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Tag: gut microbes

Published on Leave a comment on Exposure To Sunlight Improves Gut Microbes and Vitamin D Levels

Researchers in Canada found that sunlight (or UVB light) on the skin changes the gut microbes (gut microbiome), especially in people with lower levels of vitamin D, that is, who are vitamin D deficient. UVB (Ultraviolet B light) exposure increased beneficial gut microbe diversity and richness in these people, as well as increasing their vitamin D levels. However, people who had been taking vitamin D supplements prior to the study, and who had sufficient vitamin D levels, did not have significant gut microbiome changes.

The researchers viewed the study results as evidence that there may be a skin-gut axis. As the researcher Vallance said: “It is likely that exposure to UVB light somehow alters the immune system in the skin initially, then more systemically, which in turn affects how favorable the intestinal environment is for the different bacteria,” suggested Vallance.

The researchers also thought that these study results (which was conducted in Vancouver, Canada, in healthy human volunteers) could help explain the protective effect of UVB light against inflammatory diseases such as multiple sclerosis (MS) or inflammatory bowel disease (IBD). And how did the researchers know what bacteria were in the gut in the study participants? They analyzed the feces with modern genetic sequencing methods. By the way, these results match what has been found in earlier studies in humans and mice.

Bottom line: Sunlight on the skin is beneficial to the gut microbiome, by increasing gut bacteria linked to health. In the study the increases in bacteria (after UVB light exposures) were in the Lachnospiraceae, Ruminococcus, and Clostridiaeae families. And nope, none of those are found in currently available probiotics. By the way, this study was conducted in winter in Canada, so the effects of UVB light were clearly seen in the healthy volunteers. This study supports getting some sunlight exposure (on the skin), and perhaps supplementing with vitamin D in the winter.

From Medical Xpress: Where the sun doesn't shine? Skin UV exposure reflected in poop  ...continue reading "Exposure To Sunlight Improves Gut Microbes and Vitamin D Levels"

Published on Leave a comment on Children, Animals, and Gut Microbes

The evidence is growing. Another recent study found that exposure to dirt and animals in the first year of life is beneficial for development of a a rich and diverse gut microbiome - that is, for greater species "richness" as well as more beneficial microbes. This is linked to lower levels of allergies and asthma in children.

So don't worry about children being exposed to animal "germs" and getting dirty! Instead, consider the microbes as having health benefits, such as developing a "robust immune system". In summary, it now appears that in the first year of life the immune system needs lots of exposure to all sorts of microbes (e.g. from pets, animals, dirt)  to "train it" to develop normally.

The Ohio State University researchers compared 5 healthy rural Amish infants to 5 healthy non-Amish urban infants in Ohio, also found that all of the rural (Amish) children were breastfed, while 2 of the urban (non-Amish) children were only formula fed (some microbial differences there). The Amish households had farm animals (cattle, sheep, and/or horses) and pets (dogs and/or cats), while the non-Amish households had no contact with livestock, but did have a pet dog or cat. Just like in other studies, one pet doesn't seem to be enough - even more animal exposure in early childhood is best for the gut microbiome. [One study found a dose-dependent effect with exposure to 5 furry pets in early childhood was needed to prevent all allergies.]

Studies find that rural (Amish) children have a low incidence of allergies and asthma, while urban children have a high incidence of allergies and asthma. In this study, an example of microbial differences in the 2 groups of children was that Bifidobacterium bacteria were "enriched" in non-Amish (urban) infants, while Roseburia species were "enriched" in Amish (rural, farm-raised) infants. Similar gut microbe differences have been observed in other studies comparing rural and urban children, and both dietary differences (e.g. farm raised children eat lots of homegrown produce) and environmental differences (animal exposure) are thought to be responsible for the differences.

From Science Daily: Keeping livestock in the yard just might help your baby's immune system  ...continue reading "Children, Animals, and Gut Microbes"

Published on Leave a comment on Gut Bacteria Has An Effect On Some Medicines?

