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.”

Foodborne illness in Denmark

I have a soft spot for the Danes. Spending five summers hammering nails with a couple of Danish homebuilders in Ontario taught me the value of being well-read and beer at morning coffee, lunch, and afternoon coffee. My friend John Kierkegaard would say, the beer is nice, but the work, it isn’t really so good.

quotes-1600-900-wallpaperWhen I went to Copenhagen for a scientific meeting, sure enough, there was beer at morning coffee.

The Technical University of Denmark reports that almost every other registered salmonella infection in Denmark in 2014 was brought back by Danes travelling overseas. Travel thus remains the largest cause of salmonella infections. An outbreak of salmonella from Danish eggs was also recorded in 2014, which is the first time in five years and illness was again attributed Danish chicken meat.

These are some of the findings presented in the annual report on the occurrence of diseases that can be transmitted from animals and food to humans. The report was prepared by the National Food Institute, Technical University of Denmark, in cooperation with Statens Serum Institut, the national institute of public health, and the Danish Veterinary and Food Administration.

In 2014 a total of 1,122 salmonella infections were reported among Danes, which is equivalent to 19.9 infected cases per 100,000 inhabitants. The figure is in line with the previous year when a historically low number of Danes was infected with salmonella.

In all, 48% became ill with salmonella after travelling overseas in 2014. Most of those who returned home with a travel-related infection had been to Thailand (17.5%), Turkey (15.4%) and Spain (6.4%).

Thus, foreign travel is still the largest cause of salmonella infections among Danes.

tasting-midtfyns-jule-stoutIn the annual source account which the National Food Institute calculates, salmonella infections were attributed Danish chicken meat for the first time since 2011. In total 2% of the infections were estimated to be attributed this source.

“For two decades Danish producers, authorities and researchers have successfully worked hard to make fresh chicken salmonella-free. It is not allowed to sell fresh meat from Danish chickens if the flock is positive for salmonella. There will always be a small risk that positive fresh meat goes under the surveillance radar and makes its way to store refrigerators. This is why it is important to continue to have a close monitoring,” Senior Academic Officer Birgitte Helwigh from the National Food Institute says.

The first salmonella outbreak from Danish eggs for five years has also been registered in 2014. “It has been five years since we last had a foodborne outbreak caused by Danish eggs. The outbreak was associated with an outbreak of acute salmonella illness in the flock, which is extremely rare. The results show how important it is that producers and authorities continue to focus on maintaining the low incidence of salmonella in the egg production,” says Birgitte Helwigh says.

Danish pork was the food source associated with the most infections among persons infected in Denmark. Overall 15% of the reported illness cases were attributed to Danish pork. There were three outbreaks where Danish pork was registered as the source of infection, which contributed 4.6% of the cases.

Approximately one fifth of all salmonella cases in Denmark were not attributed to a specific food source. The reason may be that the cases were caused by foods which were not included in the salmonella source account, e.g. fruit and vegetables, or other sources of infection such as contact with livestock and pets.

With 3,782 cases registered in 2014, campylobacter still causes the most cases of foodborne bacterial illnesses in Denmark. In 2014 a total of 92 listeria infections were registered, which is an increase of 84% compared to the year before. The increase is mainly due to an outbreak in “rullepølse” (a Danish cold cut ready-to-eat speciality) with 41 reported cases.

In 2014, a total of 60 foodborne disease outbreaks were registered compared with 74 outbreaks the year before. An outbreak is when several people become sick from the same food source. As in previous years, norovirus caused the most outbreaks (40%). These outbreaks usually take place in restaurants, where a total of 363 people were infected in 24 of the recorded outbreaks.

UK national burger day: Idiocy on how to prepare and serve burgers safely

The Brits are forever complicating things.

barfblog.Stick It InAnd they’re supposed to be science-based, when they’re just rhetoric-based (with that charming but difficult to understand British accent; don’t get me started on Wales).

For National Burger Day, Big Hospitality provides 750 words of advice on what controls can be put in place to ensure that diners are not put at risk from the serving of pink or rare burgers.

It’s hard to blame this restaurant rag when the science-based UK government authority barfs out the same advice.

Color is a lousy indicator.

