Applications
Microbial Targeted Sequencing

Accurately achieve comprehensive sequencing of complex bacterial or viral targets from any sample type with myBaits® hybridization capture kits and myReads® NGS services.

 

Overcoming Challenges of Microbial Genome Sequencing

As many biological sample types are dominated by DNA from other sources, significant next-generation sequencing (NGS) depths are needed to resolve specific microbial genomes or to fully characterize the variation within microbial communities. Targeted sequencing, wherein background non-target DNA is excluded from samples prior to NGS, solves this problem and drastically reduces the overall costs of sequencing and data analysis per sample. Hybridization capture with myBaits Target Capture kits is currently the most versatile technique for comprehensive, cost-effective targeted NGS of both viruses and bacteria in complex samples.
 

Benefits of hybridization capture for targeted microbial sequencing:

  • Highly adaptable: Whole genome or complex gene family sequencing from any virus or bacteria
  • Greater sequencing depth: Achieve >100-fold or higher enrichment of microbial genomes from biological samples
  • Cost effective: Deliver significant savings by sequencing only target genes/genomes of interest
  • Flexible in sample type: Sequence almost any sample type, from cell culture, tissue, saliva, fecal, to environmental collections
  • Broad applications: 16S rRNA, metagenomics, whole genome sequencing

 

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Case Study:
“Resistome” Antimicrobial Resistance Gene Targeted Sequencing

Sequence many more samples per run while preserving essential gene content signals

Shotgun total sample DNA sequencing is the gold standard for metagenomic profiling, as it permits full assessment of novel microbial gene content without the limitations associated with other approaches such as amplicon sequencing or culture-based methods. However, the cost of generating sufficiently deep sequencing data can limit the number of samples that are able to be efficiently studied. By applying the hybridization capture approach, one can routinely achieve orders of magnitude greater sequencing efficiency, even for complex gene sets.

In Guitor et al. (2019), researchers design a novel myBaits hybridization capture panel targeting the “resistome” of antimicrobial resistance genes (ARGs), and favorably evaluated the panel’s performance for both control mock community samples as well as biological samples. They demonstrated that myBaits enrichment was an effective discovery tool not only enabling comprehensive ARG profiling but also detecting novel content at considerably lower sequencing depths compared to shotgun. To learn more about this cost-effective approach, read the original paper presenting this unique work.

Graph depicting enrichment specificity for mock community samples. Data depicted from Guitor et al 2019, Antimicrobial Agents and Chemotherapy.
 
Enrichment provides orders of magnitude higher target specificity. For control experiments with mock bacterial community samples of 4 or 8 different bacterial genomic DNAs, results are shown for percentage of sequencing reads mapping to the 8 different intended target regions both with (left) and without (right) myBaits enrichment with a comprehensive “resistome” ARG baitset. Figure based on Guitor et al. (2019) Fig 3A. For more details, read: Guitor et al. (2019), Antimicrobial Agents and Chemotherapy
 


“We chose the myBaits hybridization capture platform for our project aimed at capturing antimicrobial resistance genes because of the flexibility in selecting our targets, the large capacity in the sequence target range, and the clarity and ease of use of the protocol. The myBaits kits are very convenient for our research projects as they come with all materials and reagents for hybridization capture and require few additional reagents.”
– Allison Guitor, Graduate Student, Dr. Gerry Wright Lab, McMaster University

 

 


Download the Targeted Genomics for Pathogen and Microbial Communities application note to apply to your research.

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Featured Publications

Guitor, A.K. et al. 2019. Capturing the Resistome: a Targeted Capture Method To Reveal Antibiotic Resistance Determinants in Metagenomes. Antimicrobial Agents and Chemotherapy.

Forth, J.H. et al. 2019. A Deep-Sequencing Workflow for the Fast and Efficient Generation of High-Quality African Swine Fever Virus Whole-Genome Sequences. Viruses.

Trimpert, J. et al. 2019. A proofreading-impaired herpesvirus generates populations with quasispecies-like structure. Nature Microbiology.

Burrell, S. et al. 2017. Ancient Recombination Events between Human Herpes Simplex Viruses. Molecular Biology and Evolution.

Vezzulli, L. et al. 2017. Whole-Genome Enrichment Provides Deep Insights into Vibrio cholerae Metagenome from an African River. Microbial Ecology.

Campana, M.G. et al. 2016. Simultaneous identification of host, ectoparasite and pathogen DNA via in‐solution capture. Molecular Ecology Resources.

Duggan, A.T. et al. 2016. 17th Century Variola Virus Reveals the Recent History of Smallpox. Current Biology.

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