OCT 15, 2019 10:00 AM PDT

The 'Three Peak Challenge' for long-read, ultra-deep stool metagenomics on the PromethION

Sponsored by: Zymo Research
C.E. Credits: P.A.C.E. CE Florida CE
Speakers
  • Research Fellow, University of Birmingham
    Biography
      Josh is a molecular biologist finishing up his PhD at the University of Birmingham. He is a member of Nick Loman's lab which explores the use of cutting-edge genomics and metagenomics approaches to the diagnosis, treatment and surveillance of infectious disease. In 2015 during the West-African Ebola virus outbreak he travelled to Guinea with a 'lab-in-a-suitcase' to establish a sequencing laboratory to perform genome sequencing of new cases in a matter of days. Last year, over the course of three trips to Brazil, he developed a multiplex version of the tiling-amplicon approach used previously leading to the first successful sequencing of Zika virus genomes directly from clinical samples. This was successfully used by the ZiBRA consortium and other groups investigating the origins of Zika virus in the Americas. Most recently, as part of a group of developers known as the Nanopore WGS consortium, he showed it was possible to sequence extremely long reads on the MinION using optimized extraction and rapid sequencing protocols. Generating runs with read N50's over 100 kilobases it demonstrated MinION is likely to be the platform of choice for those seeking highly contiguous assemblies for complex genomes.
    • Director of Microbiome Applications - Zymo Research
      Biography
        Dr. Janina Krumbeck is the Director of Microbiome Applications at Zymo Research Corp., Irvine, California and is working towards addressing current challenges in microbiome research. Dr. Krumbeck has over ten years of experience in microbiology and molecular biology and prior to her position at Zymo Research Corp., she perused her PhD at the University of Nebraska-Lincoln, USA in genetics, cell, and molecular biology. Her PhD research has focused on gastrointestinal microbiology and microbial ecology to develop of novel microbial synbiotic applications to improve human and animal health. Dr. Krumbeck received her Master of Science degree in genetics and applied microbiology at the RWTH Aachen University in Aachen, Germany.

      Abstract

      DATE: October 15, 2019

      TIME: 10:00am PDT

      At present, most metagenomic surveys rely on high-output platforms such as Illumina. However, the short reads generated by these platforms limit specificity of taxonomic assignment and result in highly fragmented assemblies. Single molecule sequencing platforms are able to sequence much longer molecules and the output of these platforms, particular the PromethION from Oxford Nanopore now supports the study of complex microbial communities using shotgun metagenomics.

      We assessed a variety of methods using both a ten-species mock community and clinical samples seeking to find a method capable of generating ultra-long reads (>100 kb) from these sample types. The results presented here demonstrate the importance of having lysis methods capable of extracting high-molecular weight DNA from recalcitrant organisms such as Gram-positive bacteria and fungi. Development of these methods is critical to support the growing field of clinical microbiome research including the ability to perform strain tracking and produce high-quality metagenome assembled genomes (MAGs) from metagenomic samples.

       

      Learning Objectives:

      • Explain how to utilize mock microbial community standards to benchmark and optimize DNA extraction methods.
      • Explain the effects that different lysis methods have on long-read metagneomic sequencing.
      • Explain how a hybrid lysis technique can improve long-read data quality.

       

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      LabRoots is approved as a provider of continuing education programs in the clinical laboratory sciences by the ASCLS P.A.C.E. ® Program. By attending this webinar, you can earn 1 Continuing Education credit once you have viewed the webinar in its entirety.


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