The Microbiome: 33 Ways Gut Bacteria Affect Your Body & Mind

When the Menu Turns Raw, Your Gut Microbes Know What to Do

The Microbiome: 33 Ways Gut Bacteria Affect Your Body & Mind
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It was a challenge un any other the chef-turned-graduate student had faced: Vayu Maini Rekdal had to create a menu where every ingredient could be eaten either raw or cooked. No pickling was allowed, nor fermented toppings soy sauce or miso. Nothing could be processed in any way, so things tofu were out. And the more sweet potatoes he could serve up, the better.

“It was extremely challenging,” said Mr. Rekdal, a chemistry graduate student at Harvard.

Rising to the occasion, Mr. Rekdal concocted chia seed breakfast puddings that could be cooked or chilled. He made raw and cooked pea-sweet potato-tahini patties. And for three days, eight volunteers dined on the unusual menu, providing stool samples to assist in research that could eventually help illuminate the evolution of the human microbiome.

The work was led by Rachel Carmody, a professor of human evolution at Harvard, and Peter Turnbaugh, a professor of microbiology at the University of California, San Francisco. They were studying the gut microbiome, the collection of microbes that live in our intestines and influence our immune system and various other parts of our biology, as well as help us digest food.

They had discovered that mice, eating a diet of starchy foods sweet potatoes, developed vastly different microbiomes, depending on whether their food had been cooked or served raw. A switch from one to the other provoked a rapid shift in their guts’ microbial inhabitants.

Now, they wanted to see if the same was true with humans.

The results of the experiment appear in a paper published last month in Nature Microbiology. Although the sample size was small, and the effect was not as strong as in mice, people’s microbiomes do seem to shift on a raw diet, and very rapidly.

While the human study was very short, it raises intriguing questions about whether starting to eat cooked food, eons ago, shaped the evolution of the organisms that live inside us, and whether our bugs may have helped us survive times of scarcity.

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As a graduate student, Dr. Carmody found that mice fed cooked diets quickly grew plump. Cooking alters the structure of many molecules, making more energy available to the mice. But she was also interested in the microbial community living in the mouse gut, which helps digest food and interacts with its host’s biology in a variety of ways.

In the new paper, she and her collaborators found that feeding mice meat that was raw or cooked changed little about their microbiomes. But with sweet potatoes, meant to stand in for tubers that early humans might have eaten, it was a different story.

Cooking produced significant changes, affecting the kinds of microbes that thrived and which genes they used.

The scientists traced the effect to the sweet potato’s starches, which are difficult for mammals to digest raw but become more easily digestible once cooked. Depending on which kind of starch molecules arrive in the large intestine, different groups of microbes might take on the disposal job and subsequently surge in numbers.

“ any ecosystem, if you dramatically change foodstuffs coming into it, some species will thrive over others,” Dr. Carmody said.

The researchers also found that raw sweet potatoes inflicted an impressive amount of damage on the microbiome of the mouse gut, similar to what occurs in mice fed an antibiotic. That may result from antimicrobial compounds in the sweet potato, which may be inactivated by cooking.

If cooking, at least of starches, can alter the ecology of the gut, then have humans been shaping our microbiomes ever since we learned to put prehistoric tubers in the fire? If our ancestors did eat these kinds of foods, and switched to cooking them, it may be that some tasks that used to be handled by gut microbes were no longer necessary, says Stephanie Schnorr, a biological anthropologist at the University of Nevada, Las Vegas, who was not involved in the study. As a result, the bacteria might have lost the related genes or gained new roles.

The ability of the gut’s microbial residents to shift themselves so dramatically even in the short term may have had other benefits for their hosts. If microbiomes can retool themselves on little notice to handle changes in diet, they may have helped early humans cope with lean days where tubers were the only foods or times when only meat was on the menu.

“The microbiome could essentially help us, within 24 hours, maximize our ability to digest nutrients even on a low-quality diet,” Dr. Carmody said.

Still, the extent to which humans and their live-in digestion engines evolved together is debated.

Mice given human microbiomes are generally healthy, suggesting that a host and its microbes don’t fit together a lock and key, honed by eons of mutual evolution.

However, in some situations, when a mouse gets sick, it is more ly to recover when it has its own microbiome. That may imply that there has been some co-evolution between the organism and its microbiome, Dr. Carmody said.

