VISUALIZING COMPLEX BACTERIAL POPULATIONS IN ANIMAL MODELS

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Presentation transcript:

VISUALIZING COMPLEX BACTERIAL POPULATIONS IN ANIMAL MODELS Giovanni Widmer Infectious Diseases & Global Health Cummings School of Veterinary Medicine at Tufts University

According to newer estimates, there are 0 According to newer estimates, there are 0.9 x 1011 bacteria in a gram of feces.

MICROBIOME PROTECTIVE FUNCTION Science, Vol. 341; August 2, 2013

driving the science of omics: the rapidly falling cost of DNA sequencing 4000 $1,000,000,000 $4000 $10,000,000 $100,000 $0 Wikipedia

one technique - many applications an individual a bacterial microbiome genome re-sequencing population DNA RNA 16S amplicon main applications of high-throughput sequencing GWAS: Genome Wise Association Study Metagenome: the combined genomes of a population or sample (like a tumor or a tissue) Transcriptome: all transcripts (mRNA, rRNA, tRNA, ncRNA...) from a sample. GWAS, personalized medicine, conservation bacterial population, ecology transcriptome (mRNA cells, tissue, organism) metagenome (many genomes)

16S amplicon sequencing: analysis of complex bacterial populations 16S rRNA gene 16S rRNA

analysis pipeline input aligned sequences distance matrix clustering visualization hypothesis

between sequences: D=k/N MEASURES OF DISTANCE between sequences: D=k/N between samples: UniFrac distance sample 1 D = 1 sample 2 D = 0 sample 3 D = 0.5 species 1 species 2 Lozupone C, Knight R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol. 2005 Dec;71(12):8228-35.

DISTANCE MATRIX

VISUALIZATION: UNCONSTRAINED VS CONSTRAINED ORDINATION

ORDINATION AND METADATA constrained: Canonical Correspondence Analysis unconstrained PCoA of fecal microbiome Mann, Byrnes and Widmer, unpublished

(infered from 16S sequences) rat fecal microbiome taxonomy (by family) (Order Bacteriodales) (Phylum Bacteriodetes) days on diet pre 3 10-12 30 function (infered from 16S sequences) pre 30 Mann and Widmer, unpublished