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BBC – Future – What we do and do not know about gut health

Inside your gastrointestinal tract (GI) has trillions of micro-organisms, including bacteria, fungi and viruses. You have roughly the same number of micro-organisms, mostly in the large intestine, as you do human cells in your entire body.

Microbes & me

The microbes & me is a new collaborative series between BBC

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

In the series, we will be looking at the recent research into the microbiome of bacteria that lives inside us

We will be exploring how it affects our health, what could be having detrimental

These microbiomes differ greatly from person to person, depending on diet, lifestyle and other factors, and they influence everything from our health to our appetites, weight and moods. But despite being one of the most researched parts of the body, there is still a long way to go to fully understanding our guts.


Our diets have a huge influence on the gut microbiome. Research has found links between Western diet, typically high in animal and protein-rich protein and low in fiber, with increased production of cancer-causing compounds and inflammation. The Mediterranean diet, on the other hand, which is typically high in fiber and low in red meat, has been associated with increased levels of faecal short-chain fatty acids, which have been found to have anti-inflammatory effects and improve the immune system .

Scientists hope that population-wide research will advance existing findings. One such project, the ongoing American Gut Study, is collecting and comparing the gut microbiomes of thousands of people living in the US. So far, research suggests those whose diets include more plant-based foods have a more diverse microbiome, and one that is "extremely different" from those who do not, says Daniel McDonald, project's scientific director

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"We can not say one end is healthy or unhealthy yet, but we suspect that those who eat a diet rich in fruits and vegetables have very healthy microbiomes," he says. However, McDonald adds, it is unclear if and how radically switching from a diet high in a plant-based diet to a low diet in healthy food 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 used in treatments including inflammatory bowel diseases such as Crohn's disease and ulcerative colitis, several reviews suggest there needs to be further research on which strains and dosages are effective

Eran Elinav, an immunologist at the Weizmann Institute of Science in Israel, recently found that some people are immune to probiotics ̵

1; although he did this in a relatively small study that would require future research to come to any concrete answers. He gave 25 healthy individuals either 11 strains of probiotics or placebo, and tested their microbiomes and gut function with colonoscopies and endoscopies before and three weeks after the intervention.

"People could be divided into two groups – those in which probiotics were welcomed by indigenous microbiome and allowed to colonize the GI tract, where probiotics were able to change the microbiome and those who were resistant. "

The researchers were able to predict which category a person would fall into by examining features in their microbiome. Elinav says his findings suggest a need for more advanced tailoring to personalize probiotics to the needs of individuals


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

Our microbiomes start developing when we are born when microbes colonize the human intestine. Babes delivered by natural birth have been found to have higher gut bacterial counts than those delivered by the Caesarean section due to their contact with their mother's vaginal and intestinal bacteria, says Lindsay Hall, microbiome research leader at Quadram Institute Bioscience

C-section-born babies miss out on that initial inoculation, and some of the microbes they come into contact with will be from the skin and the environment, "says Hall

Numerous studies have shown that C-sections affect health long-term – Lindsay Hall

"This is very important for babies to develop their immune systems."

Numerous studies have shown that " C-sections affect health long-term, and there is strong evidence that they lead to a higher risk of developing allergies, and a less robust ecosystem, meaning you're more susceptible t

"There is no robust evidence of what this difference means specifically for the immune system."

There are also differences in the microbiomes of breast-fed and formula-fed babies. Bifidobacterium, a group of bacteria associated with health, are often found in the guts of babies who are breast-fed

"We know that Bifidobacterium are able to digest components found in breast milk. milk, which is why formula-fed babies have less of them, "Hall says.

Scientists are getting closer to understanding how the gut can also be used to treat disease. One of the newest treatments in the field is faecal microbiota transplants, where a healthy person's microbiota is put into a patient's gut.

The procedure is used to treat antibiotic-resistant intestinal bacteria clostridium difficile, which can infect the bowel and cause diarrhea . Though there is no conclusive evidence of the underlying mechanism, it is believed that the transplant repopulates a microbiome with various bacteria that helps to fight the virus off.

We have not established what's normal, but also what is normal for every individual – Fiona Pereira

"The big question about these transplants is defining what a normal gut microbiome is."

