31 sickened by E. coli O55 in Dorset: 3 years later, health-types’ report remains a secret

In Dec. 2014, an outbreak of E. coli O55 was identified in Dorset, U.K. with at least 31 sickened. Public Health England (PHE) and local environmental health officials investigated and found nothing, other than cats were also being affected.

Tara Russell of Bournemouth Echo reports again this week that a review into the outbreak in Dorset was carried out, health chiefs have insisted – but the report is not available to the public.

Public Health England (PHE) says the public can only request to see the report detailing exactly what happened when 31 people contracted the O55 strain between July 2014 and November 2015 through a Freedom of Information request.

Families including some whose children have been left with lifelong health complications say they did not know the review existed and have branded it ‘disappointing and disgusting’ they have been kept in the dark.

The Daily Echo has lodged an official FOI request on behalf of the affected families and will receive a response in July.

Nurse Jessica Archer, who today suffers crippling head pains, fatigue and depression while her nephew Isaac Mortlock (right) endures severe seizures, must be peg fed every night and will need a kidney transplant as a result of the outbreak, said: “Without the Daily Echo we wouldn’t even know this report even existed and we are very interested to see it and we have the right to know. The families affected have so many unanswered questions and have to live with the effects of this outbreak forever but yet again we feel Public Health England are trying to sweep it under the carpet and hope that it will just go away.

“It is disappointing and disgusting this report has not already been made public let alone having to wait and wait still. We feel there have been a series of failures and this is the latest.”

The news comes after Jessica last month called for PHE to be held to account telling how her and her five-year-old nephew’s Isaac Mortlock’s lives have changed irreversibly, and accused the organisation of ‘a cover up.’

In response, PHE told the Daily Echo it carries out ‘routine outbreak reviews once investigations have ended’, adding it is ‘a learning organisation and reflects on outbreaks to identify lessons learnt and to continually improve our response.’

However at the time, the organisation refused to tell the Daily Echo exactly which lessons were learned.

It was only following a further request from this newspaper, PHE said a report was compiled however it has not been available to the public.

A spokesman said: “This report was not intended for external publication – it’s not standard procedure to publish outbreak reports externally due to patient confidentiality – however if interested parties would like to request a copy they can do this via our Freedom of Information portal.”

That’s bullshit.

Outbreak investigations are routinely published while ensuring patient confidentiality.

Families say it is the latest in a string of ‘failures’ by Public Health England.

A spokesman from PHE added: “As with all outbreaks, PHE Health Protection Team ensured throughout their investigation that those affected were kept informed of any information that was uncovered at that time.”

That’s also bullshit.

And why UK health types feature prominently in our paper on when to go public for the benefit of public health.

Three years seems a bit long.

Going public: Early disclosure of food risks for the benefit of public health

Mar.17

NEHA, Volume 79.7, Pages 8-14

Benjamin Chapman, Maria Sol Erdozaim, Douglas Powell

http://www.neha.org/node/58904

Often during an outbreak of foodborne illness, there are health officials who have data indicating that there is a risk prior to notifying the public. During the lag period between the first public health signal and some release of public information, there are decision makers who are weighing evidence with the impacts of going public.

Multiple agencies and analysts have lamented that there is not a common playbook or decision tree for how public health agencies determine what information to release and when. Regularly, health authorities suggest that how and when public information is released is evaluated on a case-by-case basis without sharing the steps and criteria used to make decisions.

Information provision on its own is not enough. Risk communication, to be effective and grounded in behavior theory, should provide control measure options for risk management decisions. There is no indication in the literature that consumers benefit from paternalistic protection decisions to guard against information overload. A review of the risk communication literature related to outbreaks, as well as case studies of actual incidents, are explored and a blueprint for health authorities to follow is provided.

Handwashing is never enough: Texas family says sons infected with E. coli at petting zoo

An Azle family wants to warn others after both their young boys were hospitalized with E. coli earlier this year.

“It’s awful. You can’t do anything but just sit there and watch your child hurt,” Emily Miller told WFAA.

Miller’s sons Brayden, 7, and Dylan, 5, were both diagnosed with an E. coli infection, and Dylan’s case impacted his kidneys. Miller said he required dialysis, and he was hospitalized for 27 days, including several nights in the ICU.

“It’s such a crazy thought that this could happen,” Miller said.