New research is raising questions about the role of gut bacteria in how people react to medications and whether the medicines are effective, at least some medications such as L-dopa treatment for Parkinson's disease. Why do medicines work for some people and not others? Perhaps the gut microbes are playing a part by interacting with the medicines! The gut microbes may actually be breaking down medicines and preventing them from reaching their target.

Researchers from Harvard University and University of California found that the composition of the gut microbes has an effect on whether the medicine L-dopa is effective or becomes ineffective as a Parkinson's disease treatment. They found that some bacteria can inactivate the medicine. Definitely research that needs following up on. Also, which medications is this true for?

Excerpts from Science Daily: Gut microbes eat our medication    ...continue reading "Gut Bacteria Has An Effect On Some Medicines?"

Published on Leave a comment on High Fiber Diet Protects The Colon’s Mucus Layer

An interesting study that showed that when gut microbes are deprived of dietary fiber (their food) they start to eat the natural layer of mucus that lines the colon. (The colon is part of the large intestine). This is important because the colon's mucus layer normally acts as a barrier to pathogenic microbes. Yes, it was done in mice, but the researchers feel that this study accurately models what also happens in humans. Their conclusion: when the microbes in the gut don't get enough dietary fiber from plants (such as whole grains, fruits, vegetables, seeds, nuts), then the microbes feed on the colon's mucus layer, which results in inflammation and makes the colon more vulnerable to pathogenic (disease causing) microbes. This is what some people refer to as "leaky gut".

Research shows that changes in the diet (high fiber vs low fiber) quickly results in changes in the gut microbes in humans and rodents - so it's important to consistently eat a lot of a variety of plant fiber. Currently the recommended daily fiber intake for adults is for 28 to 35 grams (chart of some high fiber foods). They found that some bacteria strains flourished the best in low or no fiber conditions and it was these bacteria that were involved in breaking down the mucus layer. The research also showed that what are called "prebiotics" (purified forms of soluble fiber similar to what some processed foods and supplements contain) also resulted in thinning of the colon's mucus layer - they did not properly feed the gut microbes. From Medical Xpress:

High-fiber diet keeps gut microbes from eating colon's lining, protects against infection

It sounds like the plot of a 1950s science fiction movie: normal, helpful bacteria that begin to eat their host from within, because they don't get what they want. But new research shows that's exactly what happens when microbes inside the digestive system don't get the natural fiber that they rely on for food. Starved, they begin to munch on the natural layer of mucus that lines the gut, eroding it to the point where dangerous invading bacteria can infect the colon wall. In a new paper in Cell, an international team of researchers show the impact of fiber deprivation on the guts of specially raised mice. The mice were born and raised with no gut microbes of their own, then received a transplant of 14 bacteria that normally grow in the human gut. 

The findings have implications for understanding not only the role of fiber in a normal diet, but also the potential of using fiber to counter the effects of digestive tract disorders. "The lesson we're learning from studying the interaction of fiber, gut microbes and the intestinal barrier system is that if you don't feed them, they can eat you," says Eric Martens, Ph.D., an associate professor of microbiology at the University of Michigan Medical School....Using U-M's special gnotobiotic, or germ-free, mouse facility, and advanced genetic techniques that allowed them to determine which bacteria were present and active under different conditions, they studied the impact of diets with different fiber content - and those with no fiber. They also infected some of the mice with a bacterial strain that does to mice what certain strains of Escherichia coli can do to humans - cause gut infections that lead to irritation, inflammation, diarrhea and more.

The result: the mucus layer stayed thick, and the infection didn't take full hold, in mice that received a diet that was about 15 percent fiber from minimally processed grains and plants. But when the researchers substituted a diet with no fiber in it, even for a few days, some of the microbes in their guts began to munch on the mucus.They also tried a diet that was rich in prebiotic fiber - purified forms of soluble fiber similar to what some processed foods and supplements currently contain. This diet resulted in the same erosion of the mucus layer as observed in the lack of fiber.

