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Molecular Studies of Microbial Communities and the Desulfoglaeba alkanexidens genome

Molecular Studies of Microbial Communities and the Desulfoglaeba alkanexidens genome. Leonid Sukharnikov. Scheme of talk. High Thoughput Analysis of Microbial Communities Updates for Desulfoglaeba alkanexidens – a Member of Oil Microbial Community. 454 sequence data.

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Molecular Studies of Microbial Communities and the Desulfoglaeba alkanexidens genome

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  1. Molecular Studies of Microbial Communities and the Desulfoglaeba alkanexidens genome Leonid Sukharnikov

  2. Scheme of talk • High Thoughput Analysis of Microbial Communities • Updates for Desulfoglaeba alkanexidens – a Member of Oil Microbial Community

  3. 454 sequence data Contigs/Flows Orientation BlastN Generate distance matrix (Phylip) Multiple Sequence Alignment using clustalX Generate Operational Taxonomic Units (OTUs) using DOTOUR Contigs + singlets Comparative Community Analysis Analyze community profile Overview of community analysis

  4. Microbial communitydata collection pipeline Isolate microbial genomic DNA from environmental samples Genomic DNA PCR 16S rDNA (or any gene of interest) and sequence 16S rDNA sequences Blast the generated sequences against GenBank nucleotide database Unoriented BLASTed 16S rDNA sequences Orient the generated sequences

  5. Microbial communitydata analysis pipeline Align the sequences with ClustalW alignment file *.phy Use alignment file in phylip format to create a distance matrix file with Phylip Distance matrix *.dist Define OTUs with Dotur program Dotur generated OTUs file *.dotur (*list*) Analyze and combine OTUs using an in-house script “DoturReader”

  6. Evaluating Data quality - Evenness This indicates how saturation -- fzn

  7. Evaluating Data quality - Rarefaction Another analytical tool to show the saturation of your sample -- fzn (DOTOUR graph)

  8. General Diversity Comparison How oil is the least diverse of the three…

  9. 35 30 25 20 Oil Mouse Soil 15 10 5 0 otu1 otu2 otu3 otu4 otu5 otu6 otu7 otu8 otu9 Oil, Mouse, and Soil microbial communities at 15 % cutoff I think it is better to compare results side by side as it shows directly the differences -- fzn

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