The Human Microbiome - Bioconductor

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Summary: Vaginal Microbiota• The human vagina harbors communities of bacteria that arevery different from other human body sites• Bacterial diversity in subjects without BV is limited, whereassubjects with BV have a high degree of species richness thatincludes many novel and fastidious bacteria• Treatment of BV with antibiotics results in a rapid decline ofanaerobic bacteria, though relapse is common• The nature of the interactions among BV-associated bacteriais poorly understood– Functional redundancy to explain heterogeneity?– Are there syntrophic metabolic interactions?
The Human Microbiome and Omics• Single cell genomics: NIH sequencing initiative– What are the functional capabilities of individual microbes?• Metagenomics: assessing community gene content by highthroughput sequencing– What are the functional capabilities of microbial communities asassessed by gene representation?• Metatranscriptomics: mRNA and rRNA– Which genes are expressed in certain communities under definedconditions?• Proteomics: Which proteins are present and how do theychange with host factors or community composition?• Metabolomics: Which small molecule metabolites are presentin a given habitat and how do fluxes illuminate thebiochemistry of the community?
Page 1 and 2: The Human MicrobiomeDavid N. Fredri
Page 3 and 4: Human Genome Project (HGP)• 3.16
Page 5 and 6: The Human Microbiome Project Peter
Page 7: Science. 2006 Jun 2;312(5778):1355-
Page 10 and 11: The gut microbiome affects…• Vi
Page 12 and 13: The bacterial 16S rRNA genePresent
Page 14 and 15: Bacterial VaginosisThe most prevale
Page 16 and 17: Schematic for Pyrosequencing Approa
Page 18 and 19: BACTERIAL DIVERSITY - PYROSEQUENCIN
Page 21 and 22: 16S rRNA gene copies/swab16S rRNA g
Page 23: 16S rRNA gene copies/swabRecurrent

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