"We have not established what is normal, but also what is normal for every individual. has gone through, "says Fiona Pereira, Head of Business Development and Strategy for the Department of Ophthalmology and Cancer at Imperial College London, which supervises research into the relationship between microbiome and diet

Pereira says if scientists can get clear understanding what is healthy in different ethnic groups and age groups, they can then profile a person and see how their gut varies and what this is related to –

It is already well established that antibiotics can dramatically alter our gut microbiota

The gut is an environment where harmful and beneficial bacteria are in very close contact to opportunistic pathogens that cause infections, said Willem van Schaik, a professor at the University of Birmingham, and lead researcher on the identification of more than 6,000 new antibiotic-resistance genes in pathogens

He found that most of these pathogens (19659022) Our findings highlight how many resistant genes are present in the microbiome and could potentially be mobilized to be able to translate between these bacteria, opportunistic pathogens – Willem van Schaik

However, many of the genes thought to be fixed in certain bacterial environments can start with (19659010) "Our findings highlight how many resistant genes are in the microbiome and could potentially be mobilized to be opportunistic pathogens. They have to be seen as a warning that there is a large reservoir of these genes we do not want to start mobilizing, "says van Schaik.

The brain

The brain and gut have a strong, two-way communication system referred to as the gut-brain axis.This is essential for the other – studies have found that brain development is abnormal in the absence of the gut microbiome.However, recent review stated that research has not yet figured out which exact gut

Further investigation is uncovering how intertwined the gut is to the brain, however, including our mood and mental health, says Katerina Johnson, a researcher of the microbiome-gut-brain axis at the University of

"Research shows that if we take gut bacteria from depressed humans and colonize the guts of mice with it, the mice show changes in their behavior and physiology that are characteristic of depression," she says. can produces most of the neurotransmitters found in the human brain, including serotonin, which plays a key role in regulating mood. 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 like our microbiomes, including Parkinson's disease and multiple sclerosis


We've also started to glimpse how gut microbes can influence behavior. Some studies, largely conducted in animals, for example, suggest that certain types may affect brain chemistry and behaviour to make animals act more socially

Germ-free animals who have had no exposure to microbes, on the other hand, have The researchers have found that this can be restored by adding specific types of bacteria such as Lactobacillus, often found in yoghurt, according to Johnson

Behavioral changes are likely to be a by-product of processes that help microorganisms grow and compete in the gut, such as fermentation

A recent paper titled 'Why does the microbiome affect behavior?' examined the theory that the gut microbiome has evolved to manipulate its human host for its own success, much like parasites, making the host more sociable to be transmitted.

The paper argued however that this theory is unlikely, and behavioral changes are likely to be a by-product of processes that help microorganisms grow and compete in the gut, such as fermentation

"The gut microbiome is so diverse that even if there was a type of bacteria producing active chemicals it manipulates our behavior, this bacterium would quickly be outcompeted by other bacteria not investing any extra energy to produce the compound, "says Johnson, one of the paper's authors

The future

Science has not yet defined what a healthy microbiome looks like, and a conclusion seems some way off yet. But there is growing consensus that environmental factors, such as diet and antibiotics, affect our microbiome more than our genes, and that a more diverse microbiome is better for us

"While we can change our microbiome with our diet, they seem they have a set point to which they often return after a temporary disturbance, "says Johnson. "But one thing we can do is eat more fiber, to increase the diversity of the gut, which is often associated with health."

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

One of these is the reliance on a method called 16S rRNA sequencing, says McDonald, which looks at a specific region of a single gene believed to exist in all bacteria. E. coli is an example of why this method is too broad, McDonald says.

"While there are pathogenic E.coli, there are also E. coli that play a neutral or beneficial role in the gut, which would all be "

McDonald 's advice is that we should remain cautious

" There are lots of cool things microbiome research will lead to, and there are exciting developments going on now, but while continuing advances will lead to improvements in health, a lot of this stuff is tied up in basic research, and there's a lot of research we can do with mice that we can not translate to humans, because it's not safe to do so. "

In the meantime, most scientists can advise to eat our greens

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