The interaction between host and microbes is complex, and longer studies with more people eating a raw or cooked diet would be necessary to probe how such a dietary change affects the microbiome and its host in the longer term.

People actually did enjoy the menu, by and large, Mr. Rekdal said, which included salads of mushrooms, sweet potato and cauliflower, either roasted or raw, and smoothies of cooked or raw fruit in addition to the puddings and patties. Some of the raw items weren’t wildly popular, but he has received many requests for the chia pudding recipe.

He sees the study as helping advance our understanding of cooking, a particularly ancient kind of applied chemistry.

“It’s a form of science,” he said, “that humans have been practicing for thousands and thousands of years.”

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How the bacteria in your gut affect your mind and body

The Microbiome: 33 Ways Gut Bacteria Affect Your Body & Mind

Have you ever felt “butterflies in your stomach,” or made a “gut decision”?

That might have been your “second brain” — otherwise known as your gut — talking. Our guts are composed of over 100 trillion bacteria and about 100 million nerve cells line the entire gastrointestinal tract. The gut and brain are often communicating with each other along what’s known as the gut-brain axis.

Both mental and physical health — from Alzheimer’s disease to depression — can be affected by the health of our guts. Recent scientific research has shown the numerous ways our guts work and heal.

Our gut bacteria produce many of the chemicals that affect our mood

People usually assume that most of our serotonin, often known as the happy chemical, is housed in our brain.

However, approximately 95 percent of our body’s serotonin is actually found within the gut. GABA, another neurotransmitter that improves mood, is also often present in the gut.

And both are released from good bacteria, meaning that the gut has a tremendous effect on our overall health.

A large part of our immune system is also housed in the gut and it's connected to the brain via the vagus nerve, which, in addition to the digestive tract, also has crucial functions in many other parts of the body. The vagus nerve acts a highway of information between the gut and the brain, transporting inflammatory markers back and forth.

Inflammation, the body’s defense mechanism against injury or foreign invaders, is usually a healthy response. However, chronic inflammation — lasting months or even years — can slowly and subtly cause damage. It has been linked to countless chronic diseases and mental illnesses, including anxiety and depression.

Heightened inflammation alerts the central nervous system (CNS) to induce symptoms resembling depression, such as lethargy, sleep disturbances and changes in appetite. The two-way link between inflammation and depression promotes the idea that reducing inflammation through a healthier, balanced diet and by regulating stress can be beneficial to our entire health.

Chronic inflammation can be caused by autoimmune disorders and infection, but there are also unexpected causes, such as long-term exposure to pollutants, harmful industrial chemicals, unhealthy diets and chronic stress.

Bad gut bacteria have been linked to neurologic and chronic diseases

Various studies have catalogued the association between imbalanced gut microbiota — usually marked by bad bacteria — and neuroimmune and neuroinflammatory diseases, such as Alzheimer’s, multiple sclerosis and Parkinson’s disease. Gut imbalances may also contribute to other types of critical diseases, including obesity and colorectal cancer.

More research is needed to understand if these links are happenstance or if they’re actually caused by bad gut bacteria. But restoring the gut’s bacterial balance may be a crucial factor in the future for preventing and treating these types of diseases and chronic illnesses.

It's possible to cultivate a healthy gut

The good news is that there are many ways to reverse inflammatory responses that stem from an unhealthy gut. Our gut microbiota is extremely responsive to outside factors, such as diet, smoking, antibiotic use, infections and stress.

Some basics steps everyone can take to directly combat inflammation include:

Avoiding diets that are high in saturated fats and sugars. Anti-inflammatory foods include foods with healthy fats, such as walnuts, flaxseed and oily fish salmon or sardines; fruits and vegetables and whole grains.

Practicing well-being. Try mindfulness or meditation or just figure out a way to reduce stress that works for you, and commit to it.

Get physically active. Beyond the tangible benefits of improving our heart health and helping with weight control, exercise has been proven to enrich the diversity of our gut bacteria and reduce inflammation. As little as 20 minutes a day can produce anti-inflammatory benefits.

Lucille Tang is a member of the ABC News Specialized Units.

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Association between gut bacteria and emotion, suggests study

The Microbiome: 33 Ways Gut Bacteria Affect Your Body & Mind

Researchers have identified gut microbiota that interact with brain regions associated with mood and behavior. This may be the first time that behavioral and neurobiological differences associated with microbial composition in healthy humans have been identified.