The researchers also saw that the mix of bacteria changed depending on what the mice were being fed, even day by day. Some species of bacteria in the transplanted microbiome were more common - meaning they had reproduced more - in low-fiber conditions, others in high-fiber conditions. And the four bacteria strains that flourished most in low-fiber and no-fiber conditions were the only ones that make enzymes that are capable of breaking down the long molecules called glycoproteins that make up the mucus layer....  Just like the mix of bacteria, the mix of enzymes changed depending on what the mice were being fed, with even occasional fiber deprivation leading to more production of mucus-degrading enzymes.

Images of the mucus layer, and the "goblet" cells of the colon wall that produce the mucus constantly, showed the layer was thinner the less fiber the mice received. While mucus is constantly being produced and degraded in a normal gut, the change in bacteria activity under the lowest-fiber conditions meant that the pace of eating was faster than the pace of production - almost like an overzealous harvesting of trees outpacing the planting of new ones. 

When the researchers infected the mice with Citrobacter rodentium - the E. coli-like bacteria - they observed that these dangerous bacteria flourished more in the guts of mice fed a fiber-free diet. Many of those mice began to show signs of illness and lost weight. When the scientists looked at samples of their gut tissue, they saw not only a much thinner or even patchy mucus later - they also saw inflammation across a wide area. Mice that had received a fiber-rich diet before being infected also had some inflammation but across a much smaller area. [Original study]

A thick mucus layer (green), generated by the cells of the colon's wall, provides protection against invading bacteria and other pathogens. This image of a mouse's colon shows the mucus (green) acting as a barrier for the "goblet" cells (blue) that produce it. Credit: University of Michigan

Published on Leave a comment on A Fungus May Be Playing A Role In Crohn’s Disease

Image result for ibd Exciting new research about what is going on in the gut microbiome (the community of microbes) of people with Crohn's disease - a debilitating intestinal bowel disease (IBD) which causes severe abdominal pain, diarrhea, weight loss, and fatigue. A number of earlier studies focused on gut bacteria and found dysbiosis (microbial community out of whack) in those with Crohn's disease.

This new research also looked at fungal species and found that there is an "abundance" of 2 species of bacteria (Serratia marcescens and Escherichia coli) and one fungal species (Candida tropicalis) and that these interact in the gut in persons with Crohn's disease. In persons with Crohn's disease the abundance of potentially pathogenic bacteria is increased (Escherichia coli, Serratia marcescens, and Ruminococcus gnavus), while beneficial bacteria (such as Faecalibacterium prausnitzii) are decreased. From Science Daily:

Fungus in humans identified for first time as key factor in Crohn's disease

A Case Western Reserve University School of Medicine-led team of international researchers has for the first time identified a fungus as a key factor in the development of Crohn's disease. The researchers also linked a new bacterium to the previous bacteria associated with Crohn's. The groundbreaking findings, published on September 20th in mBio, could lead to potential new treatments and ultimately, cures for the debilitating inflammatory bowel disease, which causes severe abdominal pain, diarrhea, weight loss, and fatigue. "We already know that bacteria, in addition to genetic and dietary factors, play a major role in causing Crohn's disease," said the study's senior and corresponding author, Mahmoud A Ghannoum, PhD.

Both bacteria and fungi are microorganisms -- infinitesimal forms of life that can only be seen with a microscope. Fungi are eukaryotes: organism whose cells contain a nucleus; they are closer to humans than bacteria, which are prokaryotes: single-celled forms of life with no nucleus. Collectively, the fungal community that inhabits the human body is known as the mycobiome, while the bacteria are called the bacteriome. (Fungi and bacteria are present throughout the body; previously Ghannoum had found that people harbor between nine and 23 fungal species in their mouths.)

