Story Behind the Paper: A comparison of methods used to unveil the genetic and metabolic pool in the built environment.

­­(This is a blog post by Cinta Gomez-Silvan, the first author on this paper) Story behind the paper: A comparison of methods used to unveil the genetic and metabolic pool in the built environment.   It seems pretty obvious that in the field of microbial ecology we need to understand how living microorganism interact. Nevertheless, …

Paper of Interest: Drinking water microbiome assembly induced by water stagnation

Just came across this paper today from the University of Illinois, “Drinking water microbiome assembly induced by water stagnation“.  Looks like a good study on actual residential tap water systems.   Was also happy to see that the press release didn’t dip too much into scare-mongering.   Worth a read by folks interested in water systems.  Abstract …

The Bath Toy Microbiome

I just got pointed to this article today “Ugly Ducklings – the dark side of plastic materials in contact with potable water“, along with the accompanying commentary “About duck, pipes, and microbiomes“.  I think this is a fascinating study for a few reasons.  Firstly, like probably most parents, I observed and wondered about the biofilms …

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 …

Watercolours “created” by bacteria (sort of, but still really cool)

OK this is cool :This watercolour painting was created by artistic bacteria | WIRED UK Though not quite what the headline says. From the article With Park’s guidance, Roberts placed Serratia marcescens – a red pigmented bacteria – on to agar plates previously painted with watercolours. When coming into contact with the paint, the bacteria …

Another RDP for microbiologists to check out ..

Just came across this paper on bioRXiv. A Measure of Open Data: A Metric and Analysis of Reusable Data Practices in Biomedical Data Resources by Seth Carbon, Robin Champieux, Julie McMurry, Lilly Winfree, Letisha R Wyatt, and Melissa Haendel Abstract Data is the foundation of science, and there is an increasing focus on how data can be reused …

One last call for help with Sloan-funded MoBE paper collection

Back in September we posted a call for help with our “comprehensive” database of publications resulting from the Alfred P. Sloan Foundation program in the Microbiology of the Built Environment.   We’ve tried database scanning, begging people for help, public posting, manually digging through Google Scholar, grant reports, etc.  Our hope is to use this collection …

Paper of possible interest: KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples

This may be of interest to people out there.  Source: KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples | mSystems Abstract: Microbiome analyses of low-biomass samples are challenging because of contamination and inefficiencies, leading many investigators to employ low-throughput methods with minimal controls. We developed a new automated protocol, KatharoSeq (from the Greek katharos [clean]), …

Upcoming reddit “Ask Me Anything” #AMA on the Microbiology of the Built Environment

This Friday, March 16th at 1:00pm (EDT), the folks over at the National Academy of Sciences (NAS) will be participating in a reddit AMA (Ask Me Anything) on the Microbiology of the Built Environment.  The featured experts are Diane Gold, Vivian Loftness, and Jordan Peccia.  All three were committee members on the NAS group that …