Harnessing microbial potential
To meet global demand for pharmaceutical products, environmental remediation, and chemical commodity production, microbial biotechnology must be rooted in a foundation of complete genomic information.
The advent of Single Molecule, Real-Time (SMRT) Sequencing on PacBio Systems delivers a more comprehensive view of individual organisms and microbial communities, fueling discovery research for scientists developing microbial biological products. With PacBio sequencing, scientists have the ability to:
- Generate complete assemblies of industrially important microbes, confidently reconstruct intact genes, and discover gene clusters
- Explore how epigenetic regulation improves the efficiency of microbial genetic manipulation
- Identify critical members of complex microbial communities to isolate and develop commercial microbial products
- Resolve viral populations to facilitate successful design and evaluation of drugs and vaccines
- Sequence intact transcriptome and metatranscriptomes to directly define the full-length bacterial operons generating industrially important microbial products
- Validate targets
Spotlight: Genetic variation among microbes in food production
Scientists employed SMRT Sequencing to obtain species-level resolution of the bacterial microbiota used in artisanal cheese production. Their findings demonstrated the breadth of microbial diversity in cheese-making within and beyond Kazakhstan. Explore this research further:
Li, J. et al., 2017. Bacterial microbiota of Kazakhstan cheese revealed by single molecule real time (SMRT) sequencing and its comparison with Belgian, Kalmykian and Italian artisanal cheeses. BMC Microbiology, 17(1), p.13.
Spotlight: Tracking the genetic basis of improved microbial production
Scientists used long-read sequencing to construct complete microbial genomes to track gene shuffling events in bacteria with the goal of enhancing production of propionic acid. Explore this research further:
Luna-Flores, C.H. et al., 2017. Improved production of propionic acid using genome shuffling. Biotechnology Journal, 12(2), p.1600120.
Selected Resources
- Cartwright, Joseph F et al. (2018) Highly sensitive detection of mutations in CHO cell recombinant DNA using multi-parallel single molecule real-time DNA sequencing. Biotechnology and Bioengineering
- 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
- Beaulaurier, John et al. (2017) Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation. Nature Biotechnology
- Jayakumar, Vasanthan et al. (2017) Comprehensive evaluation of non-hybrid genome assembly tools for third-generation PacBio long-read sequence data. Briefings in Bioinformatics
- Conway, Jonathan M et al. (2017) Functional analysis of the Glucan Degradation Locus (GDL) in Caldicellulosiruptor bescii reveals essential roles of component glycoside hydrolases in plant biomass deconstruction. Applied and Environmental Microbiology
- Fraiture, Marie-Alice et al. (2017) An integrated strategy combining DNA walking and NGS to detect GMOs. Food Chemistry
- Nakano, Kazuma et al. (2017) Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area. Human Cell
- Jia, Fang-Fang et al. (2017) Complete genome sequence of bacteriocin-producing Lactobacillus plantarum KLDS1.0391, a probiotic strain with gastrointestinal tract resistance and adhesion to the intestinal epithelial cells. Genomics
- 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
- Song, Lijiang et al. (2017) Discovery and biosynthesis of gladiolin: A Burkholderia gladioli antibiotic with promising activity against Mycobacterium tuberculosis. Journal of the American Chemical Society
- Latimer, Luke N et al. (2017) Iterative optimization of xylose catabolism in Saccharomyces cerevisiae using combinatorial expression tuning. Biotechnology and Bioengineering
- Yue, Jia-Xing et al. (2017) Contrasting evolutionary genome dynamics between domesticated and wild yeasts. Nature Genetics
- Kelleher, Philip et al. (2017) Comparative and functional genomics of the Lactococcus lactis taxon; insights into evolution and niche adaptation. BMC Genomics
- McRose, Darcy L et al. (2017) Diversity and activity of alternative nitrogenases in sequenced genomes and coastal environments. Frontiers in Microbiology
- Luna-Flores, Carlos H et al. (2017) Improved production of propionic acid using genome shuffling. Biotechnology Journal
- Hagen, Live H et al. (2017) Quantitative metaproteomics highlight the metabolic contributions of uncultured phylotypes in a thermophilic anaerobic digester. Applied and Environmental Microbiology
- Li, Jing et al. (2017) Bacterial microbiota of Kazakhstan cheese revealed by single molecule real time (SMRT) sequencing and its comparison with Belgian, Kalmykian and Italian artisanal cheeses BMC Microbiology
- Eudes, Aymerick et al. (2016) Exploiting members of the BAHD acyltransferase family to synthesize multiple hydroxycinnamate and benzoate conjugates in yeast. Microbial Cell Factories
- Weigele, Peter et al. (2016) Biosynthesis and function of modified bases in bacteria and their viruses. Chemical Reviews
