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 …

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 …

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 …

Strain-resolved analysis of hospital rooms & infants reveals overlap between human & room microbiome 

Of potential interest – new paper from the Banfield Lab – thanks to Elisabeth Bik for pointing me to this on Twitter.   Preterm infants exhibit different microbiome colonization patterns relative to full-term infants, and it is speculated that the hospital room environment may contribute to infant microbiome development. Here, we present a genome-resolved metagenomic …

Worth a look: Communicating promise, risks, & ethics of large-scale, open space microbiome & metagenome research 

At the recent NAS MOBE meeting there was some discussion of some potential ethical concerns associated with one of the projects discussed (work of Eric Alm where he was collecting samples from urban water systems and trying to infer information about communities and residents).   OK #MOBE17 and others out there – I am getting …

Postdoctoral positions in engineering the microbiome – Cornell University

The Brito Lab at Cornell University in Ithaca, NY works in the area of systems biology of the human microbiome. We are looking for talented postdocs to fill two open positions for postdoctoral researchers interested in investigating mechanistic linkages between microbes and human health outcomes. Postdoctoral candidates can have an experimental or computational background, or both. One of …

KU: Asst Prof. in Microbial Environmental Metagenomics & Bioinformatics

Source: University of Kansas – Job details “The University of Kansas seeks a tenure-track assistant professor in Microbial Environmental Metagenomics and Bioinformatics.  This position is a full-time, academic year appointment.  The faculty member will conduct research in microbial environmental genomics, metagenomics and bioinformatics leading to publication in appropriate media; procure external funding as appropriate; participate …

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  

Journal Club: Metagenomics on the Space Station

Microbes in space have been of interest to the folks at various space agencies for as long as we’ve been sending people into space.  Rampant mold growth on the Russian Space Station Mir was probably one of the reasons for the decision to “deorbit” the station (a fancy way of describing crashing into the ocean).  …