Genomes from metagenomics: pulling the needles from the haystack.

Shotgun whole genome sequencing revolutionized how we study single, microbial isolates. By breaking the genome into small reads in vitro, we are able to parallelize sequencing and decrease costs before bioinformatic assemblers put the puzzle back together again in silico. However, re-building the genomic puzzle gets more complicated in metagenomic samples and bioinformatic tools are still being developed in order to improve our abilities to re-compile multiple genomic puzzles from a given sample.

Nadel im Heuhaufen

One way of doing this is to separate the puzzles from each other by organizing metagenomic information into bins which can each be dealt with independently. Many tools exist to separate metagenomic information based on the composition of sequences, and the relative abundance within and across samples; however, we have found that the output of these tools can vary substantially, making biological interpretation of the data difficult.

Recently, Sieber et al. released a possible improvement to these approaches in the DAS Tool. This tool takes the output of multiple binning strategies and dereplicates, aggregates, and scores these to produce an optimal binning output. On March 31st at 3pm in 3N10A, I will lead the Club through this approach. The goals of this journal club will be:

  1. To provide amble background information. Shotgun metagenomic sequencing is not yet as universal as 16S rRNA gene sequencing approaches, so I will make sure to spend time explaining this technique and the accompanying literature to-date.
  2. To assess the DAS Tool compared to other binning strategies in terms of (i) accuracy, (ii) ease-of-use, and (iii) feasibility on our own human microbiota datasets.

Afterwards, I hope to continue with whiteboard discussions of metagenomic sequencing strategies in general… which may relocate to the Phoenix as necessary.

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