She was surprised by the intensity of the illness, but also by where her boys may have come into contact with E. coli. She said doctors believe they were likely contaminated while the family was visiting a petting zoo.

“I wasn’t aware that you could get it from animals and livestock,” Miller said.

She took the boys to the petting zoo back in January, and four days later her oldest was in the hospital.

Both brothers are now doing well, though Dylan is still on blood pressure medicine due to the illness, Miller said.

The Centers for Disease Control says petting zoos do pose risks, as livestock can carry E. coli bacteria. The CDC’s advice is to wash hands with soap and water immediately after being near animals, whether you touch them or not.

The CDC also says that soap and water is more effective than instant hand sanitizers, and if sanitizers are the only option, go ahead and use them but follow up with soap and water as soon as possible.

A table of petting zoo outbreaks is available at http://barfblog.com/wp-content/uploads/2014/04/Petting-Zoo-Outbreaks-Table-4-8-14.xlsx.

Erdozain G, Kukanich K, Chapman B, Powell D. 2012. Observation of public health risk behaviours, risk communication and hand hygiene at Kansas and Missouri petting zoos – 2010-2011. Zoonoses Public Health. 2012 Jul 30. doi: 10.1111/j.1863-2378.2012.01531.x. [Epub ahead of print]

Abstract below:

Observation of public health risk behaviors, risk communication and hand hygiene at Kansas and Missouri petting zoos – 2010-2011Outbreaks of human illness have been linked to visiting settings with animal contact throughout developed countries. This paper details an observational study of hand hygiene tool availability and recommendations; frequency of risky behavior; and, handwashing attempts by visitors in Kansas (9) and Missouri (4), U.S., petting zoos. Handwashing signs and hand hygiene stations were available at the exit of animal-contact areas in 10/13 and 8/13 petting zoos respectively. Risky behaviors were observed being performed at all petting zoos by at least one visitor. Frequently observed behaviors were: children (10/13 petting zoos) and adults (9/13 petting zoos) touching hands to face within animal-contact areas; animals licking children’s and adults’ hands (7/13 and 4/13 petting zoos, respectively); and children and adults drinking within animal-contact areas (5/13 petting zoos each). Of 574 visitors observed for hand hygiene when exiting animal-contact areas, 37% (n=214) of individuals attempted some type of hand hygiene, with male adults, female adults, and children attempting at similar rates (32%, 40%, and 37% respectively). Visitors were 4.8x more likely to wash their hands when a staff member was present within or at the exit to the animal-contact area (136/231, 59%) than when no staff member was present (78/343, 23%; p<0.001, OR=4.863, 95% C.I.=3.380-6.998). Visitors at zoos with a fence as a partial barrier to human-animal contact were 2.3x more likely to wash their hands (188/460, 40.9%) than visitors allowed to enter the animals’ yard for contact (26/114, 22.8%; p<0.001, OR= 2.339, 95% CI= 1.454-3.763). Inconsistencies existed in tool availability, signage, and supervision of animal-contact. Risk communication was poor, with few petting zoos outlining risks associated with animal-contact, or providing recommendations for precautions to be taken to reduce these risks.

Best practices for planning events encouraging human-animal interactions

Zoonoses and Public Health 62:90-99, 2015

G. Erdozain , K. KuKanich , B. Chapman  and D. Powell

http://onlinelibrary.wiley.com/doi/10.1111/zph.12117/abstract?deniedAccess

Educational events encouraging human–animal interaction include the risk of zoonotic disease transmission. It is estimated that 14% of all disease in the US caused by Campylobacter spp., Cryptosporidium spp., Shiga toxin-producing Escherichia coli (STEC) O157, non-O157 STECs, Listeria monocytogenes, nontyphoidal Salmonella enterica and Yersinia enterocolitica were attributable to animal contact. This article reviews best practices for organizing events where human–animal interactions are encouraged, with the objective of lowering the risk of zoonotic disease transmission.

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petting2-791x1024 

2-year-old on life support in Texas after contracting E. coli

An Ennis family says the CDC is investigating after their 2-year-old was exposed to a dangerous strain of E.coli.

Landon Huston is now on life support at Children’s Medical Center Dallas.

“He’s usually up, rambunctious, running around,” said his mother, Lindsey Montgomery. “I’m ready for my little boy to be back.”

