Get ready for a microbiome and metagenome festival in NYC! We are excited to announce the first international summit on metagenomics and metadesign of subways and urban biomes (MetaSUB), held in New York City (NYC) on June 20, 2015, at the New York Genome Center (NYGC). This will be held right after a related meeting at …
Dear metagenome method developers, The first challenge of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI) begins right now! Over the last three months, we received valuable feedback from the community playing with our toy data sets. We incorporated many of your suggestions, thanks again! Today, we proudly release the official data sets …
In this week’s Best of MicrobiomeDigest, we’ll look at the effect of a “sea voyage” on the human oral and belly button microbiome. For those of you who are not familiar with Fisherman’s Friend (I am not sure if these are as popular in the rest of the world as they are in parts of Europe), it’s a British …
Really nice article from Sarah Zhang at Gizmodo “Not Even Science Could Explain the Bacteria In My Apartment“. In it, she discusses the results of her participation in the Wildlife of Our Home study, the NY metagenomic data, and the fact that we’re still in the “exploration” phase of DNA-based microbial ecology. I think it’s …
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 …
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 …
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, …
We publish a newsletter every month here at microBEnet. And I thought it would be good to also publish to the blog the various summaries and roundups from the newsletter. Past newsletters are archived here. Here are some of the highlights from this latest newsletter. MicroBEnet Blogs A summary of the recent topics posted on microBE.net …
The idea for GenomePeek began two years ago when I was working with Karl Klose, Liz Dinsdale, and Rob Edwards to assemble a P. salmonis genome that was being particularly difficult, even though we had 9 gigabases of sequencing. To check whether it was a single isolated genome I pulled out all the 16S reads …