Skip to content

Category: human microbiome

Published on

Another reason to wash your hands before handling food. From The Scientist:

Money Microbiome

Analyzing the genetic material on 80 $1 bills sampled from a Manhattan bank, researchers from New York University (NYU) have discovered a diverse array of microbes, most of which are relatively harmless to humans, but a few that may leave you washing your hands after every cash transaction. It total, they found more than 3,000 bacterial types, including some drug-resistant species, and known microbes accounted for just 20 percent of the non-human DNA the researchers isolated; the rest belongs to as-yet unidentified species.

The most abundant species the researchers identified were those that cause acne, followed by benign skin flora. More alarming discoveries included pathogenic Staphylococcus species as well as bacteria associated with gastric ulcers, pneumonia, and food poisoning. The researchers also found DNA from antibiotic-resistance genes, such as those carried by the deadly methicillin-resistantStaphylococcus aureus (MRSA).

The researchers even found evidence of anthrax, although Carlton notes this shouldn’t necessarily be cause for concern. “Anthrax is a very common bacteria in soil."

Nevertheless, the microbial diversity identified highlights the likelihood that cash—one of the most common items to be distributed internationally—could spread disease around the world. A 2010 study that investigated currencies from 10 different countries, including Australia, China, the U.K., Ireland, Mexico, and the U.S., found similarly dirty money, and the authors recommended “that current guidelines as they apply in most countries with regard to the concurrent hygienic handling of foods and money should be universally adopted.”

Published on

Flatulence is good, and up to 18 a day is totally normal! From NPR:

Got Gas? It Could Mean You've Got Healthy Gut Microbes

We know that air often comes after eating nutrient-packed vegetables, such as cabbage, kale and broccoli. And researchers have found that fiber-rich foods, like beans and lentils, boost the levels of beneficial gut bacteria after only a few days, as we reported in December.

So all this got us wondering: Could passing gas, in some instances, be a sign that our gut microbes are busy keeping us healthy? Absolutely, says Purna Kashyap, a gastroenterologist at the Mayo Clinic in Rochester, Minn. "Eating foods that cause gas is the only way for the microbes in the gut to get nutrients," he says. "If we didn't feed them carbohydrates, it would be harder for them to live in our gut."

And we need to keep these colon-dwelling critters content, Kashyap says. When they gobble up food — and create gas — they also make molecules that boost the immune system, protect the lining of the intestine and prevent infections.

"A healthy individual can have up to 18 flatulences per day and be perfectly normal," he adds.

Gas gets into the digestive tract primarily through  two routes: Swallowing air (which we all do when we eat and chew gum) and your microbiome. That's the collection of organisms in the GI tract that scientists and doctors are currently all fired up about. (Check our colleague Rob Stein's recent series on it.) That microbiome includes hundreds of different bacteria. But there are also organisms from another kingdom shacking up with them: the archaea.

All these microbes are gas-making fools. They eat up unused food in your large intestine, like fiber and other carbohydrates we don't digest, and churn out a bunch of gases as waste. But that's not all they make. They also produce a slew of molecules (called short chain fatty acids) that may promote the growth of other beneficial bacteria and archaea.

And the more fiber you feed these friendly inhabitants, the more types of species appear, studies have found. "Undigested carbohydrates allow the whole ecosystem to thrive and flourish," Kashyap says. Most gas made by the microbiome is odorless. It's simply carbon dioxide, hydrogen or methane. But sometimes a little sulfur slips in there."That's when it gets smelly," Kashyap says.

But here's the hitch: Many of the smelly sulfur compounds in vegetables have healthful properties. Take for instance, the broccoli, mustard and cabbage family. These Brassica vegetables are packed with a sulfur compound, called sulforaphane, that is strongly associated with a reduced risk of cancer. Another possible benefit of a little smelly gas? It may reduce the total volume of air in the gut, Kashyap says. 

Published on

Excerpts from a very interesting NPR interview with Dr. Martin Blaser and his views on the human microbiome. The big take-away: our modern life-style is not good for the gut microbiome. His recently published book is Missing Microbes: How the Overuse of Antibiotics is Fueling Our Modern Plagues.

From NPR News: Modern Medicine May Not Be Doing Your Microbiome Any Favors

There are lots of theories about why food allergies, asthma, celiac disease and intestinal disorders like Crohn's disease have been on the rise. Dr. Martin Blaser speculates that it may be connected to the overuse of antibiotics, which has resulted in killing off strains of bacteria that typically live in the gut.

