Recent Built Environment Microbiology papers, July 6 edition

Several new papers about microbes and the built environment came out or came up in my searches this weekend, so time for another installment. Since one of the papers is about prison workers, you could play Johnny Cash’s Folsom Prison Blues while reading this post.

Open Access: Coccidioides Exposure and Coccidioidomycosis among Prison Employees, California, United States – Marie A. de Perio – Emerging Infectious Diseases

Screen Shot 2015-07-06 at 01.41PM, Jul 06Responding to a request by corrections agency management, we investigated coccidioidomycosis in prison employees in central California, a coccidioidomycosis-endemic area. We identified 103 cases of coccidioidomycosis that occurred over 4.5 years. As a result, we recommended training and other steps to reduce dust exposure among employees and thus potential exposure to Coccidioides. ….. We .. could not determine if each confirmed coccidioidomycosis case in an employee was because of exposure at work or outside of work….Almost all interviewed employees at each prison reported spending time outdoors at work, and almost one third, specifically custody and plant operations employees, reported work involving soil disruption.

Open Access: Bacteriological assessment of the hospital environment in two referral hospitals in Yaoundé-Cameroon – Kamga Hortense Gonsu – Pan African Medical Journal

Screen Shot 2015-07-06 at 01.46PM, Jul 06The aim of this study was to identify potential bacteria reservoirs that may be responsible for nosocomial infection in surgical services in the Yaoundé University Teaching Hospital (YUTH) and the Central Hospital Yaoundé (CHY)…..a total of 143 surface samples were collected. Bacteria were isolated in all surfaces except from one trolley sample and a surgical cabinet sample. The predominant species in all services was coagulase negative Staphylococcus (CNS). The average number of colonies was132. 82CFU/25cm2. The bacteria isolated in the air were similar to those isolated from surfaces. From the 16 water samples cultured, an average of 50.93 CFU/100ml bacteria were isolated. The distribution of isolated species showed a predominance of Burkholderia cepacia.

Paid AccessGreen spaces and cognitive development in primary schoolchildren – Payam Dadvand – PNAS. This is not a microbiology paper, but interesting enough to include here.

Screen Shot 2015-07-06 at 01.52PM, Jul 06This study aimed to assess the association between exposure to green space and measures of cognitive development in primary schoolchildren. This study was based on 2,593 schoolchildren in the second to fourth grades (7–10 y) of 36 primary schools in Barcelona, Spain (2012–2013)….We assessed exposure to green space by characterizing outdoor surrounding greenness at home and school and during commuting by using high-resolution (5 m × 5 m) satellite data on greenness (normalized difference vegetation index). Multilevel modeling was used to estimate the associations between green spaces and cognitive development….Our study showed a beneficial association between exposure to green space and cognitive development among schoolchildren that was partly mediated by reduction in exposure to air pollution.

Paid Access: House microbiotas as sources of lactic acid bacteria and yeasts in traditional Italian sourdoughs – Fabio Minervini – Food Microbiology

Screen Shot 2015-07-06 at 01.59PM, Jul 06This study aimed at understanding the extent of contamination by lactic acid bacteria (LAB) and yeasts from the house microbiotas during sourdough back-slopping. Besides sourdoughs, wall, air, storage box, dough mixer and flour of four bakeries were analyzed. Based on plate counts, LAB and yeasts dominated the house microbiota. Based on high throughput sequencing of the 16S rRNA genes, flour harbored the highest number of Firmicutes, but only few of them adapted to storage box, dough mixer and sourdough. Lactobacillus sanfranciscensis showed the highest abundance in dough mixer and sourdoughs. Lactobacillus plantarum persisted only in storage box, dough mixer and sourdough of two bakeries. Weissella cibaria also showed higher adaptability in sourdough than in bakery equipment, suggesting that flour is the main origin of this species. Based on 18S rRNA data, Saccharomyces cerevisiae was the dominant yeast in house and sourdough microbiotas, excepted one bakery dominated by Kazachstania exigua. The results of this study suggest that the dominat species of sourdough LAB and yeast dominated also the house microbiota.

