Sequence the microbial world with confidence
Microbes account for most of the diversity of life on our planet, yet fewer than 1% have been identified. To understand this ever-evolving world, scientists need the unbiased, accurate, and comprehensive information that only PacBio long-read sequencing can provide.
See the details that drive biological insights with highly accurate, closed genomes that include epigenetic information.
Prokaryotic methylation | Why closed genomes?
Address global needs for novel therapeutics, environmental remediation, and efficient chemical production by mining even the most difficult to sequence microbial genomes.
Biofuel research at JGI | Natural product discovery | Scalable biosynthesis
Advance human health worldwide with new insights into the viruses, bacteria, and protozoa that cause infectious disease.
HIV | Cholera | Malaria | Sleeping sickness | Chagas | Leishmania
Protect public health by finding all the variant types that drive the spread of antimicrobial resistance and contribute to bacterial virulence.
Klebsiella in hospitals | Carbapenem resistance | Shiga-toxigenic E. coli | Tuberculosis virulence
Explore the role of microbial symbionts and pathogens in plant and animal health and disease.
Entomopathogen biology | Closed Xanthomonas genomes | Methylation directs a pathogen lifecycle
 | Whole Genome Sequencing Assemble microbial genomes that are the gold standard for both completeness and accuracy with ease and confidence |
 | Metagenomics Comprehensively characterize metagenomes with long, highly accurate, single-molecule reads – no assembly required |
 | Bacterial Epigenetics Detect the recognition motifs of active R-M systems at coverage levels recommended for assembly |
| | Viral Populations Use long, highly accurate single-molecule reads to deconvolute complex populations, track viral evolution and quantify minor variants |
Selected Resources
- Tørresen, Ole K et al. (2019) Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases. Nucleic acids research
- 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
- Jensen, Torbjørn Ølshøj et al. (2019) Genome-wide systematic identification of methyltransferase recognition and modification patterns. Nature communications
- 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
- Forde, Brian M et al. (2019) SMRT sequencing reveals differential patterns of methylation in two O111:H- STEC isolates from a hemolytic uremic syndrome outbreak in Australia. Scientific reports
- Zan, Jindong et al. (2019) A microbial factory for defensive kahalalides in a tripartite marine symbiosis. Science
- Davies, Mark R et al. (2019) Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics. Nature genetics
- Nye, Taylor M et al. (2019) DNA methylation from a Type I restriction modification system influences gene expression and virulence in Streptococcus pyogenes. PLoS pathogens
- Breitwieser, Florian P et al. (2019) Human contamination in bacterial genomes has created thousands of spurious proteins. Genome research
- Johnston, Christopher D et al. (2019) Systematic evasion of the restriction-modification barrier in bacteria. Proceedings of the National Academy of Sciences of the United States of America
- Stinson, Lisa F et al. (2019) The Not-so-Sterile Womb: Evidence That the Human Fetus Is Exposed to Bacteria Prior to Birth. Frontiers in microbiology
- Tedersoo, Leho et al. (2019) Towards PacBio-based pan-eukaryote metabarcoding using full-length ITS sequences. Environmental microbiology reports
- Su, Bin et al. (2019) Detection of pretreatment minority HIV-1 reverse transcriptase inhibitor-resistant variants by ultra-deep sequencing has a limited impact on virological outcomes. The Journal of antimicrobial chemotherapy
- Jamy, Mahwash et al. (2019) Long metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity BioRxiv
- Lui, Wing-Yu et al. (2019) SMRT sequencing revealed the diversity and characteristics of defective interfering RNAs in influenza A (H7N9) virus infection. Emerging microbes & infections
- Ashton, P M et al. (2019) Three phylogenetic groups have driven the recent population expansion of Cryptococcus neoformans. Nature communications