- Sturmberger, Lukas et al. (2016) Refined Pichia pastoris reference genome sequence. Journal of Biotechnology
- Gesudu, Qimu et al. (2016) Investigating bacterial population structure and dynamics in traditional koumiss from Inner Mongolia using single molecule real-time sequencing. Journal of Dairy Science
- Zheng, Yi et al. (2016) Using PacBio long-read high-throughput microbial gene amplicon sequencing to evaluate infant formula safety. Journal of Agricultural and Food Chemistry
- Ricker, N et al. (2016) PacBio SMRT assembly of a complex multi-replicon genome reveals chlorocatechol degradative operon in a region of genome plasticity. Gene
- Armanhi, Jaderson Silveira Leite et al. (2016) Multiplex amplicon sequencing for microbe identification in community-based culture collections. Scientific Reports
- Bao, Weichen et al. (2016) Assessing quality of Medicago sativa silage by monitoring bacterial composition with single molecule, real-time sequencing technology and various physiological parameters. Scientific Reports
- Frank, J A et al. (2016) Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data. Scientific Reports
- Badran, Ahmed H et al. (2016) Continuous evolution of Bacillus thuringiensis toxins overcomes insect resistance. Nature
- Thomma, Bart P H J et al. (2016) Mind the gap; seven reasons to close fragmented genome assemblies. Fungal Genetics and Biology
- Gomez-Escribano, Juan Pablo et al. (2016) Next generation sequencing of Actinobacteria for the discovery of novel natural products. Marine Drugs
- Grau, Jan et al. (2016) AnnoTALE: bioinformatics tools for identification, annotation, and nomenclature of TALEs from Xanthomonas genomic sequences. Scientific Reports
- Studholme, David J et al. (2016) Genome Update. Let the consumer beware: Streptomyces genome sequence quality. Microbial Biotechnology
- Faino, Luigi et al. (2015) Single-Molecule Real-Time Sequencing combined with optical mapping yields completely finished fungal genome. mBio
- Gordon, Sean P et al. (2015) Widespread polycistronic transcripts in fungi revealed by single-molecule mRNA sequencing. PLoS One
- Roberts, Richard J et al. (2015) REBASE–a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Research
- Hüser, Daniela et al. (2014) Adeno-associated virus type 2 wild-type and vector-mediated genomic integration profiles of human diploid fibroblasts analyzed by third-generation PacBio DNA sequencing. Journal of Virology
- Poster: Heiner, Cheryl et al. (2018) Multiplexed Complete Microbial Genomes on the Sequel System
- 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, C. et al. (2017) Profiling complex population genomes with highly accurate single molecule reads: cow rumen microbiomes
- Poster: Oh, S. et al. (2016) Minimization of chimera formation and substitution errors in full-length 16S PCR amplification
- Poster: Baybayan, Primo et al. (2016) Application specific barcoding strategies for SMRT Sequencing
- Poster: Heiner, Cheryl et al. (2016) Low-input long-read sequencing for complete microbial genomes and metagenomic community analysis
- Poster: Chin, Jason et al. (2016) Un-zipping diploid genomes – revealing all kinds of heterozygous variants from comprehensive hapltotig assemblies
- Presentation: Chin, Jason et al. (2016) Diploid genome assembly and comprehensive haplotype sequence reconstruction
- Poster: Hall, Richard J et al. (2016) Profiling metagenomic communities using circular consensus and Single Molecule, Real-Time Sequencing
- Poster: Sethuraman, Anand et al. (2015) Analysis of full-length metagenomic 16S genes by Single Molecule, Real-Time Sequencing
- Poster: Lee, Walter et al. (2015) Barcoding strategies for multiplexing of samples using a long-read sequencing technology.
- Poster: Badalamenti, Jonathan P. et al. (2015) Metagenomes of native and electrode-enriched microbial communities from the Soudan Iron Mine.
- Hatas, Emily (2017) Webinar: SMRT Sequencing applications in plant and animal sciences: an overview
- (2017) Tutorial: Minor Variant Analysis
- Auvignen, Petra (2017) AGBT Virtual Poster: Interspecies interation amoung meat spoilage-related lactic acid bacteria
- 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
- Morey, Robert (2016) AGBT Virtual Poster: Using PacBio sequencing as a synthetic biology error analysis tool
- Blow, Matthew (2015) AGBT Conference: Functional genomics – gene annotation and methylome analysis in bacteria
- 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 Brief: Microbial whole genome sequencing – Best Practices. (2017)
- Application Brochure: Microbial Communities – Complex microbial populations simplified. (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)
- Targeted Sequencing Application Brochure: Capture your regions of interest in high resolution. (2015)
- Microbiology and Infectious Disease Brochure: Novel insights into microbial and viral complexity. (2015)
- Certified Service Provider Profile: GATC Biotech expands applications with unique attributes of SMRT Sequencing. (2015)