In PLoS ONE this week, Danish researchers report on their analysis of insertions and deletions in the human genome. The team sifted through published re-sequencing data in the Seattle SNPs and National Institute of Environmental Health Sciences databases to find polymorphism patterns in the human genome, comparing these with chimpanzee indels. "Our data strongly suggest that deletions are more deleterious than insertions," they write, "but that insertions and deletions are otherwise generally governed by the same genomic factors."
J. Craig Venter Institute and Macquarie University researcher Ian Paulsen and his team describe their sequencing and analysis of the genome of an antibiotic resistant Pseudomonas aeruginosa strain called PA7 from Argentina. After using a whole-genome shotgun approach to sequence the 6.6 million base genome, the researchers compared the sequence to that of other strains, identifying virulence factors, genes involved in antibiotic resistance, and more.
As part of the Trial of Infant Probiotic Supplementation or TIPs study, University of California of San Francisco gastroenterologist Susan Lynch and her co-workers investigate how the infant gut microbiome changes in babies given Lactobacillus casei subspecies rhamnosus supplements. As part of the double blind, randomized trial, the team used 16S rRNA PhyloChip to compare the gut microbial community in infants receiving the supplements for their first six months with infants receiving a placebo. Their results suggest the L. casei supplements are linked to gut microbial communities containing other known probiotics, including Lactobacillaceae and Bifidobacteriaceae species.
A team of researchers from the UK and US report that they have sequenced the genome of an Escherichia coli strain called E. coli 042. First isolated from a child with diarrhea in Peru in the early 1980s, the strain belongs to a group of intestinal infection-causing bacteria called enteroaggregative E. coli. The researchers sequenced the genome to about eight times coverage and used microarrays to profile the bug's metabolism, turning up differences between E. coli 042 and other E. coli strains. "This study provides a genetic context for the vast amount of experimental and epidemiological data published thus far and provides a template for future diagnostic and intervention strategies," they write.