Brain-gut-microbiota interactions may play an important role in human health and behavior.

Previous research suggests that microbiota, a community of microorganisms in the gut, can influence behavior and emotion.

Rodent models have demonstrated the effects of gut microbiota on emotional and social behaviors, such as anxiety and depression. There is, however, little evidence of this in humans.

For this study the researchers sought to identify brain and behavioral characteristics of healthy women clustered by gut microbiota profiles.

Forty women supplied fecal samples for profiling, and magnetic resonance images were taken of their brains as they viewed images of individuals, activities or things that evoked emotional responses.

The women were divided by their gut bacteria composition into two groups: 33 had more of a bacterium called Bacteroides; the remaining seven had more of the Prevotella bacteria. The Bacteroides group showed greater thickness of the gray matter in the frontal cortex and insula, brain regions involved with complex processing of information.

They also had larger volumes of the hippocampus, a region involved in memory processing. The Prevotella group, by contrast, showed more connections between emotional, attentional and sensory brain regions and lower brain volumes in several regions, such as the hippocampus.

This group's hippocampus was less active while the women were viewing negative images. They also rated higher levels of negative feelings such as anxiety, distress and irritability after looking at photos with negative images than did the Bacteroides group.

These results support the concept of brain-gut-microbiota interactions in healthy humans.

Researchers do not yet know whether bacteria in the gut influence the development of the brain and its activity when unpleasant emotional content is encountered, or if existing differences in the brain influence the type of bacteria that reside in the gut. Both possibilities, however, could lead to important changes in how one thinks about human emotions.

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Story Source:

Materials provided by University of California – Los Angeles Health Sciences. Note: Content may be edited for style and length.

Journal Reference:

  1. Kirsten Tillisch, Emeran Mayer, Arpana Gupta, Zafar Gill, Rémi Brazeilles, Boris Le Nevé, Johan E.T. van Hylckama Vlieg, Denis Guyonnet, Muriel Derrien, Jennifer S. Labus. Brain structure and response to emotional stimuli as related to gut microbial profiles in healthy women. Psychosomatic Medicine, 2017; 1 DOI: 10.1097/PSY.0000000000000493


Psychobiotics: How your microbiome can improve your mental health

The Microbiome: 33 Ways Gut Bacteria Affect Your Body & Mind

There’s a school of thought that says you are not one single organism, but rather a superorganism made up of many.

Human cells make up less than half of what you call ‘you’ – the rest are trillions of bacteria, fungi and viruses in your gut, on your skin and throughout your tissues, collectively known as your microbiome.

You need them because of the role they play in digesting your food and maintaining a healthy immune system. They need you because they need somewhere to live.

Now research is providing evidence that you have an extra reason to treasure the microbes living in the depths of your bowels: if they’re happy, you’re happy too.

The hitherto ludicrous-sounding idea that what happens in your intestines affects your mood has now got scientific backing.

And it’s become clear that it’s your gut bacteria that are doing the communicating with your brain and affecting your state of mind.

Scientists are providing evidence for this link, which they refer to as the ‘microbiome-gut-brain axis’.

Not only that, but they are showing that altering your gut bacteria (microbiota) by administering probiotics (live bacterial supplements) and prebiotics (dietary fibre supplements that encourage bacterial growth), you can actually improve stress response, reduce anxiety and mitigate the effects of other mental health problems.

These findings are giving rise to a whole new class of medicines: psychobiotics. The hope is that they will eventually provide powerful new treatments for depression and other mental health conditions, as well as helping us to deal with everyday stress and anxiety.

Read more about your microbiome:

This year a large review of studies found that probiotics yielded a small but significant effect in reducing anxiety and depression. A smaller study, published in the journal Translational Psychiatry, found that introducing a Bifidobacterium probiotic into the guts of healthy volunteers reduced their feelings of stress and improved their memory.

“I think the link is pretty strong,” says Tim Spector, professor of genetic epidemiology at King’s College London. “I’m not meeting anyone in the field who is saying there’s no link between your gut microbes and mental health.”

Such mind-body associations sound they belong to the province of alternative medicine. But doctors have long known that mental health problems, such as bipolar disorder and even autism, are often associated with gut problems, for example inflammation.

