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.”

Surf cops: Investigating microbes of surfers and the sea to understand resistance

Peter Andrey Smith of the New York Times writes that on a recent trip, Cliff Kapono hit some of the more popular surf breaks in Ireland, England and Morocco. He’s proudly Native Hawaiian and no stranger to the hunt for the perfect wave. But this time he was chasing something even more unusual: microbial swabs from fellow surfers.

Mr. Kapono, a 29-year-old biochemist earning his doctorate at the University of California, San Diego, heads up the Surfer Biome Project, a unique effort to determine whether routine exposure to the ocean alters the microbial communities of the body, and whether those alterations might have consequences for surfers — and for the rest of us.

Mr. Kapono has collected more than 500 samples by rubbing cotton-tipped swabs over the heads, mouths, navels and other parts of surfers’ bodies, as well as their boards. Volunteers also donate a fecal sample.

He uses mass spectrometry to create high-resolution maps of the chemical metabolites found in each sample. “We have the ability to see the molecular world, whether it’s bacteria or a fungus or the chemical molecules,” he said.

Then, working in collaboration with U.C.S.D.’s Center for Microbiome Innovation — a quick jaunt across the quad from his lab — Mr. Kapono and his colleagues sequence and map the microbes found on this unusually amphibious demographic.

He and his colleagues are looking for signs of antibiotic-resistant organisms. Part of their aim is to determine whether, and to what extent, the ocean spreads the genes for resistance.

Many antibiotics used today derive from chemicals produced by microbes to defend themselves or to attack other microorganisms. No surprise, then, that strains of competing bacteria have also evolved the genetic means to shrug off these chemicals.

While drug resistance comes about because of antibiotic overuse, the genes responsible for creating resistance are widely disseminated in nature and have been evolving in microbes for eons. Startlingly, that means genes giving rise to drug resistance can be found in places untouched by modern antibiotics.

Several years ago, researchers identified antibiotic-resistant genes in a sample of ancient permafrost from Nunavut, in the Canadian Arctic. William Hanage, an epidemiologist at the Harvard School of Public Health, was among those showing that these genes conferred a resistance to amikacin, a semi-synthetic drug that did not exist before the 1970s.

“There was a gene that encoded resistance to it in something that was alive 6,000 years ago,” he said in an interview.

Another group led by Hazel Barton, a microbiologist at the University of Akron, discovered microorganisms harboring antibiotic-resistance genes in the Lechuguilla Cave in New Mexico. These bacteria, called Paenibacillus sp. LC231, have been isolated from Earth’s surface for four million years, yet testing showed they were capable of fending off 26 of 40 modern antibiotics.

It’s all cool research, but all I could think of was Celebrity, a skit by The Kids in the Hall.

Hang 10, you’re booked.

Michael Pollan didn’t invent microbiome research, he’s a demagogue: Set of 15 bacterial species protects mice from Salmonella as effectively as natural gut microbiota

The mammalian gut harbors thousands of microbial species – collectively known as the microbiota or microbiome – that interact with each other and with their host to form a complex ecosystem.

lmu-set-of-15-bacterial-species-protects-mice-from-salmonella-infections-as-effectively-as-does-the-natural-gut-microbiotaIn healthy organisms, this community provides an effective shield against infection by many pathogenic organisms, such as Clostridium difficile (which is responsible for antibiotic-associated diarrhea) and various Salmonella species.

Researchers led by LMU microbiologist Professor Bärbel Stecher, in cooperation with colleagues from the University of Vienna and the Technical University of Munich, now show that, in the mouse, a defined group of 15 bacterial species confers the same degree of protection against Salmonella infections as does the host’s natural microbiota. The work establishes a new model system for the investigation of the interaction between the gut microbiome and infectious pathogens, which could in turn provide new approaches to the treatment of gastrointestinal infections. The new findings appear in the journal Nature Microbiology.

The protective effect provided by the gut microbiota against infection by invasive pathogens is referred to as colonization resistance. Exposure to antibiotics can disrupt this mechanism because these drugs typically alter the composition of the bacterial population in the gastrointestinal tract. “However, the contribution made by individual bacterial species to colonization resistance remains unclear,” says Stecher, who is also member of the German Center for Infection Research (DZIF).

“In order to gain a better understanding of the functions of the gut microbiota in this context, we had already established in my laboratory a minimal consortium comprising 12 bacterial species which are representative for the gut microbiome of the mouse.” This set of species, which is referred to as Oligo-MM-12, can be introduced into germ-free mice and is stably maintained over several generations. However, while mice colonized by the Oligo-MM-12 species are more resistant to infection by Salmonella enterica than their germ-free relatives, they are not as well protected as mice with a normal microbiome.

pollan-microbiomeThe team then went on to develop a new strategy, called genome-guided microbiota design, to identify species required to confer the same measure of protection as the natural gut microbiome of the mouse.

