MAY 10, 2018 10:30 AM PDT

Strain Level Microbiome Profiling Using rRNA Gene Amplicons

C.E. Credits: CEU P.A.C.E. CE Florida CE
Speaker
  • Chief Scientific Officer, Co-Founder, Shoreline Biome, LLC
    Biography
      Mark has led and supported teams launching transformative new innovations globally at Molecular Stagings and 454 Life Sciences. In 2004, he led the development team at 454 Life Sciences that launched the GS 20, the first of the NGS (Next Generation Sequencing) systems, which revolutionized the world of DNA sequencing. He was part of the development teams that launched the GS FLX, the GS FLX+, and the GS Junior, the first of the benchtop sequencers. Mark has experience leading a development team consisting of subteams in hardware, software, informatics, reagents, marketing, and customer support.

      Mark received his Ph.D. in Biochemistry from the University of Rochester and his B.S. in Biology from the University of Buffalo.

    Abstract

    An ideal microbiome profiling method would produce strain level taxonomic classification of organisms and their relative quantities. We demonstrate proof of principle experiments that sequencing methods using amplicons derived from rRNA gene clusters can be designed to differentiate between known strains of Clostridium difficile, a common hospital acquired pathogen. Obtaining consistent and reproducible results depends on overcoming challenges in microbial lysis, amplicon design, PCR primer degeneracy, sample multiplexing technology, and sequence database analysis. Novel approaches developed for each of these challenges are discussed.


    Show Resources
    You May Also Like
    OCT 02, 2019 11:00 AM PDT
    OCT 02, 2019 11:00 AM PDT
    DATE: October 2, 2019TIME: 11:00am PDT, 2:00pm EDT Ditch the Excel spreadsheets and manage your molecular workflows entirely in your LIMS Achieve configuration of molecular workf...
    NOV 18, 2019 7:00 AM PST
    C.E. CREDITS
    NOV 18, 2019 7:00 AM PST
    DATE: November 18, 2019TIME: 7:00am PST, 11:00am EST, 4:00pm CEWT How often do you pipette in your cell culture lab every day? Usually, we do it so often that we tend stop th...
    JAN 23, 2020 9:00 AM PST
    C.E. CREDITS
    JAN 23, 2020 9:00 AM PST
    DATE: January 23, 2020 TIME: 9:00am PST, 12:00pm EST...
    APR 07, 2020 8:00 AM PDT
    Add to Calendar Select one of the following: iCal Google Calendar Outlook Calendar Yahoo Calendar
    C.E. CREDITS
    APR 07, 2020 8:00 AM PDT
    Add to Calendar Select one of the following: iCal Google Calendar Outlook Calendar Yahoo Calendar
    DATE: April 7, 2020 TIME: 8:00am PT, 11:00am ET This webinar sets out to establish why quality control is key to robust, reliable, reproducible science. We will look at best practice criteri...
    MAY 08, 2020 10:00 AM PDT
    Add to Calendar Select one of the following: iCal Google Calendar Outlook Calendar Yahoo Calendar
    C.E. CREDITS
    MAY 08, 2020 10:00 AM PDT
    Add to Calendar Select one of the following: iCal Google Calendar Outlook Calendar Yahoo Calendar
    DATE: May 8, 2020 TIME: 10:00am PT, 11:00am MT, 1:00pm ET The application of next generation sequencing to interrogate immune repertoires and methods in which these highly complex dataset...
    MAR 03, 2020 9:00 AM JST
    C.E. CREDITS
    MAR 03, 2020 9:00 AM JST
    DATE: March 3, 2020 TIME: 9:00am JST A major limitation in the ex vivo expansion of harvested human hematopoietic stem-progenitor cells (HSPCs) is the rapid differentiation of HSPCs at the e...
    Loading Comments...
    Show Resources