Nikki Perkins Microbial Communities Labs

Nicole Perkins Microbial Communities Core Labs

The Nicole Perkins Microbial Communities Core Labs are dedicated to characterizing host pathogens interaction and the role of the microbial communities in health and disease using state-of-the technologies to identify new targets for research. The core is to enhance the ability to deliver translational research and foster bench-to-bedside research collaboration between basic scientist and clinicians. 


Our history

The Nicole Perkins Microbial Communities Core Labs were named after Nicole Perkins, Director of the Summit Foundation, who has been suffering from cystic fibrosis and is a spokesperson for the Snyder Institute for Chronic Diseases. This facility would not have been possible without her continued support. We thank you, Nikki!

Nicole Perkins Microbial Communities Core Labs Information


  • Flow Cytometry Cell Analysis and Cell Sorting
    • Core stuff assisted or user-run flow cytometry on BD Canto2 and LSRII & cell sorting on Aria II
    • Assistance with development & optimization of cytometric techniques and methods
    • Software for data analysis (FlowJo X dongles and workstation)
  • Next Generation Sequencing
    • WGS of bacteria and viruses, 16S Amplicon Sequencing, RNA-Seq
  • Instruments for culturing aerobe & anaerobes & DNA Fingerprinting bacterial isolates
  • CyTOF Helios: Expected operational in early 2016

Key Areas of Research

  • Culturing and isolating of bacteria from samples & DNA ingerprinting of isolates
  • Whole Genome Sequencing (WGS) bacteria & viruses on the MiSeq
  • 16S Amplicon Sequencing for Microbial Communities (Microbiome) on MiSeq
  • Flow Cytometry Analysis and Cell Sorting
  • Mass Cytometry on the CyTOF Helios

Select Publications

  • Halverson, T.W. et al., PLoS Pathog. 2015 Jan 15; 11 (1)
  • Byaih, AB et al., PLoS Negl Trop Dis 2014 Dec 11; 8 (12)
  • Miyata ST et al., PLoS Pathog. 2013, Dec 9 (12)


Karen K. H. Poon, PhD
Department of Microbiology, Immunology & Infectious Diseases
Manager of the Nicole Perkins Microbial Communities Core Labs
Labs: HSC 2580, 2896, 2590, Lab: 403.210.6853
Office: 403.210.7816

Karen Poon, PhD

Karen Poon, PhD

Bruce Perrault

Core Personnel

Dr. Karen K. H. Poon, PhD
Manager and Application Specialist

Manager and Application Specialist of the Nicole Perkins Microbial Communities Core Labs since June, 2009. Dr. Poon obtained her PhD in molecular microbiology and B Sc in Biochemistry from the University of Calgary. She did a post-doctoral research in LPS biosynthesis in Pseudomonas aeruginosa at the University of Guelph. Between 2006 and 2009, Karen worked as the manager for the Leukocyte Trafficking Molecular Core (LTMC), assisting various labs in molecular techniques. Since 2009, she worked in attained expertise in flow cytometry analysis and cell sorting applications, next generation sequencing of small genomes and 16S metagenomics on the MiSeq platform.

Specialization / Applications

Flow Cytometry: analytical and cell sorting applications

  • Multicolor analysis
  • Develop cytometry methods for bacteria
  • Cellular kinetics and physiological cellular responses
  • Cell cycle analyses (DNA, RNA content)
  • Train clientele in the use of the instruments (BD FACSCanto-3 laser-4B-3R-3V; BD LSRII-3 laser-2B-4G-2R)
  • Train clientele on the analysis of data as well as consulting on experimental design
  • Cell sorting to recover a subset of cells from a sample. Cells can be deposited into tubes or 96-well plates for further analysis

CyTOF Helios Mass Cytometer (Fluidigm)

  • Flow Cytometry with heavy-metal tagged antibodies
  • Immunophenotyping, intracellular cyotkines, and phospo-CyTOF

Next Generation Sequencing on the MiSeq


  • Library Preparation and QA/QC of Libraries for Sequencing
  • 16S Variable PCR Amplicons Sequencing : Barcode Primer sets for V3-V4, V3-V5, V3-V6
  • Sequencing on libraries on V3 and V2 MiSeq cartridges