The Impact of a Consortium of Fermented Milk Strains on the Gut Microbiome of Gnotobiotic Mice and Monozygotic Twins

“The results also showed that (i) consumption of an FMP containing five bacterial strains was not associated with a statistically significant change in the proportional representation of resident community members within and between individuals; (ii) the appearance and disappearance of strains comprising the FMP consortium did not exhibit familial patterns in the fecal microbiota; and […]

Genome Sequence of E. coli O104:H4 Leads to Rapid Development of a Targeted Antimicrobial Agent against This Emerging Pathogen – PLoS ONE

“A recent widespread outbreak of Escherichia coli O104:H4 in Germany demonstrates the dynamic nature of emerging and re-emerging food-borne pathogens, particularly STECs and related pathogenic E. coli. Rapid genome sequencing and public availability of these data from the German outbreak strain allowed us to identify an O-antigen-specific bacteriophage tail spike protein encoded in the genome. […]

Bacterial genomics: A new source of antimicrobial targets : Nature Reviews Microbiology

“Bacterial clone-based genome sequencing frequently results in gaps, which harbour hypothetical genes of unknown function. Sorek and colleagues show that these gaps contain a vast array of genes encoding proteins that are toxic to the sequencing host (Escherichia coli), including previously uncharacterized restriction enzymes, toxin–antitoxin systems and non-coding RNAs.” Of course, to me, this is […]

Macro and Micro Diversity of Clostridium difficile Isolates from Diverse Sources and Geographical Locations – PLoS ONE

“Clostridium difficile has emerged rapidly as the leading cause of antibiotic-associated diarrheal disease, with the temporal and geographical appearance of dominant PCR ribotypes. We have undertaken a breadth genotyping study using multilocus sequence typing (MLST) analysis of 385 C. difficile strains from diverse sources by host (human, animal and food), geographical locations (North America, Europe […]

Patterns of Gene Flow Define Species of Thermophilic Archaea: PLoS Biology

“Patterns of homologous gene flow among genomes of 12 strains from a single hot spring in Kamchatka, Russia, demonstrate higher levels of gene flow within than between two persistent, coexisting groups, demonstrating that these microorganisms fit the biological species concept. Furthermore, rates of gene flow between two species are decreasing over time in a manner […]

The Visionary

“Seeking to spur drug development, Stephen Friend has launched a daring series of initiatives to make biomedical research more open and effective.” Interesting fellow. He’s a mover and shaker in the bioinformatics “data must be free” crowd. It’s a very good article. Read it. Read this article…

China’s Sequencing Powerhouse Comes of Age

“With new sequencing centers in Europe and the United States, BGI hopes its growing clout will help deliver the benefits promised by genomics—and revenue to pay off a mounting debt.” Genomics at a scale only China could do. Oh, my. Read this article…

Outbreak Detectives Embrace the Genome Era: Science

“Genomic epidemiologists say, it’s time to use the technique to track microbial movements on a global scale. By routinely sequencing bacterial samples—perhaps up to a billion a year—scientists could pinpoint the sources of new outbreaks faster, determine whether a bug is resistant to antibiotics, and investigate how public policies or the use of certain drugs […]