Paper of interest: Predicting antibiotic resistance from full genome sequences 

This preprint seems like it may be of interest to folks: Precise prediction of antibiotic resistance in Escherichia coli from full genome sequences | bioRxiv Basically, the authors showed that, using a machine learning approach, they can quite accurately predict antibiotic resistance in E. coli from whole genome data. The emergence of microbial antibiotic resistance …

The Built Environment Reference Genome Collection… A First Taste

Over the last several years our lab has spent a fair bit of effort on collecting and sequencing genomes of bacteria from the built environment.  Genome sequences are useful for a number of reasons including facilitating metagenomics and understanding the actual metabolic capacity of particular microbes.  In particular we hope that genome sequences will facilitate …

Sequencing bacterial genomes in a class: a Swiss project

Isolating interesting bacteria and sequencing their genomes has never been easier and our lab has worked extensively on this topic, particularly in the context of undergraduate education.   Our first foray into this field came in 2011 with a group of students working on the “Built Environment Genomes Project” and eventually culminated in our Swabs to …

Swabs to Genome Workflow available as pre-print on PeerJ

Almost exactly a year ago we finally wrapped up our undergraduate project focusing on sequencing and assembling reference genomes from the built environment.  This project aimed to take undergrads through every step from starting with a swab to ending with a published genome announcement and data in NCBI. Over the course of the work, we …