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In this issue of microBEnet News, we are featuring the portion of our site dedicated to  Citizen Science.   On this page you will find links to projects as well as examples of protocols, kits and consent forms. MicroBEnet is always seeking new information and projects. If your lab is involved in Citizen Science, please share what you know about this valuable aspect of scientific research.


MicroBEnet Blogs

A brief summary of the recent topics posted on microBE.net  


Posts highlighting People Behind the Science:


Posts related to Sloan:


Notable Posts:


There was also an eclectic mix of topics covered including meningitis, bacterial concrete, MRSA, growing houses,  navel gazing, toxicity of indoor mold, chickens, asthma,  moldy documents, bacterial snow, and Christmas trees.



People Behind the Science
People Behind the Science


UC Davis undergraduate students in a research experience with built environment genomes.   




Complete video interview can be seen here.  


Built Environment Genomes

UC Davis Undergraduate Research Experience


People spend over 90% of their time indoors, yet our understanding of the microbiology of the built environment is surprisingly shallow.


To address this, the Alfred P. Sloan Foundation has funded a multi-year program focused on fundamental research in this area.


This video describes an undergraduate research project undertaken with funding from the Sloan Foundation.   The goals of this project were two-fold.


Firstly, to produce a number of sequenced reference genomes from the built environment, in order to facilitate ongoing metagenomic studies.   Secondly, to provide a unique research experience for undergrads while demonstrating the feasibility of microbial genome sequencing at this educational level.


To accomplish this we isolated, cultured, and identified bacteria from a variety of built environments. We then selected candidates for sequencing, prepared DNA libraries and sequenced the genomes. This was followed by genome assembly, annotation, and publication of the results.


To begin, we collected samples from numerous places in the built environment including homes, offices, and vehicles.


Bacteria were cultured in rich media, and grown at a variety of temperatures. Once single colonies were established by dilution streaking, overnight cultures were grown.


This was followed by isolation of DNA, then amplification of the 16S ribosomal RNA gene in order to establish the identity of the bacteria. You can think of this gene sequence as a "barcode" for identifying organisms.


Once a large number of bacteria had been isolated, we selected candidates for sequencing. Our primary considerations were that they had never been sequenced and that they might play a role in the microbial ecology of the built environment.


This was followed by paired-end Illumina library construction and sequencing here at UC Davis.


Once the sequencing was complete, the students had to make the difficult shift from being lab biologists to bioinformaticians.


They began with genome assembly using the a5 assembly pipeline and an assessment of the quality of the assembly.   This was followed by annotation of the genomes using RAST, which is a program that predicts the presence and function of genes in the sequence.


From this point the students branched out. They created phylogenetic trees to see where their bacteria fit in, they performed comparative genomics to other close relatives that had been sequenced, and they dug deeper into the biochemistry as predicted by the annotation.


Results and data are currently being condensed into a series of genome papers, authored by the students themselves.


Along the way these students got to experience all the ups and downs of science; contamination, failure of reagents, broken machines, inexplicable results, and fear of the command line.  


At the end of the day however, they walked away with a unique research experience and a feeling that they had really contributed to the body of scientific knowledge.


And we had plenty of fun along the way...


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Featured Articles

Well, the meningitis outbreak tied to steroid injections gets scarier and scarier by the day: Poor Sanitation Found at Pharmacy Linked to Meningitis Outbreak - NYTimes.com. One of the latest pieces of news is that the pharmacy that was "compounding" the steroids for injection appears to have been a "microbiology of the built environment" nightmare. Some key pieces of detail from this NY Times story:


   "A federal inspection ... found greenish-yellow residue on sterilization equipment, surfaces coated with levels of mold and bacteria that exceeded the company's own environmental limits, and an air-conditioner that was shut off nightly despite the importance of controlling temperature and humidity."


   "... 83 out of 321 vials ... contained "greenish black foreign matter" and another 17 vials had "white filamentous material."


   "... surfaces in the clean rooms contaminated with either bacteria or mold exceeding the levels at which the company's own procedures called for remedial measures. In some cases, there were so many bacteria or fungi in a sample that the whole testing dish was overrun with a so-called overgrowth."


and more.


All of this to me is yet another reason why we need to know more about the microbial ecology in buildings. Although clearly one solution to the problems described here is to be more careful and cleaner, it is also possible that better design of buildings where drugs are produced to reduce some of the contamination risks.

French archive employees handling moldy documents were found to be more likely to experience headaches, fatigue, eye or throat irritation, coughing, and rhinorrhea (stuffy nose) than their co-workers breathing the same air but not handling moldy documents . The culture and qPCR-based analysis of air samples showed Penicillium chrysogenum, Cladosporium sphaerospermum, and Aspergillus versicolor were the three main fungi found in terms of frequency and quantity in air and dust samples in the ten French archives where the research was done. The strongest effects were seen in frequency of eye irritation and coughing. Other symptoms included throat irritation, fatigue, and rhinorrhea. Workers in the archives with the highest mold concentrations in air and dust reported no more symptoms than workers in the other archives. It appears that handling the moldy documents was the key factor in symptom prevalence.

The researchers recommend that future studies also consider concentrations of fungal metabolites and chemical substances as potential confounders in investigations of the effects of molds.

The article is available in the current issue of Indoor Air 22 (6) 514-512. (ISIAQ members have free access through their membership by logging in to the ISIAQ web site).


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