Those subway germs: They’re the harmless kind (mostly)

Nicholas Bakalar of the New York Times reports that with the cooperation of the Massachusetts Bay Transit Authority, researchers at Harvard swabbed seats, walls, poles, hand grips and ticket machines in the Boston transit system, and then did DNA analyses to figure out what kinds of organisms they had collected. The study is online in mSystems.

poleAll the surfaces were contaminated with generally innocuous human skin bacteria, including various strains of propionibacterium, corynebacterium, staphylococcus and streptococcus, among others. Some strains of these bacteria can cause disease under certain circumstances, but all are carried by healthy people and usually cause no problems.

Unsurprisingly, oral germs were found on poles at mouth level, and microbes that infest the skin on hand grips. Outdoor ticket machines had microbes that are prevalent in soil and the air.

“We were specifically checking for bad bugs or the kind of DNA that can make good bugs go bad,” said the lead author of the study, Curtis Huttenhower, an associate professor at the Harvard T.H. Chan School of Public Health. “But even though we think of it as dirty, the transit system has only the kind of microbes you run into shaking people’s hands.”


Bugs at home: Citizen science effort highlights how little we know about invisible life

We got 6-year-old Sorenne a microscope and a telescope (although I haven’t set them up yet) so she can begin to appreciate the world, big and small.

OLYMPUS DIGITAL CAMERAMatt Shipman of North Carolina State University writes that in a new paper, scientists are announcing the discovery of thousands of unidentified species living in and around homes in the United States. The work relied on advanced technologies and scientific expertise from multiple disciplines, but none of it would have been possible without one critical resource – a group of non-scientists who wanted to be part of making a discovery.

The paper, published Aug. 26 in Proceedings of the Royal Society B, comes out of a project called the Wild Life of Our Homes, led by Rob Dunn of NC State University and Noah Fierer of the University of Colorado at Boulder.

“When we started this project, we wanted to see what invisible lifeforms were sharing our homes,” Dunn says. “Which species of fungi and bacteria live with us? And what’s responsible for determining which species live in which homes? No one really knew.

“But we also wanted to devise a study that stirred the public imagination, and made the public a meaningful part of the scientific process,” Dunn says.

To that end, the research team, called Your Wild Life, created an online campaign to recruit study participants, who were asked to swab the inside and outside of their front doors and send those samples in for analysis. As a result, the Aug. 26 paper includes samples from more than 1,100 homes across the United States.

The samples, analyzed by Noah Fierer’s team at Colorado, revealed a staggering amount of data: they found genetic traces of more than 72,000 taxa of fungi and more than 125,000 taxa of bacteria.

“We found tens of thousands of bacteria that no one knows anything about – they don’t even have names,” Dunn says. Including hundreds of “mystery” bacteria that were more common inside homes than outside. To prioritize the data for analysis, the researchers decided to focus on those bacteria and fungi found inside people’s homes.

And as they sifted through the mountain of data, there were surprises. For example, while the fungi found inside a home varied widely from region to region, bacteria really didn’t. And the setting of a home within a region didn’t seem to influence bacteria in a home either: a rural home from one part of the country could very likely have similar populations of bacteria to an urban home thousands of miles away. But there were factors that appeared to influence bacterial biodiversity.

WILDLIFE-HEADER-720x405Homes that had a cat appeared to favor specific bacteria. Homes with dogs appeared to favor other bacteria. And the types of bacteria found in a home were also influenced by the ratio of men to women in a home.

“We can tell if there are more men than women in a home, for example, because those homes have more armpit bacteria,” Dunn says. “Seriously.”

“We’re just starting to look at what lives in our homes,” Dunn says. “These findings are not an exhaustive answer, they’re a first step – and the study highlights just how much we don’t know.

“But it does give us a baseline understanding of bacterial biodiversity that can inform future research.”

“We’re now starting to let study participants know what we’ve found,” says Holly Menninger, co-author of the paper and director of public science in NC State’s College of Sciences. “And anyone who’s interested can go through a data visualization we’ve done of the findings. We want to bring the public into the process of steering future research on this. What questions do people have? And how can science help us answer those questions?”