Blaser is an expert on the human microbiome, which is the collection of bacteria, viruses, fungi and other microbes that live in and on the body. In fact, up to 90 percent of all the cells in the human body aren't human at all — they're micro-organisms. Blaser is the director of NYU's Human Microbiome Program and a former chairman of medicine there. His new book is called Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues.

"Since World War II, we've seen big rises in a number of diseases: asthma, allergies, food allergies, wheat allergy, juvenile diabetes, obesity. ... These are all diseases that have gone up dramatically in the last 50 or 70 years. One of the questions is: Why are they going up? Are they going up for 10 different reasons, or perhaps there is one reason that is fueling all of them."

"My theory is that the one reason is the changing microbiome; that we evolved a certain stable situation with our microbiome and with the modern advances of modern life, including modern medical practices, we have been disrupting the microbiome. And there's evidence for that, especially early in life, and it's changing how our children develop."

"There's a choreography; there's a normal developmental cycle of the microbiome from birth over the first few years of life, especially the first three years, [that] appear[s] to be the most important. And that's how nature has, how we have, evolved together so that we can maximize health and create a new generation, which is nature's great purpose. And because of modern practices, we have disrupted that. And then the question is: Does that have consequence[s]?"

"As far as we know, when the baby is inside the womb it is apparently sterile. ... The big moment of truth is when the membranes rupture, the water breaks, and the baby starts coming out. And that's where they first get exposed to the bacteria of the world, and the first bacteria they're exposed to is their mother's bacteria in the birth canal. So as labor proceeds, the babies are in contact with the microbes lining their mother's vagina and, as they're going out, they're covered by these bacteria. They swallow the bacteria; it's on their skin. ..."

"That's their initial exposure to the world of bacteria. That's how mammals have been doing it for the last 150 million years, whether they're dolphins or elephants or humans. ... And we know a little about what those bacteria are. The most common bacteria are lactobacillus and there's evidence that over the course of pregnancy the microbiome in the vagina changes, just as many other parts of the body are changing. The microbiome is changing in its composition in terms of maximizing lactobacilli, and these are bacteria that eat lactose, which is the main component of milk. So the baby's mouth is filled with lactobacilli. The first thing that happens is they go up against their mom's breast and they inoculate the nipple with lactobacilli and now milk and lactobacilli go into the new baby and that's the foundation for their microbiome and that's how they start their life. ..."

"You could project that if they didn't acquire these organisms or they didn't acquire them normally or at the normal time, then the foundations might be a little shaky."

"Shortly after birth, they compared the microbiomes in the babies that came out. The babies that were born vaginally, their microbiome, not surprisingly, looked like the mom's vagina everywhere in the body — in their GI tract, on their skin, in their mouth. But the babies born by C-section, their microbiome looked like skin and it didn't even necessarily look like the mom's skin, maybe it was somebody else in the operating room. So it's clear that the microbiome is different immediately depending on the kind of birth."

"What I can tell you is that our immune system is quite complex. There are many kinds of immune cells. There are cells that strongly recognize foreign substances, there are ones that try to damp [the immune system] and down-regulate it. There's what we call innate immunity, which is the immunity we're all born with, and then there's adaptive immunity — the immunity that develops when we experience different kinds of exposures. So it's very complex."

"There are many different probiotics.  I think I can say three things: The first is that they're almost completely unregulated; second is that they seem to be generally safe; and third is that they're mostly untested. ... I'm actually a big believer in probiotics; I think that's going to be part of the future of medicine, that we're going to understand the science of the microbiome well enough so that we can look at a sample from a child and say this child is lacking such-and-such an organism and now we're going to take it off the shelf and we're going to give it back to that child. ... "

Published on

An argument for the need for human exposure to the microbes in rural environments. However, the role of diesel exhaust and other urban air pollutants is not discussed here (for example, diesel exhaust is linked to asthma). From Science Daily:

Rural microbes could boost city dwellers' health, study finds

The greater prevalence of asthma, allergies and other chronic inflammatory disorders among people of lower socioeconomic status might be due in part to their reduced exposure to the microbes that thrive in rural environments, according to a new scientific paper co-authored by a University of Colorado Boulder researcher.

The article, published in the journal Clinical & Experimental Immunology, argues that people living in urban centers who have less access to green spaces may be more apt to have chronic inflammation, a condition caused by immune system dysfunction.

When our immune systems are working properly, they trigger inflammation to fight off dangerous infections, but the inflammation disappears when the infection is gone. However, a breakdown in immune system function can cause a low level of inflammation to persist indefinitely. Such chronic inflammation can cause a host of health disorders.