Stick it in: use a thermometer.

hamburger-safe and unsafe-thumb-450x138-175

Watch NFL linebacker Brian Cushing puke an endless stream of vomit

In hockey coaching camp, we’re told, the old school ways of making kids skate until they puke is a no-no.

I agree.

Apparently, the concussion-free National Football League hasn’t gotten that message, as Houston Texans linebacker Brian Cushing demonstrated at a NFL training camp.

Watch Cushing prove to everyone that he’s only human by puking for nearly a minute during last night’s episode of HBO’s Hard Knocks.

Consumers in Bangladesh feel unsafe about food

Nearly two years into passage of the Food Safety Act 2013 and six months into formation of the Bangladesh Food Safety Authority (BFSA), consumers are still anxious about food adulteration in the country, said speakers yesterday.

Food-security_bdMany consumers, agricultural scientists, right activists, and policy planners, at a seminar, demanded that the BFSA inform the public about its progress in enforcing the act which came into force amidst a huge public outcry over widespread food adulteration.

Lemon juice and human norovirus

Brisbane is equidistant from the equator as Sarasota, Florida, and we have fabulous citrus.

lemon.lime.bittersLemon-lime-and-bitters has become my go-to drink, along with the bubbly water provided by our soda stream.

But will lemon juice reduce my risk of contracting Norovirus?

Maybe.

Researchers at the German Cancer Research Center say that lemon juice could be a potentially safe and practical disinfectant against Norovirus.

I wouldn’t rely on it.

Human noroviruses does not grow in cell culture, so they tested the effects of increasing concentrations of citric buffer on the so called norovirus virus-like particles, which have the same surface characteristics as real viruses. Dr Grant Hansman, head of CHS junior research group at the German Cancer Research Center noroviruses and the University of Heidelberg and his staff show that the virus particles change their shape after citrate binding. X-ray crystal structures revealed that the citrate – from lemon juice or citrate disinfectants – precisely interacts at the binding pocket on the particle that is involved in attaching to host ligands – the so-called histo-blood group antigens.

These new results may explain why citrate reduces the infectivity of noroviruses. “Maybe a few drops of lemon juice on contaminated food or surfaces may prevent the transmission of these viruses,” speculates Hansman. With his staff, he now plans to investigate if citric acid could reduce symptoms in those already infected with noroviruses.

That’s a lot of maybes.

Anna D. Koromyslova, Peter White, and Grant S. Hansman: Citrate alters norovirus particle morphology. Virology 2015, DOI: 10.1016/j.virol.2015.07.009

77 sick at Calif. Chipotle

Ventura County health officials say at least 60 customers reported feeling sick after eating at a Chipotle restaurant in Simi Valley last week.

It’s unclear what made the customers ill – test results were pending Monday.

Mike Byrne, food safety supervisor for the Ventura County Environmental Health Division, said the restaurant also sent home 17 employees for being sick, closed the business to clean it for a day and brought in new food before reopening.

Health officials inspected the restaurant at 1263 Simi Town Center Way on Monday.

NBC4 reviewed the restaurant’s health inspection reports on the Environmental Health Division website. Violations posted Monday included:

The premises and/or floors, walls, or ceiling are in an unsanitary condition.

Equipment or utensils are not clean, fully operative and in good repair.

Flying insects observed within the food facility.

Food handlers employed at this facility do not possess a valid food handler card and/or records documenting that food employees possess a valid food handler card are not maintained by the food facility for review as required.

The restroom is unclean or in disrepair.

NBC4 found the restaurant has repeated violations for some of the same issues dating back to January 2015.

Despite the findings, health officials said the Simi Valley Chipotle passed Monday’s inspection and found no major violations.

In a statement to NBC4, Chipotle said: “The safety and well being of our customers is always our highest priority. When we were contacted by customers who reported feeling poorly after visiting our restaurant in Simi Valley, we notified health department officials, immediately began a review of the incident, and have taken all of the necessary steps to ensure that it is safe to eat there.”

Cyclospora will do that: Cilantro shortage hits Illinois restaurants, grocery stores

In the produce aisle at a Round Lake Beach grocery store, Valerie Brown hesitated before plucking a bunch of cilantro from between the parsley and green onions.

cilantro.slugs.powell.10She’s used to paying 75 cents for a bundle of the leafy green herb, she said. Today, the price read $1.99.

