approaches. Long-read sequencing enables species-level resolution and drives functional insights with full-length 16S sequencing and 10 kb HiFi reads for metagenome profiling and assembly.
Highly accurate long reads – HiFi reads – with single-molecule resolution make Single Molecule, Real-Time (SMRT) Sequencing ideal for full-length 16S rRNA sequencing, shotgun metagenomic profiling, and metagenome assembly, so that you can:
- Identify 6-8 full-length genes in every HiFi read, without assembly, with cost-effective metagenomic profiling
- Determine community composition at the species or strain-level with affordable full-length 16S sequencing
- Generate reference-quality assemblies with 15-fold coverage of HiFi metagenome data for comparative genomics
- Leverage epigenomic data to associate contigs and plasmids from closely related strains
 | Library Preparation |
| Prepare targeted sequences or shotgun libraries to characterize your microbial community. |
 | Sequencing |
| Use the Sequel II System for affordable, high-quality metagenomic sequencing |
 | Data Analysis |
| Make discoveries using bioinformatics tools in SMRT Analysis or PacBio DevNet. |
Application Brief: Learn more these best practices for metagenomic sequencing with HiFi reads
Spotlight: Strain-level identification of bacterial communities with the unprecedented accuracy of PacBio full-length 16S sequencing
Using DADA2 software, all copies of the 16S housekeeping gene can be recovered from microbial communities. 16S sequence variants from the same strain appear in the data in integer ratios that reflect their copy number in each genome. In some cases, for example E. coli O157:H7 in the Zymo mock community, this high-resolution information can be used to unambiguously identify not only the species but the strain present. Explore this research further:
Callahan, B. J., et al. (2019). High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution. Nucleic Acids Research.
Long reads and methylation profiles enable binning of metagenome assembly contigs and plasmids
SMRT Sequencing of metagenomes enables highly contiguous assemblies of community members, but leveraging the associated methylation information further allows those contigs to be associated into near-complete genome bins. Plasmids of sufficient size can also be associated with hosts via their methylation fingerprints. Explore this research further:
Beaulaurier, J., et al. (2017). Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation. Nature Biotechnology, 36(1), 61–69.
Selected Resources
- Bickhart, Derek M et al. (2019) Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation. Genome biology
- Loit, Kaire et al. (2019) Relative Performance of MinION (Oxford Nanopore Technologies) vs. Sequel (Pacific Biosciences) Third-Generation Sequencing Instruments in Identification of Agricultural and Forest Fungal Pathogens. Applied and environmental microbiology
- Martijn, Joran et al. (2019) Confident phylogenetic identification of uncultured prokaryotes through long read amplicon sequencing of the 16S-ITS-23S rRNA operon. Environmental microbiology
- Callahan, Benjamin J et al. (2019) High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution. Nucleic acids research
- Zan, Jindong et al. (2019) A microbial factory for defensive kahalalides in a tripartite marine symbiosis. Science
- Tedersoo, Leho et al. (2019) Towards PacBio-based pan-eukaryote metabarcoding using full-length ITS sequences. Environmental microbiology reports
- Zhang, Peng et al. (2019) Full-Length Multi-Barcoding: DNA Barcoding from Single Ingredient to Complex Mixtures. Genes
- Jamy, Mahwash et al. (2019) Long metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity BioRxiv
- Hiraoka, Satoshi et al. (2019) Metaepigenomic analysis reveals the unexplored diversity of DNA methylation in an environmental prokaryotic community. Nature communications
- Nilsson, R Henrik et al. (2019) Mycobiome diversity: high-throughput sequencing and identification of fungi. Nature reviews. Microbiology
