So you want to run FACS on your microbiome samples…

So you want to run FACS on your microbiome samples… By Cara Pardon Although optimized for eukaryotic cell research, an increasingly common technique used in the microbiome field is Fluorescence Activated Cell Sorting (FACS).  From sorting cells for single cell genomics to identifying the host range of a plasmid; from detecting metabolically active cells in …

Method of interest: Leaf-FISH: Microscale Imaging of Bacterial Taxa on Phyllosphere

This paper may be of use to people working on plant microbiomes. Peredo EL and Simmons SL (2018) Leaf-FISH: Microscale Imaging of Bacterial Taxa on Phyllosphere. Front. Microbiol. 8:2669. doi: 10.3389/fmicb.2017.02669 Abstract Molecular methods for microbial community characterization have uncovered environmental and plant-associated factors shaping phyllosphere communities. Variables undetectable using bulk methods can play an …

Help wanted: looking for a recent (post 2012) #openaccess review on molecular phylogenetic methods

I am getting ready for my “EVE161” class on Sequence based studies of the diversity of microbes.  For more about past versions of the class see here: https://www.microbe.net/eve161/. Anyway – I am working on the reading for the class and I am looking for a good, recent, open access review of molecular phylogenetic methods.  Any recommendations …

Why genome completeness and contamination estimates are more complicated than you think

Genome-resolved metagenomics is the process of recovering de novo genomes belonging to individual organisms present in a community using DNA extracted from the whole community. These genomes are sometimes referred to as MAGs (metagenome-assembled genomes), and are recovered by associating assembled contigs together in “bins” in a process known as genome binning. As opposed to …

Networks shed new light on microbiota literature

Thanks to rapid and relatively inexpensive techniques, anything that can be swabbed, scooped and sequenced is fair game for bacterial community analyses. And, microbiome-mania aside, we are still discovering incredible things about the invisible microbial world everyday. Fellow microBEnet author David Coil has suggested that it is timely to collate the wealth of information that …

Paper generating a lot of buzz: Nucleic acid purification from plants, animals and microbes in under 30 seconds

Well, this paper is generating a lot of buzz on social media.  Nucleic acid purification from plants, animals and microbes in under 30 seconds.  For example see Eric Topol’s Tweet about it Now this is innovative: paper dipstick extraction of DNA or RNA in < 30 seconds https://t.co/RKuLsAW7fM @PLOSBiology @UQ_News pic.twitter.com/FH1krTFYMw — Eric Topol (@EricTopol) …