The family took a trip to Oklahoma two weeks ago, cooling down in a hotel pool and at a natural spring.

“I’d never heard of people swimming and get E. oli,” said his father, John Huston.

Unfortunately, many, many people have been identified as getting sick with Shiga-toxin producing E. coli from swimming, water parks, or water supplies.

“Three, four days later, Landon’s got fever, diarrhea, really sick,” said Montgomery.

But by the time a test confirmed E.coli, his kidneys were shutting down. Montgomery said the CDC interviewed her trying to determine the source of the infection.

“They asked me where he had been, what food he had ate, any restaurants,” she said.

Dr. Jeffrey Kahn, Children’s Health Chief of Pediatric Infections Diseases, said it’s normal for a case like this to trigger a public health investigation.

“That suggests that there’s some contamination somewhere. It’s usually water or food and typically that means it’s not just one individual who’s been exposed,” he said.

Hummus sucks, especially with Listeria

Winnipeg, Manitoba, Canada correspondent Rob Mancini writes:

I hate hummus.

My wife loves it.

Concerns with potential Listeria contamination and food are on-going due to the ubiquitous nature of this pathogen. In Nov. 2016, there was a significant recall of hummus due to potential Listeria concerns with certain Sabra brand hummus products in both Canada and the US. Food producers, manufacturers, retail and foodservice operations are in a constant battle to control this problem and continually seeking new innovative products/solutions for its’ control.

A study published in 2006 found that a combination of citric acid, nisin, and proper hygienic practices served as an effective means to minimize growth of the pathogen in hummus. It may also be a good idea to take into consideration where the ingredients were sourced and ensuring that your facility are following and adhering to good GMP’s.

Either way, still hate the stuff.

Daily Hornet reports:

Lantana Foods, the company that supplied the hummus, notified Harris Teeter of the possible contamination, and the grocer promptly removed it from its cases.

Affected products include Fresh Foods Market Artisan Hummus Pine Nuts with UPC 7203602705.

Harris Teeter is using transaction data to notify shoppers who may have purchased the hummus, according to a press release on the company’s website.

If you purchased any hummus affected by the recall you should discard it immediately or return it to Harris Teeter for a full refund.

Listeriosis is a severe infection caused by eating food contaminated with Listeria monocytogenes, according to the Centers for Disease Control and Prevention (CDC). The disease typically affects children, the elderly, and adults with weakened immune systems.

To date, no listeria infections have been associated with the Harris Teeter hummus recall.

 Al-Holy, M,  Al-Qadiri,H,  Lin, M,  and  Rasco, B. Inhibition of Listeria innocua in Hummus by a Combination of Nisin and Citric Acid.  Journal of Food Protection, Vol. 69, No. 6, 2006, Pages 1322–1327

 

Salmonella and hockey don’t mix: 250 sickened at Riga Cup in 2015

(Thanks to a Brisbane-based colleague and barfblog.com fan who passed this along.)

In April 2015, Finnish public health authorities alerted European Union member states of a possible multi-country Salmonella enteritidis outbreak linked to an international youth ice-hockey tournament in Latvia.

The European Centre for Disease Prevention and Control (ECDC), Finnish and Latvian authorities initiated an outbreak investigation to identify the source. The investigation included a description of the outbreak, retrospective cohort study, microbiological investigation and trace-back. We identified 154 suspected and 96 confirmed cases from seven countries.

Consuming Bolognese sauce and salad at a specific event arena significantly increased the risk of illness. Isolates from Finnish, Swedish and Norwegian cases had an identical multiple-locus variable-number of tandem repeats analysis-profile (3-10-6-4-1).

Breaches in hygiene and food storing practices in the specific arena’s kitchen allowing for cross-contamination were identified. Riga Cup participants were recommended to follow good hand hygiene and consume only freshly cooked foods.

This investigation demonstrated that the use of ECDC’s Epidemic Intelligence Information System for Food- and Waterborne Diseases and Zoonoses platform was essential to progress the investigation by facilitating information exchange between countries. Cross-border data sharing to perform whole genome sequencing gave relevant information regarding the source of the outbreak.

