A fascinating side story to brain-defect microbiome study – major role of the built environment

So there is a new paper out that is incredibly interesting and has been getting lots of press coverage.  The paper was in Nature: Endothelial TLR4 and the microbiome drive cerebral cavernous malformations. Sadly it is behind a paywall, so not everyone out there will have free access to it. But it is available in sci-hub …

This is calling out for a large microbiome study: Salt from icy roads is contaminating North America’s lakes

It seems to me that this is calling out for some large scale comparative microbial community study: Salt from icy roads is contaminating North America’s lakes – The Washington Post Basically, there is evidence that lakes throughout North America have seen a big increase in salt levels connected to salt used to try and deal …

Of possible interest: Special Issue on emerging aquatic microbial and chemical contaminants 

Just a quick post here.  There is a “special issue of International Journal of Environmental Research and Public Health (ISSN 1660-4601).” that may be of interest.  The issue is on “Emerging Aquatic Microbial and Chemical Contaminants of Concern and Their Impact on Human Health” and it currently has seven papers and apparently more coming. A brief …

Journal of Bacteriology minireview collection on host-microbe interactions

Just got this announcement via email and thought it might be of interest. New eBook Special Collection of JB Minreviews Dear Colleague, The microbial world is a competitive place, and bacteria have evolved diverse strategies to sense their environment and survive in it. These strategies involve acquiring necessary nutrients, particularly when inside a mammalian host, …

Paper of interest comparing taxonomies of SILVA, RDP, Greengenes, NCBI and OTT 

Just a quick post here.  There is a paper of interest I thought I would call attention to: Source: SILVA, RDP, Greengenes, NCBI and OTT — how do these taxonomies compare? | BMC Genomics  by Monika Balvočiūtė and Daniel H. Huson Abstract: Background A key step in microbiome sequencing analysis is read assignment to taxonomic units. …

ASM Press Release: Bacteria Fight Corrosion on Ancient Iron Artifacts

This is a cross-posting of a Press Release from the American Society for Microbiology. A team of Swiss chemists and microbiologists have shown that a species of anaerobic bacterium can inhibit corrosion on archeological artifacts made of iron. The research is published March 10 in Applied and Environmental Microbiology, a journal of the American Society …

Genomes of eight bacteria from the built environment

We just published an extended genome report from eight bacteria that were sequenced as part of the “Built Environment Reference Genome” (BERG) project. BERG is a microBEnet run effort to increase the number of reference genomes in the Built Environment (BE) by offering free genome sequencing to a number of labs working in the field. …

Call for Papers MoBE 2017 Microbiome Special Issue

Call for Papers: MoBE 2017 Special Issue of BioMed Central’s Microbiome Journal  (Submission Guidelines) We invite submissions of MoBE papers highlighting recent research and emerging hot topics along the theme of “MoBE Research to Applications” for our peer-reviewed MoBE special issue. Publishing charges are sponsored by the MoBE meeting and BioMed Central’s Microbiome Journal. This special issue will be available by October 1st, …

From genomes to phenotypes: Traitar, the microbial trait analyzer

There is an increasing number of studies with a large number genomes recovered from isolate, metagenome, or single cell sequencing. To bridge the gap between the available genome sequences and available phenotype information, we have developed Traitar, a bioinformatics software to phenotype bacteria based on their genome sequence (see workflow below) . Traitar includes phenotype models for …

16S rRNA Sequencing Using the Oxford Nanopore Minion

There has been some interest in our recent preprint describing Oxford Nanopore MinIONTM sequencing for 16S rRNA microbiome characterization and I was asked to write a post for microbenet on this technology. Disclaimers – this paper is a work in progress – our paper has not yet been peer-reviewed and we are continuing to revise …