Paid AccessMicrobial diversity in bioaerosol samples causing ODTS compared to reference bioaerosol samples as measured using Illumina sequencing and MALDI-TOF – Anne Mette Madsen – Environmental Research

Screen Shot 2015-07-06 at 01.56PM, Jul 06The aim of this paper is to gain knowledge on the bacterial and fungal communities in dust causing organic dust toxic syndrome (ODTS) and in reference dust not causing ODTS. Bacterial and fungal communities were described in personal exposure samples from grass seed workers developing ODTS, in dust generated from grass seeds causing ODTS and in dust generated from reference seeds not causing ODTS. … After only a few hours of unloading and cleaning of the lot of problematic grass seeds workers began to experience airway symptoms and flu-like symptoms along with malaise. … The sequencing data revealed more than 150 bacterial and 25 fungal genera present in each sample. Streptomyces spp., Aspergillus fumigatus and Rhizopus microsporus were dominating in the dust causing ODTS but not in the reference dust.

Paid Access, but you can request full text at Research Gate: Concentration and determinants of molds and allergens in indoor air and house dust of French dwellings – Arnaud Dallongeville – Science of the Total Environment. Note: Supplementary materials 1 and 2 appear to have been switched.

Screen Shot 2015-07-06 at 02.06PM, Jul 06The aims of this study were to assess the concentrations of common molds in indoor air and floor dust and the concentrations of house dust mite, cat and dog allergens in mattress dust in French dwellings, and to assess predictors of these concentrations. A sample of 150 houses in Brittany (western France) was investigated. … Multivariate linear models for mold levels, explaining up to 62% of the variability, showed an influence of the season, of the age of the dwelling, of aeration habits, presence of pets, smoking, signals of dampness, temperature and relative humidity. Allergens in the dust of the mattress were strongly related to the presence of pets and cleaning practices of bedsheets, these factors accounting for 60% of the variability. This study highlights ubiquitous contamination by molds and underlines complex interaction between outdoor and indoor sources and factors.

This Bacteria-Slaying Light Fixture Is Perfectly Safe For Humans – Andrew Liszewski – Gizmodo. Note: I wonder what effect this would have on the normal skin microbiome of healthcare workers and patients. I am not sure if the qualification “safe for patients or caregivers” is really true if you take the effects of the light on our skin symbionts into account.

Screen Shot 2015-07-06 at 02.11PM, Jul 06Bacteria-killing ultraviolet lights can sterilize everything from toothbrushes to bedsheets. But a new type of light fixture called the Indigo-Clean is able to wipe out those same dangerous pathogens while still being safe for patients or caregivers in a hospital. … To anyone in the room, the HINS light looks blueish in color, which might be slightly annoying for those who prefer warmer hues. But it’s more than just an issue of preferable color temperature for bacteria and other harmful micro-organisms lurking in the room. The HINS light is absorbed by molecules inside them which starts a chemical chain reaction that stops their growth, prevents reproduction, and eventually kills them.

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Air Quality on Airplanes

Happy 4th of July! Given how many people in the US are travelling this long weekend, this article about air quality on airplanes caught my eye. And, while you are reading this post, may I suggest the following song: B.o.B – Airplanes ft. Hayley Williams of Paramore ?

In this short article called Air Quality on Airplanes 4th of July Air Travel Update, Charlie Seyffer from Camfil, a manufacturer of air filters talks about the recycling and treatment of air on airplanes.

The recirculated air is passed through industrial grade HEPA air filters that are capable of removing particles that are hundreds of times smaller than the eye can see. Airliner manufacturer’s say that between 94 and 99.9 percent of airborne microbes are captured, and that there is a total changeover of all of the cabin air every two or three minutes.