The researchers assessed the mycobiome and bacteriome of patients with Crohn's disease and their Crohn's-free first degree relatives in nine families in northern France and Belgium, and in Crohn's-free individuals from four families living in the same geographic area....The researchers found strong fungal-bacterial interactions in those with Crohn's disease: two bacteria (Escherichia coli and Serratia marcescens) and one fungus (Candida tropicalis) moved in lock step. The presence of all three in the sick family members was significantly higher compared to their healthy relatives, suggesting that the bacteria and fungus interact in the intestines. Additionally, test-tube research by the Ghannoum-led team found that the three work together (with the E. coli cells fusing to the fungal cells and S. marcescens forming a bridge connecting the microbes) to produce a biofilm -- a thin, slimy layer of microorganisms found in the body that adheres to, among other sites, a portion of the intestines -- which can prompt inflammation that results in the symptoms of Crohn's disease.

This is first time any fungus has been linked to Crohn's in humans; previously it was only found in mice with the disease. The study is also the first to include S. marcescens in the Crohn's-linked bacteriome. Additionally, the researchers found that the presence of beneficial bacteria was significantly lower in the Crohn's patients, corroborating previous research findings.

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Another interesting factoid about the human gut microbiome - it has circadian rhythms. This also has implications for timing of medical treatments and medicines. From Science Daily:

Jet lag can cause obesity by disrupting the daily rhythms of gut microbes

Organisms ranging from bacteria to humans have circadian clocks to help them synchronize their biological activities to the time of day. A study now reveals that gut microbes in mice and humans have circadian rhythms that are controlled by the biological clock of the host in which they reside. Disruption of the circadian clock in the host alters the rhythms and composition of the microbial community, leading to obesity and metabolic problems.

Disruption of the circadian clock in humans is a hallmark of relatively recent lifestyle changes involving chronic shift work or frequent flights across time zones. These widespread behavioral patterns have been linked to a wide range of diseases, including obesity, diabetes, cancer, and cardiovascular disease. But, until now, it has not been clear how changes in circadian rhythms increase the risk for these diseases.

In the new study, Elinav and his team set out to determine whether gut microbes could be the missing link. When they analyzed microbes found in fecal samples collected from mice and humans at different times of day, they discovered rhythmic fluctuations in the abundance of microbes and their biological activities. The host's circadian clock and normal feeding habits were required for the generation of these rhythmic fluctuations in the gut microbes.

When mice were exposed to changing light-dark schedules and abnormal 24 hr feeding habits, the microbial community lost its rhythmic fluctuations and changed in composition. Moreover, a high-fat diet caused these jet-lagged mice to gain weight and develop metabolic problems associated with diabetes. Similarly, jet lag in two humans who had traveled from the United States to Israel changed the composition of gut microbes, favoring the growth of bacteria that have been linked to obesity and metabolic disease.

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Sad, but not surprising results. It highlights the damage repeated courses of antibiotics, and even illness, do to gut microbial communities. The researchers write that during a prolonged stay in ICU they found the emergence of "ultra-low-density communities" (only 1 to 4 bacteria species) in patients. From Science Daily:

Critically ill ICU patients lose almost all of their gut microbes and the ones left aren't good

Researchers at the University of Chicago have shown that after a long stay in the Intensive Care Unit (ICU) only a handful of pathogenic microbe species remain behind in patients' intestines. The team tested these remaining pathogens and discovered that some can become deadly when provoked by conditions that mimic the body's stress response to illness.

"Our hypothesis has always been that the gut microflora in these patients are very abnormal, and these could be the culprits that lead to sepsis," he says. The current study supports this idea. Alverdy and Olga Zaborina, a microbiologist, wanted to know what happens to the gut microbes of ICU patients, who receive repeated courses of multiple antibiotics to ward off infections.

They found that patients with stays longer than a month had only one to four types of microbes in their gut, as measured from fecal samples -- compared to about 40 different types found in healthy volunteers.

Four of these patients had gut microbe communities with just two members-- an infectious Candida yeast strain and a pathogenic bacterial strain, such as Enterococcus faecium or Staphylococcus aureus and other bugs associated with hospital-associated infections. Not surprisingly, almost all of the pathogenic bacteria in these patients were antibiotic resistant.

