This month’s journal club will continue on the topic of increasing the resolution of human microbiome studies, through a novel metagenomics analysis pipeline developed by Greenblum et al. In the human microbiome, bacterial strains of the same species may possess different genes or different copy numbers of genes, which affects the functionality encoded by the entire community. However, this strain-level information is usually lost in 16S rRNA gene sequencing and metagenomic studies.
In this paper, the authors analyze the intra-species copy number variation from shotgun metagenomic data of 109 gut microbiome samples. They found that copy-number variation of genes was wide-spread across different species, with genes important for environmental adaptation more likely to be variable. Additionally, correlations were found between strain variation and host states, including IBD and obesity.
Please join us at 3:30pm on Friday, August 28 at West End Pub for a lively discussion on this novel method of determining strain-level copy number variability and the results obtained by the authors when this method was applied to microbiome data sets; the applicability of this analysis for other data sets, and any limitations of the overall study or method.