A microbial sequencing discussion course built around a paper and a blog post

So – just a quick post for now.  More details to come.  But I wanted to get a little bit about this out there. For a few years I have been teaching a mid-level course at UC Davis on “DNA sequencing based studies of microbial diversity’.  The course has evolved over the years from a …

US Interagency Strategic Plan for Microbiome Research

Some important reading for those interested in microbiomes. NSF’s mission is to advance the progress of science, a mission accomplished by funding proposals for research and education made by scientists, engineers, and educators from across the country. From NSF: A group of 23 U.S. government agencies, including the National Science Foundation (NSF), have joined to …

Special issue of mSystems: Essays by Early-Career Systems Microbiology Scientists

This should be of interest to many: mSystems has a whole issue dedicated to essays by “Early-Career Systems Microbiology Scientists”. Early-Career Systems Microbiology Scientists Jack A. Gilbert mSystems March/April 2018 3:e00002-18; doi:10.1128/mSystems.00002-18 http://msystems.asm.org/content/3/2/e00002-18   Conflict of Interest Declarations by Contributing Editors of the Special Issue on Early-Career Systems Microbiology Scientists, Sponsored by Janssen Human Microbiome …

Looks great: 7th Conference on Beneficial Microbes at UW-Madison 7/8-11

Conference announcement: The 7th Conference on Beneficial Microbes will be held at UW-Madison on July 8-11, 2018. The abstract submission deadline is May 2. https://uwmadison.eventsair.com/QuickEventWebsitePortal/BENEFICIALMICROBES/18 The conference was formerly the “ASM Conference on Beneficial Microbes,” with a long history of combining model and natural systems to understand the ecology and functions of host-associated microbes. When ASM …

Who are the microbes in your neighborhood mice? In your neighborhood mice? In your neighborhood mice?

  Just a quick post here pointing people to some new papers of potential interest.  The papers in are mBio and are from Ian Lipkin’s lab (with others) on bacteria and viruses in mice in New York City papers in mBio Viral Diversity of House Mice in New York City mBio 9:2 march/april 2018; doi:10.1128/mBio.01354-17 New York …

New tool of interest: GraftM: “a tool for scalable, phylogenetically informed classification of genes within metagenomes”

This could be of use to many people: Source: GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes | Nucleic Acids Research | Oxford Academic Large-scale metagenomic datasets enable the recovery of hundreds of population genomes from environmental samples. However, these genomes do not typically represent the full diversity of complex microbial …

New paper of interest on Hospital Plumbing and Carbapenem Resistance

New paper of interest:: Genomic Analysis of Hospital Plumbing Reveals Diverse Reservoir of Bacterial Plasmids Conferring Carbapenem Resistance Weingarten RA, Johnson RC, Conlan S, Ramsburg AM, Dekker JP, Lau AF, Khil P, Odom RT, Deming C, Park M, Thomas PJ, NISC Comparative Sequencing Program, Henderson DK, Palmore TN, Segre JA, Frank KM. 2018. Genomic analysis …

New Report on The Struggle for Water Justice from the UC Davis Center for Regional Change

Of potential interest:: The Struggle for Water Justice from the Center for Regional Change at UC Davis. Summary: The Struggle for Water Justice: Disadvantaged Unincorporated Communities in California’s San Joaquin ValleyFebruary 2018 In California, lack of access to clean, safe, and affordable water is a threat to public health and well-being, and violates the state’s newly codified …

Watercolours “created” by bacteria (sort of, but still really cool)

OK this is cool :This watercolour painting was created by artistic bacteria | WIRED UK Though not quite what the headline says. From the article With Park’s guidance, Roberts placed Serratia marcescens – a red pigmented bacteria – on to agar plates previously painted with watercolours. When coming into contact with the paint, the bacteria …