Sifting through microbial lineages within metagenomes

We’re starting the year off by discussing a new paper out this month on metagenomic data analysis (Darling et al. 2014 PeerJ 2:e243). Members of the Matsen and Eisen labs came together to explore methods for phylogenetic-based microbial community analysis and the result is their open-source software package PhyloSift. Bring your low-tech paper and pen to discuss this high-tech article at the Phoenix pub next Monday, January 20th, at 3 pm. The highlights of the paper include:

  • Studying microbial communities with metagenomes (i.e. entire genomes of all the microbes in the sample) instead of the amplicon-based single gene methods (i.e. PCR amplification of the 16S rRNA genes from all microbes in the sample).
  • The software incorporates 37 marker genes as well as all other gene families.
  • They use a phylogenetic methods for studying microbial communities  – we’ll talk about what this means and how it’s different from OTU-based taxonomies.
  • Bayesian hypothesis testing, edge PCA over PCoA or CA based on UniFrac, alpha diversity based on phylogenetic methods versus OTU-based methods, and much more…

We’ll talk about the pros and cons of their method, how this applies to us and metagenome analysis in general and about how they show the taxonomic ambiguities in their data instead of ignoring it. PeerJ is even set up to accept comments and question on the article website, so if we have some burning questions remaining we might even post them. Great, see you there.


About Jennifer Stearns

Farncombe Family Chair in Microbial Ecology and Bioinformatics and Assistant Professor at McMaster University
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