Maybe it’s the remaining 6 percent of microbes that are still being blown into my face, but I often catch a cold within hours of air travel. Or is it just the fact that in an airplane with 300 passengers there is always a person near your seat who has a cold and will sneeze on you. Charlie Seyffer offers the following advice:

To reduce your probability of breathing in these contaminants turn the air vent above your seat on and aim the clean air current slightly in front of your face so that germs from infectious passengers that are nearby will be redirected away from you.

So there you have it. The article also links to a Camfill video about this topic. Happy travels and don’t catch a cold.

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Inside Philanthropy covers the BioBE Center and Sloan MoBE Program 

Just a quick post.  There is a story of interest at “Inside Philanthropy” on the Sloan Foundation MoBE (microbiology of the built environment) Program and the renewal of the BioBE center project.  See Sloan’s Deep (and Kind of Gross) Probe Into the Microbes Crawling All Around You – Inside Philanthropy: Fundraising Intelligence – Inside Philanthropy

Although I would like to debate the calling it kind of gross, I will let that slide.

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Recent Built Environment Microbiology papers, July 2 edition

Just in time for the long weekend (where we all will be catching up with the literature – ahem), here is another collection of recent papers about microbiology of the built environment. The first paper is about the mattress microbiome, so the video song Jump from Glee came to mind (“Here at Mattress Land we believe that mattresses are not just for sleeping and fornicating anymore.”).

First, some papers about the great indoors:

Open Access: Bacterial Exposures and Associations with Atopy and Asthma in Children – Maria Valkonen – PLOS ONE

Screen Shot 2015-07-02 at 04.56PM, Jul 02DGGE was applied to mattress dust samples of farm children and control children…. Quantitative DNA based assays (qPCR) for four bacterial groups were applied on the dust samples to seek quantitative confirmation of associations indicated in DNA fingerprinting….. Several statistically significant associations between individual bacterial signals and also bacterial diversity in DGGE and health outcomes in children were observed. The majority of these associations showed inverse relationships with atopy, less so with asthma. Also, in a subsequent confirmation study using a quantitative method (qPCR), higher mattress levels of specifically targeted bacterial groups – Mycobacterium spp., Bifidobacteriaceae spp. and two different clusters of Clostridium spp. – were associated with a lower prevalence of atopy.

Paywalled: Intensive care unit environmental surfaces are contaminated by multidrug-resistant bacteria in biofilms: combined results of conventional culture, pyrosequencing, scanning electron microscopy, and confocal laser microscopy – H. Hu – The Journal of Hospital Infection

Screen Shot 2015-07-02 at 05.28PM, Jul 02The intensive care unit (ICU) of a tertiary referral hospital was decommissioned and the opportunity to destructively sample clinical surfaces was taken in order to investigate whether multidrug-resistant organisms (MDROs) had survived the decommissioning process and whether they were present in biofilms….Multidrug-resistant bacteria were cultured from 52% (23/44) of samples cultured. S. aureus PCR was positive in 50%. Biofilm was demonstrated in 93% (41/44) of samples by CLSM and/or SEM. Pyrosequencing demonstrated that the biofilms were polymicrobial and contained species that had multidrug-resistant strains.

Open Access: Exposure to soil, house dust and decaying plants increases gut microbial diversity and decreases serum immunoglobulin E levels in BALB/c mice – Dongrui Zhou – Environmental Microbiology

Screen Shot 2015-07-02 at 05.12PM, Jul 02…we raised BALB/c mice under three distinct environmental conditions: a specific pathogen-free animal room (SPF), a general animal room (XZ) and a farmhouse (JD). … Using high-throughput sequencing of the 16S rRNA gene, we found that each mouse group had a specific structure of the gut microbial community. Groups JD and XZ harboured a significantly more diverse and richer gut microbiota than did group SPF….. Total serum immunoglobulin E (IgE) levels were significantly lower in groups XZ and JD than in group SPF.

