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
- Fallon, Timothy R et al. (2018) Firefly genomes illuminate parallel origins of bioluminescence in beetles. eLife
- 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
- Mehta, Devang et al. (2018) CRISPR-Cas9 interference in cassava linked to the evolution of editing-resistant geminiviruses BioRxiv
- Xin, Tianyi et al. (2018) Biomonitoring for traditional herbal medicinal products using DNA metabarcoding and single molecule, real-time sequencing. Acta pharmaceutica Sinica. B
- 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
- 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. (2018) Bioengineered AAV capsids with combined high human liver transduction in vivo and unique humoral seroreactivity. Molecular therapy
- 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
- Deptula, Paulina et al. (2017) De novo assembly of genomes from long sequence reads reveals uncharted territories of Propionibacterium freudenreichii. BMC genomics
- 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
- 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
- Nakano, Kazuma et al. (2017) Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area. Human Cell
- 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
- D'Amore, Rosalinda et al. (2017) SMRT Gate: A method for validation of synthetic constructs on Pacific Biosciences sequencing platforms. BioTechniques
- Tai, Phillip WL et al. (2018) Adeno-associated virus genome population sequencing achieves full vector genome resolution and reveals human-vector chimeras Molecular therapy
- Xu, Haiyan et al. (2017) The effects of probiotics administration on the milk production, milk components and fecal bacteria microbiota of dairy cows Science bulletin
- 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
- 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
- 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: 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 [SMRT Link v5.0.0]
- 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
- PacBio Certified Service Providers (2018)
- SMRT Sequencing Brochure: Revolutionize genomics with SMRT Sequencing (2018)
- Application Brief: Microbial whole genome sequencing – Best Practices (2018)
- Application Brochure: Microbial communities – Complex microbial populations simplified. (2017)
- 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)