Multi-country outbreak of Salmonella enteritidis infection linked to the international ice hockey tournament

Epidemiology and Infection, pages 1-10, 14 Jun 2017, Pärn T, Dahl V, Lienemann T, Perevosčikovs J, DE Jong B

https://doi.org/10.1017/S0950268817001212

https://www.ncbi.nlm.nih.gov/pubmed/28610640

Blame Qatar? No, blame poor food handling as 825 sickened at Mosul camp

The first time I understood the term displaced person, was from my carpenter friend John Kierkegaard who, in the Danish tradition, had a beer at morning coffee, one at lunch, and one at afternoon coffee.

John would often tell me, it tastes good, but the work is not so good.

He told tales of bicycling 20-30 km/h with full infantry gear during WW II, and how he migrated to Canada at the end of the war as a displaced person.

On June 12, 2017, at sundown, hundreds of residents of one of the many tent camps that have sprawled across the barren landscape around Mosul gathered for iftar, the evening meal to break the day’s Ramadan fast. They were treated to a meal of chicken, rice, soup, beans and yogurt — paid for by a Qatari charity and prepared by a restaurant in Erbil, the capital of the autonomous Kurdish region.

Within hours, hundreds fell sick, vomiting and suffering from diarrhea. Overnight, until about 4 a.m., ambulances and cars rushed victims to hospitals, said Alaa Muhsin, an ambulance driver from Baghdad who works at the camp.

The period between when the food was cooked and then transported to the IDP camps resulted in the food poisoning of over 825 displaced persons from Mosul in southwestern Erbil.

 

“After we carried out an investigation of the case, we found out the cause of the food poisoning was due to the long period between preparing and consuming the food as it was packed in plastic containers and transferred to the camps,” Erbil Governor Nawzad Hadi said on Monday in a press conference.

“There were no deliberate intentions to poison IDPs by those who cooked the food,” he added.

“The food itself was okay, but the delay between the preparation of the meals and their distribution, along with the improper storing of the food, was the reason hundreds of IDPs became ill,” Hadi emphasized, stating the case had been sent to court.

The Governor previously mentioned the food was cooked at 9:00 a.m. then transferred to the camp at 1:00 p.m. The food was later distributed between 4:00 and 5:00 p.m.

Following the incident, seven people were arrested, six from the restaurant where the meals were prepared and one from a charity organization.

The restaurant was also closed, Erbil police previously informed.

Hadi noted the food should be prepared at the camps and that premade meals are forbidden.

He thanked the Peshmerga and security members for quickly transporting 638 IDPs to hospitals in Erbil to receive prompt medical treatment, while the remaining were treated at the camps.

The Erbil Health Department’s Director-General Saman Hussein Barzinjy told Kurdistan24 the group which delivered the donation did not take into consideration health hazards related to food preparation and distribution.

At the time, Barzinjy mentioned one of the camp’s inhabitants had died from food poisoning.

However, a statement released on Tuesday apologized for the misinformation, assuring no one had died, adding the condition of the child who was thought dead was “stable.”

The Kurdistan Region is home to almost two million IDPs and refugees who fled from the threat of the Islamic State in Iraq and Syria.

Two separate outbreaks send thousands of Turkish soldiers to hospital

The leading cause of immobilizing U.S. troops?

Foodborne illness.

My former dean was known as Dr. Clorox while serving in Vietnam.

I used to give these training sessions to food types headed for Iraq and Afghanistan from Fort Riley (in Manhattan, Kansas) and would sheepishly say, I have no idea what you’re going to face in terms of potable water, but bleach is your friend.

Prayer won’t make food safe, but science can help.

An outbreak of foodborne illness was first detected on May 23, 2017 at the training center of the First Manisa Infantry Brigade in western Manis in Turkey. Up to 1,000 were sickened, with one death and 46 hospitalizations.

Dr. Tur Yildiz Bicer, who is also a deputy of the main opposition group, the Republican People’s Party (CHP), visited the soldiers attended at the provincial hospital and the tests concluded that soldiers were infected with salmonellosis through game meat which was on the barracks menu.

“In the samples were traces of the bacterium Salmonella, which is transmitted through meat, especially poultry, If not well cooked or stored according to health regulations,” said the doctor, and recalled that the soldiers ate turkey meat the night the infection began.

On June 17, 2017, the Daily Sabah reported a total of 590 Turkish soldiers were hospitalized in the western province of Manisa following complaints of nausea and vomiting. It is the latest case of mass poisoning at military bases in Manisa that have been plagued by such incidents since late May. An investigation is already underway while police early Sunday arrested 21 employees, including executives of the catering firm that provides food to the base and others in the province.