Even that was better than last week, said Brown, who lives in Antioch. Her husband visited three grocery stores and couldn’t find a single sprig. Cilantro is her parakeets’ favorite food, so she put a bundle in her cart despite the sticker shock.

Grocery stores and restaurants in the area said they’ve been noticing the same higher-than-usual prices and tighter-than-usual supply since officials implemented a partial import ban on some cilantro imported from Mexico.

The Centers for Disease Control and Prevention, Food and Drug Administration and state public health officials linked cilantro from the state of Puebla, Mexico to outbreaks of cyclosporiasis in the U.S. in 2013 and 2014 and identified it as the possible cause of a 2015 outbreak, according to an import alert the FDA posted in July. About 40 percent of cilantro sold in the U.S. is grown in Puebla, said FDA spokeswoman Lauren Sucher.

Egg moguls belong behind bars

The Des Moines Register writes in this editorial that four months ago, Iowa egg producers Austin “Jack” DeCoster and his son, Peter, were each sentenced to 90 days in prison for their role in the nation’s largest egg-related Salmonella outbreak.

decosterNow, however, the Chamber of Commerce of the United States, the National Association of Manufacturers and other major business organizations are fighting to keep the DeCosters out of prison.

They’ve filed briefs with the Eighth Circuit Court of Appeals, siding with the DeCosters in arguing that while fines and probation are acceptable in such cases, it’s unconstitutional to put corporate executives behind bars for the criminal actions of their underlings.

It’s an interesting case with major legal and ethical implications. After all, mere fines aren’t much of a deterrent to executives who collect multi-million-dollar salaries. But a 90-day stint in prison, as the DeCosters themselves argue in their court filings, carries with it the “personal loss and stigma” associated with becoming a convict.

In this case, a prison sentence certainly seems warranted. The Quality Egg salmonella outbreak of 2010 sickened at least 56,000 people (about 1,800 confirmed) and triggered a record-setting recall of more than half a billion eggs.

salmonella.eggsAs to whether the DeCosters themselves were to blame for the outbreak, U.S. District Court Judge Mark Bennett found the two men had created a “culture of rampant safety violations” and a “work environment where employees not only felt comfortable disregarding regulations and bribing USDA officials, but may have even felt pressure to do so.”

The editorial conclueds that tens of thousands of people were sickened as a direct result of the manner in which the DeCosters managed — or, rather, mismanaged — Quality Egg and its employees. For that, the DeCosters should be held accountable. A prison sentence is entirely appropriate.

Not just a Europe thing: DNA testing reveals horse meat in two products bought in US

Horse meat has been detected in two of 48 samples of ground meat products purchased from retailers in California.

horse.meat.butcher.france.07It is illegal for horse meat to enter the food chain in the United States.

The presence of horse meat in the two samples was detected during a study undertaken by researchers in the Food Science Program at California’s Chapman University.

The discovery comes after the 2013 horse-meat scandal in Europe, which saw a range of ready-made meals pulled from supermarket freezers across the continent after beef was found to have been contaminated with horse meat.

The resulting international investigation revealed the complexities of the food chain and its vulnerability to rogue traders.

Researchers at Chapman University have just published two separate studies exploring meat mislabeling in consumer products. One focused on identification of the species found in ground meat products and the other investigated game meat species labeling.

Both studies examined products sold in the US commercial market; and both identified species mislabeling.

In the study on identification of species found in ground meat products, 48 samples were purchased from five online specialty meat distributors and four retail outlets (three supermarkets and one butcher) in Orange County, California. The samples represented 15 different meat types.

They were tested for the presence of beef, chicken, lamb, turkey, pork and horse using a combination of DNA barcoding and real-time polymerase chain reaction (PCR).

Thirty-eight of them were found to have been labeled correctly.

However, 10 were found to have been mislabeled. Of these, nine were found to contain additional meat species and one sample was mislabeled in its entirety. Horse meat was detected in two of the samples.

One of the samples containing horse was labeled as ground bison and the other as ground lamb meat.

Both had been purchased from two different online specialty meat distributors.