Compiling some of the more interesting tools I have seen recently. Some I have plyed with but most I have just looked at the papers briefly. Microbiome | Abstract | VizBin – an application for reference-independent visualization and human-augmented binning of metagenomic data. Global biogeographic sampling of bacterial secondary metabolism GrammR: Graphical Representation and Modeling …
Quick post here. Just got alerted to this paper by automated searches from Pubchase: Construction of a dairy microbial genome catalog opens new perspect… – PubMed – NCBI. This paper provides a really good example of how researchers interested in microbial ecology of a particular system (in this case, dairies and cheese) can use culturing and …
In just over a decade, metagenomics has developed into a powerful and productive method in microbiology and microbial ecology. The ability to retrieve and organize bits and pieces of genomic DNA from any natural context has opened a window into the vast universe of uncultivated microbes. Tremendous progress has been made in computational approaches to …
So many new tools and methods in microbiome and microbial community studies and it is just really hard to keep up with them. Here are some that have caught my eye recently: PLOS ONE: IM-TORNADO: A Tool for Comparison of 16S Reads from Paired-End Libraries. Jeraldo P, Kalari K, Chen X, Bhavsar J, Mangalam A, …
The spread of antibiotic resistance traits is an ongoing and important issue that is poorly studied. This PLoS One study by Lerma et al. is the first to use a culture independent approach to characterize antibiotic resistance traits in the total microbiota present in a goat and lamb slaughterhouse. Lerma et al. found that tetracycline resistance genes (tetA and tetB) and Sulfonamide …
Every day, diverse microbial communities with cell levels of 106-108 cells/liter migrate from drinking water treatment plants through a complex network of pipes in drinking water distribution systems and into our built environment. Managing this mass migration is critical from multiple perspectives. Some of these microorganisms can make consumers ill, some can contribute to pipe …
So – just was reading this paper: Healthcare Workers’ Hand Microbiome May Mediate Carriage of Hospital Pathogens. Basically, they showed that the microbiome on health care worker’s hands was correlated with estimates of pathogen carriage. And, it seems to be of potential interest to the microBEnet community. I confess, I am skeptical of the validity of some …
When I first saw this headline: Fox 25 Investigates: Hidden hospital germs I geared up for YASS – yet another swab story (this is a bit of a play on the “swab story” complaint Mark Martin uses for stories that report on microbes found by swabbing. Nooooooooooo- there are bacteria in our homes —- run run run — aaarrgg …
Rob Knight, together with science journalist Brendan Buhler, has written a witty synopsis (entitled “Follow Your Gut: The Enormous Impact of Tiny Microbes”) about the human microbiome and how it affects human life in the form of a TED book, now available for pre-order on Amazon.com. The description from Amazon’s webpage is below: “Allergies, asthma, obesity, …
Today, humans spend ~90% of their lives roaming the ‘great indoors’, which is very different from the outdoor environments where we co-evolved with our commensal microbiota (Kelley and Gilbert, 2013). We are just beginning to understand how the design of built environments (BEs) influences our microbiome, and how these interactions, in turn, might affect human …