From genomes to phenotypes: Traitar, the microbial trait analyzer

There is an increasing number of studies with a large number genomes recovered from isolate, metagenome, or single cell sequencing. To bridge the gap between the available genome sequences and available phenotype information, we have developed Traitar, a bioinformatics software to phenotype bacteria based on their genome sequence (see workflow below) . Traitar includes phenotype models for …

16S rRNA Sequencing Using the Oxford Nanopore Minion

There has been some interest in our recent preprint describing Oxford Nanopore MinIONTM sequencing for 16S rRNA microbiome characterization and I was asked to write a post for microbenet on this technology. Disclaimers – this paper is a work in progress – our paper has not yet been peer-reviewed and we are continuing to revise …

New papers on Microbiology of the Built Environment, January 29, 2017

Microbes indoors Building-related symptoms are linked to the in vitro toxicity of indoor dust and airborne microbial propagules in schools: A cross-sectional study – JT Salin – Environmental Research ($41.95) We examined whether the in vitro toxicity of indoor samples from school buildings was associated with work-related health symptoms (building-related symptoms, BRS). Administrators of the Helsinki …

New papers on Microbiology of the Built Environment, January 21, 2017

  Microbes in the house and office A survey of xerophilic Aspergillus from indoor environment, including descriptions of two new section Aspergillus species producing eurotium-like sexual states – Cobus M. Visagie – MycoKeys (OA) Xerophilic fungi grow at low water activity or low equilibrium relative humidity and are an important part of the indoor fungal …

Paper of possible interest: Microbial analysis of Heating systems’ surfaces 

Just a quick post – this may be of interest to some: An analysis of experimental investigation focused on microbial pollution of heated was carried out for heating systems installed in different types of buildings as residential houses and civil buildings. The results point on importance of maintenance and cleaning the heating systems for quality …

Humans as collectors and emitters of environmental microbes

As part of the Healthy Buildings 2015 America Conference, there was a technical session on Indoor Microbiome Research where we discussed strategies on, among other things, how to sample and analyze bioaerosols using modern high throughput sequencing techniques. In that workshop, we did a small exercise highlighting the potential for humans to transport microbes into …

What kind of DNA lingers on ATM keypads? Your food, your skin microbes…and (maybe) parasites

Amidst the November/December holiday chaos, myself and co-authors were proud to witness the publication of a neat new paper focused on ATM keypads in New York City. Yes, just like all other surfaces in the Built Environment, those ATM keypads are harboring lots of microbes and bits of orphaned DNA! This ATM keypad study was work that …

The concept of hygiene and the human microbiome.

(This post was written by Roo Vandegrift at the University of Oregon) I was recently asked to spearhead the writing of a review centered around the interaction between the concept of hygiene and our increasingly nuanced understanding of the human skin microbiome for the Biology and the Built Environment (BioBE) Center at the University of …

New papers on Microbiology of the Built Environment, January 7, 2017

Microbes around the house Editorial: An emerging paradox: Toward a better understanding of the potential benefits and adversity of microbe exposures in the indoor environment – J. Mensah-Attipoe – Indoor Air (OA) In order to further explore indoor microbial exposures and their associated health effects, and to help establish research agenda priorities, a two-day workshop to …

Upcoming National Academies Study on Legionella in Drinking Water Systems

Just got this from the a representative of the National Academy of Sciences who asked me to post here. UPDATED June 13, 2017 (based on email from NAS) Scope of work: An ad hoc committee of The National Academies will review the state of science with respect to Legionella contamination of water systems and issue …