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  

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 …

Indexed PCR Primers Induce Template-Specific Bias in Large-Scale DNA Sequencing Studies

So I had two thoughts when I read the article title “Indexed PCR Primers Induce Template-Specific Bias in Large-Scale DNA Sequencing Studies“… #1:  Ack!  Yet another thing to worry about in the insanely complicated craziness that is 16S amplicon sequencing. #2: I probably shouldn’t be the person to blog about this because I’ve honestly never …

Behind the paper: 16Stimator

In scientific manuscripts, we tell stories of our research, generally in straight-line fashion with clear motivations and results. This type of research is rare (in my experience), with stories, motivations, and applications only realized post hoc. This is the nature of science, and our recent ISMEJ publication is no different. With “16Stimator: statistical estimation of …

High throughput full length 16S sequencing

Microbial ecology has benefited enormously from the development of high throughput sequencing technologies, driving the discovery of massive diversity in environments from the ocean to the human body.  Where sequencing of less than one hundred 16S rRNA genes from several samples used to be common place with cloning and Sanger sequencing, we can now generate tens …

Challenges and Opportunities of Airborne Metagenomics

There is a new #openaccess paper out that may be of interest to many working on microbes in the built envronment or microbes in air (indoors or outdoors): Challenges and Opportunities of Airborne Metagenomics by Behzad et al. in Gebome Biology and Evolution.  There are some useful things in this paper and some strange things but …

Best practices for sample processing and storage prior to microbiome DNA analysis freeze? buffer? process?

So – we have been having a running discussion with people in my lab about one key issue in microbiome studies – how does one store samples prior to doing DNA extractions and does it matter?  As background for those who do not do this kind of work – the general principle behind DNA based …