PaywalledTriclosan and prescription antibiotic exposures and enterolactone production in adults – Margaret A. Adgent – Environmental Research

Screen Shot 2015-07-02 at 05.16PM, Jul 02We examined urinary triclosan and enterolactone for 2005-2008 U.S. National Health and Nutrition Examination Survey subjects, aged ≥20 years (n=3041). We also examined the association between prescription antibiotic use and enterolactone to confirm its susceptibility to changes in bacterial composition of the body….Triclosan was detected in 80% of subjects …, while enterolactone was detected in >99% of subjects….Any antibiotic use, as compared to no antibiotic use, was associated with significantly lower enterolactone…, with no sex-specific effects.

Here are some new papers about drinking/recreational water:

Open Access: Prevalence of tetracycline resistance genes among multi-drug resistant bacteria from selected water distribution systems in southwestern Nigeria – Ayodele. T. Adesoji – Annals of Clinical Microbiology and Antimicrobials

Screen Shot 2015-07-02 at 05.01PM, Jul 02Multi-drug resistant (MDR) bacteria, including resistance to tetracycline, were isolated from treated and untreated water distribution systems in southwest Nigeria. MDR bacteria were resistant to >3 classes of antibiotics based on break-point assays. Isolates were characterized using partial 16S rDNA sequencing and PCR assays for six tetracycline-resistance genes. Plasmid conjugation was evaluated using E. coli strain DH5α as the recipient strain…… This study found a high prevalence of plasmid-encoded tet(A) among Alcaligenes isolates, raising the possibility that this strain could shuttle resistance plasmids to pathogenic bacteria.

Open Access Review: Waterborne Viruses: A Barrier to Safe Drinking Water – Aimee M. Gall – PLOS Pathogens

Screen Shot 2015-07-02 at 05.18PM, Jul 02No abstract, but structured around the following questions:
– What is the Global Status of Access to Safe, Pathogen-Free Drinking Water?
– Are Waterborne Viruses a Particular Concern?
– What is the State of the Art for Control of Viruses in Water?
– What are the Barriers toward Disinfecting Viruses in Drinking Water?
– What is the Future of Waterborne Virus Research?

PaywalledMathematical Model of Dynamic Behavior of Microbial Desalination Cells for Simultaneous Wastewater Treatment and Water Desalination – Qingyun Ping – Environmental Science & Technology

Screen Shot 2015-07-02 at 05.23PM, Jul 02This work presents a mathematical model to simulate dynamic behavior of MDCs for the first time through evaluating multiple factors such as organic supply, salt loading, and current generation. Ordinary differential equations were applied to describe the substrate as well as bacterial concentrations in the anode compartment. Local sensitivity analysis was employed to select model parameters that needed to be re-estimated from the previous studies….It was able to predict the response of the MDC with time under various conditions, and also provide information for analyzing the effects of different operating conditions.

Open Access: Constitutive presence of antibiotic resistance genes within the bacterial community of a large subalpine lake – Andrea Di Cesare – Molecular Ecology

Screen Shot 2015-07-02 at 05.31PM, Jul 02Although of diverse origin, the persistence of ARGs in aquatic environments is highly influenced by anthropic activities, allowing potential control actions in well-studied environments. However, knowledge of abundance and space-time distribution of ARGs in ecosystems is still scarce. Using qPCR, we investigated the presence and the abundance of twelve ARGs … at different sampling sites, depths and seasons, in Lake Maggiore, a large subalpine lake, and in the area of its watershed. We then evaluated the correlation between each ARG and a number of ecological parameters in the water column in the deepest part of the lake.

Finally, some papers about microbiology of corroded or polluted sites:

Open Access: Microbially influenced corrosion communities associated with fuel-grade ethanol environments – Charles H. D. Williamson – Applied Microbiology and Biotechnology

Screen Shot 2015-07-02 at 05.03PM, Jul 02Reports of suspected MIC in systems handling FGE and water prompted an investigation of the microbial diversity associated with these environments. Small subunit ribosomal RNA gene pyrosequencing surveys indicate that acetic-acid-producing bacteria (Acetobacter spp. and Gluconacetobacter spp.) are prevalent in environments exposed to FGE and water. Other microbes previously implicated in corrosion, such as sulfate-reducing bacteria and methanogens, were also identified.