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Here are some more articles that I found regarding psychobiotics or the use of probiotics to affect behavior and treat psychiatric disorders.  A probiotic is a microorganism introduced into the body for its beneficial properties. Even though the articles are from 2013, they all give slightly different information about this emerging and exciting new field. Please note that psychotropic means having an effect on how the mind works (and it usually refers to drugs that affect a person's mental state). Remember that this area of research and terminology used is in its infancy. From Medscape (November 2013):

Probiotics a Potential Treatment for Mental Illness

Probiotics, which are live bacteria that help maintain a healthy digestive system, are now often promoted as an important part of dietary supplements and natural food products. "Many of the numerous health-improvement claims have yet to be supported scientifically..."

They note that the term "psychobiotic" was created as recent studies have begun to explore a possible link between probiotics and behavior.  "As a class of probiotic, these bacteria are capable of producing and delivering neuroactive substances such as gamma-aminobutyric acid [GABA] and serotonin, which act on the brain-gut axis," they write.

For this review, the investigators sought to examine studies that assessed whether ingesting these bacteria "in adequate amounts" could potentially lead to an effective treatment for depression and other stress-related disorders. In 1 of the preclinical studies examined, mice that ingested L rhamnosus showed reduced anxiety scores and "altered central expression" on both the GABA type A and type B receptors.

And a study of human patients with chronic fatigue syndrome showed that those who consumed an active strain of L casei 3 times a day had significantly higher improvement scores on anxiety measures than did those who received matching placebo. This provides "further support for the view that a probiotic may have psychotropic effects," write the researchers.

Still, Dr. Dinan called for caution. "What is clear at this point is that, of the large number of putative probiotics, only a small percentage have an impact on behavior and may qualify as psychobiotics," said Dr. Dinan. He added that for now, the field needs to wait for large-scale, placebo-controlled trials to provide definitive evidence of benefit and to detect which probiotics have psychobiotic potential.

Dr. Camille Zenobia wrote this in August 2013. From Real Clear Science:

Can 'Psychobiotic' Bacteria Affect Our Mood?

But what about your brain? Apparently, bacteria influence what’s going on up there, too. Within the last several years, a blossoming field of study called “microbial endocrinology” has provided some provocative insights about the relationship between our GI microbiota and our mood and behavior.

Studies in the field of microbial endocrinology have implicated GI microbes as a factor that can regulate the endocrine system. This could have both good and bad effects since the endocrine system is responsible for the production of hormones and coordinates metabolism, respiration, excretion, reproduction, sensory perception and immune function.

From Nov. 2013 Popular Science:

Forget Prozac, Psychobiotics Are The Future Of Psychiatry

The answer lies in the fact that many psychiatric illnesses are immunological in nature through chronic low level inflammation. There is a plethora of evidence showing the link between gut microbiota and inflammation and studies on probiotic strains have revealed their ability to modulate inflammation and bring back a healthy immunological function.  In this regard, by controlling inflammation through probiotic administration, there should be an effect of improved psychiatric disposition.

The authors bring up another reason why psychobiotics are so unique in comparison to most probiotics.  These strains have another incredible ability to modulate the function of the adrenal cortex, which is responsible for controlling anxiety and stress response. Probiotic strains, such as Lactobacillus helveticus and Bifdobacterium longum have shown to reduce levels of stress hormones and maintain a calmer, peaceful state.  There may be a host of other probiotic bacteria with the same ability although testing has been scant at best.

Finally, the last point in support of psychobiotics is the fact that certain strains of bacteria actually produce the chemicals necessary for a happy self.  But as these chemicals cannot find their way into the brain, another route has been found to explain why they work so well.  They stimulate cells in the gut that have the ability to signal the vagus nerve that good chemicals are in the body.  The vagus nerve then submits this information to the brain, which then acts as if the chemicals were there.  