- Jayaraman, Siddharth et al. (2019) Application of long read sequencing to determine expressed antigen diversity in Trypanosoma brucei infections. PLoS neglected tropical diseases
- Murphy, Timothy F et al. (2019) Persistence of Moraxella catarrhalis in Chronic Obstructive Pulmonary Disease and Regulation of the Hag/MID Adhesin. The Journal of infectious diseases
- Fischer, Sebastian et al. (2019) A unique methylation pattern by a type I HsdM methyltransferase prepares for DpnI rare cutting sites in the Pseudomonas aeruginosa PAO1 genome. FEMS microbiology letters
- Sierra, Johanna C et al. (2019) a-Difluoromethylornithine reduces gastric carcinogenesis by causing mutations in Helicobacter pylori cagY. Proceedings of the National Academy of Sciences of the United States of America
- Beaulaurier, John et al. (2019) Deciphering bacterial epigenomes using modern sequencing technologies. Nature reviews. Genetics
- Olarte, Rodrigo A et al. (2019) Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum. BMC genomics
- Pinzone, Marilia Rita et al. (2019) Longitudinal HIV sequencing reveals reservoir expression leading to decay which is obscured by clonal expansion. Nature communications
- Masonbrink, Rick et al. (2019) The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes. BMC genomics
- Kingan, Sarah et al. (2019) A high-quality de novo genome assembly from a single mosquito using PacBio sequencing Genes
- Mehta, Devang et al. (2019) A new full-length circular DNA sequencing method for viral-sized genomes reveals that RNAi transgenic plants provoke a shift in geminivirus populations in the field. Nucleic acids research
- Sullivan, Mitchell J et al. (2019) Complete genome screening of clinical MRSA isolates identifies lineage diversity and provides full resolution of transmission and outbreak events BioRxiv
- Biessy, Adrien et al. (2019) Diversity of phytobeneficial traits revealed by whole-genome analysis of worldwide-isolated phenazine-producing Pseudomonas spp. Environmental microbiology
- 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
- Liang, Quanhui et al. (2019) Sequencing and Genomic Diversity Analysis of IncHI5 Plasmids. Frontiers in microbiology
- Ameur, Adam et al. (2019) Single-Molecule Sequencing: Towards Clinical Applications. Trends in biotechnology
- Chen, Yujiao et al. (2019) Study of the whole genome, methylome and transcriptome of Cordyceps militaris. Scientific reports
- 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: Hong, Bo-young et al. (2019) Microbiome profiling at the strain level using rRNA amplicons
- Poster: Ekholm, Jenny et al. (2019) Streamlines SMRTbell library generation using addition-only, single tube strategy for all library types reduces time to results
- Poster: Wong, J. et al. (2018) Single chromosomal genome assemblies on the Sequel System with Circulomics high molecular weight DNA extraction for microbes
- Poster: Boitano, M. et al. (2018) Full-length cDNA sequencing of prokaryotic transcriptome and metatranscriptome samples
- Poster: Heiner, Cheryl et al. (2018) Multiplexed complete microbial genomes on the Sequel System
- Poster: Lambert, C. et al. (2017) Multiplexing strategies for microbial whole genome sequencing using the Sequel System
- Poster: Kingan, Sarah et al. (2017) A high-quality genome assembly of SMRT sequences reveals long range haplotype structure in the diploid mosquito Aedes aegypti
- 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: Kingan, S. et al. (2017) A high-quality genome assembly of SMRT Sequences reveals long-range haplotype structure in the diploid mosquito Aedes aegypti
- Poster: Concepcion, G. et al. (2017) Phased diploid genome assembly with single-molecule real-time sequencing
- Poster: Heiner, C. et al. (2017) Profiling complex population genomes with highly accurate single molecule reads: cow rumen microbiomes
- (2020) Video: Introduction to PacBio highly accurate long-read sequencing
- Ashby, Meredith and Eversole, Kelley (2019) Webinar: Unbiased, efficient characterization of metagenome functions with PacBio HiFi sequencing
- Wheeler, Nic (2019) User Group Meeting: Long-read RNA Sequencing in neglected human parasites
