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Tag: gut microbes

Published on Leave a comment on Altered Gut Microbiomes In Persons With Pain Conditions
Wrist pain Credit: Wikipedia

We know that there are microbiomes  (communities of bacteria, viruses, fungi) throughout the body, and that there are microbial patterns or "microbial signatures" found in different diseases. But now it appears that there are microbial signatures for a whole list of pain conditions, such as fibromyalgia, complex regional pain syndrome (CRPS), arthritis, and migraine.

In other words, the gut microbiome is different between those with a pain condition compared to healthy individuals without the condition. One question is: does chronic pain cause the microbiome to change or do microbial changes or shifts cause chronic pain? Or does the presence of certain bacteria protect against different pain conditions?

It is still unknown whether probiotic supplementation would help these conditions because the studies are not yet done. But researchers do suggest eating an anti-inflammatory diet - which means a diet rich in fruits, vegetables, whole grains, legumes (includes beans), fish, seeds, nuts, and olive oil. This kind of diet has lots of fiber to feed and support beneficial bacteria.

Also, avoid ultra-processed food as much as possible, including processed meats and soda, because these are associated with harmful bacteria in the gut. Read the ingredient list, and try to avoid foods with ingredients not found in your kitchen (e.g., emulsifiers, colors, natural flavors, artificial flavors, carrageenan, soy lecithin, guar gum)

From Medscape: Gut Microbiome Changes in Chronic Pain — Test and Treat?

A new study adds to what has been emerging in the literature — namely that there appear to be gut microbiome “signatures” for various pain conditions — suggesting that microbiome-based diagnostics and therapeutics may one day be routine for a broad range of pain conditions. ...continue reading "Altered Gut Microbiomes In Persons With Pain Conditions"

Published on Leave a comment on Exercise Is Beneficial In Cancer

Exercise helps fight cancer. Wow! What a headline. But is it true?

Researchers studied exercise, and its effect on gut microbes and the molecules they produce in response to the exercise. They found that certain gut microbes produce a metabolite (formate) that is increased with exercise and which boosts the potency of CD8 T cells in the immune system – which are key to fighting cancer. The initial tests were done in mice, but then the researchers took their results and applied them to humans with melanoma.

They found that in humans with melanoma, high levels of formate had longer progression-free survival (they live with the cancer, but it doesn't get worse). This is big news! Of course, further studies are ongoing.

Bottom line: Exercise is beneficial for all sorts of reasons, but one may be its effects on cancer. Studies find that exercise is known to help prevent cancer and suppress the growth of existing tumors.

From New Scientist: Exercise helps fight cancer – and we may finally know why

Exercise seems to help prevent cancer and reduce the growth of tumours, and that protective effect may be due to the way working out changes the gut microbiome. ...continue reading "Exercise Is Beneficial In Cancer"

Published on Leave a comment on A Mediterranean Style Diet Feeds Beneficial Gut Bacteria

The incidence of both intestinal bowel diseases (IBD) and colorectal cancer is rapidly increasing in developed countries (e.g., US, Canada, Europe). There are many theories over why this is occurring, with most researchers thinking a person's diet plays a role. A big suspect in promoting IBD and colorectal cancer is the Western diet, which has lots of ultra-processed foods and is also low in fiber.

A recent large study looked at 6 major diets and how they impact the gut microbiome. The six dietary patterns were: Western diet, Mediterranean diet, high-fiber diet, plant-based diet, high protein diet, and ketogenic diet.

And surprise, surprise - eating a Western diet resulted in having an increase in gut bacterial species linked to chronic inflammation, heart disease, colorectal cancer, IBD, and diabetes. The Mediterranean style diet had an increase in bacterial species linked to a lower risk of cardiovascular disease, IBD, and type 2 diabetes. In fact, all 6 diets had distinct bacterial profiles in the gut.

Bottom line: The foods a person eats can either feed and nourish beneficial bacteria or harmful bacteria (linked to cancer and IBD). Best for health is a Mediterranean style diet (lots of fruits, vegetables, whole grains, legumes, seeds, nuts), and avoiding ultra-processed foods. You are what you eat!

From Medical Xpress: Western diets pose greater risk of cancer and inflammatory bowel disease, study finds

Western diets pose a greater risk of inflammatory bowel disease (IBD) and colorectal cancer, according to a milestone review of what people eat around the world. ...continue reading "A Mediterranean Style Diet Feeds Beneficial Gut Bacteria"

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.

Published on

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.

Published on

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.