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Explore complete microbial characterization
Advancing our understanding of the microbial world through discovery-based research entails comprehensive analysis of microbial genomes, their interactions, communities, and environments in which they live.
Single Molecule, Real-Time (SMRT) Sequencing on the PacBio Systems provides a deeper understanding of microbes and microbial communities by giving scientists the ability to:
- Resolve complete microbial genomes and detail their mobile elements
- Characterize epigenetic modifications
- Investigate viral pathogenicity, evolution, and selection
- Understand microbial communities
- Discover novel genes and transcript isoforms
Spotlight: Species-precise identification of microbial population members
Scientists used SMRT Sequencing to generate near full-length 16S rRNA sequences for metataxonomic profiling of the Tibet-Qinghai Plateau vultures. The results of the study indicated that the vultures may serve as a reservoir for microbial pathogens. Explore this research further:
Meng, X. et al., (2017) Metataxonomics reveal vultures as a reservoir for Clostridium perfringens. Emerging Microbes and Infections, 6(2), 9.
Spotlight: Improved genome assembly corrects understanding of virulence
SMRT Sequencing corrected errors in the Mycobacterium tuberculosis H37Rv reference genome originally produced using Sanger Sequencing. The improved reference genome revealed important variant strain differences that affect virulence. Explore this research further:
Elghraoui, A., Modlin, S.J. & Valafar, F., 2017. SMRT genome assembly corrects reference errors, resolving the genetic basis of virulence in Mycobacterium tuberculosis. BMC Genomics, 18(1), p.302.
Selected Resources
- 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
- Tedersoo, Leho et al. (2019) Towards PacBio-based pan-eukaryote metabarcoding using full-length ITS sequences. Environmental microbiology reports
- 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
- 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
- Bao, Jiandong et al. (2017) PacBio sequencing reveals transposable element as a key contributor to genomic plasticity and virulence variation in Magnaporthe oryzae. Molecular plant
- Wlodarska, Marta et al. (2017) Indoleacrylic acid produced by commensal Peptostreptococcus species suppresses inflammation. Cell host & microbe
- Sinha, Sunita et al. (2017) Insight into the recent genome duplication of the halophilic yeast Hortaea werneckii: combining an improved genome with gene expression and chromatin structure. G3
- 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
- Ortiz-Merino, Raúl A et al. (2017) Evolutionary restoration of fertility in an interspecies hybrid yeast, by whole-genome duplication after a failed mating-type switch. PLoS biology
- Yue, Jia-Xing et al. (2017) Contrasting evolutionary genome dynamics between domesticated and wild yeasts. Nature genetics
- 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
- Fischer, Matthias G et al. (2016) Host genome integration and giant virus-induced reactivation of the virophage mavirus. Nature
- Singer, Esther et al. (2016) High-resolution phylogenetic microbial community profiling. The ISME journal
- Frank, J A et al. (2016) Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data. Scientific reports
- Thomma, Bart P H J et al. (2016) Mind the gap; seven reasons to close fragmented genome assemblies. Fungal genetics and biology
- Ikuta, Tetsuro et al. (2016) Heterogeneous composition of key metabolic gene clusters in a vent mussel symbiont population. The ISME journal
- Dickey, Aaron M et al. (2016) Large genomic differences between Moraxella bovoculi isolates acquired from the eyes of cattle with infectious bovine keratoconjunctivitis versus the deep nasopharynx of asymptomatic cattle. Veterinary research
- Poster: Jain, S. et al. (2019) Comparison of sequencing approaches applied to complex soil metagenomes to resolve proteins of interest
- 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: Seetin, M. et al. (2016) Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome using long-read sequencing
- Poster: Laird Smith, M. et al. (2016) An improved circular consensus algorithm with an application to detect HIV-1 Drug Resistance Associated Mutations (DRAMs)
- 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: Hepler, N. Lance et al. (2016) An improved circular consensus algorithm with an application to detection of HIV-1 Drug-Resistance Associated Mutations (DRAMs)
- Poster: Baybayan, Primo et al. (2016) Application specific barcoding strategies for SMRT Sequencing
- Poster: Seetin, Matthew et al. (2016) Long-read assembly of the Aedes aegypti Aag2 cell line genome resolves ancient endogenous viral elements
- 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: Seetin, Matthew G et al. (2016) Long-read assembly of the Aedes aegypti Aag2 cell line genome resolves ancient endogenous viral elements
- 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
- 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
- Application Brief: Metagenomic sequencing with HiFi reads – Best Practices (2020)
- Application Brief: Microbial whole genome sequencing – Best Practices (2020)
- SMRT Sequencing Brochure: Delivering highly accurate long reads to drive discovery in life science (2019)
- Case Study: Sequencing an historic bacterial collection for the future (2019)
- Epigenetics Application Brochure: Characterize the epigenetic landscape of your genome (2016)