PaywalledAn in-depth analysis of actinobacterial communities shows their high diversity in grassland soils along a gradient of mixed heavy metal contamination – Tomáš Větrovský – Biology and Fertility of Soils

Screen Shot 2015-07-02 at 05.06PM, Jul 02Several previous studies indicated that Actinobacteria may be enriched in soils with elevated content of heavy metals. In this study, we have developed a method for the in-depth analysis of actinobacterial communities in soil through phylum-targeted high-throughput sequencing and used it to address this question and examine the community composition in grassland soils along a gradient of heavy metal contamination (Cu, Zn, Cd, Pb). The use of the 16Sact111r primer specific for Actinobacteria resulted in a dataset obtained by pyrosequencing where over 98 % of the sequences belonged to Actinobacteria.


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Update on An Introduction to Applied Bioinformatics

About a year ago, I posted here about my free, interactive text: An Introduction to Applied Bioinformatics. The project is now Sloan-funded (as of April 2015), so there will be a lot of changes and expanded content coming down the pipe over the next few months.

One major change that went in recently, and which I think will be of general interest to anyone who uses IPython (Jupyter) Notebooks as part of their bioinformatics workflows, is that the content is now written in markdown and converted to IPython Notebooks at build time. This has a lot of benefits, including that it’s vastly easier for readers to submit changes to content, and for me to review and merge those changes (watch a five-minute video showing how this works). I also think that it will be much easier to write content this way, but time will tell…

I wrote a post about this change for the Mozilla Science Lab blog. You can find that here. Enjoy!

Greg Caporaso

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The case of the warehouse mystery pooper

Suppose you owned a warehouse that serves as a distribution hub for grocery stores, and you find that every so often, someone is pooping in your warehouse. Not only is that insulting and obnoxious, but it also has the potential to make a lot of people very sick. You take the shift schedule, and you correlate it with the times the mystery pooper has struck. You find that there are two employees who had the opportunity to do the dastardly deed.

You might reason something like this : Poop has human DNA in it. Why not tell the employees they have to submit buccal swabs for testing if they want to keep their jobs? After all, if they weren’t the ones pooping all over the place, the test will exonerate them. Seems reasonable, yes?

Turns out, no. This sort of practice is prohibited under the Genetic Information Nondiscrimination Act (GINA). The warehouse operator argued, unsuccessfully, that the law only applies to genetic tests that could reveal health information. The US District Court found otherwise, and the grad jury awarded damages of $250,000 and $225,000 to each of the employees. Moreover, the grand jury was asked,

Do you find from a preponderance of the evidence that Atlas Logistic Group Retail Services (Atlanta), LLC acted with malice or with reckless indifference to the Plaintiffs’ federally protected rights such that punitive damages should be assessed against them?

They concluded that yes, the employer had acted with malice or reckless indifference to federally protected rights, and levied $1.75 million in punitive damages. This is probably worth pondering before you go around playing CSI without a badge and a warrant.

But of course, what you are really wondering is if the DNA tests unmasked the mystery pooper. Turns out, no. If either of the two employees were responsible, they were enterprising enough not to use their own poop.

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Recent Built Environment Microbiology papers, June 21 edition

What’s new in the built environment microbiology literature? Here is my selection of the new papers from the past 2 weeks. And, since one of them is about the microbiome of gyms, I thought “Pump It” by the Black Eyed Peas would fit nicely with this post. And I apologize that only two of these papers are Open Access. Dear microbiologists of the world, please make your papers accessible for all, by only publishing in the Open Access format! Thank you… Let’s start.

