When I jetted off to South America a year and a half ago, my doctor sent me with a bottle of Ciprofloxacin in case of an unfortunate bout of food poisoning. I thought little of it then, but what does it mean when millions of travelers head to developing countries with antibiotics? You guessed it …
Great article about a great study. Read them both. Failing that, here’s my short version: A study entitled “Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics” came out yesterday that is just fascinating on multiple levels. This article describes a large-scale metagenomics study carried out by the PathoMap project at Weill Cornell Medical …
Well, the stories just keep coming about antimicrobial agents we can use to kill off some pathogen in our environment. Today’s is about plasma – yes plasma – and how it can deactivate norovirus in the environment: ‘Cold plasma’ kills off norovirus from the BBC. The article discusses a new study in the journal mBio. Some key …
When we take a swab and perform 16S sequencing we assume that this gives us a picture of who is present in a bacterial community. But actually what we’re measuring is what DNA is present on that surface. This technique doesn’t tell us who is alive, who is dead, who is viable, who is non-viable, …
By Amanda Makowiecki 1st Year Mechanical Engineering PhD Student Miller Research Group, University of Colorado Boulder Researchers at the University of Oregon recently published a paper examining the connection between architectural design and microbial diversity in our buildings (Kembel et al. 2014). Although occupancy type was identified as the strongest predictor of microbial variation, several …
IBM and Mars put out a joint press release today announcing a new effort to use metagenomics to study microorganisms in the food supply chain. The new initiative, called the Sequencing the Food Supply Chain Consortium (SFSC), will use metagenomics and metatranscriptomics to establish what they call a “microbial baseline” that can later be used …
From the perspective of biothreat detection, one of the biggest questions is “what is the background?”. If you sample the air near a farm, there’s a good bet that you’ll find anthrax (or at least a close relative indistinguishable by a 16S PCR survey). But that’s just because anthrax lives in the soil, not because …
Saw an interesting talk yesterday from Karen Guillemin of the University of Oregon. I made a storification of the Twitter posts from the talk. See it at the end of this post. I note – I think there are some important lessons in the work on germ free animals that could be applied to studies …
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 …
There is an abundance of literature on how microbes can obtain antibiotic resistance, but not as much about how antibiotic resistance can spread. Jonathan drew my attention to this article today, which highlights the fact that antibiotic resistance can be spread through the air. While I didn’t find the conclusions all that surprising, I was …