Some scientists have hypothesized that the increase of chronic inflammation in wealthier Western countries is connected to lifestyles that have essentially become too clean. The so-called "hygiene hypothesis" is based on the notion that some microbes and infections interact with the immune system to suppress inflammation and that eliminating exposure to those things could compromise your health.

The authors agree that microbes and some types of infections are important because they can keep the immune system from triggering inflammation when it's not necessary, as happens with asthma attacks and allergic reactions.

But they say the infections that were historically important to immune system development have largely been eliminated in developed countries. The modern diseases we pick up from school, work and other crowded areas today do not actually lead to lower instances of inflammatory disorders.

During our evolutionary history, the human immune system was exposed to microbes and infections in three important ways: commensal microbes were passed to infants from their mothers and other family members; people came into contact with nonpathogenic microbes in the environment; and people lived with chronic infections, such as helminths, which are parasitic worms found in the gut and blood.

In order for those "old infections" to be tolerated in the body for long periods of time, they evolved a mechanism to keep the human immune system from triggering inflammation. Similarly, environmental bacteria, which were abundant and harmless, were tolerated by the immune system. According to Rook, a professor at UCL, "Helminthic parasites need to be tolerated by the immune system because, although not always harmless, once they are established in the host efforts by the immune system to eliminate them are futile, and merely cause tissue damage."

In contrast, relatively modern "crowd infections," such as measles or chicken pox, cause an inflammatory response. The result is that either the sick person dies or the infection is wiped out by the inflammation and the person becomes immune from having the same infection again in the future.

Collectively, the authors refer to the microbes and old infections that had a beneficial impact on the function of our immune systems as "old friends." Exposure to old friends plays an important role in guarding against inflammatory disorders, the authors said. Because the "old infections" are largely absent from the developed world, exposure to environmental microbes -- such as those found in rural environments, like farms and green spaces -- has likely become even more important.

The authors say this would explain why low-income urban residents -- who cannot easily afford to leave the city for rural vacations -- are more likely to suffer from inflammatory disorders. The problem is made worse because people who live in densely populated areas also are more likely to contract crowd infections, which cause more inflammation.

Published on

Important to know about this nasty bacterial strain for those who use contact lenses. From Science Daily:

Bacteria survive longer in contact lens cleaning solution than previously thought, study shows

Each year in the UK, bacterial infections cause around 6,000 cases of a severe eye condition known as microbial keratitis -- an inflammation and ulceration of the cornea that can lead to loss of vision. The use of contact lenses has been identified as a particular risk factor for microbial keratitis. New research, presented today at the Society for General Microbiology Annual Conference in Liverpool, shows that a bacterial strain associated with more severe infections shows enhanced resistance to a common contact lens disinfectant solution.

Researchers from The University of Liverpool and The Royal Liverpool University NHS Trust tested different strains of the keratitis-causing bacterium Pseudomonas aeruginosa for their ability to survive in a commonly used contact lens cleaning solution. The team compared nine clinical strains of P. aeruginosa, taken from hospital patients in the UK, with P. aeruginosa strain 9027, the standard strain used by lens solution manufacturers.

The results showed that the majority of clinical strains tested were killed within 10 minutes of being immersed in the contact lens solution, comparable with the standard reference strain. However, one clinical isolate, P. aeruginosa strain 39016 -- associated with a more severe case of keratitis with a prolonged healing time -- was able to survive for over four hours, much longer than the reference strain.

Professor Craig Winstanley, who led the research, says: "Microbial keratitis can be devastating for a patient -- it is important that the risk of developing this condition is reduced in contact lens wearers by improving contact lens disinfectant solutions."

Published on

Another reason to avoid products with Triclosan. From Science Daily:

Antimicrobial from soaps promotes bacteria buildup in human noses

An antimicrobial agent found in common household soaps, shampoos and toothpastes may be finding its way inside human noses where it promotes the colonization of Staphylococcus aureus bacteria and could predispose some people to infection. 

Triclosan, a human-made compound used in a range of antibacterial personal care products such as soaps, toothpastes, kitchen surfaces, clothes and medical equipment, was found in nasal passages of 41% of adults sampled. A higher proportion of subjects with triclosan also had S. aureus colonization. S. aureus could promote infection in some populations such as people undergoing surgery.

