Exploring the world of microbes
The importance of the diversity of the microbes on earth is only just beginning to come to light. To continue exploring the world of microbes, complete characterization of genomes and communities will be necessary to improve global health, protect our agriculture and livestock, and fuel discovery research.
Single Molecule, Real-Time (SMRT) Sequencing empowers scientists to:
- Generate near-complete de novo assemblies of microbes and their accessory plasmids
- Confidently resolve viral diversity
- Characterize microbial populations down to the species level
See how SMRT Sequencing can drive your science
 | Discovery-based Microbiology Advance understanding of the microbial world |  | Industrial Microbiology Address global challenges by evolving industrial microbiology | |||
 | Infectious Disease Combat infectious disease to promote human health |  | Public Health Inform global health and surveillance of pathogens | |||
 | Plant and Animal Microbiology Explore the role of microbial symbionts in plant and animal health and disease |
Selected Resources
- Poulter, Russell T. M. et al. (2018) Comparison between complete genomes of an isolate of Pseudomonas syringae pv. actinidiae from Japan and a New Zealand isolate of the pandemic Scientific Reports
- Castellanos, Mildred et al. (2018) A Borrelia burgdorferi mini-vls system that undergoes antigenic switching in mice: investigation of the role of plasmid topology and the long inverted repeat. Molecular Microbiology
- Douglass, Alexander P et al. (2018) Population genomics shows no distinction between pathogenic Candida krusei and environmental Pichia kudriavzevii: One species, four names. PLoS Pathogens
- Pollard, Martin O et al. (2018) Long reads: their purpose and place. Human Molecular Genetics
- Mehta, Devang et al. (2018) CRISPR-Cas9 interference in cassava linked to the evolution of editing-resistant geminiviruses BioRxiv
- Verhey, Theodore B et al. (2018) Antigenic variation in the lyme spirochete: Insights into recombinational switching with a suggested role for error-prone repair. Cell Reports
- 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
- Harumoto, Toshiyuki et al. (2018) Male-killing toxin in a bacterial symbiont of Drosophila. Nature
- Zhao, Liang et al. (2018) The highly heterogeneous methylated genomes and diverse restriction-modification systems of bloom-forming Microcystis. Harmful Algae
- Vincent, Antony T et al. (2018) Unexpected diversity in the mobilome of a Pseudomonas aeruginosa strain isolated from a dental unit waterline revealed by SMRT Sequencing. Genome
- Berná, Luisa et al. (2018) Expanding an expanded genome: long-read sequencing of Trypanosoma cruzi. Microbial Genomics
- Otto, Thomas D et al. (2018) Long read assemblies of geographically dispersed Plasmodium falciparum isolates reveal highly structured subtelomeres. Wellcome Open Research
- Slager, Jelle et al. (2018) Deep genome annotation of the opportunistic human pathogen Streptococcus pneumoniae D39 BioRxiv
- Heeger, Felix et al. (2018) Long-read DNA metabarcoding of ribosomal rRNA in the analysis of fungi from aquatic environments BioRxiv
- Frank, Jeroen et al. (2018) Resolving the complete genome of Kuenenia stuttgartiensis from a membrane bioreactor enrichment using Single-Molecule Real-Time sequencing. Scientific Reports
- Hu, Yi et al. (2018) Herbivorous turtle ants obtain essential nutrients from a conserved nitrogen-recycling gut microbiome. Nature Communications
- Bruijnesteijn, Jesse et al. (2018) Human and rhesus macaque KIR haplotypes defined by their transcriptomes. Journal of Immunology
- Magrini, Vincent et al. (2018) Improving eukaryotic genome annotation using single molecule mRNA sequencing. BMC Genomics
- Yadav, Vikas et al. (2018) RNAi is a critical determinant of centromere evolution in closely related fungi. Proceedings of the National Academy of Sciences of the United States of America
- Haig, Sarah-Jane et al. (2018) A high-throughput approach for identification of nontuberculous mycobacteria in drinking water reveals relationship between water age and Mycobacterium avium. mBio
- Weingarten, Rebecca A et al. (2018) Genomic analysis of hospital plumbing reveals diverse reservoir of bacterial plasmids conferring carbapenem resistance. mBio
- Schwessinger, Benjamin et al. (2018) A near-complete haplotype-phased genome of the dikaryotic wheat stripe rust fungus Puccinia striiformis f. sp. tritici reveals high interhaplotype diversity. mBio
- Atack, John M et al. (2018) Phasevarions of bacterial pathogens: Methylomics sheds new light on old enemies. Trends in Microbiology
- Ardui, Simon et al. (2018) Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics. Nucleic Acids Research
- Kjærbølling, Inge et al. (2018) Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species. Proceedings of the National Academy of Sciences of the United States of America
- Paulk, Nicole K et al. (2017) Bioengineered AAV capsids with combined high human liver transduction in vivo and unique humoral seroreactivity. Molecular Therapy
- Palmer, Jonathan M et al. (2018) Extreme sensitivity to ultraviolet light in the fungal pathogen causing white-nose syndrome of bats. Nature Communications
- Acuña-Amador, Luis et al. (2018) Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains. BMC Genomics
- Li, M et al. (2017) High frequency of mitochondrial DNA mutations in HIV-infected treatment-experienced individuals. HIV Medicine
- Pfeiffer, Friedhelm et al. (2018) The complete and fully assembled genome sequence of Aeromonas salmonicida subsp. pectinolytica and its comparative analysis with other Aeromonas species: investigation of the mobilome in environmental and pathogenic strains. BMC Genomics
- Fallon, Timothy R et al. (2017) Firefly genomes illuminate the origin and evolution of bioluminescence BioRxiv
- Hemadou, Audrey et al. (2017) Pacific Biosciences sequencing and IMGT/HighV-QUEST analysis of full-length single chain fragment variable from an in vivo selected phage-display combinatorial Library. Frontiers in Immunology
- Revez, Joana et al. (2017) Survey on the use of whole-genome sequencing for infectious diseases surveillance: Rapid expansion of European national capacities, 2015-2016. Frontiers in Public Health
- Beaulaurier, John et al. (2017) Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation. Nature Biotechnology
- Lu, You et al. (2017) Comparative genomic analyses of Clavibacter michiganensis subsp. insidiosus and pathogenicity on Medicago truncatula. Phytopathology
- Poster: Heiner, C. 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
- (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
- Korlach, Jonas (2017) AGBT PacBio Workshop: SMRT Sequencing roadmap: better throughput, lower costs
- 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
- Suzuki, Yoshihiko (2016) AGBT Virtual Poster (Japanese): Meta-methylome of human gut microbiome using SMRT Sequencing
- 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
- Chin, Jason (2016) PAG Conference: Diploid genome assembly and comprehensive haplotype sequence reconstruction
- Application Brief: Microbial whole genome sequencing – Best Practices. (2018)
- Application Note: Microbial multiplexing workflow on the Sequel System (2018)
- 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)
- Product Note: Fast, high-resolution DNA Sizing with the Fragment Analyzer system (2016)