Resolving complexity
Generating new insights into how microbial communities function requires improved approaches. Long-read sequencing enables species-level resolution and drives functional insights with full-length 16S rDNA and shotgun sequencing for metagenomic profiling and assemblies.
Single Molecule, Real-Time (SMRT) Sequencing for metagenomics pairs long reads with high accuracy, enabling you to:
- Understand key community functions by sequencing complete operons at 99.9% accuracy with long-insert metagenomic profiling – no assembly required
- Identify microbial community members with strain-level resolution using full-length 16S rDNA or shotgun sequencing
- Discover novel genes and gene clusters by reconstructing multi-kilobase long contigs with whole genome shotgun metagenomic assembly
- Leverage epigenomic data to associate contigs and plasmids from closely related strains
Workflows: from DNA to resolved microbial communities
 | Library Preparation
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| SMRT Sequencing with the Sequel System
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| Data Analysis through SMRT Analysis, PacBio DevNet or Service Partners
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Spotlight: Accurately mapping mycobiota to understand human health
Scientists explored various sequencing techniques to establish the most rigorous method to map human gut mycobiota of healthy individuals. Their results showed that PacBio SMRT Sequencing most accurately represented the metagenomic population profile. Explore this research further:
Motooka, D. 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, 8, p.238.
Selected Resources
- P.E. Zida 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
- Heeger, Felix et al. (2018) Long-read DNA metabarcoding of ribosomal rRNA in the analysis of fungi from aquatic environments BioRxiv
- Beaulaurier, John et al. (2017) Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation. Nature Biotechnology
- 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
- Tedersoo, Leho et al. (2017) PacBio metabarcoding of fungi and other eukaryotes: errors, biases and perspectives. The New Phytologist
- 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
- Nakano, Kazuma et al. (2017) Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area. Human Cell
- Tai, Phillip WL et al. (2018) Adeno-associated virus genome population sequencing achieves full vector genome resolution and reveals human-vector chimeras Molecular Therapy
- 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
- Lam, Ka-Kit et al. (2016) BIGMAC : breaking inaccurate genomes and merging assembled contigs for long read metagenomic assembly. BMC Bioinformatics
- Gesudu, Qimu et al. (2016) Investigating bacterial population structure and dynamics in traditional koumiss from Inner Mongolia using single molecule real-time sequencing. Journal of Dairy Science
- Zheng, Yi et al. (2016) Using PacBio long-read high-throughput microbial gene amplicon sequencing to evaluate infant formula safety. Journal of Agricultural and Food Chemistry
- Singer, Esther et al. (2016) High-resolution phylogenetic microbial community profiling. The ISME Journal
- Gall, Cory A et al. (2016) The bacterial microbiome of Dermacentor andersoni ticks influences pathogen susceptibility. The ISME Journal
- Armanhi, Jaderson Silveira Leite et al. (2016) Multiplex amplicon sequencing for microbe identification in community-based culture collections. Scientific Reports
- Bao, Weichen et al. (2016) Assessing quality of Medicago sativa silage by monitoring bacterial composition with single molecule, real-time sequencing technology and various physiological parameters. Scientific Reports
- Myer, Phillip R et al. (2016) Evaluation of 16S rRNA amplicon sequencing using two next-generation sequencing technologies for phylogenetic analysis of the rumen bacterial community in steers. Journal of Microbiological Methods
- Frank, J A et al. (2016) Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data. Scientific Reports
- Ikuta, Tetsuro et al. (2016) Heterogeneous composition of key metabolic gene clusters in a vent mussel symbiont population. The ISME Journal
- Tsai, Yu-Chih et al. (2016) Resolving the complexity of human skin metagenomes using single-molecule sequencing. mBio
- Broecker, Felix et al. (2016) Long-term changes of bacterial and viral compositions in the intestine of a recovered Clostridium difficile patient after fecal microbiota transplantation Molecular Case Studies
- Chen, Yuan et al. (2015) Next generation multilocus sequence typing (NGMLST) and the analytical software program MLSTEZ enable efficient, cost-effective, high-throughput, multilocus sequencing typing. Fungal Genetics and Biology
- 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
- Hatas, Emily (2017) Webinar: SMRT Sequencing applications in plant and animal sciences: an overview
- Auvignen, Petra (2017) AGBT Virtual Poster: Interspecies interation amoung meat spoilage-related lactic acid bacteria
- (2017) Tutorial: Circular Consensus Sequence analysis application [SMRT Link v5.0.0]
- Suzuki, Yoshihiko (2016) AGBT Virtual Poster (Japanese): Meta-methylome of human gut microbiome using SMRT Sequencing
- 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
- SMRT Sequencing Brochure: Revolutionize genomics with SMRT Sequencing. (2018)
- PacBio Certified Service Providers (2018)
- Plant and Animal Sciences Brochure: A comprehensive view of genetic diversity (2017)
- Application Brochure: Microbial communities – Complex microbial populations simplified. (2017)
- SMRT Analysis Brochure: Gain a deeper understanding of your sequencing data (2017)
- Case Study: Scientists advance understanding of microbial genomes, epigenomes and communities with SMRT Sequencing. (2016)
- Industrial Biotechnology Brochure: Fuel biotech discovery with confident characterization of microbes and their communities. (2016)
- Epigenetics Application Brochure: Characterize the epigenetic landscape of your genome. (2016)