Triclosan has been around for the past 40 years, says senior study author Blaise Boles, PhD, an assistant professor of molecular, cellular and developmental biology at the university, and has been incorporated into many antibacterial household products within the past decade. Other studies have found traces of triclosan in human fluids including serum, urine and milk, and studies in mammals have found that high concentrations of triclosan can disrupt the endocrine system and decrease heart and skeletal muscle function.

"It's really common in hand soaps, toothpastes and mouthwashes but there's no evidence it does a better job than regular soap," Boles says. "This agent may have unintended consequences in our bodies. It could promote S. aureus nasal colonization, putting some people at increased risk for infection."

Additional experiments found that S. aureus grown in the presence of triclosan was better able to attach to human proteins, and that rats exposed to triclosan were more susceptible to S. aureus nasal colonization.

Published on

This exciting research opens a whole new way of thinking about the female breast and breast cancer. First of all, note that the study found that even our breasts have a microbiome (the microbial community).

Key finding: the breast microbial population (specifically the bacteria) is different in healthy breasts (in the breast tissue) as compared to cancerous breasts.

From Science Daily: First look at breast microbiota raises tantalizing questions

The female breast contains a unique population of microbes relative to the rest of the body, according to the first-ever study of the breast microbiome. That study sought to lay the groundwork for understanding how this bacterial community contributes to health and disease, says first author Camilla Urbaniak, a PhD student at the University of Western Ontario. 

"Proteobacteria was the dominant phylum in healthy breast tissue," says Urbaniak, noting that it is found only in small proportions at other sites in the body. That may reflect the fact that breast tissue produces high concentrations of fatty acids, and these bacteria are fatty acid metabolizers. Proteobacteria is also the predominant phylum in human milk.

"The fact that beneficial bacteria, such as Lactobacillus and Bifidobacteria, were also detected makes us wonder whether their presence might be protective for both mother and child," says principal investigator Gregor Reid of the University of Western Ontario. Breast milk is one of the initial sources of gastrointestinal (GI) bacteria for newborns, and their GI microbiota are different if they are formula fed, says Urbaniak.

Conversely, Escherichia and Bacillus predominated in cancerous breasts.

"Strains of Escherichia have been shown to have mutagenic and carcinogenic activity in the gut and the bladder," says Urbaniak.

In the study, the investigators collected breast tissue from 81 women. Ten of these had undergone breast reduction, and their breast microbiota served as controls. The remaining women had had benign or cancerous tumors. The tissue collected from these women was taken from about five centimeters from the tumor, from what is known as "normal adjacent" tissue. Bacterial censuses were taken using a molecular technique known as 16S ribosomal sequencing, and with cultures.

Studies of the microbiome in other parts of the body, most notably the gastrointestinal tract, have shown that certain changes in bacterial populations can lead to a variety of ills, from obvious gastrointestinal conditions such as inflammatory bowel disease to those more unexpected, such as diabetes, obesity, cancer and even neurological conditions.

The complete reference: C. Urbaniak, J. Cummins, M. Brackstone, J. M. Macklaim, G. B. Gloor, C. K. Baban, L. Scott, D. M. O'Hanlon, J. P. Burton, K. P. Francis, M. Tangney, G. Reid.Bacterial microbiota of human breast tissue. Applied and Environmental Microbiology, 2014; DOI: 10.1128/AEM.00242-14

Published on

The United Nations has proclaimed today as the International Day of Happiness. In that spirit is the following article. From Science Daily:

Precise reason for health benefits of dark chocolate: Thank hungry gut microbes

The health benefits of eating dark chocolate have been extolled for centuries, but the exact reason has remained a mystery -- until now. Researchers have just reported that certain bacteria in the stomach gobble the chocolate and ferment it into anti-inflammatory compounds that are good for the heart.

"We found that there are two kinds of microbes in the gut: the 'good' ones and the 'bad' ones," explained Maria Moore, an undergraduate student and one of the study's researchers.

"The good microbes, such as Bifidobacterium and lactic acid bacteria, feast on chocolate," she said. "When you eat dark chocolate, they grow and ferment it, producing compounds that are anti-inflammatory." The other bacteria in the gut are associated with inflammation and can cause gas, bloating, diarrhea and constipation. These include some Clostridia and some E. coli.

"When these compounds are absorbed by the body, they lessen the inflammation of cardiovascular tissue, reducing the long-term risk of stroke," said John Finley, Ph.D., who led the work. He said that this study is the first to look at the effects of dark chocolate on the various types of bacteria in the stomach. The researchers are with Louisiana State University.

