Advance microbiology with complete microbial characterization
Advancing our understanding of the microbial world and its interactions is only possible though comprehensive characterization of microbial genomes, communities, and their interactions with hosts and environments.
The PacBio Systems provide a deeper understanding of microbes and microbial communities by giving scientists the ability to:
Featured research: a biphasic epigenetic switch regulates immune evasion in Haemophilus influenzae
Non-typeable Haemophilus influenzae infection is significantly associated with middle ear infections in children, community-acquired pneumonia, and chronic obstructive pulmonary disease. Here, scientists have used SMRT genome and methylome analysis of H. influenzae to discover an epigenetically modulated “ON/OFF” switch that regulates the expression of multiple genes important in immune evasion, antibiotic resistance, and biofilm formation1.
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Complex linkage and reassortment patterns in Influenza A
Using single-molecule sequencing, the mutational spectrum of an H3N2 influenza A virus population documented the complex dynamics underlying the evolution of antiviral resistance. The figure shows a schematic representation of lineage dynamics for Influenza A segments HA, M, NA, and NP, and consensus (a) and haplotype (b) frequencies across time points2.
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References
- Atack et al., (2015) A biphasic epigenetic switch controls immunoevasion, virulence and niche adaptation in non-typeable Haemophilus influenzae. Nature Communications. 6(7828).
- Rogers M., et al., (2015) Intrahost dynamics of antiviral resistance in influenza A virus reflects complex patterns of segment linkage, reassortment, and natural selection. mBio. 6(2), e02464-14.
Selected Resources
- 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
- Le Nouën, Cyril et al. (2017) Genetic stability of genome-scale deoptimized RNA virus vaccine candidates under selective pressure. Proceedings of the National Academy of Sciences of the United States of America
- Caskey, Marina et al. (2017) Antibody 10-1074 suppresses viremia in HIV-1-infected individuals. Nature Medicine
- Retchless, Adam C et al. (2016) The establishment and diversification of epidemic-associated serogroup W meningococcus in the African meningitis belt, 1994 to 2012. mSphere
- Singer, Esther et al. (2016) High-resolution phylogenetic microbial community profiling. The ISME Journal
- Betz-Stablein, B D et al. (2016) Single-molecule sequencing reveals complex genomic variation of hepatitis B virus during 15 years of chronic infection following liver transplantation. Journal of Virology
- Laird Smith, Melissa et al. (2016) Rapid sequencing of complete env genes from primary HIV-1 samples Virus Evolution
- Steinberg, Barrett et al. (2016) Shifting fitness and epistatic landscapes reflect trade-offs along an evolutionary pathway. Journal of Molecular Biology
- Rutledge, Gavin G et al. (2016) Elusive Plasmodium species complete the human malaria genome set bioRxiv
- 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
- Bull, Rowena A et al. (2016) A method for near full-length amplification and sequencing for six hepatitis C virus genotypes. BMC Genomics
- 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
- Tsai, Yu-Chih et al. (2016) Resolving the complexity of human skin metagenomes using single-molecule sequencing. mBio
- Poon, Leo L M et al. (2016) Quantifying influenza virus diversity and transmission in humans. Nature Genetics
- 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
- Huang, Da Wei et al. (2016) Towards better precision medicine: PacBio single-molecule long reads resolve the interpretation of HIV drug resistant mutation profiles at explicit quasispecies (haplotype) level. Journal of Data Mining in Genomics & Proteomics
- Poster: Boitano, M. et al. (2017) Full-length cDNA sequencing of prokaryotic transcriptome and metatranscriptome samples
- Poster: Lambert, C. et al. (2017) Multiplexing strategies for microbial whole genome sequencing using the Sequel System
- Poster: Heiner, Cheryl et al. (2017) Profiling complex communities with highly accurate single molecule reads: cow rumen microbiomes
- 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
- Korlach, J. and Kingan, S. (2016) i5K Webinar: High-quality de novo insect genome assemblies using PacBio sequencing
- 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
- Application Brief: Microbial Whole Genome Sequencing – Best Practices (2017)
- Application Brochure Microbial Communities: Complex microbial populations simplified (2017)
- SMRT Sequencing Brochure: Revolutionize genomics with SMRT Sequencing (2017)
- Case Study: Scientists advance understanding of microbial genomes, epigenomes and communities with SMRT Sequencing (2016)
- Epigenetics Application Brochure: Characterize the epigenetic landscape of your genome (2016)