Until recently, the main clues that this had something to do with the bacteria in our bowels came from animal experiments. Studies on mice indicated that the bacteria in their guts were creating some sort of pathway between their bowels and their brains.

For example, research from the University of Colorado Boulder has shown that stress disrupts the normally stable relationship between gut bacteria and their host, resulting in gut inflammation. Giving rats a probiotic containing a bacterium known to be important to immune system function not only clears up the inflammation but reduces stress-related behaviour.

The large intestine is home to trillions of bacteria, fungi and viruses © Getty Images

Only in the past year have large population studies provided strong evidence that the same principle applies to humans. Patterns of anxiety and depression tally with certain patterns of gut microbes.

An analysis of data from more than 1,000 people in Belgium and Holland found that the presence of some types of gut bacteria was consistently associated with higher quality of life, while their absence was consistently associated with depression.

After the results were published, author Prof Jeroen Raes, a microbiologist at Belgium’s Katholieke Universiteit Leuven, said: “If you would have asked a neuroscientist 10 years ago whether they thought the gut microbiota could be linked to depression, many of them would have said you were crazy.”

Spector, whose microbiome research forms the basis of his book The Diet Myth, agrees that new studies are making scientists think differently. “But we still haven’t done the really big studies in humans,” he says. “We’re over the first hurdle of saying there’s a link, but we’re a long way from pinning down the exact mechanisms and treatments.”

The Alimentary Pharmabotic Centre (APC), part of University College Cork, Ireland, is at the forefront of trying to explain the microbiome-gut-brain axis.

Scientists there were the first to discover that transplanting gut microbes from a depressed rodent to a non-depressed rodent causes behaviour changes that indicate depression.

They are trying to use this new knowledge to develop ways of making us healthier and happier.

According to Ted Dinan, professor of psychiatry at University College Cork and the APC’s lead investigator on the microbiome-gut-brain axis, there are three ly communication routes between gut microbiota and the brain.

The brain needs a constant supply of tryptophan and the microbiota play a part in providing it

First, chemicals produced by bacteria may influence signals being sent from the millions of nerve endings in the digestive system to the brain via the vagus nerve, which runs all the way from the colon to the brain stem.

Second, research at the APC has indicated that some gut bacteria such as Bifidobacteria produce an amino acid called tryptophan. This is an important building block for the neurotransmitter serotonin – an essential brain chemical known to influence mood. “The brain needs a constant supply of tryptophan and the microbiota play a part in providing it,” says Dinan.

The third possibility is that bacteria are influencing gene expression in the brain. When microbes digest fibre, short-chain fatty acids are released as a by-product. It now seems ly, explains Dinan, that these acids travel through the bloodstream to the brain, where they act as epigenetic modulators, reprogramming some brain functions and influencing mood.

It’s thought that there are as many bacteria living in you as there are human cells in your body. The lodgers in your gut metabolise the food and drink you consume, eking out extra nutrients for your body as they do.

But the diversity of these bacteria and the way they interact can affect the signals that are sent to your brain via the nerves and chemical pathways based in your digestive system. As such, any nutritional deficiencies in your diet that lead to a drop in the diversity of your gut bacteria population could have a negative impact on your mental wellbeing.

Potential treatments and prevention

Researchers at the APC are focusing on the effects of probiotics and prebiotics on healthy volunteers, rather than those with clinically diagnosed depression. But already the evidence suggests doctors will, one day, be recommending such supplements to fill microbiota gaps that may be contributing to their patients’ mental health issues.

“We will see a scenario where probiotics or prebiotics will be recommended for people with milder forms of depression or anxiety,” says Dinan. “We don’t have the trials at the moment to make those recommendations, but it will happen in the future.”

Some of the most exciting potential lies in conditions for which treatment is currently difficult, ineffective or brings unpleasant side effects.

There is some research indicating that microbial transplants might be of use in people with autism spectrum disorders (ASD).

Arizona State University researchers have reported that by treating the gastrointestinal problems of children with ASDs with a transplant of microbes from a healthy donor, they also brought about improvements in language skills, social interaction and behaviour.

Prof Ted Dinan says that lots of plant-based foods can help boost the microbiome © Clare Keogh/University College Cork

In the battle against depression, which is triggered by a complex mix of genetic and environmental factors, probiotics could provide another weapon. “The effect size is pretty small for most pharmaceutical antidepressants, so the evidence so far is that some of these probiotics might do just as well as the more commonly prescribed drugs, which can have dangerous side effects,” says Spector.

