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Microbiome Sciences�Research Limitations

Nichole Ginnan, PhD

Project Manager

One Health Microbiome Center Penn State University

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Introduction and Perspectives

Plant Pathology

Ecology & Evolutionary Biology

Partnerships, communications, center-level grant writing, community building, interdisciplinary collaborations

Project Manager

Microbiome-mediated defenses + development

Local adaptations and host-microbiome evolution

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One Health Microbiome Center�Penn State University

microbiome.psu.edu

@PSUmBiome

1st Microbiome Sciences Dual Title PhD

500+ Members

115 Faculty in 42 Dept.

Award-winning faculty and trainees

Broad Expertise

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Center-level Survey Results

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1. Graduate Training Gaps

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  • 2011: Estimated that PhD graduates outnumber new faculty positions in STEM fields 7:1

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  • Microbial bioproducts market has a projected annual growth of 5.4%

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Industry or Corporate

Need for diverse career training

Need for workforce development

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Graduate student fellowships or research support

Graduate student Internships/Co-op

Industry mentoring and visits

1. Graduate Training Gaps

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2. Low Biomass Samples

  • Arid/desert soils
  • Clay-based soils
  • Rainwater
  • Leaf dew

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Kit contamination

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Personal Experience

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Plant Microbiome Research

Complexity Continuum

Gnotobiotics

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Gnotobiotics

Semi-Standardized Systems

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3. Gnotobiotic Plant Systems

  • Does not work with larger seeds/plants
  • Poor for inoculations, especially fungi
  • High humidity
  • Difficult/time consuming
  • High contamination
  • Difficult to water

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4. Community Complexity

Causal agent discovery

Culturable and unculturable

less studied microbes

Meta-Omics sequencing

Host contamination

Beyond bacterial genomes

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Live Cell Fractionation

  • Separate soil particles and plant cells from protist, fungi, bacteria, viruses, etc.

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  • Re-inoculate fractions for functional assays

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  • Sequence fractions separately for easier assembly

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  • Standard “ladder”
    • Size
    • Stains

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Summary: Limitations

Academic-Industry partnership

Visits + mentoring

Internships/ co-ops

Graduate support

Contaminant-free kits

Specialized extraction kits

Ready to use and standardized growth systems

Live cell fractionation

1. Graduate Training Gaps

2. Low Biomass Samples

3. Gnotobiotic Plant Systems

4. Community Complexity