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 …

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) …

Indoor microbiology paper of interest on effects of moisture & interventions

For those interested in microbiology of the built environment this paper seems definitely worth checking out: Indoor microbiota in severely moisture damaged homes and the impact of interventions. Jayaprakash B, Adams RI, Kirjavainen P, Karvonen A, Vepsäläinen A, Valkonen M, Järvi K, Sulyok M, Pekkanen J, Hyvärinen A, Täubel M. Microbiome. 2017 Oct 13; 5(1):138 Abstract …

New standards recommendations on minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Of possible interest – a new paper (on which I am a coauthor) on standards for minimum information about single cell genomes and genomes assembled from metagenomes.  See link below: Source: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea : Nature Biotechnology : Nature Research  

Full-length #16S rRNA #nanopore sequencing of dog #skin microbiota

We are a research group working on Genetics in a Vet School and closely collaborating with veterinary clinicians and dermatologists. We moved from specific pathogens, such as Leishmania, to specific commensals such as Demodex… and finally ended studying the whole: the skin microbiota on healthy dogs. Vets are always wondering why there are differences among …

Everyone should read this piece by Ed Yong: Norm Pace Blew The Door Off The Microbial World

There is a wonderful tribute to Norm Pace in the Atlantic by Ed Yong. Norm Pace truly did blow the door off the microbial world. Source: Norm Pace Blew The Door Off The Microbial World – The Atlantic Lots of good stuff in there about Pace and his career.  See for example this: Pace also …