“This highlights the value of citizen science,” Dunn says. “We couldn’t have done this research if we hadn’t been able to work with more than a thousand people who wanted to help us shed light on a scientific mystery.”

More goop: Micro risk in fish spas

In fish spas, clients may submerge their hands, feet or whole body in basins with Garra rufa fish, for dead skin removal.Skin infections may result from using these spas, transmitted from fish to clients, through either fish or water, or from client to client.

fish.spaThe microbiological water quality was determined in 24 fish spas in 16 companies in the Netherlands through analysis of a single water sample per fish spa. Water samples were tested for the presence of Aeromonas spp., Vibrio spp., Pseudomonas aeruginosa, nontuberculous mycobacteria, and faecal indicator bacteria by using standard culture methods. The majority of the examined fish spas contained Aeromonas spp. (n = 24), P. aeruginosa (n = 18), Vibrio spp. (n = 16) including V. cholerae non-O1/O139 and V. vulnificus, and several rapid growing Mycobacterium spp. (n = 23) including M. fortuitum, M. conceptionense, M. abscessus and M. chelonae. Faecal contamination of the fish spa water was low. Based on the detected concentrations of Aeromonas spp., Vibrio spp., and P. aeruginosa, the detected Mycobacterium spp., and the health implications of these bacteria, the health risk from using fish spas is considered limited for healthy people with an intact skin and no underlying disease.

 The Microbiological Quality of Water in Fish Spas with Garra Rufa Fish, the Netherlands, October to November 2012

Eurosurveillance, Volume 20, Issue 19, 14 May 2015

F M Schets, H H van den Berg, R de Zwaan, D van Soolingen, A M de Roda Husman


What are the bugs – or the fabrics — that make hockey equipment smell?

Nothing has quite the stench of (ice) hockey equipment.

Entire cleansing cabinets have been created to lessen the smell. I played hockey I’d wash my jersey maybe once a year.

The stench imparted by the gloves is equivalent to the stench imparted to the hands of a fish monger.

However in all the years coaching girls’ hockey, I can generally say the girls are somewhat more particular to the odor aspect.


On Sunday, the team I coach had an hour practice.

This was followed by a girls only session sponsored by the IIHF (International Ice Hockey federation, below, exactly as shown) for their annual World Girls Weekend.

Sorenne was back out on the ice.

Then I coached a come-and-try session for kids learning how to play from  3:30-4:30 (Sorenne wasn’t on the ice for that) followed by the final league games of the season (Sorenne played, I helped ref).

That’s a lot of hockey.

And a lot of smell.

Whereas I’d leave my stuff to ferment in the bag, Amy ensures Sorenne’s stuff is aired and washed regularly.

Callewaert, et al. examined the microbial basis of exercise stench and concluded they type of undergarments determines the stench of the smell.

Abstract below:

Clothing textiles protect our human body against external factors. These textiles are not sterile and can harbor high bacterial counts as sweat and bacteria are transmitted from the skin. We investigated the microbial growth and odor development in cotton and synthetic clothing fabrics. T-shirts were collected from 26 healthy individuals after an intensive bicycle spinning session and incubated for 28 h before analysis. A trained odor panel determined significant differences between polyester versus cotton fabrics for the hedonic value, the intensity, and five qualitative odor characteristics. The polyester T-shirts smelled significantly less pleasant and more intense, compared to the cotton T-shirts. A dissimilar bacterial growth was found in cotton versus synthetic clothing textiles. Micrococci were isolated in almost all synthetic shirts and were detected almost solely on synthetic shirts by means of denaturing gradient gel electrophoresis fingerprinting.

A selective enrichment of micrococci in an in vitro growth experiment confirmed the presence of these species on polyester. Staphylococci were abundant on both cotton and synthetic fabrics. Corynebacteria were not enriched on any textile type. This research found that the composition of clothing fibers promotes differential growth of textile microbes and, as such, determines possible malodor generation.
Microbial odor profile of polyester and cotton clothes after a fitness session

Appl. Environ. Microbiol. November 2014 80:6611-6619;
15 August 2014, doi:10.1128/AEM.01422-14

Chris Callewaert, Evelyn De Maeseneire, Frederiek-Maarten Kerckhof, Arne Verliefde, Tom Van de Wiele, and Nico Boon