I wrote a post on the Seagrass Microbiome website yesterday about my struggles with fungal ITS sequencing data which I thought I’d share here as well in case anyone is looking to jump into the fungal fray. To summarize: changing the default method of the QIIME assign_taxonomy.py script from “UCLUST” to “blast” dramatically increased the …
Quick post here. I discovered this a few weeks ago but just have not had time to write about it in detail or even scrutinize it exceptionally carefully but it seems of interest to the theme here at microBEnet: Invisible City Life: The Urban Microbiome | The Nature of Cities. By Marina Alberti from the University of …
One activity we have been hoping to do more of here at microBEnet is to catalyze the development and sharing and evaluation of course materials (preferably free and open) for teaching about microbiology of the built environment. I confess this is just not my area of expertise so I am going to be writing a …
Laura Williams recently posted a great writeup of some of the materials she covered with her microbiology class – specifically focused on microbes in the built environment. It turns out they were reading one of the papers we recently published (!) about how humans can influence the microbes indoors by the way we interact with …
When drainage systems fail, a lot of undesirable effects may follow, from leaks that cause mold to fecal-laden water contaminating groundwater and houses. A study from the Heriot Watt University in Edinburgh, Scotland found yet another concern we should have about broken or inadequate building drainage. Airflows in pipes can contain aerosolized pathogens and then escape into …
Finally got around to reading “Impacts of Flood Damage on Airborne Bacteria and Fungi in Homes after the 2013 Colorado Front Range Flood” from the labs of Shelly Miller and Noah Fierer. The massive floods in 2013 provided the researchers with an opportunity to examine the lingering effects of flood damage, even post remediation. Ideally …
This semester, I’m teaching a microbiology course for non-majors. The course was originally designed to focus on microbial diseases and public health, but as I crafted my version of the course, I wanted to broaden our view of microbiology and include the fascinating field of microbiome research. In our first few weeks (relentless winter weather …
I. Introduction There is an oft-cited hierarchy for data, wherein ideally it should flow: Data –>Information –>Knowledge –>Wisdom (DIKW). Just because you have data, it takes some processing to get quality information, and even good information is not necessarily knowledge, and knowledge often requires context or application to become wisdom. For example, you could have …
The Alfred P. Sloan foundation has approved a grant to organize a workshop on indoor microbiome in Finland in Fall 2015. The workshop is designed for a scientific exchange including a workshop and researcher exchanges that will bridge the Sloan grantees in US and Canada with the research groups in Finland and neighboring countries. The workshop organizing committee, …
I’m currently attending the inaugural conference of the Citizen Science Association… “Citizen Science 2015“. Over 650 participants from around the world have arrived in San Jose to talk about all the various flavors and implications of citizen science. It’s been a fascinating conference so far, not least because there’s very little agreement on what the …