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Lately some articles have been mentioning the amazing possibility of new treatments for psychiatric disorders using bacteria as psychobiotics. Think of probiotics (microorganisms that have beneficial effects when consumed) that affect the brain. Researchers promoting the use of this term define a psychobiotic as "a live organism that, when ingested in adequate amounts, produces a health benefit in patients suffering from psychiatric illness". This new emerging field is just in its infancy. Lots of speculation and anecdotal evidence, and a few tantalizing studies.

I think the following article is a good introduction to this research area of the gut and mind/brain interaction, even though it was published in late 2013. Or you could order the newly published scholarly book "Microbial Endocrinology: The Microbiota-Gut-Brain Axis in Health and Disease" (Editors M.Lyte and J.F.Cryan) with a $189. purchase price (!).  From November 2103 NPR:

Gut Bacteria Might Guide The Workings Of Our Minds

Could the microbes that inhabit our guts help explain that old idea of "gut feelings?" There's growing evidence that gut bacteria really might influence our minds. 

"I'm always by profession a skeptic," says Dr. Emeran Mayer, a professor of medicine and psychiatry at the University of California, Los Angeles. "But I do believe that our gut microbes affect what goes on in our brains." Mayer thinks the bacteria in our digestive systems may help mold brain structure as we're growing up, and possibly influence our moods, behavior and feelings when we're adults. "It opens up a completely new way of looking at brain function and health and disease," he says.

So Mayer is working on just that, doing MRI scans to look at the brains of thousands of volunteers and then comparing brain structure to the types of bacteria in their guts. He thinks he already has the first clues of a connection, from an analysis of about 60 volunteers. Mayer found that the connections between brain regions differed depending on which species of bacteria dominated a person's gut. 

But other researchers have been trying to figure out a possible connection by looking at gut microbes in mice. There they've found changes in both brain chemistry and behavior. One experiment involved replacing the gut bacteria of anxious mice with bacteria from fearless mice. "The mice became less anxious, more gregarious," says Stephen Collins of McMaster University in Hamilton, Ontario, who led a team that conducted the research. It worked the other way around, too — bold mice became timid when they got the microbes of anxious ones. And aggressive mice calmed down when the scientists altered their microbes by changing their diet, feeding them probiotics or dosing them with antibiotics. 

Scientists also have been working on a really obvious question — how the gut microbes could talk to the brain. A big nerve known as the vagus nerve, which runs all the way from the brain to the abdomen, was a prime suspect. And when researchers in Ireland cut the vagus nerve in mice, they no longer saw the brain respond to changes in the gut. "The vagus nerve is the highway of communication between what's going on in the gut and what's going on in the brain," says John Cryan of the University College Cork in Ireland, who has collaborated with Collins.

Gut microbes may also communicate with the brain in other ways, scientists say, by modulating the immune system or by producing their own versions of neurotransmitters. "I'm actually seeing new neurochemicals that have not been described before being produced by certain bacteria," says Mark Lyte of the Texas Tech University Health Sciences Center in Abilene, who studies how microbes affect the endocrine system. "These bacteria are, in effect, mind-altering microorganisms."

This research raises the possibility that scientists could someday create drugs that mimic the signals being sent from the gut to the brain, or just give people the good bacteria — probiotics — to prevent or treat problems involving the brain. Experiments to test whether changing gut microbes in humans could affect the brain are only just beginning. 

One team of researchers in Baltimore is testing a probiotic to see if it can help prevent relapses of mania among patients suffering from bipolar disorder."The idea is that these probiotic treatments may alter what we call the microbiome and then may contribute to an improvement of psychiatric symptoms," says Faith Dickerson, director of psychology at the Sheppard Pratt Health System.

Mayer also has been studying the effects of probiotics on the brain in humans. Along with his colleague Kirsten Tillisch, Mayer gave healthy women yogurt containing a probiotic and then scanned their brains. He found subtle signs that the brain circuits involved in anxiety were less reactive, according to a paper published in the journal Gastroenterology.

But Mayer and others stress that a lot more work will be needed to know whether that probiotic — or any others — really could help people feel less anxious or help solve other problems involving the brain. He says, "We're really in the early stages."

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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.