“We compared DNA sequences from the 12 species represented in Oligo-MM-12 with homologous sequences derived from the total mouse microbiome, and were able to identify groups of genes that were missing from our set,” Stecher explains. Some of these genes turned out to be characteristic for so-called facultative anaerobes, i.e. bacterial species that grow best in the presence in oxygen, but are nevertheless capable of proliferating in its absence. Indeed, the genus Salmonella consists of facultative anaerobes, while almost all the species that make up the Oligo-MM-12 consortium are obligate anaerobes – for which oxygen is toxic.

“We therefore supplemented our original consortium with three facultatively anaerobic species that are found in the microbiota of healthy mice,” Stecher says, “and we were able to demonstrate experimentally that this combination confers the same level of colonization resistance against Salmonella as that observed in mice that have a natural microbiota.” Stecher and her colleagues believe that their new “mini-microbiota”, together with the use of genome-guided microbiota design, provides a powerful new tool for the identification of hitherto unknown functions mediated by natural microbiota. This opens a route to the identification of specific bacterial species that could ameliorate the effects of disease-dependent dysfunction of the gut microbiota.

More microbiome (use it a lot in grant applications): Proteins secreted by beneficial gut microbes inhibit Salmonella, invasive E. coli

Few treatments exist for bacteria-caused intestinal inflammation that leads to diarrhea, fever and abdominal cramps. But University of California, Irvine microbiologists have demonstrated a new approach that may lead to more effective remedies.

activiaIn the journal Nature, Manuela Raffatellu, associate professor of microbiology & molecular genetics, and colleagues provide the first evidence that small protein molecules called microcins, produced by beneficial gut microbes, play a critical part in blocking certain illness-causing bacteria in inflamed intestines.

In their study, the researchers show that a probiotic strain of E. coli called Nissle 1917 utilizes microcins to inhibit the pathogen salmonella and an invasive form of E. coli (isolated from patients with inflammatory bowel disease).

“Although an in vivo role for microcins has been suggested for 40 years, it has never been convincingly demonstrated,” said Raffatellu, who’s affiliated with UCI’s Institute for Immunology. “We hypothesize that their role was missed because, as our data indicate, microcins do not seem effective in noninflamed intestines. In contrast, we show that in an inflamed intestine, microcins help a probiotic strain limit the growth of some harmful bacteria.”

She added that microcins are essential for the therapeutic activity of E. coli Nissle, and her next step is to purify microcins and test whether they can be given as targeted antibiotics.

Martina Sassone-Corsi, Sean-Paul Nuccio, Henry Liu, Dulcemaria Hernandez, Christine Vu, Amy Takahashi and Robert Edwards of UCI contributed to the study, which is abstracted at http://www.nature.com/nature/journal/vaap/ncurrent/full/nature20557.html

It’s hard to poop on vacation

More than 100 million people in the U.S. are expected to travel at some point between this Christmas and New Year’s Day—and each and every one of them will take roughly 100 trillion intestinal microbes along for the ride.

poop.travelsAmong the various other things influenced by these gut bacteria—like eating habits, for example—they also help control how much, or how little, a person poops. For many travelers, “how little” is the operative phrase: By one estimate, as many as 40 percent of people experience constipation while they’re away from home, due partially to their gut bacteria’s reaction to the change of setting.

“Any time you leave your general habitat, it’s throwing your gut microflora off balance,” says Brooke Alpert, a New York-based registered dietician. Sometimes, that begins before you reach your new destination: In some people, the very act of traveling from point A to point B can cause constipation. Movement stimulates the gut, so sitting on a plane or in a car for long periods of time can cause the intestines to clog; ignoring the urge to go while in the air or on the road can also make it more difficult once you finally sit down on the toilet.

Time differences can also pose a problem. Many people have a normal bowel-movement routine, pooping at regular intervals throughout the day. But when jetlag or a new time zone shifts that schedule ahead or backwards by a few hours, it can mess up that routine, causing constipation.

Even the stress of traveling can make it difficult for people to poop while they’re away. Researchers have nicknamed the gut “the second brain” for the millions of neurons that line the intestines. These cells play a role in digestion, but less understood is the interplay between a person’s gut and her mental state. Researchers do know, however, that things like anxiety can affect the way this “second brain” functions. (Think of butterflies in the stomach, or a stomach tied up in knots.)

And some aren’t; some of my best friends are germs

Fresh off Michael Pollan’s New York Times magazine feature on microbiomes – the totality of microbes, their genomes and particular environments, such as the human digestive tract —  new research has shown mixed potential for diet in reducing the risk of E. coli O157:H7 infection, at least in mice.

