Journal Club: “Pre- and post-sequencing recommendations for functional annotation of human fecal metagenomes”

This is a pre-print that just came out from several UC Davis colleagues.  I actually think the title is a bit misleading because these recommendations are a lot broader than just human fecal metagenomes.  Definitely worth a read! Abstract below: Background Shotgun metagenomes are often assembled prior to annotation of genes which biases the functional …

Network analysis of the Sloan-funded MoBE program publications

~15 years after the first project was funded, the Sloan “Microbiology of the Built Environment” program has pretty much wrapped up.  Here at microBEnet, we wanted to take a deeper look at the impact of the program on the published literature in the field.  There were over 300 publications from the program through the end …

Job Posting: Microbial Ecology and Evolution at University of Toronto Mississauga

  Assistant Professor – Microbial Ecology and Evolution – 1902892 The Department of Biology at the University of Toronto Mississauga (UTM) invites applications for a tenure-stream appointment in Microbial Ecology and Evolution, at the rank of Assistant Professor, commencing July 1, 2020, or shortly thereafter. Applicants must have a Ph.D. in Biology or closely related …

Postdoc at UC Davis in metagenomics bioinformatics

Job posting from here at UC Davis: The laboratories of Danielle Lemay (USDA Western Human Nutrition Research Center) and David Mills (UC Davis Food Science) seek a motivated postdoctoral scholar for a one year project. The goal of the project is to determine how dietary intake influences antimicrobial resistance in fecal metagenomes of healthy adults. The …

New wastewater anammox project

So our lab appears to be digging deeper and deeper into the world of wastewater treatment, especially the process of removing ammonia from wastewater in the final steps.  I’ve posted before about our sample collection from a pilot wastewater treatment facility.   We’ve been sequencing those samples like crazy… we’ve thrown Nanopore, Illumina, and PacBio data …

Job posting for Nanopore bioinformatics at NASA

Just got pointed to this really awesome sounding job posting at NASA.   Text below: Job Description Bioinformatics Scientist – 1079705 The Microbiology Laboratory at the NASA Johnson Space Center is seeking a highly motivated individual to fill a bioinformatics research position. The goal of the laboratory is to mitigate microbial risk to crew health, …

Quick journal club post on Legionella and Mycobacterium in premise plumbing

Came across this relevant article today; “The sporadic nature of Legionella pneumophila, Legionella pneumophila Sg1 and Mycobacterium avium occurrence within residences and office buildings across 36 states in the United States“.   Abstract Aim Premise plumbing may disseminate the bacteria Legionella pneumophila and Mycobacterium avium, the causative agents for legionellosis and pulmonary nontuberculous mycobacterium disease …