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Inside your gastrointestinal (GI) tract are trillions of micro-organisms, including bacteria, fungi and viruses. You have roughly the same number of micro-organisms in there, as you do human cells in your whole body. But only 10% to 20% of the bacteria you have in your gut will be shared with anyone else.
Microbes & me
The life inside all of us
Microbes & me is a new collaborative series between BBC Future and BBC Good Food.
In the series, we'll be looking at recent research into the microbiome of bacteria that lives inside us.
We'll be exploring how it affects our health, what could be causing effects on it, and recommending recipes that may help it thrive.
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's still a long way to go to fully understand our guts. BBC Future reviewed the findings of some of the science so far.
Diet
Our diets have a huge influence on the gut microbiome. Research has found links in Western diet, typically high in animal fat and protein and low in fiber, with increased production of cancer-causing compounds and inflammation. The mediterranean diet, on the other hand, is typically high in fiber and low red meat, has been reported to have increased levels of faecal short-chain fatty acids, which have 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 "very different" from those who do not, says Dennis McDonald, the 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's unclear if and how radically switching from a diet high in plant-based food to a diet low in the health food would change the microbiome.
Probiotics
There have been a lot of hype around the 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, many 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, has recently found that some people are immune to probiotics – 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 or 11 strains of probiotics or placebos, 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 colonise the GI tract, where probiotics were able to change the microbiome, and those who were resistant.In this group, the probiotics were not allowed to settle in, and did almost nothing, "he says.
The researchers were able to predict which category a person would fall into the examining features in their microbiome. Elinav says his findings suggest a need for more advanced tailoring to personalize probiotics to the needs of individuals.
Health
Gut microbiota has a major role to play in the health and function of the GI tract, with evidence that conditions such as 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 when we're born, when microbes colonise the human gut. Babies delivered by natural birth have found to have higher gut bacterial counts than those delivered by the cesarean section because of contact they make with their mother's vaginal and intestinal bacteria, says Lindsay Hall, microbiome research leader at Quadram Institute Bioscience.
"C-section-born infants miss out on that initial inoculation, and some of the microbes they come into contact with will be from the skin and environment" says Hall.
Numerous studies have shown that C-sections affect health long-term – Lindsay Hall
"This is very important for infants to develop their immune systems." Recent work has suggested that the disruptions in early life gut microbiome have negative consequences for host health, "she says.
"Numerous studies have shown that C-sections affect health long-term, and there's strong evidence to suggest they lead to a higher risk of developing allergies, and a less robust ecosystem, meaning you're more susceptible to changes and disurbances, such as antibiotics.
"However, there is no robust evidence on 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 parts found in breast milk These are not normally found in formula milk, which is why the formula-fed babies have less of them," Hall says.
Scientists are getting closer to understanding how the gut can also be used to treat the disease. One of the newest treatments in the field is the transformation of microbiota, where a healthy person's microbiota is put into a patient's gut.
The procedure is used to treat an antibiotic-resistant intestinal bacteria clostridium difficile, which can infect the bowel and cause diarrhea. Although there's no conclusive evidence on the underlying mechanism, it's believed that the transplant repopulates a microbiome with diverse bacteria that helps to fight the virus off.
We have not established what's normal, but also what's normal for each individual – Fiona Pereira
The big question around these transplants is defining what a normal gut microbiome is.
"We have not established what's normal, but also what's normal for every individual. It depends on their ethnicity, environment and other things they body has gone through," says Fiona Pereira, head of business development and strategy for the department of surgery and cancer at London Imperial College, which oversees research into the relationship between the microbiome and diet.
Predir says if scientists can get a clear understanding of 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 could be diet, environment, or genetic predispositions to certain diseases.
Antibiotics
It is already well established that antibiotics can dramatically change our gut microbiota.
The gut is an environment where the harmless and beneficial bacteria are in very close contact to opportunistic pathogens that cause infections, says Willem van Schaik, professor at the University of Birmingham and lead researcher of a new study identifying more than 6,000 new antibiotic-resistance genes in pathogens.
He found that most of these pathogens were not associated with DNA that can transfer between bacteria, which means there is no immediate risk of spread of these genes from normal bacteria to pathogens.
Our findings highlight how many resistant genes are in the microbiome and could potentially be mobilized to be opportunistic pathogens – Willem van Schaik
However, many of the genes thought to be fixed in certain bacterial environments can start spreading by overuse of antibiotics, which can put pressure on the resistant genes locked up inside a single bacterial cell, causing them to mobilize.
"Our findings highlight how many resistant genes are in the microbiome and could potentially be mobilized to be opportunistic pathogens.They should be seen as a warning that there is a huge reservoir of these genes we do not want to start mobilizing," van Schaik says.
The brain
The brain and gut have a strong, two-way communication system referred to as the gut-brain axis. Each are essential to the other – studies have found that brain development is abnormal in the absence of the gut microbiome. However, a recent review stated that research has not yet figured out which bacterium is crucial for brain development.
Further investigation is uncovering how interlinked 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 Oxford.
"Research shows that if we take gut bacteria from depressed humans and colonise the guts of mice with it, the mice show changes their behavior and physiology that are characteristic of depression," she says.
Gut microbes can produce 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 produce neurotransmitters to treat psychiatric and neurologic disorders like to our microbiomes, including Parkinson's disease and multiple sclerosis.
Behaviour
We've also started to glimpse how gut microbes can influence behaviour. Some studies, largely conducted in animals, for example, suggest that certain types can affect brain chemistry and behaviour to make animals act more socially.
Germa-free animals who have had no exposure to microbes, have shown that deficits in social behavior, and researchers have found that this can be restored by adding specific types of bacteria such as Lactobacillus, often found in yoghurt 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 Influence Behavior? The researched the theory that the gut microbiome has evolved to manipulate its human host for its own success, much like parasites, by making the host more sociable in order to be transmitted.
The paper argued, however, that this theory is unlikely, and the behavioral changes are likely to be a by-product of processes that help the microorganisms grow and compete in the gut, such as fermentation.
"The gut microbiome is so diverse, even if there was a type of bacteria producing active chemicals to manipulate our behavior, this bacteria would soon 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 appears 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 to have a set point to which they often return after a temporary disruption," says Johnson. "But one thing we can do is eat more fibre, to increase the diversity of the gut, which is often associated with health."
While there have been many advancements in microbiome research in recent years, there also remain some challenges.
One of these is the 16S rRNA sequencing, says McDonald, which looks at a specific region of a single gene believed to exist in all the 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 be all indistinguishable with the current method we use. mean it's bad for you. "
McDonald's advice is that we must remain cautious.
"There are a lot of cool things in my life, 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 not 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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