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Introduction: Quantitative Ecology

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Elisa Margolis

on 3 March 2017

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Transcript of Introduction: Quantitative Ecology

Introduction: Quantitative Ecology
Ellie Margolis MD PhD
observations
Mathematical Models
experiments
statistical inference
mechanism
tools to describe observations better
test whether different mechanisms would differ in resulting observations or experimental results
a) improving resolution and reproducibility of microbiome analysis
sample
DNA sequencing
Classification Pipeline
Results
Clostridiales in Simulated Gut Community
b) improving ability to detect interactions or community functions in temporal microbiome data
whether bacteria persistence during antibiotic treatment is due to a particular species producing a biofilm?
which Lactobacillus species responsible for low vaginal pH in vivo?
identify particular bacteria linked to recovery from childhood malnutrition
Convergent Cross Mapping
Mechanistic model to test why there has been an increase in community-acquired C. difficile in last decade?
epidemiology SEIR model
-spill-over from hospitals
-increase hospital community contact
-increase virulence
-longer colonization of infants
-more antibiotics
hypotheses to test:
what allows infants to have no apparent disease when colonized with pathogenic C. difficile?
Conventional wisdom of infant lack receptors
never demonstrated
explore alternative hypotheses:
-infant microbiome reduces toxin production
-infant immune tolerance reduces pathogenesis
infant longitudinal
stool collection
hamster colonization
model
experiments
Full transcript