Research on microbiomes has been around for awhile, but as humans, we’re limited in understanding how to strategically lever gut activity to reduce the human-microbiome-change_1risk of foodborne illness.

A cocktail of non-pathogenic bacteria naturally occurring in the digestive tract of healthy humans can protect against a potentially lethal E. coli infection in animal models according to research presented today at the 113th General Meeting of the American Society for Microbiology. The research, conducted by scientists at the University of Michigan Medical School in Ann Arbor, could have important implications for the prevention or even treatment of this disease.

Enterohemorrhagic Escherichia coli (EHEC) O157:H7 is a food-borne pathogen that has been responsible for several recent outbreaks of potentially fatal disease. Severe manifestations of this disease include both hemorrhagic colitis (HC) and hemolytic uremic syndrome (HUS), a form of acute renal disease that can result in death or permanent disability.

“EHEC is of primary concern because HUS, the most severe outcome, preferentially targets young children,” says Kathryn Eaton, a researcher on the study. “Tragically, HUS occurs late in the course of disease, often after the child has recovered from the enteric form. Thus, children who appear to have recovered may relapse and even die.”

HUS is caused by absorption of Shigatoxins (Stx) that are produced by the bacteria in the intestine. Stx production occurs within a few days of bacterial colonization and once it is present in the intestines it can be absorbed into the bloodstream where it may cause systemic disease and even death. There is no specific treatment or preventative measure that prevents progression from HC to HUS.

The overall goal of research in Eaton’s laboratory is to identify potential therapies to prevent production or absorption of Stx before it can cause disease.

“In brief, the results of our study show that in a mouse model, non-pathogenic bacteria that are normal inhabitants of the human intestine can eliminate Stx from the intestinal contents and completely prevent HUS,” says Eaton.

In the study, the researchers gave EHEC to two groups of mice: one that had been been pre-colonized with a mix of bacterial species derived from normal human intestines and one that had not. In the pre-colonized mice, Stx levels microbiome 1remained undetectable and all mice remained completely healthy. In contrast, the control group had high levels of Stx and all developed kidney disease within one week of infection.

“The discovery that normal intestinal bacteria can prevent intestinal Stx accumulation and disease in an animal model may have important implications for prevention of HUS in people infected with EHEC,” says Eaton.

First, it could help explain why not everyone infected with EHEC develops HUS. Second, and most importantly says Eaton, it identifies specific, non-pathogenic, probiotic bacteria that could be used to prevent or treat Stx-mediated diseases

Zumbrun, et al, of the Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, write in today’s PNAS that “dietary fiber content affects susceptibility to Shiga toxin (Stx)-producing Escherichia coli (STEC) infection in mice. We showed that high fiber diet (HFD)-fed mice had elevated levels of butyrate, a beneficial gut metabolite that paradoxically enhances the cell-killing capacity of Stx. We also found that the amount of gut bacteria in HFD-fed mice increased whereas the percent of commensal Escherichia species (spp) decreased compared with animals fed a low fiber diet (LFD). These changes led to higher E. coli O157:H7 colonization levels, more weight loss, and greater rates of death in HFD-fed than in LFD-fed STEC-infected animals.

Abstract

The likelihood that a single individual infected with the Shiga toxin (Stx)-producing, food-borne pathogen Escherichia coli O157:H7 will develop a life-threatening sequela called the hemolytic uremic syndrome is unpredictable. We reasoned that conditions that enhance Stx binding and uptake within the gut after E. coli O157:H7 infection should result in greater disease severity. Because the receptor for Stx, globotriaosylceramide, is up-regulated in the presence of butyrate in vitro, we asked whether a high fiber diet (HFD) that reportedly enhances butyrate production by normal gut flora can influence the outcome of an E. coli O157 infection in mice. To address that question, groups of BALB/c mice were fed high (10%) or low (2%) fiber diets and infected with E. coli O157:H7 strain 86-24 (Stx2+). Mice fed an HFD exhibited a 10- to 100-121022_r22702_p233fold increase in colonization, lost 15% more body weight, exhibited signs of morbidity, and had 25% greater mortality relative to the low fiber diet (LFD)-fed group. Additionally, sections of intestinal tissue from HFD-fed mice bound more Stx1 and expressed more globotriaosylceramide than did such sections from LFD-fed mice. Furthermore, the gut microbiota of HFD-fed mice compared with LFD-fed mice contained reduced levels of native Escherichia species, organisms that might protect the gut from colonization by incoming E. coli O157:H7. Taken together, these results suggest that susceptibility to infection and subsequent disease after ingestion of E. coli O157:H7 may depend, at least in part, on individual diet and/or the capacity of the commensal flora to produce butyrate.