BBC – Future – What we do and don't know about intestinal health


In your gastrointestinal (GI) tract there are trillions of microorganisms, including bacteria, fungi, and viruses. You have the same number of microorganisms there, mostly in the large intestine, as do human cells throughout your body. But only 10% to 20% of the bacteria in your intestine will be shared with other people.

Microbial & me

Life in all of us

Microbes & me is a new collaboration series between BBC Future and BBC Good Food.

In this series, we will look at the latest research on bacterial microbiomes that live in us.

We will explore how it affects our health, what might have an adverse effect on it, and recommend recipes that might help it develop.

These microbiomes are very different from person to person, depending on diet, lifestyle and other factors, and they affect everything from health to taste, weight, and our mood. But even though it is one of the most studied body parts, there is still a long way to go to fully understand our guts. BBC Future examines the findings of several sciences so far.


Our food has a big influence on the intestinal microbiome. Research has found an association between Western diets, usually high in fat and animal protein and low in fiber, with increased production of compounds that cause cancer and inflammation. The Mediterranean diet, on the other hand, which is usually high in fiber and low in red meat, is likened to an increase in fecal short-chain fatty acid levels, which have been found to have anti-inflammatory effects and enhance the immune system.

Scientists hope that research across the population will advance existing findings. One such project, the ongoing American Gut Study, collects and compares intestinal microbiomes of thousands of people living in the US. So far, research shows that those on diets including more plant foods have more diverse microbiomes, and those that are "very different" from those who don't, said Daniel McDonald, the project's scientific director.

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"We cannot say that one end is healthy or unhealthy, but we suspect that those who eat fruits and vegetables have very healthy microbiomes," he said. However, McDonald added, it was unclear whether and how to radically switch from a diet high in plant foods to a diet low in healthy foods would change the microbiome.


There has been a lot of hype around the health benefits of prebiotics and probiotics in recent years, but while they are increasingly being used in treatments including inflammatory bowel diseases such as Crohn's disease and ulcerative colitis, some reviews suggest there needs to be further research on strains and which doses are effective.

Eran Elinav, an immunologist at the Weizmann Institute of Science in Israel, recently discovered that some people are immune to probiotics – although he did this in a relatively small study that would require future research to arrive at concrete answers. He gave 25 healthy people both 11 types of probiotics or placebo, and tested their microbiomes and intestinal function with colonoscopy and endoscopy before and three weeks after the intervention.

"People can be divided into two groups – the probiotics are welcomed by native microbiomes and allowed to colonize the GI tract, where probiotics can change microbiomes, and those who are resistant. In this group, probiotics are not allowed to settle, and do almost nothing. even so, "he said.

Researchers can predict which category someone will fall into by examining the features in their microbiome. Elinav said his findings suggested the need to adjust further to personalize probiotics with individual needs.


Intestinal microbiota has a major role in the health and function of the GI tract, with evidence that conditions such as irritable bowel syndrome (IBS) often coincide with changing microbiota. But it also plays a much wider role in our health, and this is very much determined in the first few years of life.

Our microbiomes begin to develop when we are born, when microbes colonize the human intestine. Babies born naturally are known to have a higher number of intestinal bacteria than those born by caesarean section because of the contact they make with their mother's vaginal and intestinal bacteria, said Lindsay Hall, leader of microbiome research at Quadram Institute of Bioscience.

"Babies born by caesarean section lose the initial inoculation, and some microbes that come into contact with it come from the skin and environment," Hall said.

A number of studies have shown that caesarean section affects long-term health – Lindsay Hall

"It is very important for babies to develop their immune systems. Recent work has shown that disturbances in the early life of intestinal microbiomes have negative consequences for the health of the host," he said.

"A number of studies have shown that caesarean section affects long-term health, and there is strong evidence that this operation is at higher risk of allergies, and a less powerful ecosystem, which means you are more susceptible to changes and disorders, such as antibiotics.

"However, there is no strong evidence about what this difference specifically means for the immune system."

There are also differences in microbiomes of breastfed infants and formula milk. Bifidobacterium, a group of bacteria related to health, is often found in the stomach contents of breastfed babies.

"We know that Bifidobacterium is able to digest the components found in breast milk. This component is usually not found in formula milk, which is why formula-fed babies have less than that," Hall said.

Scientists are increasingly understanding how the intestines can also be used to treat diseases. One of the latest treatments in the field is fecal microbiota transplants, in which microbiota of healthy people is inserted into the patient's intestine.

This procedure is used to treat antibiotic-resistant clostridium difficile intestinal bacteria, which can infect the intestines and cause diarrhea. Although there is no conclusive evidence about the underlying mechanism, it is believed that transplants will replenish the microbiome with a variety of bacteria that help fight viruses.