- Nakanishi, Masako (2019) User Group Meeting: Modulation of gut microbiome in mice with differential susceptibility to colonic ulceration
- Polson, Shawn (2019) User Group Meeting: New genotype to phenotype associations in viral metagenomes enabled by SMRT Sequencing
- 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
- Ashby, Meredith (2019) Webinar: Long-read sequencing and infectious disease: New insights into longstanding challenges
- Auch, Ben, and Sheik, Cody and van Bakel, Harm (2019) Webinar: Complete genomes within reach – Closing bacterial genomes from the lakes of Minnesota to NYC hospitals
- Korlach, Jonas and Corney, Dave (2018) Webinar: A new paradigm in DNA sequencing – Highly accurate single-molecule long reads
- 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
- Korlach, Jonas (2018) Webinar: New PacBio solutions for high-resolution microbiology & immunology analysis
- Pillai, Nisha (2018) Webinar: Assessing the targeted regions using a PacBio Amplicon analysis applications
- (2018) Tutorial: Multiplexed Microbial Assembly [SMRT Link v5.1.0]
- Hatas, Emily (2017) Webinar: SMRT Sequencing applications in plant and animal sciences: an overview
- (2017) Tutorial: Minor variant analysis [SMRT Link v5.0.0]
- Kingan, Sarah (2017) Webinar: Understanding, curating, and analyzing your diploid genome assembly
- Turner, Stephen (2017) Webinar: An introduction to PacBio’s long-read sequencing & how it has been used to make important scientific discoveries
- Neafsey, Daniel (2017) AGBT Conference: A community effort using multiple technologies to produce a dramatically improved genome assembly of the Zika virus mosquito vector
- Auvignen, Petra (2017) AGBT Virtual Poster: Interspecies interation amoung meat spoilage-related lactic acid bacteria
- Paulin, Lars (2017) AGBT Virtual Poster: Single-molecule sequencing reveals the presence of distinct JC polyomavirus populations in patients with progressive multifocal leukoencephalopathy
- (2017) Tutorial: Base modification detection, base modification and motif analysis application [SMRT Link v5.0.0]
- (2017) Tutorial: HGAP4 de novo assembly application [SMRT Link v5.0.0]
- Matthews, Ben (2017) PAG PacBio Workshop: Genome assembly and molecular genetics of the dengue, yellow fever, and zika vector Aedes aegypti
- Laird Smith, Melissa (2016) ASHG PacBio Workshop: SMRT Sequencing as a translational research tool to investigate germline, somatic and infectious diseases
- Korlach, J. and Kingan, S. (2016) i5K Webinar: High-quality de novo insect genome assemblies using PacBio sequencing
- Hannigan, Brett (2016) DNAnexus Webinar: Simplifying de novo assembly with PacBio tools available on DNAnexus: FALCON
- Ameur, Adam (2016) AGBT Roche and PacBio Workshop: Clinical SMRT Sequencing – from single genes to complete genomes
- Murrell, Ben (2016) AGBT Roche and PacBio Workshop: Deeply sequencing entire genes from rapidly evolving viruses
- Paxinos, Ellen (2016) AGBT Virtual Poster: An improved circular consensus algorithm with an application to detect HIV-1 Drug Resistance Associated Mutations (DRAMs)
- Seetin, Matthew (2016) AGBT Virtual Poster: Long-read assembly of the Aedes aegypti Aag2 cell line genome resolves ancient endogenous viral elements
- 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: Delivering highly accurate long reads to drive discovery in life science (2019)
- Application Brochure: What can you do with one SMRT Cell? (2019)
- Case Study: Sequencing an historic bacterial collection for the future (2019)
- Infographic: A brief history of microbiology (2019)
- Application Brief: Microbial whole genome sequencing – Best Practices (2019)
- Application Brochure: Explore metagenomes in high resolution (2019)
- Case Study: Mining complex metagenomes for protein discovery with long-read sequencing (2019)
- PacBio Certified Service Providers (2019)
- Product Note: SMRTbell express template prep 2.0 for microbial multiplexing (2019)
- Application Note: Microbial multiplexing workflow on the Sequel System (2019)
- SMRT Analysis Brochure: Gain a deeper understanding of your sequencing data (2018)
- 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)