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Links 1 through 10 of 72 by Charlie Schick tagged microbiology

ICYMI @_zoonotica_ started a #Microbiology Twitter Journal Club. 1st paper being discussed right now! http://t.co/nXnOLk27 Use #microtwjc.

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"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 and Australia) and PCR ribotypes. Results identified 18 novel sequence types (STs) and 3 new allele sequences and confirmed the presence of five distinct clonal lineages generally associated with outbreaks of C. difficile infection in humans."

A broad survey to understand the nature of this pesky and increasingly common pathogen.

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"We report on the remarkable degree of biodiversity in the wine yeast populations naturally present in a small area of Sicily where traditional (non-industrial) winery practices are still in place. Out of more than 900 yeast isolates recovered from late spontaneous fermentations, we detected at least 209 strains. Given that the characteristics of the wines produced were found to be industrially appealing, the study demonstrated the economic potential of preserving the patrimony of Sicilian yeast biodiversity and highlighted the importance of maintaining traditional wine making practices."

This is a great paper - studying the biodiversity of yeast obtained from traditional wineries; analyzing their genetic and metabolic qualities; and even using a few to make wines.

How fun. How inspiring.

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"This study demonstrates that the milk-feeding type and the HLA-DQ genotype differently influence the bacterial colonization pattern of the newborn intestine during the first 4 months of life and, therefore, could also influence the risk of developing CD in later life. Breast-feeding reduced the genotype-related differences in microbiota composition, which could partly explain the protective role attributed to breast milk in this disorder."

Interesting study doing two things: 1) showing an effect of genotype on bacterial populations in the gut - and that they are different for those at risk for celiac disease; and, 2) showing a difference between the bacterial populations of breast-fed and formula-fed children, and a possible microbial reason why breast-feeding protects against celiac disease.

Very cool. And scary how it makes such good sense.

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"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 consistent with incipient speciation."

This is a really cool paper analyzing speciation in action. It shows how microbes slowly become less likely to swap genetic information as they differentiate. A key concept, too, is that each species has its own genetic island.

Great stuff.

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"For decades, Robert Daum has studied the havoc wreaked by methicillin-resistant Staphylococcus aureus. Now he thinks he can stop it for good."

Excellent story of the fight against MRSA by the guy who first made us aware of it.

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"There is a common conceit among we DIYbio enthusiasts, namely to suggest that one could opt to create “glow-in-the-dark yoghurt” using DIYbio-oriented techniques as a nigh trivial matter. Indeed, this conceit led to my recently being queried by twitter and email about the possibility; where are the guides and how-tos, if it is so trivial? While a conceit it may be to suggest that glow-in-the-dark yoghurt would be trivial, that’s not to say it’s at all out of reach to the dedicated biohacker. Here, I will lay out a suggested course of action based on the available literature."

Quite cool.

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"The Earth Microbiome Project (EMP) is the most ambitious attempt to provide a systematic characterization of the microbial world that dominates this planet. The ecosystem services provided by microbes in every environment (including the human body) are fundamental to the survival of life on this planet and the continued economic and physical health of the human race. The pilot study of the EMP started in March 2011 and is now reaching its zenith."

This session has four interesting talks on handling the data deluge, a field guide, why we should care, and mathematical modeling. Cool. Can't wait for the speaker notes and the like.

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"A mouthwash that kills S. mutans and leaves the rest of the bacteria to take over S. mutans‘s real estate could spell the end of cavities. In a small clinical study last year, one team found that one application of the mouthwash knocked down S. mutans levels, and that harmless bacteria grew back in its place. If the mouthwash pans out, it could join the ranks of an emerging new type of treatment: better living through hacking the microbiome."

This is really cool. And this article get extra points for the endnotes on probiotics and fecal transplants.

I totally believe we are entering an age where we are going to manipulate our microbiome for health and medicine.

[via @edyong209]

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"Artificial two-dimensional biological habitats were prepared from porous polymer layers and inoculated with the fungus Penicillium roqueforti to provide a living material. Such composites of classical industrial ingredients and living microorganisms can provide a novel form of functional or smart materials with capability for evolutionary adaptation. We demonstrated a design of such living materials and showed both active (eating) and waiting (dormant, hibernation) states with additional recovery for reinitiation of a new active state by observing the metabolic activity over two full nutrition cycles of the living material (active, hibernation, reactivation). This novel class of living materials can be expected to provide nonclassical solutions in consumer goods such as packaging, indoor surfaces, and in biotechnology."

Hm. Some really practical uses of microbes - impregnating fabrics to provide bioactive activity.

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