The team tested three cocoa powders using a model digestive tract, composed of a series of modified test tubes, to simulate normal digestion. They then subjected the non-digestible materials to anaerobic fermentation using human fecal bacteria, according to Finley.

He explained that cocoa powder, an ingredient in chocolate, contains several polyphenolic, or antioxidant, compounds such as catechin and epicatechin, and a small amount of dietary fiber. Both components are poorly digested and absorbed, but when they reach the colon, the desirable microbes take over. "In our study we found that the fiber is fermented and the large polyphenolic polymers are metabolized to smaller molecules, which are more easily absorbed. These smaller polymers exhibit anti-inflammatory activity," he said.

Finley also noted that combining the fiber in cocoa with prebiotics is likely to improve a person's overall health and help convert polyphenolics in the stomach into anti-inflammatory compounds. "When you ingest prebiotics, the beneficial gut microbial population increases and outcompetes any undesirable microbes in the gut, like those that cause stomach problems," he added. Prebiotics are carbohydrates found in foods like raw garlic and cooked whole wheat flour that humans can't digest but that good bacteria like to eat. This food for your gut's helpful inhabitants also comes in dietary supplements.

Published on

Another article reporting on the Crohn's disease study I posted yesterday. But this article lists the depleted bacteria and also which ones there are too much of in Crohn's patients. It illustrates that gut microbial communities being out of whack go hand in hand with disease. Remember: dysbiosis means an imbalance in the microbial populations. Interestingly, just like in the 2012 sinusitis study (see my December 4, 2013 post) - it's biopsies that found the specific bacterial imbalances, and not fecal samples or mucus/phlegm swabs (typically done in sinusitis). Big step forward in human microbiome research. And again antibiotics are not the answer.

From Science magazine:

Crohn's Disease Marked by Dramatic Changes in Gut Bacteria

The largest clinical study of its kind is revealing new insights into the causes of Crohn's disease, a periodic inflammation of the intestines. The research, which involved 668 children, shows that numbers of some beneficial bacteria in the gut decrease in Crohn's patients, while the number of potentially harmful bacteria increases. The study could lead to new, less invasive diagnostic tests; it also shows that antibiotics—which aren't recommended for Crohn's but are often given when patients first present with symptoms—may actually make the disease worse.

Crohn’s disease is one of the two major inflammatory bowel diseases (IBDs); the other is ulcerative colitis, a similar condition that affects only the colon. Both have been on the rise in the developing world since the early 1950s; now, an estimated 1.4 million people suffer from IBD in the United States alone. Symptoms include diarrhea, abdominal pains and cramping, and intestinal ulcers.

But genes alone can't explain the sharp rise in IBD incidence, and scientists have looked at the environment—in particular diet and antibiotic use—for answers.

Several studies have shown that Crohn’s disease is characterized by microbial dysbiosis, a shift in the microbial populations inhabiting the gut, but it's difficult to unravel cause and effect: A change in gut microbiota can cause inflammation, but the reverse can also occur. Complicating the picture is the fact that before being diagnosed with IBD, patients often receive antibiotics to fend off a supposed gut infection that could be causing the symptoms, which also have a powerful impact on the microbial populations living in our guts.

Now, a group headed by Ramnik Xavier, a gastroenterologist at Harvard Medical School in Boston, has collected fecal samples and taken biopsies of the lower part of the small intestine and rectum from 447 children who had just been diagnosed with Crohn's, and a control group of 221 kids who had noninflammatory abdominal symptoms, such as bloating and diarrhea. In contrast with previous studies, the majority of patients had not yet received antibiotics or anti-inflammatory drugs. Based on their genetic material, the researchers determined the relative abundance of a range of microbial species in the samples.

Some potentially harmful microbial species were more abundant in Crohn's patients, such as those belonging to the Enterobacteriaceae, Pasteurellaceae, Veillonellaceae, and Fusobacteriaceae; numbers of the Erysipelotrichales, Bacteroidales, and Clostridiales, generally considered to be beneficial, were lower. The disappearance and appearance of species can be equally important, says Dirk Gevers of the Broad Institute in Cambridge, Massachusetts, who performed most of the work. "There has been a shift in the ecosystem, which affects both types.”

But those differences were found mostly in the biopsy samples; there weren't many differences between the feces from Crohn's patients and the control group. At this early stage of the disease, "the dysbiosis seems not to have reached the stool yet," Gevers says.

The dysbiosis was also more pronounced in patients who had received antibiotics. "This study confirms that these drugs don’t do any good to people with Crohn’s disease," says gastroenterologist Séverine Vermeire of the Catholic University of Leuven in Belgium, who was not involved in the study. "We knew antibiotic use increases the risk to develop the disease; now we know they can worsen it, too."