The soldiers’ complaints at the 1st Infantry Training Battalion Command began following a dinner. The Manisa Prosecutor’s Office said in a statement Sunday that 731 soldiers were affected by the tainted meal.

The Manisa governorate announced yesterday that food services from the catering firm were suspended and meals will be provided to the base temporarily. Manisa Governor Mustafa Hakan Güvençer said a delegation from the Public Health Institute, the highest public health authority and a delegation from the Land Forces Command that oversees military bases hosting training for conscripts, were investigating the issue. Military compounds in Manisa function as two main training bases for thousands of conscripts who are dispatched to other cities after completing a month-long training course there.

Color sucks: Use a thermometer and stick it in for food safety

safefood Ireland has joined the UK Food Standards Agency in providing terrible advice about how to cook burgers.

A recipe for summer beef burgers (may a fine solstice greet our Northern and Southern friends) endorsed by safefood says:

“Before serving, ensure that the burgers are cooked thoroughly. Cut into them with a clean knife and check that they are piping hot all the way through, there is no pink meat remaining and that the juices run clear.”

Meanwhile, FSA issued a Safe Summer Food guide as UK picnickers head out in the sun (there’s sun in the UK?). The guidelines were in part based results of a self-reported survey, which is largely meaningless but something FSA likes to do.

The Morning Advertiser has more details on the hoops FSA seems willing to jump through to ensure the safety of rare burgers including:

  • sourcing the meat only from establishments which have specific controls in place to minimise the risk of contamination of meat intended to be eaten raw or lightly cooked;
  • ensuring that the supplier carries out appropriate testing of raw meat to check that their procedures for minimising contamination are working;
  • Strict temperature control to prevent growth of any bugs and appropriate preparation and cooking procedures;
  • notifying their local authority that burgers that aren’t thoroughly cooked are being served by the business; and,
  • providing advice to consumers, for example on menus, regarding the additional risk.

The advice from these self-proclaimed science-based agencies is at odds with, uh, science.

It has been known for over two decades that color is a lousy indicator of safety in hamburger.

The latest addition to this work comes from Djimsa et al. in the Dept. of Animal Science at Oklahoma State Univ., who wrote in the Journal of Food Science earlier this year that:

Premature browning is a condition wherein ground beef exhibits a well-done appearance before reaching the USDA recommended internal cooked meat temperature of 71.1 °C; however, the mechanism is unclear.

The objectives of this study were: (1) to determine the effects of packaging and temperature on metmyoglobin reducing activity (MRA) of cooked ground beef patties and (2) to assess the effects of temperature and pH on thermal stability of NADH-dependent reductase, lactate dehydrogenase (LDH), and oxymyoglobin (OxyMb) in-vitro.

Beef patties (lean: fat = 85:15) were packaged in high-oxygen modified atmosphere (HiOX-MAP) or vacuum (VP) and cooked to either 65 or 71 °C. Internal meat color and MRA of both raw and cooked patties were determined. Purified NADH-dependent reductase and LDH were used to determine the effects of pH and temperature on enzyme activity. MRA of cooked patties was temperature and packaging dependent (P < 0.05). Vacuum packaged patties cooked to 71 °C had greater (P < 0.05) MRA than HiOX-MAP counterparts.

Thermal stability of OxyMb, NADH-dependent reductase, and LDH were different and pH-dependent. LDH was able to generate NADH at 84 °C; whereas NADH-dependent reductase was least stable to heat.

The results suggest that patties have MRA at cooking temperatures, which can influence cooked meat color.

Effects of metmyoglobin reducing activity and thermal stability of NADH-dependent reductase and lactate dehydrogenase on premature browning in ground beef

Journal of Food Science, 2017 Feb, 82(2):304-313, doi: 10.1111/1750-3841.13606. Epub 2017 Jan 18.

https://www.ncbi.nlm.nih.gov/pubmed/28099768

Hucksterism gets richer: Amazon to buy Whole Foods in $13.4 billion deal

When you’re the second richest guy on the planet, what do you pick up when you go to the shops for a little retail therapy?

Buy Whole Foods for $13.4 billion (U.S.).

