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This Week in PLOS: Sep 9, 2013

In PLOS Genetics, Danish researchers describe findings from a genomic analysis of bacteria from a Pseudomonas aeruginosa lineage capable of being passed from one individual infected with cystic fibrosis to another. The team sequenced 55 P. aeruginosa isolates found in 21 Danish cystic fibrosis patients over nearly four decades, from 1972 to 2008. The data made it possible for investigators to untangle relationships between the bugs — including those from an especially mutagenic sub-population of the lineage known as DK2. The group also tracked down genes that appear to have bolstered pathogenicity and patient adaptation.

A Boston-based team performed high-throughput sequencing on a transposon insertion library for an independent P. aeruginosa study in appearing in PLOS Pathogens. The insertion-sequencing, or INSeq, strategy offered clues about which non-essential genes that contribute to fitness in the P. aeruginosa strain PA14 — both in the lab and in a mouse model of infection. "These experiments resulted in the identification of the P. aeruginosa strain PA14 genes necessary for optimal survival in the mucosal and systemic environments of a mammalian host," the study's authors note.

Researchers from Canada, the US, and Austria report on the human urine metabolome in PLOS One. The group brought together existing information in the literature with experimental data determined with the help of nuclear magnetic resonance, liquid chromatography, and various forms of mass spectrometry to get at the metabolite makeup of human urine. On the experimental side, investigators tracked down 450 different urine-based metabolites, including 378 that could be quantified. Information in the literature led to another 2,208 compounds, which the team combined with experimental and structural data in an online urine metabolite clearinghouse found at

The Scan

Machine Learning Helps ID Molecular Mechanisms of Pancreatic Islet Beta Cell Subtypes in Type 2 Diabetes

The approach helps overcome limitations of previous studies that had investigated the molecular mechanisms of pancreatic islet beta cells, the authors write in their Nature Genetics paper.

Culture-Based Methods, Shotgun Sequencing Reveal Transmission of Bifidobacterium Strains From Mothers to Infants

In a Nature Communications study, culture-based approaches along with shotgun sequencing give a better picture of the microbial strains transmitted from mothers to infants.

Microbial Communities Can Help Trees Adapt to Changing Climates

Tree seedlings that were inoculated with microbes from dry, warm, or cold sites could better survive drought, heat, and cold stress, according to a study in Science.

A Combination of Genetics and Environment Causes Cleft Lip

In a study published in Nature Communications, researchers investigate what combination of genetic and environmental factors come into play to cause cleft lip/palate.