In Nature Methods this week, an international team presents the results of the Critical Assessment of Metagenome Interpretation (CAMI) effort, a community-driven benchmarking challenge for metagenomics software. Participants were tasked with benchmarking their programs on complex and realistic datasets generated from roughly 700 newly sequenced microorganisms, as well as around 600 novel viruses and plasmids. Among the findings were that assembly and genome binning programs performed well for species represented by individual genomes, but were affected by the presence of related strains. Taxonomic profiling and binning programs were proficient at high taxonomic ranks, meanwhile, with "a notable performance decrease below family level." And parameter settings had a major impact on performance, highlighting their importance for program reproducibility. Overall, the results "provide a roadmap for software selection to answer specific research questions," the authors write.
And in Nature Biomedical Engineering, a group led by University of California, Berkeley, researchers reports a novel non-viral method for delivering CRISPR/Cas9 molecules in vivo. The researchers used gold nanoparticles surrounded by a protective polymer as carriers for the CRISPR machinery, which allowed them to avoid the safety and efficacy issues commonly associated with viral delivery. In addition to demonstrating that CRISPR cargo could be delivered into a variety of cell types, the investigators used the approach to correct the genetic mutation associated with Duchenne muscular dystrophy in the muscle tissue of a mouse model of the disease. They further showed that the observed gene editing occurred via the preferred homology-directed repair mechanism.