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
  • Chief Scientific Officer, Co-Founder, Shoreline Biome, LLC
      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.


    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.

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