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This Week in Nature: Feb 7, 2019

In this week's Nature, University of California, Berkeley scientists and others investigate a new CRISPR nuclease — dubbed CasX — that can edit the human genome with different functionality than Cas9 and Cas12a. CasX was isolated from groundwater microbes and is smaller than other CRISPR nucleases at fewer than 1,000 amino acids. The authors show that CasX can modify both human and E. coli genomes, and demonstrate its unique features including a domain involved in DNA unwinding and minimal trans-cleavage activity relative to other Cas systems. GenomeWeb and the Scan have more on this, here and here.

And in Nature Biotechnology, a team of Chinese investigators from industry and academia reports on 1,520 reference genomes from cultivated human gut bacteria for microbiome research. Called the Culturable Genome Reference, the collection was generated from more than 6,000 bacteria cultivated from fecal samples of healthy humans. The genomes were chosen to cover all major bacterial phyla and genera in the human gut, and 264 of them are not represented in existing reference genome catalogs. The scientists show that this increased number of reference bacterial genomes improves the rate of mapping metagenomic sequencing reads from 50 percent to more than 70 percent, enabling higher-resolution descriptions of the human gut microbiome.

Also in Nature Biotechnology, a group led by Wellcome Sanger Institute scientists presents the Human Gastrointestinal Bacteria Culture Collection, a set of 737 whole genome-sequenced bacterial isolates representing 273 species — including 105 novel species — from 31 families found in the human gastrointestinal microbiota. This collection increases the number of bacterial genomes derived from human gastrointestinal microbiota by 37 percent, the authors state, "circumvents dependence on de novo assembly of metagenomes, and enables accurate and cost-effective shotgun metagenomic analyses of human gastrointestinal microbiota."

GenomeWeb also covers these papers, here.