I’m working on a manuscript where we analyze OTU co-occurrence patterns using network analyses as well as the traditional approaches (ordination, alpha diversity, etc.). This means that we have to include some equations in our methods and so for the first time, I am using Authorea and LaTeX. I am getting used to working with the …
Last week I had the opportunity to present a lecture on the history of DNA sequencing in Jonathan Eisen’s EVE 161 Microbial Phylogenomics course. This lecture uses Elaine Mardis’ excellent review papers on the next generation sequencing methods as a guide (and required reading). You can see videos of both Dr. Mardis and Dr. Eisen presenting lectures on this topic. …
Here are my notes from day 3 of the Mothur Workshop that is taught by Pat Schloss (pdschloss at gmail.com) at a hotel that is conveniently located near the Detroit airport. Of all of the bioinformatic workshops I have attended, this group of students was my favorite so far. We had a lot of fun …
Here are my notes from day 2 of the Mothur workshop taught by Pat Schloss (pdschloss at gmail.com) in December 2015. For those who are interested in learning to use Mothur for microbiome studies, Pat will be teaching another one in February. Mothur is better for bacterial characterization than eukaryotes because the sequences are aligned before OTU clustering. This …
Pat Schloss (pdschloss at gmail.com) offers excellent workshops on the Mothur software for analyzing 16S rRNA data for bacteria. He’s just announced the next one (February 8 to 10, 2016 near the Detroit airport). I had the pleasure of attending the December workshop. A diverse and international group attended the workshop, with many folks who are interested in the human microbiome. …
Here is a fun recent article by Vilanova et al. on the coffee machine bacteriome (open access in Nature’s Scientific Reports) that made me wonder why didn’t we think of doing this. In this study, the authors sampled the inner drip tray (below the capsule container) of nine different Nespresso capsule coffee machines. They found that Enterococcus sp. and Pseudomonas sp. were abundant in most …
Sometimes efforts to be environmentally friendly can give rise to microbial challenges. This was nicely described by Katie Dahlhausen in her recent post about water quality about green buildings. Other examples include observations that Legionella pneumophila can be contracted from shower heads and the use of low flow shower heads and lower water temperatures may increase its transmission. Likewise, wastewater (e.g., Environmental and …
More good news for animal lovers! A recent study on the effects of exposure to dogs and farm animals on childhood asthma was just published in JAMA Pediatrics. The article is entitled Early Exposure to Dogs and Farm Animals and the Risk of Childhood Asthma by T. Fall, C. Lundholm, A.K. Örtqvist, K. Fall, F. Fang, Ã…. Hedhammar, O. Kämpe, E. Ingelsson, C. Almqvist. Here is the …
Last year I posted here about how amazing termite mounds are and how they often tilt towards the equator. Termites make them from saliva, poop and soil, and use them to regulate temperature and humidity and farm fungus. In addition to what must be some fascinating microbiology, we could learn a lot about how to design …
Antibiotic resistance is a global problem, threatening both human and animal health. A recent study shows that antibiotic resistance has spread into wildlife populations in Chobe National Park, a spectacular park located along the Chobe River in Botswana. In this region, humans and wildlife live in close proximity and significant antimicrobial resistance occurs in human populations. In a study published in the …