Open AccessAthletic equipment microbiota are shaped by interactions with human skin – Mariah Wood – Microbiome

Screen Shot 2015-06-21 at 3.13.34 PMBacterial assemblages associated with different surfaces in three athletic facilities, including floors, mats, benches, free weights, and elliptical handles, were sampled every other hour (8 am to 6 pm) for 2 days. Surface and equipment type had a stronger influence on bacterial community composition than the facility in which they were housed. Surfaces that were primarily in contact with human skin exhibited highly dynamic bacterial community composition and non-random co-occurrence patterns, suggesting that different host microbiomes—shaped by selective forces—were being deposited on these surfaces through time. However, bacterial assemblages found on the floors and mats changed less over time, and species co-occurrence patterns appeared random, suggesting more neutral community assembly.

Paid AccessProfiling microbial community structures across six large oilfields in China and the potential role of dominant microorganisms in bioremediation – Weimin Sun – Applied Microbiology and Biotechnology

Screen Shot 2015-06-21 at 3.17.31 PMNineteen oil-contaminated soil samples and five uncontaminated controls were taken from six major oilfields across different geoclimatic regions in China to investigate the spatial distribution of the microbial ecosystem. Microbial community analysis revealed remarkable variation in microbial diversity between oil-contaminated soils taken from different oilfields. Canonical correspondence analysis (CCA) further demonstrated that a suite of in situ geochemical parameters, including soil moisture and sulfate concentrations, were among the factors that influenced the overall microbial community structure and composition. ……Euryarchaeota may play an important ecological role in some oil-contaminated soils.

Book chapter, paid access only: Bacteria and Fungi in Green Roof Ecosystems – Krista L. McGuire – Green Roof Ecosystems

Screen Shot 2015-06-21 at 3.20.50 PMMicroorganisms such as fungi and bacteria have been found to be diverse and abundant components of green roof growing substrate and may contribute to some of the other benefits green roofs provide such as the removal of organic pollutants from precipitation. Here, we review several functional groups of microbes that may be useful for understanding in terms of green roof design and maintenance: mycorrhizal fungi, decomposer fungi, endophytes, N-fixing bacteria, and pathogens. These microbes interact with plant species and growing substrate in complex ways that require further investigation. The ecology of these microbial groups should also be considered, including their dispersal rates and how they respond to regional differences such as climate and seasonality.

Paid Access: Impact of disinfectant wipes on the risk of Campylobacter jejuni infection during raw chicken preparation in domestic kitchens – G.U. Lopez – Journal of Applied Microbiology

Screen Shot 2015-06-21 at 3.28.24 PMIn the present study, we conducted a quantitative microbial risk assessment forecasting the exposure to Campylobacter jejuni contaminated surfaces during preparation of chicken fillets and how using a disinfectant-wipe intervention to clean a contaminated work area decreases the risk of infection following the preparation of raw chicken fillet in a domestic kitchen. Using a Monte Carlo simulation of the risk of transferring Camp. jejuni strain A3249, from various surfaces to hands and subsequently transferring it to the mouth was forecasted. The use of a disinfectant-wipe intervention to disinfect contaminated surface area was also assessed. Several assumptions were used as input parameters in the classical Beta-Poisson model to determine the risk of infection. The disinfectant-wipe intervention reduced the risk of Camp. jejuni infection by 2–3 orders on all fomites.

Paid Access: The effects of different hygiene procedures in reducing bacterial contamination in a model domestic kitchen – Elin Røssvoll – Journal of Applied Microbiology

Screen Shot 2015-06-21 at 3.33.55 PMWe report results from two surveys on Norwegian consumers’ cleaning procedures. Laboratory models involving cutting boards, tap handles and mobile phones contaminated with E. coli and S. aureus were used to compare the hygiene efficacy of commonly used cleaning methods together with new technologies (sprays, single use wipes, and chlorinebased disinfectants). Commonly used cleaning methods produced a mean log10 reduction (LR) in contamination of 1.5-2.5. The efficacy could be improved by drying or including a disinfection step (mean LR 3.1-4.6). Cleaning of mobile phones was common and was improved by including humidity (1.5-1.9 mean LR). In many situations, traditional methods used by consumers may be sufficient to hygienically clean surfaces. However, in some situations, such as where there are infected or immune compromised individuals, or where high risk foods are being handled, hygiene practices resulting in higher LR should be recommended.

