Metagenomics at Second Genome

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Presentation transcript:

Metagenomics at Second Genome Tanya Yatsunenko tanya@secondgenome.com

Taking a mechanistic approach to discovery San Francisco based company leveraging microbiome science to enable the discovery and development of human health products through services, collaborations and internal R&D Taking a mechanistic approach to discovery First-of-kind microbiome drug discovery platform with pharma partner validation Not Dx, not nutrition, not fecal transplant, not strains as drugs Curator of Greengenes™ database (Todd DeSantis) Qiime developer (Justin Kuczynski from Rob Knight Lab) Over 200 microbiome studies completed to date across industry, government, academic researchers, nutrition companies, and pharma

Metagenomic (and RNA-seq) Pipeline at SG Sample1_Right.fastq Sample1_Left.fastq Remove adapters prinseq-lite Remove poor quality bases and short reads Remove Host DNA Bowtie2 Remove rRNA SortmeRNA Filtered sequences Metaphlan Taxonomic Table Functional Annotation RapSearch BioCyc Database Samples comparison: PCoA, Hierarchical Clustering; Discriminatory Organisms and Pathways Genes, Genomes, Pathway abundance and coverage Open source software Cloud = Amazon AWS spot instances fastq-mcf

Functional annotation Genes -> Enzymes -> Pathways and Strains 1 Query Sequence from Sample1: KDYDTAQRVLGNVLVLNIIIGLAFTVLTLIFLD Functional assignments Bacterial strain assignments Genes 1 2 GJXV-1205, GTP cyclohydrolase GJXV-2161, Na+-driven multidrug pump 10 Strains 1 2 Faecalibacterium prausnitzii M-65 100 Acidovorax sp.JS42 Enzymes 1 2 ENZRXNJXV-1763 ENZRXNJXV-1765 10 Connecting genes/enzymes to bacterial genomes Pathways 1 2 NAGLIPASYN-PWY PWY-5687 10

Challenges ~1% filtered sequences with a significant hit to BioCyc database Assembly with complex microbiota? Paired-end sequences are treated independently (for hi-seq) Confidence in identification of strains hits from metagenomic and transcriptomic datasets Database: KEGG vs BioCyc vs others Some samples forward and reverse reads result in different microbiome profiles

Correlating human with microbial transcriptome +Rho Microbial gene -Rho Human gene Get correlation coefficient (Rho) and p value 23 mln correlations, 400 after bonferroni correction

Best correlation: Peptidoglycan glycosyltransferase vs Human gene (inflammasome related) Microbial enzyme expression Human gene expression Sample ID

Best correlation: microbial enzyme vs 5 human genes Peptidoglycan glycosyltransferase.

Summary Will be happy to discuss our methods and some of the findings Currently working on relating human and microbiome functions in disease states tanya@secondgenome.com