- Redondo, Miguel A et al. (2018) Contrasting distribution patterns between aquatic and terrestrial Phytophthora species along a climatic gradient are linked to functional traits. The ISME journal
- Beaulaurier, John et al. (2018) Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation. Nature biotechnology
- Heeger, Felix et al. (2018) Long-read DNA metabarcoding of ribosomal RNA in the analysis of fungi from aquatic environments. Molecular ecology resources
- Zida, P.E. et al. (2018) Increasing sorghum yields by seed treatment with an aqueous extract of the plant Eclipta alba may involve a dual mechanism of hydropriming and suppression of fungal pathogens Crop protection
- Tedersoo, Leho et al. (2018) PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives. The New phytologist
- Perraudeau, Fanny et al. (2017) Accurate determination of bacterial abundances in human metagenomes using full-length 16S sequencing reads BioRxiv
- Wang, Yuan et al. (2017) Profiling of oral microbiota in early childhood caries using Single-Molecule Real-Time Sequencing Frontiers in microbiology
- Edwards, Joan E et al. (2017) PCR and omics based techniques to study the diversity, ecology and biology of anaerobic fungi: Insights, challenges andopportunities. Frontiers in microbiology
- Costa, Stephen K et al. (2017) Bypassing the Restriction System To Improve Transformation of Staphylococcus epidermidis. Journal of bacteriology
- Zhao, J et al. (2017) Reduction in fecal microbiota diversity and short-chain fatty acid producers in Methicillin-resistant Staphylococcus aureus infected individuals as revealed by PacBio single molecule, real-time sequencing technology. European journal of clinical microbiology & infectious diseases
- Wlodarska, Marta et al. (2017) Indoleacrylic acid produced by commensal Peptostreptococcus species suppresses inflammation. Cell host & microbe
- Nakano, Kazuma et al. (2017) Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area. Human cell
- Xu, Haiyan et al. (2017) The effects of probiotics administration on the milk production, milk components and fecal bacteria microbiota of dairy cows Science bulletin
- Pootakham, Wirulda et al. (2017) High resolution profiling of coral-associated bacterial communities using full-length 16S rRNA sequence data from PacBio SMRT sequencing system. Scientific reports
- Sadowsky, Michael J et al. (2017) Analysis of gut microbiota – An ever changing landscape. Gut microbes
- McRose, Darcy L et al. (2017) Diversity and activity of alternative nitrogenases in sequenced genomes and coastal environments. Frontiers in microbiology
- Meng, Xiangli et al. (2017) Metataxonomics reveal vultures as a reservoir for Clostridium perfringens. Emerging microbes and infections
- Motooka, Daisuke et al. (2017) Fungal ITS1 deep-sequencing strategies to reconstruct the composition of a 26-species community and evaluation of the gut mycobiota of healthy Japanese individuals. Frontiers in microbiology
- Driscoll, Connor B et al. (2017) Towards long-read metagenomics: complete assembly of three novel genomes from bacteria dependent on a diazotrophic cyanobacterium in a freshwater lake co-culture. Standards in genomic sciences
- Hagen, Live H et al. (2017) Quantitative metaproteomics highlight the metabolic contributions of uncultured phylotypes in a thermophilic anaerobic digester. Applied and environmental microbiology
- Li, Jing et al. (2017) Bacterial microbiota of Kazakhstan cheese revealed by single molecule real time (SMRT) sequencing and its comparison with Belgian, Kalmykian and Italian artisanal cheeses BMC microbiology
- Poster: Baybayan, Primo et al. (2020) New advances in SMRT Sequencing facilitate multiplexing for de novo and structural variant studies
- Poster: Ashby, Meredith et al. (2020) Unbiased characterization of metagenome composition and function using HiFi sequencing on the PacBio Sequel II System
- Poster: Ashby, Meredith et al. (2019) Unbiased characterization of metagenome composition and function using HiFi sequencing on the PacBio Sequel II System
- Poster: Jain, S. et al. (2019) Comparison of sequencing approaches applied to complex soil metagenomes to resolve proteins of interest