We have not set what is normal, but also what is normal for each individual – Fiona Pereira

The big question about this transplant is determining what the normal intestinal microbiome is.

"We have not set what is normal, but also what is normal for each individual. It depends on their ethnicity, environment and other things they have been through," said Fiona Pereira, head of business development and strategies for the department of surgery and cancer in Imperial College London, which oversees research on the relationship between the microbiome and diet.

Pereira said that if scientists can get a clear understanding of what is healthy in different ethnic groups and age groups, they can then profile someone and see how their intestines vary and what they have to do with this – can be diet, environment, or genetic predisposition for certain diseases.


It is well known that antibiotics can dramatically change our intestinal microbiota.

The intestine is an environment where harmless and beneficial bacteria are in close contact with opportunistic pathogens that cause infection, said Willem van Schaik, professor at the University of Birmingham and lead researcher from the new study that identified more than 6,000 new antibiotic resistance genes in pathogens .

He found that most of these pathogens are not related to DNA that can transfer between bacteria, which means there is no immediate risk of spreading these genes from normal bacteria to pathogens.

Our findings highlight how many genes are resistant in the microbiome and can potentially be mobilized to become opportunistic pathogens – Willem van Schaik

However, many genes that are thought to have been repaired in certain bacterial environments can begin to spread with excessive use of antibiotics, which can put pressure on resistant genes confined within a single bacterial cell, causing them to move.

"Our findings highlight how many genes are resistant in the microbiome and potentially can be mobilized to become opportunistic pathogens. They should be seen as a warning that there is a large reservoir of these genes that we do not want us to start mobilizing," van Schaik said.


The brain and intestine have a strong two-way communication system called the intestinal-brain axis. Each is very important for others – studies have found that abnormal brain development in the absence of intestinal microbiomes. However, a recent review states that research has not found the right intestinal bacteria that are important for brain development.

Further investigations reveal how the intestines link with the brain, including our moods and mental health, said Katerina Johnson, a researcher from intestinal brain microbiomas at the University of Oxford.

"Research shows that if we take intestinal bacteria from humans that are suppressed and colonize the intestines of mice, mice show changes in their behavior and physiology which are characteristic of depression," he said.

Intestinal microbes can produce most of the neurotransmitters found in the human brain, including serotonin, which play a key role in regulating moods. It is hoped that scientists will soon be able to understand how microbes can be used to produce neurotransmitters to treat psychiatric and neurological disorders that our microbiomes favor, including Parkinson's disease and multiple sclerosis.


We have also begun to see how intestinal microbes can affect behavior. Some studies, mostly carried out on animals, for example, show that certain types can influence brain chemistry and behavior to make animals act more socially.

Germ-free animals that have no microbial exposure, on the other hand, have shown deficits in social behavior, and researchers have found that this can be recovered by adding certain types of bacteria such as Lactobacillus, often found in yogurt, according to Johnson.

Behavior change tends to be a by-product of processes that help microorganisms grow and compete in the intestine, such as fermentation

A recent paper titled & # 39; Why does the microbiome affect behavior? & # 39; examines the theory that intestinal microbiomes have evolved to manipulate human hosts for their own success, such as parasites, by making hosts more friendly to be transmitted.

This paper argues, however, that this theory is not possible, and behavior change tends to be a by-product of processes that help microorganisms grow and compete in the intestine, such as fermentation.

"Intestinal microbiomes are so diverse that, even if there are types of bacteria that produce active chemicals to manipulate our behavior, these bacteria will be quickly defeated by other bacteria that do not invest extra energy to produce compounds," said Johnson, one of the paper's authors.


Science has not defined what a healthy microbiome is like, and the conclusion is still a little far away. But there is a growing consensus that environmental factors, such as diet and antibiotics, affect our microbiomes more than our genes, and that more diverse microbiomes are better for us.

"Although we can change our microbiome with our diet, they seem to have a set point that they often return after a temporary disruption," Johnson said. "But one thing we can do is eat more fiber, to increase intestinal diversity, which is often associated with health."

While there have been many advances in microbiome research in recent years, there are still some challenges.

One of them is dependence on a method called 16S rRNA sequencing, said McDonald, who looked at the specific region of a single gene that is believed to exist in all bacteria. E. coli is an example of why this method is too broad, McDonald said.

"Although there are pathogenic E. coli, there is also E. coli which plays a neutral or beneficial role in the intestine, all of which cannot be distinguished from the current method we use. Increasing E. coli levels does not mean it is bad for you."

McDonald's advice is we must remain cautious.

"There are a lot of cool things that microbiome research will aim at, and there are interesting developments that are happening now, but while continued progress will lead to improved health, many of these are related to basic research, and there is a lot of research that we can do with mice that don't we can translate it to humans, because it's not safe to do it. "

Meanwhile, what is most recommended by scientists is to eat our vegetables.

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