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This Week in Genome Biology: Jan 23, 2019

University of Pennsylvania genetics researcher Sarah Tishkoff and colleagues present findings from a gut microbiome study involving individuals from seven rural, non-industrialized populations in Tanzania and Botswana. Using 16S ribosomal RNA sequencing, the team profiled bacterial diversity, phylogenetics, and population structure in bacterial communities in the fecal samples from 60 Tanzanians and 54 individuals from Botswana, comparing the bacterial communities to those in 12 individuals from urban Philadelphia. The analysis pointed to distinct gut bacteria phylogenetic features in the hunter-gathers, though the authors saw overlap between agropastoralist and pastoralist microbiomes as well as similarities between gut microbial members in some agropastoralist individuals in Botswana and urban individuals from Philadelphia.

A team from the Francis Crick Institute and King's College London reveals details about the sixth version of the Network of Cancer Genes (NCG) database, a collection containing almost 2,400 manually curated genes marked by somatic alterations expected to spur on one or more cancer types. The current catalogue includes altered genes identified in more than 34,900 cases from 119 cancer types that were profiled for almost 300 studies published over a decade, the researchers say, along with expression, protein, and other related data. "The present release of NCG describes a substantial advance in annotations of known and candidate cancer driver genes," they note, "as well as an update and expansion of their systems-level properties."

Finally, researchers from the University of Toronto and New Zealand's Landcare Research report on Pseudomonas syringae relationships gleaned from whole-genome sequences for 391 agricultural or environmental strains from 11 P. syringae phylogroups. The team's analyses highlighted 2,410 core genes as well as 77,728 orthologous gene families spanning the P. syringae pan-genome, pointing to the presence of primary and secondary phylogroups within a single P. syringae species capable of recombination. "While inter-phylogroup recombination occurs relatively rarely," the authors write, "it is an important force maintaining the genetic cohesion of the species complex, particularly among primary phylogroup strains."