Metagenomics workshop taught by Titus Brown and Harriet Alexander

This is definitely worth checking out. Titus Brown and Harriet Alexander taught a two day metagenomics workshop at UCSD and they have written up some details about it and posted videos. Wrap up blog: titus-blog/2016-metagenom ics-workshop-at-sio.rst at public · ctb/titus-blog · GitHub All the docs here: http://2016-metagenomics-sio.readthedocs.io/en/latest/ Videos

Wanted – recommended service providers for microbial sequencing (genomes, rRNA, metagenomes, etc)

In January 2014 I wrote this post about “microbiome” sequencing services. I have gotten many outside requests for the following information — what places (companies, Universities, government agencies, etc) provide contract services for rRNA PCR and sequencing? Source: Request — Information on Places that do rRNA sequencing as a service — microBEnet: the microbiology of the …

IRIS AI and a wondrous rabbit hole of a labelled network of scientific papers

Got an email from the developers of IRIS AI the other day: And decided to play around with it. So I went to our Zotero collection on microbiology of the built environment: From there I got a paper and found it’s URL: Meadow, J. F., Altrichter, A. E., Kembel, S. W., Kline, J., Mhuireach, G., Moriyama, M., Northcutt, …

OMG – I want one: “Smartphone Microscope Lets You Play Games With Microbes”

OMG.  I want one. I want two. No – I want dozens. Caption from Gizmodo: “Introducing the LudusScope, a 3D-printed, open-sourced system that lets you control and play games with living microbes on your smartphone. Tormenting single-celled organisms has never been so much fun.” Source: This Smartphone Microscope Lets You Play Games With Microbes   …

Method of interest: precision sequencing of near full 16S rRNA genes on a MiSeq (from @Cath_B & @koadman)  

Definitely worth checking this one (from Burke and Darling) out if you do microbial diversity studies … Background The bacterial 16S rRNA gene has historically been used in defining bacterial taxonomy and phylogeny. However, there are currently no high-throughput methods to sequence full-length 16S rRNA genes present in a sample with precision. Results We describe …

Software of interest: MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples

New software/tool of possible interest: Source: MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples Software: http://segatalab.cibio.unitn.it/tools/metamlst/ Abstract: Metagenomic characterization of microbial communities has the potential to become a tool to identify pathogens in human samples. However, software tools able to extract strain-level typing information from metagenomic data are needed. Low-throughput molecular typing schema such as Multilocus …

The hot new 10 questions concerning the microbiomes of buildings will surprise you

Ok so I made this into Clickbait.  But you really should read this and that has nothing to do with me being a co-author. The paper is “Ten questions concerning the microbiomes of buildings” and it is in “Building and Environment” a journal that I am becoming more and more appreciative of every month.  The …

Today & tomorrow – live webcast – Standards for Microbiome Measurements @NIST

Definitely worth checking this out. NIST is running a meeting on Standards for Microbiome Measurements From the site: This workshop will seek input on defining reference materials, reference data and reference methods for human microbiome community measurements. This workshop is sponsored by NIST and NIH’s National Institute of Allergy and Infectious Diseases and the Human Microbiome …

Mick Watson (@BioMickWatson) is on a mission – collecting papers about bias in microbiome studies 

So I just saw this Tweet @BioMickWatson can’t find paper I’m thinking of, but OTU calling software/algorithm matters a lot – David Baltrus (@surt_lab) August 6, 2016 So I went to Mick Watson’s site and saw this: This is my attempt to collate the literature on how easy it is to introduce bias into microbiome …