That’s what Jeff Bezos, the head of Amazon, with a personal wealth of $84.7 billion, did on Friday on his way home with some all-organic crap bread, cheese and ice cream.
I’d be more like Jimmy Buffett: “I went to Buckhead to get some ice cream and next thing I knew I was on I-75 headed for Florida.”

According to Michael J. de la Merced and Nick Wingfield of The New York Times the Amazon deal marks an ambitious push into the mammoth grocery business, an industry that in the United States accounts for around $700 to $800 billion in annual sales. Amazon is also amplifying the competition with Walmart, which has been struggling to play catch-up to the online juggernaut.

For Whole Foods, the deal represents a chance to fend off pressure from activist investors frustrated by a sluggish stock price. Whole Foods last month unveiled a sweeping overhaul of its board, replacing five directors, naming a new chairwoman and bringing in a new chief financial officer. It also laid out plans to improve operations and cut costs.

Forget all the organic, sustainable, dolphin-friendly products: Whole Foods is a cut-throat business that attracts gullible consumers to drop extra cash on food with a lot of adjectives.

A couple of centuries ago they would be called hucksters, or medicine-men.

With Amazon, Whole Foods gets a deep-pocketed owner with significant technological expertise and a willingness to invest aggressively in a quest for dominance.

Amazon has designs on expanding beyond online retail into physical stores. The company is slowly building a fleet of outlets, and much attention has been focused on its supermaket dreams. It has already made an initial push through AmazonFresh, its grocery delivery service.

The e-commerce giant has been testing a variety of other retail concepts. It has opened a convenience store that does not need cashiers, and has explored another grocery store concept that could serve walk-in customers and act as a hub for home deliveries.

Under the terms of the proposed deal, Amazon would pay $42 a share for Whole Foods, a 27 percent premium to Thursday’s closing price. After the deal was announced, shares of Amazon rose as much as 3.3 percent while other major retailers, including Target, Walmart and Costco Wholesale fell sharply.

Whole Foods, which was founded in 1978 in Austin, Tex., is best known for its organic foods. The company built its brand on healthy eating and staked its reputation on fresh, local produce, albeit with a high price tag.

But the company has increasingly faced fierce competition from rival supermarkets. National retailers like Costco, Safeway and Walmart have begun offering organic produce and kitchen staples, forcing Whole Foods to slash prices.

 

The miracle of poop

It’s a question that has perplexed scientists: does diarrhea have a purpose?

That is, is diarrhea is a symptom of disease, or does diarrhea actually help clear the bacteria causing an infection.

Cecile Borkhataria of the Daily Mail reports that scientists have found in sick mice, proteins caused microscopic leaks in the intestinal wall that let water in, making the mouse poop looser and limiting disease severity. 

The study, conducted by researchers at Brigham and Women’s Hospital (BWH), looked at the immune mechanisms that drive diarrhea.

Diarrhea can have many different causes, including infections, certain types of medications, too much caffeine or alcohol and many more. 

It happens when there’s an excess of water in the intestines, which is normally re-absorbed by the body. 

The intestinal wall is lined with cells, and some water can pass through the cells, holes in the lining or via junctions between the cells.  

‘The hypothesis that diarrhea clears intestinal pathogens has been debated for centuries,’ said corresponding author of the study Dr Jerrold Turner of the BWH Departments of Pathology and Medicine. 

‘Its impact on the progression of intestinal infections remains poorly understood. 

‘We sought to define the role of diarrhea and to see if preventing it might actually delay pathogen clearance and prolong disease.’

To conduct the study, the researchers used a mouse infected with a bacteria called Citrobacter rodentium – the mouse equivalent of an E. coli infection. 

Within two days of the mouse being infected, the researchers saw an increase in the permeability of the mouse’s intestinal barrier – leading to water entering the intestines, causing diarrhea.

This occurred well before inflammation cellular damage of the intestines. 

The researchers discovered two new proteins involved in causing diarrhea – interleukin-22 and claudin-2, which humans possess too. 

They found that when the mouse was infected, immune cells travelled to the intestinal wall and produced interleukin-22. 

Interleukin-22 binds to cells on the intestinal wall, causing the release of another protein called claudin-2. 

It’s claudin-2 that causes the leak in cellular junction in the intestinal wall, allowing water to enter it and cause diarrhea. 

