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Genomics of Microbes and Microbiomes Overview

Listed below is a brief overview of the talk and the papers referenced throughout the talk.

Recently, the NHGRI published a series on Current Topics in Genome Analysis. One of the talks was of special interest to me, Genomics of Microbes and Microbiomes by Julie Segre.

Topic 1 Bacterial Diversity Studies with 16S rRNA Sequencing

Important issues to consider in experiment:

  • Study design?
  • Sequencing platform?
  • 16S rRNA region?
  • Number of reads?
  • Hidden technical issues?
  • Analysis tools?
  • Visualize data?
  • Comparison to previous studies?
  • What information will yield testable hypothesis?

Describing diversity:

  • richeness - number of OTUs
  • evenness - Shannon equitability index
  • Shannon diversity index - accounts for both richness and evenness of OTUs

Papers:

Topic 2 Fungal Diversity

Topic 3 Bacterial Genomes

Need to consider similar issues as 16S rRNA, but also the following:

  • Existing reference genome?
  • Sequencing depth?

Papers:

Topic 4 Metagenomics

Databases:

  • KEGG
  • MetaCyc
  • the Gene Ontology
  • eggNOG

Goals:

  • Who’s there and abundance?
  • Function?
    • Genes
    • Pathways
    • Strains
  • Recover genomes?
  • Novel pathogenic organisms?

Papers:

Topic 4 Sequencing Technology

Illumina MiSeq dominates, but PacBio gives long reads for reference genomes. There may be talk of MinION from Oxford Nanopore in teh future for long read sequencing.