Put microbes to work
Modern pharmaceutical discovery, environmental remediation, and chemical commodity production increasingly rely upon harnessing the power of microbes. To identify and develop complex biological products, microbiologists rely on comprehensive genomic information. Draft microbial genome assemblies based on short-read DNA sequencing technologies often miss critical genes or fragment metabolic gene clusters. These incomplete assemblies may undermine and restrict functional genomics and genome engineering efforts. Moreover, draft genomes do not provide information regarding restriction-modification (R-M) systems. Without this knowledge, ill-matched plasmid DNA may have low transformation efficiency during genetic manipulation.
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
Featured research: complete genome of Clostridium autoethanogenum facilitates accurate inference of critical metabolic pathways.
Scientists generated a complete assembly using only PacBio data of an industrial strain of Clostridium autoethanogenum, a microbe capable of fermenting waste gases into biofuels and commodity chemicals. Their analysis of the assembly revealed numerous metabolically important genes had been missed entirely or only partially covered in their previous short-read draft assemblies.
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Featured research: identification of restriction-modification systems in Bifidobacterium animalis
Scientists employed SMRT Sequencing to generate the complete genome and methylome of Bifidobacterium animalis species, a component of a commercialized, fermented dairy product known to have health benefits. Restriction-modification systems have been a major barrier to genetic manipulation of bifidobacteria. SMRT Sequencing predicted this bilfobacterium strain harbored two R-M systems (BanLI and Ban LII). By using appropriately methylated plasmid DNA, scientists achieved 22-fold higher transformation efficiency compared to unmethylated DNA.
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Reference
- Brown et al., (2014) Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia. Biotechnology for Biofuels. 7, 40.
- Motherway et al., (2014) Identification of Restriction-Modification Systems of Bifidobacterium animalis subsp. lactis CNCM I-2494 by SMRT Sequencing and Associated Methylome Analysis. PLoS One. 9(4) E94875
Selected Resources
- 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
- 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
- Armanhi, Jaderson Silveira Leite et al. (2016) Multiplex amplicon sequencing for microbe identification in community-based culture collections. Scientific Reports
- Weigele, Peter et al. (2016) Biosynthesis and function of modified bases in bacteria and their viruses. Chemical Reviews
- 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
- Sturmberger, Lukas et al. (2016) Refined Pichia pastoris reference genome sequence. Journal of Biotechnology
- 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
- Grau, Jan et al. (2016) AnnoTALE: bioinformatics tools for identification, annotation, and nomenclature of TALEs from Xanthomonas genomic sequences. Scientific Reports
- Hou, Qiangchuan et al. (2015) Evaluation of bacterial contamination in raw milk, ultra-high temperature milk and infant formula using single molecule, real-time sequencing technology. Journal of Dairy Science
- Alt, Silke et al. (2015) Biosynthesis of the novel macrolide antibiotic anthracimycin. ACS Chemical Biology
- Sit, Clarissa S et al. (2015) Variable genetic architectures produce virtually identical molecules in bacterial symbionts of fungus-growing ants. Proceedings of the National Academy of Sciences of the United States of America
- O'Callaghan, A et al. (2015) Pangenome analysis of Bifidobacterium longum and site-directed mutagenesis through by-pass of restriction-modification systems. BMC Genomics
- Schulze, Christopher J et al. (2015) Genome-directed lead discovery: biosynthesis, structure elucidation, and biological evaluation of two families of polyene macrolactams against Trypanosoma brucei. ACS Chemical Biology
- Cline, Lauren C et al. (2015) Initial colonization, community assembly and ecosystem function: fungal colonist traits and litter biochemistry mediate decay rate. Molecular Ecology
- Faino, Luigi et al. (2015) Single-Molecule Real-Time Sequencing combined with optical mapping yields completely finished fungal genome. mBio
- Kleigrewe, Karin et al. (2015) Combining mass spectrometric metabolic profiling with genomic analysis: a powerful approach for discovering natural products from cyanobacteria. Journal of Natural Products
- Wilkins, Katherine E et al. (2015) TAL effectors and activation of predicted host targets distinguish Asian from African strains of the rice pathogen Xanthomonas oryzae pv. oryzicola while strict conservation suggests universal importance of five TAL effectors. Frontiers in Plant Science
- Gordon, Sean P et al. (2015) Widespread polycistronic transcripts in fungi revealed by single-molecule mRNA sequencing. PLoS One
- Taniguti, Lucas M et al. (2015) Complete genome sequence of Sporisorium scitamineum and biotrophic interaction transcriptome with sugarcane. PLoS One
- Monk, Ian R et al. (2015) Complete bypass of restriction systems for major Staphylococcus aureus lineages. mBio
- Utturkar, Sagar M et al. (2015) Sequence data for Clostridium autoethanogenum using three generations of sequencing technologies. Scientific Data
- Tanizawa, Yasuhiro et al. (2015) Complete genome sequence and analysis of Lactobacillus hokkaidonensis LOOC260(T), a psychrotrophic lactic acid bacterium isolated from silage. BMC Genomics
- Roberts, Richard J et al. (2015) REBASE–a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Research
- 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.
- 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
- Blow, Matthew (2015) AGBT Conference: Functional genomics – gene annotation and methylome analysis in bacteria
- Application Brief: Microbial Whole Genome Sequencing – Best Practices (2017)
- Application Brochure Microbial Communities: Complex microbial populations simplified (2017)
- PacBio Certified Service Providers (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)
- 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)
- De Novo Assembly Application Brochure: Bring the “W” back to Whole genome sequencing (2015)
- Targeted Sequencing Application Brochure: Capture your regions of interest in high resolution (2015)
- Plant and Animal Sciences Brochure: A comprehensive view of genetic diversity (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)