The researchers tested three different kinds of mice – regular mice, genetically modified mice that produce large amount of claudin-2, and mice that didn’t make any claudin-2. 

The regular mice had diarrhea when they got sick, and the mice that made more claudin-2 always had diarrhea. 

The mice that didn’t make any claudin-2 had more e injuries to their intestinal lining, and they still had diarrhea because it seemed as though their immune system attacked the cells help make some diarrhea. 

In related poop news, Rob Knight, one of the founding fathers of gut microbiome research, in 2012, used the crowdfunding platform FundRazr to coax more than 9,000 volunteers into first donating money, and then sending samples of their poop through the mail. A team of researchers probed these samples for bacterial DNA to create the first census of the 40 trillion or so bacteria that call our guts their home.

Kyle Frischkorn of the Smithsonian quotes Knight, who directs of the Center for Microbiome Innovation at the University of California at San Diego, as saying, “You get an ongoing input of microbes from your environment—microbes you eat on food itself.”

One of the mysteries sparked by the American Gut Project was why two people who claimed to follow the same diet could have such different communities of gut microbes. For the study, volunteers had self-reported their diets, with the vast majority following omnivorous diets, and less than 3 percent each identifying as “vegetarian” or “vegan.” When researchers crunched the numbers, however, they found no discernible correlations between gut communities and those with seemingly similar diets. 

“Diet categories were completely useless and didn’t correlate with the microbiome communities at all,” says Knight.

In other words, the bacteria in poop were telling a different dietary story than the people making that poop. “You can be a vegan who mostly eats kale, or you can be a vegan who mostly eats fries,” Knight explains. “Those have totally different consequences for your microbiome.” Anyone can claim to be a die-hard adherent to the Paleo Diet, it seems, but the data suggested that the microbiome remembers all those midnight ice cream transgressions.

Knight realized that the results of the American Gut Project were missing something crucial: A deeper dive into the food we eat. Filling that gap would mean analyzing all the food going in, and seeing how it correlated with the patterns in what comes out. But while collecting poop was, in some sense, straightforward—each person “submits a sample” in the same way—tallying up all the many foods people eat would be a lot more ambitious.

Every time you ingest, you change the interior landscape of you. Because the bulk of bacteria in the microbiome live in the gut, when we feed ourselves, we feed them too. The chemistry of what we eat, be it fries or kale, alters the chemical landscape of the gut, making it more cozy for some and less hospitable for others. 

It gets livelier. Because microbes are everywhere—on the table, in the air, on the surface of the muffin you left out on the counter—you’re also adding new microbes to the mix. Some stroll through your body like polite tourists. Others stick around and interact with the locals. Every bite has the potential to alter the microbiome, and subsequently human health. But researchers have yet to figure out how.

That’s because, until now, we didn’t have the platform to embark on the massive endeavor of collecting and analyzing food samples from around the world. Thanks to the American Gut Project, Knight and his team aren’t starting from scratch. Initially, the researchers plan to collect 1,000 samples from every brick of the familiar food pyramid, and then they’ll open it for the public to submit whatever foods they’re curious about. 

“We know about calorie count, and about different food groups, but the whole world of the molecules and the microbes in our food is a black box,” says Julia Gauglitz, a post-doctoral researcher at the Center for Microbiome Innovation who will direct a new project. As the old adage goes, “we are what we eat,” she says. And yet, when you get down to the microscopic level, “we know very little about what we’re consuming.”

Everything we eat is the cumulative product of the chemistry and microbes in the soil where it was grown, the factory where it was processed, and whatever you touched right before you ate it. Why is that important? Ultimately, the team hopes, demystifying the microbial patterns in our food will help us better engineer our diets to improve our health and ward off disease.

Knight draws a historical parallel to the discovery of essential nutrients. In the last century, researchers figured out that industrially processed foods had become nutrient-depleted. By artificially adding vitamins and minerals back in, deficiency diseases like rickets and beriberi were largely eliminated from the Western world. Similarly, understanding the health effects of the microbiome could allow us to engineer those missing microbes back into our meals.

“It’s fairly likely that our modern lifestyles are stripping out a whole lot of live microbes that we need to maintain health,” says Knight. “Getting an understanding of that could be as important as the understanding that vitamin C is necessary and making sure that everyone got enough of it.”