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This Week in Genome Research: Apr 17, 2013

An international team led by investigators with the Wellcome Trust Sanger Institute's pathogen genomics group describes a strategy for sequencing the genomes of Chlamydia trachomatis isolates nabbed from clinical swabs without a separate bacterial culturing step. As they report in the early, online edition of Genome Research, the researchers relied on multiple displacement amplification, or MDA, to up the levels of DNA in clinical samples after enriching for the sexually transmitted bugs using a so-called immunomagnetic separation method. Combining the amplification and enrichment techniques helped to sequence the genomes of a significant subset of C. trachomatis specimens found in clinical and archived samples, the team reports, providing "new avenues of investigation for genomic research into difficult-to-culture and fastidious bacteria."

Meanwhile, researchers from the J. Craig Venter Institute and elsewhere explain how they used single-cell sequencing to characterize the genomes of Porphyromonas gingivalis pathogens from the sink drain of a hospital bathroom. That team came up with an automated approach for performing MDA on hundreds of individual bacterial cells in parallel, producing amplified DNA that was then tested by 16S ribosomal RNA sequencing to characterize the microbes present. From there, investigators narrowed in on sequence data for the periodontal disease culprit P. gingivalis, using single-cell sequence assembly software to put an almost complete P. gingivalis genome — a sequence that researchers subsequently compared with existing P. gingivalis genomes.

EMBL's Peer Bork and colleagues used metagenomic sequencing to look at ways in which antibiotic use in food and medicine influences the resistance genes found in microbial communities in the human gut. Using metagenomic sequence data on more than 250 fecal samples from 207 individuals in three countries, the team searched for sequences implicated in resistance to dozens of antibiotic types. Results of the "resistome" analysis indicated that resistance gene representation tends to coincide with the suite of antibiotics that have been long present and/or currently used in agricultural animals in each area.

The Scan

Study Finds Sorghum Genetic Loci Influencing Composition, Function of Human Gut Microbes

Focusing on microbes found in the human gut microbiome, researchers in Nature Communications identified 10 sorghum loci that appear to influence the microbial taxa or microbial metabolite features.

Treatment Costs May Not Coincide With R&D Investment, Study Suggests

Researchers in JAMA Network Open did not find an association between ultimate treatment costs and investments in a drug when they analyzed available data on 60 approved drugs.

Sleep-Related Variants Show Low Penetrance in Large Population Analysis

A limited number of variants had documented sleep effects in an investigation in PLOS Genetics of 10 genes with reported sleep ties in nearly 192,000 participants in four population studies.

Researchers Develop Polygenic Risk Scores for Dozens of Disease-Related Exposures

With genetic data from two large population cohorts and summary statistics from prior genome-wide association studies, researchers came up with 27 exposure polygenic risk scores in the American Journal of Human Genetics.