His twin studies have indicated that, although genes are clearly important in determining who gets depression, adjusting the microbiome can help override genetic factors. “That gives me a lot of optimism,” he says.

There may also be a role for probiotics and prebiotics in promoting longer-term mental health, even if someone has had a previous mental health episode. A fascinating trial by researchers in Baltimore found that giving probiotics to people discharged from hospital following a ‘manic’ phase of bipolar disorder significantly reduced their chances of being re-hospitalised.

The dangers of hype

Sadly, we’re unly to see any of these treatments very soon. One problem is that there are currently no dose studies showing how much of a probiotic you have to take to make a difference.

Another problem, says Spector, is that every person’s microbiome is different.

“That means that one standard treatment won’t work on everybody, so we may well end up needing personalised probiotics, which will be expensive.”

Read more about mental health:

The public too have become wary. The hype that has surrounded probiotic and prebiotic food products, with companies claiming that sugary products with added bacteria improve gut health and boost your immune system, has often not been backed up by good science.

The danger now is that the genuine promise of psychobiotics may be underestimated. “Regulation of the food industry has been very lax in the past, so people have been able to make a lot of claims without very good data,” says Dinan.

“Fortunately, I think that’s changing now.”

Good diet, good mental health

But waiting for new psychobiotic treatments may be overlooking the single most important lesson from this research: that our diet has a crucial effect on our mental health. Psychiatrists and dietitians have, for years, been saying that changing our eating habits can make us happier, or at least help keep us on an even emotional keel.

“We may not have the trials at the moment to make exact recommendations,” says Dinan. “But I’m of the view that, even now, in psychiatry, there is no question that a poor diet is associated with poor mental health.

I run clinics for people with severe forms of depression who are not responding to antidepressants and if you give them appropriate dietary advice, in association with antidepressants, there’s no doubt you can get responses that you don’t get with the antidepressants alone.”

The happiness diet? © Getty Images

Dietary diversity is the key. The reason that probiotics work as treatments is that they fill a gap in your gut microbiome that disrupts its normal functioning. There’s enough evidence to suggest that a wide-ranging diet results in a microbiome full of different types of bacteria and leads to better mental health.

A diversity of plant-based food is particularly important, says Dinan (such as the Mediterranean diet below). He points out that studies have indicated that, because of the rise of processed food, most of us have many fewer different types of gut microbes than our grandparents and great grandparents. “We’re missing microbes,” he says.

“That might mean we’re dealing with stress less effectively.”

Spector agrees. “I do think the first thing to do before thinking about probiotics is to improve your diet first. We have to realise that one of the reasons we’re getting so much depression and anxiety in the UK is because of our very poor diet and our high rate of eating processed food. We need to get our diet diverse and cut out the chemicals before thinking about psychobiotics.”

The Mediterranean diet – is this the happiness diet?

The ‘Mediterranean diet’, long touted for its heart health benefits, is now being recommended as a diet that can make you happy because it encourages a diverse and healthy gut microbiome.

Scientists and health professionals define the Mediterranean diet loosely: eating lots of fresh fruit, vegetables, beans and lentils, nuts, whole grains and olive oil; occasional fish, chicken, eggs and dairy; and avoiding red meat, sweets, cakes and biscuits. The traditional foods of Cyprus, Croatia, Greece, Italy, Morocco, Portugal and Spain all generally fit the bill.

In October 2018, a review of evidence from four large diet studies involving 36,000 adults from Spain, France, the United Kingdom, Australia and the United States, concluded that people who follow this kind of diet have a 33 per cent lower risk of depression than people who don’t. Separate research presented to the American Psychiatric Association a year later also suggested that keeping to a Mediterranean diet protects against depression in later life.

Prof Ted Dinan, principal investigator at the Alimentary Pharmabotic Centre (APC) at University College Cork, says the secret of the diet is the diversity of plant products it introduces into the gut, thus encouraging a wide range of microbes to thrive there.

The (APC) is currently investigating what happens when people change to the diet. Early findings are that, in people who experience improvements in mental health as a result of going on the Mediterranean diet, there are significant changes in gut bacteria not apparent in control groups.