Vermeire says it's a "missed opportunity" that the researchers didn't look at the patients' diets. "That could have helped elucidate why this disease occurs so much more in the Western world than elsewhere." In 2011, Vermeire’s group published a study showing that healthy family members of Crohn's disease patients have a slight dysbiosis as well. Vermeire is convinced that even in these families, it's not genetics but some lifestyle factor that causes the phenomenon. "If we could identify the dysbiosis in an early stage, and we knew the causative factors,” she says, “we could prevent disease occurrence by bringing about lifestyle changes.”

Published on

Two related studies showing the importance of the intestinal bacterial community for health and preventing diseases. Both also discuss how antibiotics disrupt the gut microbial community. From Science Daily:

Microbes help to battle infection: Gut microbes help develop immune cells, study finds

The human relationship with microbial life is complicated. Although there are types of bacteria that can make us sick, Caltech professor of biology and biological engineering Sarkis Mazmanian and his team are most interested in the thousands of other bacteria -- many already living inside our bodies -- that actually keep us healthy. Now, he and his team have found that these good bugs might also prepare the immune cells in our blood to fight infections from harmful bacteria.

In the recent study, published on March 12 in the journal Cell Host & Microbe, the researchers found that beneficial gut bacteria were necessary for the development of innate immune cells -- specialized types of white blood cells that serve as the body's first line of defense against invading pathogens.

In addition to circulating in the blood, reserve stores of immune cells are also kept in the spleen and in the bone marrow. When the researchers looked at the immune cell populations in these areas in so-called germ-free mice, born without gut bacteria, and in healthy mice with a normal population of microbes in the gut, they found that germ-free mice had fewer immune cells -- specifically macrophages, monocytes, and neutrophils -- than healthy mice. Germ-free mice also had fewer granulocyte and monocyte progenitor cells, stemlike cells that can eventually differentiate into a few types of mature immune cells. 

Khosravi and his colleagues next wanted to see if the reduction in immune cells in the blood would make the germ-free mice less able to fight off an infection by the harmful bacterium Listeria monocytogenes -- a well-studied human pathogen often used to study immune responses in mice. While the healthy mice were able to bounce back after being injected with Listeria, the infection was fatal to germ-free mice. When gut microbes that would normally be present were introduced into germ-free mice, the immune cell population increased and the mice were able to survive the Listeria infection.

The researchers also gave injections of Listeria to healthy mice after those mice were dosed with broad-spectrum antibiotics that killed off both harmful and beneficial bacteria. Interestingly, these mice also had trouble fighting the Listeria infection. "We didn't look at clinical data in this study, but we hypothesize that this might also happen in the clinic," says Mazmanian. "For example, when patients are put on antibiotics for something like hip surgery, are you damaging their gut microbe population and making them more susceptible to an infection that had nothing to do with their hip surgery?"

More importantly, the research also suggests that a healthy population of gut microbes can actually provide a preventative alternative to antibiotics, Khosravi says. 

From Science Daily:

Large study identifies exact gut bacteria involved in Crohn's disease

While the causes of Crohn's disease are not well understood, recent research indicates an important role for an abnormal immune response to the microbes that live in the gut. In the largest study of its kind, researchers have now identified specific bacteria that are abnormally increased or decreased when Crohn's disease develops. The findings, which appear in the March 12 issue of the Cell Press journal Cell Host & Microbe, suggest which microbial metabolites could be targeted to treat patients with this chronic and currently incurable inflammatory bowel disease.

Twenty-eight gastroenterology centers across North America have been working together to uncover how microbes contribute to the inflammatory cascade of Crohn's disease. Researchers took biopsies from 447 individuals with new-onset Crohn's disease and 221 nonaffected individuals at multiple locations along the gastrointestinal tract and then looked for differences between the two groups. They also validated their methods in additional individuals, resulting in a total of 1,742 samples from pediatric and adult patients with either new-onset or established disease.

The team found that microbial balance was disrupted in patients with Crohn's disease, with beneficial microbes missing and pathological ones flourishing. Having more of the disease-associated organisms correlated with increasing clinical disease activity. 

When the researchers analyzed the effects of antibiotics, which are sometimes used to treat Crohn's disease symptoms prior to diagnosis, they found that antibiotic usage in children with Crohn's disease could be counterproductive because it causes a loss of good microbes and an increase in pathological ones.