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This Week in PLOS: Jul 28, 2014

In PLOS Genetics, an international team led by investigators in Cuba, Canada, and Denmark describes findings from an effort to assess population admixture and pigmentation-related variants in more than 1,000 individuals from Cuba. With information at 128 ancestry informative markers, the researchers determined the proportions of African, European, and Native American ancestry in the genomes of 1,109 Cubans from across the country. That analysis pointed to enhanced Native American ancestry in provinces such as Granma, Holguin, and Las Tunas, for example, as well as particularly pronounced African ancestry in individuals from the Guantanamo and Santiago de Cuba provinces. Meanwhile, a search for SNPs influencing skin pigmentation led to variants in two main genes: SLC24A5 and SLC45A2.

Using sequence typing, genome sequencing, and other approaches, researchers from Saudi Arabia, India, the UK, and Australia characterized more than three dozen Vibrio cholerae isolates from a 2009 cholera outbreak in the Indian region of Chandigarh — work they present in PLOS Neglected Tropical Diseases. Within the genome sequence data, the team saw cholera-causing bugs belonging to two main clades with distinct drug resistance and cholera toxin expression profiles. "The limited capacity of [multi-locus sequence typing] and [multi-locus variable-length tandem-nucleotide repeat analysis] to discriminate between the clones that circulated in the 2009 Chandigarh outbreak highlights the value of whole-genome sequencing as a route to the identification of further genetic markers to subtype V. cholerae isolates," researchers write.

A PLOS One study by Boston University researchers suggests keystone species in the gut microbiome interact with other bacteria to produce networks of bugs that vary from one individual to the next. Using metagenomic sequence data and a strategy known as "learning interactions from microbial time series," or LIMITS, the investigators followed gut microbial community interactions and dynamics over time in two individuals. In those subjects, study authors say, levels of bacteria from the Bacteroides fragilis and Bacteroided stercosis species largely shaped gut microbial community structure. "Our prediction is that most perturbations will have little impact on the overall structure of the microbial community," they write, "but perturbations applied to a small number of keystone species will have a large impact on the structure of the community."