- Poster: McComb, E. et al. (2019) High-resolution evaluation of gut microbiota associated with intestinal maturation in early preterm neonates
- Poster: Boitano, M. et al. (2018) Full-length cDNA sequencing of prokaryotic transcriptome and metatranscriptome samples
- Poster: Hall, Richard et al. (2017) Using the PacBio Sequel System to taxonomically and functionally classify metagenomic samples in a trial of patients undergoing fecal microbiota transplantation
- Poster: Heiner, C. et al. (2017) Profiling complex population genomes with highly accurate single molecule reads: cow rumen microbiomes
- Poster: Oh, S. et al. (2016) Minimization of chimera formation and substitution errors in full-length 16S PCR amplification
- Poster: Heiner, C. et al. (2016) WGS SMRT Sequencing of patient samples from a fecal microbiota transplant trial
- Poster: Hall, R. et al. (2016) Workflow for processing high-throughput, Single Molecule, Real-Time Sequencing data for analyzing the microbiome of patients undergoing fecal microbiota transplantation
- Poster: Heiner, Cheryl et al. (2016) Low-input long-read sequencing for complete microbial genomes and metagenomic community analysis
- Poster: Hall, Richard et al. (2016) Profiling the microbiome in fecal microbiota transplantation using circular consensus and Single Molecule, Real-Time Sequencing
- Poster: Hall, Richard J et al. (2016) Profiling metagenomic communities using circular consensus and Single Molecule, Real-Time Sequencing
- Ashby, Meredith and Ma, Bing and Weinstock, George (2020) Webinar: A HiFi view – Sequencing the gut microbiome with highly accurate long reads
- Mars, Kristin and Laird Smith, Melissa and Vinnere Pettersson, Olga and Hardigan, Michael (2020) Webinar: Sequencing 101 – How long-read sequencing improves access to genetic information
- (2020) Video: Introduction to PacBio highly accurate long-read sequencing
- Vierra, Michelle (2020) PAG Conference: PacBio update on products and HiFi applications
- Ashby, Meredith and Eversole, Kelley (2019) Webinar: Unbiased, efficient characterization of metagenome functions with PacBio HiFi sequencing
- Nakanishi, Masako (2019) User Group Meeting: Modulation of gut microbiome in mice with differential susceptibility to colonic ulceration
- Korlach, Jonas (2019) User Group Meeting: Sequencing chemistry & application updates
- Ashby, Meredith (2019) User Group Meeting: Unbiased characterization of metagenome composition and function using HiFi sequencing on the PacBio Sequel II System
- Korlach, Jonas and Garimella, Kiran and Tallon, Luke and McCarthy, Shane (2019) Webinar: Sequence with Confidence – Introducing the Sequel II System
- Ehrlich, Garth (2018) User Group Meeting: Development, validation, and applications of a high-fidelity, species-specific, eubacterial pan-domain microbiome assay on the PacBio System
- Singh, Siddharth (2017) Webinar: Beginner’s guide to PacBio SMRT Sequencing data analysis
- (2017) Tutorial: Circular Consensus Sequence analysis application [SMRT Link v5.0.0]
- Heiner, Cheryl (2016) AGBT Virtual Poster: Low-input long-read sequencing for complete microbial genomes and metagenomic community analysis
- Heiner, Cheryl (2016) AGBT Virtual Poster: Minimization of chimera formation and substitution errors in full-length 16S PCR amplification
- Hall, Richard (2016) AGBT Virtual Poster: Profiling the microbiome in fecal microbiota transplantation using circular consensus and Single Molecule, Real-Time Sequencing
- Application Brief: Metagenomic sequencing with HiFi reads – Best Practices (2020)
- Application Brochure: What can you do with one SMRT Cell? (2020)
- Case Study: Diving Deep – Revealing the mysteries of marine life with SMRT Sequencing (2019)
- SMRT Sequencing Brochure: Delivering highly accurate long reads to drive discovery in life science (2019)
- Case Study: Mining complex metagenomes for protein discovery with long-read sequencing (2019)
- PacBio Certified Service Providers (2019)
- Industrial Biotechnology Brochure: Fuel biotech discovery with confident characterization of microbes and their communities (2016)