Open Access:Prokaryotic Diversity in the Rhizosphere of Organic, Intensive, and Transitional Coffee Farms in Brazil – Adam Collins Caldwell – PLOS ONE

Screen Shot 2015-06-21 at 3.36.40 PMThis study aimed to characterize and determine the differences in the prokaryotic soil microbiology of three Brazilian coffee farms: one practicing intensive farming, one practicing organic farming, and one undergoing a transition from intensive to organic practices. Soil samples were collected from 20 coffee plant rhizospheres (soil directly influenced by the plant root exudates) and 10 control sites (soil 5 m away from the coffee plantation) at each of the three farms for a total of 90 samples. Profiling of 16S rRNA gene V4 regions revealed high levels of prokaryotic diversity in all three farms, with thousands of species level operational taxonomic units identified in each farm. Additionally, a statistically significant difference was found between each farm’s coffee rhizosphere microbiome, as well as between coffee rhizosphere soils and control soils. ….many new groups may exist in these samples that can be further studied as potential plant growth-promoting bacteria to improve coffee production while diminishing negative environmental impacts.


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Berkeley balcony collapse: A failure at the intersection of building science and microbiology

I saw the tweet below from James Scott first thing this morning, linking to a NY Times article about the tragic balcony collapse in Berkeley, CA two days ago:

From the article:

The engineers said photographs taken by news organizations, as well as what they had observed, showed that seven joists, or wooden beams, extending from the stucco wall of the apartment, on which the balcony was built, had rotted through. They suggested that construction defects had allowed water to seep into the deck, rather than rolling off the edge of it, leading to the growth of fungus and long-term decay of the wood.

“The most likely scenario is water got into the joint between the balcony and the wall, permeated the joist, sat in there, and then eventually deteriorated the joist where it couldn’t handle any kind of a load,” said Gene St. Onge, a civil and structural engineer based in Oakland, Calif. “It’s fairly clear it’s dry-rotted. The timber had all turned to dust.”

Bernard R. Cuzzillo, a mechanical engineer based in Berkeley, said that from his observation, the joists were “completely rotten. Falling apart rotten. They were soaking in water most of the time they were there.”

The LA Times also has an article this morning, Berkeley balcony collapse puts new focus on wood dry rot, which includes more details on the construction of the building and its balconies and potential paths for failure. From the article:

Wood construction of the balconies is common for low-rise residential buildings. Most often, horizontal beams, or joists, that hold up the floor inside the apartment simply extend through the exterior wall to hold up the deck.

But wood rot, also known as dry rot, can make a beam that appears sturdy porous, enough to crumble on contact, due to the growth of a fungus that feeds on the wood.

There are a variety of ways water could have leaked into the wood joists. “It could’ve been that the door above the balcony didn’t have a proper waterproof seal below it,” St. Onge said. “It could’ve been water coming in from the roof down the interior of the wall. It’s a tricky matter and it takes some investigation to determine where it came from.”

Another possibility is the lack of flashing underneath the door — a piece of angled sheet metal that diverts water draining down the stucco away from the wall.

In general, before the stucco layer is applied during construction, wood balconies can be wrapped in waterproof membranes — like sticky asphalt — and then sealed to the waterproofing of the exterior wall.

Any gaps could allow water to seep in.

The quotes from the LA Times article likely get it right. There was most likely a large source of water in this building that was unable to drain properly, which would have wetted the balcony for a long period of time and allowed sustained fungal growth, which would have fed on the wood and led to rotting and structural failure. If this is indeed the case, this tragic and extremely unfortunate event clearly illustrates the importance of understanding intersections between building science and the microbiology of the built environment.

