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 |
The 2019 HiFi for All SMRT Grant Program is Now Open!
Sequence All Life with Confidence Using HiFi Reads
Tell us how highly accurate long reads (HiFi reads) will drive new discoveries in your research for a chance to win free sequencing.
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
- 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
- Morey, Robert (2016) AGBT Virtual Poster: Using PacBio sequencing as a synthetic biology error analysis tool
- 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)