Water in buildings is something that building scientists, including engineers and architects, spend a lot of time thinking about. Water problems (and solutions) in buildings are complex in practice, yet relatively simple in concept. All buildings have to manage water somehow, and proper drainage is an obvious key element for doing so. But maintaining drainage planes — both during design and construction — is tough to do in practice. As I teach in my Building Enclosure Design course at IIT, the solutions are really more of an art than a science, requiring clear details from engineers and architects, but more importantly, requiring good judgment and understanding by trades and construction teams (as well as strong oversight).

Unfortunately, these kinds of wooden structure balcony failures are all too common. The Building Inspection website InspectAPedia has an entire page devoted to balcony and porch/deck problems: Porch & Deck Ledger Flashing Errors Cause Leaks & Rot. The American Society of Home Inspectors (ASHI) wrote about this common balcony failure back in 2007. A common element of these kinds of failures is typically improper flashing.

Flashing is simple in concept: flashing refers to impervious materials that are installed in critical areas of the building enclosure and designed to serve as a guide for directing water in the direction you would prefer it to go. Generally that direction is away from the building enclosure assembly and away from joints and penetrations through which water almost always finds its way. There are a number of details that have to be done correctly in order for flashing to work properly, including sloping in the correct direction (always slope down and out) and overlapping layers in the correct order (so top layers drain to the bottom layers). Also, individual areas for flashing don’t operate in a vacuum. The entire enclosure has to be treated as a weather resistant barrier system, as a water entry problem at the roofline can just as easily lead to a water/moisture/dampness/mold problem multiple stories below in the basement.

If you’re interested in learning more about moisture management in buildings, there are plenty of resources online. The Building Science Corporation (BSC) has a number of helpful materials on flashing and other strategies for water management. Their 2007 document, Water Management Details, is a great resource to start learning about house wraps, flashings, and windows. They also have a shorter digest from 2006 on draining planes. BSC also has some information on stucco wall construction, the same type of construction used in this Berkeley apartment building. Other trade magazines such as The Construction Specifier have published articles in recent years on waterproofing buildings and ensuring wood balcony durability, as well as GreenBuilder Magazine.

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Should you worry about whether your cat is making you crazy?

Here is a guest post by UC Berkeley junior Alex Martin who is working with us on a study of the Berkeley Animal Shelter

It’s no secret that animals – including humans – serve as a nutrient-rich reservoir for microorganisms. And while the grooming habits of felines may have earned them a reputation as refreshingly clean, just like any other pet, household cats introduce unwanted microorganisms into the homes of their owners. Many of these are harmless or not transmissible to humans; a few are not. One belonging to the latter group is the Toxoplasma gondii, a protozoan that infects cats, humans, and a host of other species (sea otters, dogs, mice, basically all mammals), causing Toxoplasmosis.
Though there is evidence to suggest that a surprisingly high percentage of people have been exposed to the protozoan, healthy individuals are usually asymptomatic and may be unaware that they have been infected. Individuals with compromised immune systems, such as infants and people with HIV/AIDS, may develop flu-like symptoms. Rarely, people experience seizures and fatal brain damage.
Though clinical symptoms are rare, there is evidence to suggest that people with latent infections are more likely to die in car accidents and behave impulsively. One study released earlier this year lends support to earlier studies, identifying a link between childhood cat ownership and the development of schizophrenia later in life.
If these things seem reason enough to immediately cease all contact with cats, however, there are a few things to note. Firstly, no one has been able to prove that Toxoplasma gondii – let alone cat ownership – causes car accidents, impulsiveness, or mental illness. As of now, they are merely correlated. Secondly, people are infected with the Toxoplasma parasite all over the world – including places in which people don’t keep cats as pets. The protozoan can be found on undercooked meat and unwashed produce, and gardeners or young children who dig in the soil where a cat has buried its feces are also risk.
Instead of trying to avoid exposure at all costs, then, perhaps we should work to better understand Toxoplasma gondii, and to establish the nature of its connection (or lack thereof) to mental illness and maladaptive behaviors. An in-depth study of the parasite seems to be a promising way to further our understanding of human health through the lens of the felids.

How can you resist? Photo by Russell Neches
How can you resist? Photo by Russell Neches

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