Fecal Microbiota Transplant (FMT): a name which is redolent of innovation and the biotech world. However, it was used 1,700 years ago in China, where diarrhea was treated by drinking a broth of fermented stools–the aptly named “yellow soup”. In the Middle Ages, the Bedouins protected themselves against dysentery (a bacterial infection causing serious diarrhea) by ingesting the droppings of their camels. The first modern fecal transplants were performed in the 1950s to combat Clostridium difficile infection, a bacterium which takes advantage of the microbial imbalance triggered by an antibiotic treatment to proliferate within the intestinal flora. We had to wait until the 2000s for FMT to be taken into account in the treatment of metabolic diseases, and in the cages of laboratory rodents.

Conclusive first steps

But trials in humans in this field are just beginning. The first study was carried out in 2012 in Dutch patients: half of them received the stools of healthy donors; the others received their own stools (placebo group). The donor stools were analyzed carefully to eliminate any risk of infection by viruses, parasites or harmful bacteria. Then the transplant took place over a thirty-minute period by injection into a tube, introduced into the noses of patients, which opened out into the small intestine. Six weeks later, those who received “healthy” stools exhibited improved insulin sensitivity and increased numbers of bacteria producing metabolically beneficial butyric acid. This first attempt can thus be counted as a success!

A modus operandi to be refined

The use of FMT in metabolic diseases still has a long way to go, with manychallenges to be faced: the medical history and the microbiotas of donors must be irreproachable to avoid any transmission of diseases and strains chosen in an appropriate manner and in the right quantity. Other issues: how will the donor flora be welcomed by that of the recipient? Will a single injection be sufficient for long-term colonization? Finally, a considerable psychological limitation: the inevitable repulsion of some patients in the face of this still little-known treatment, unless FMT becomes a common therapeutic practice, knowing that its spectrum of potential applications could extend to multiple sclerosis, Parkinson’s Disease or chronic fatigue syndrome. Who knows? Perhaps the future will see the advent of stool banks and capsules.

Far from being a French specialty, “fatty liver” syndrome (foie gras in French) is driving up the number of hepatitis cases all around the world. Research is turning with increasing seriousness towards probiotics to stem these new epidemics⁹. And the gamble seems to have paid off.

Cases of viral, alcoholic, and now increasingly fatty, hepatitis are soaring due to obesity and type 2 diabetes. Excess fat accumulates in liver tissue, first causing non-alcoholic hepatic steatosis (NAFLD¹⁰) which can escalate into non-alcoholic steatohepatitis (the famous NASH¹¹), itself heralding cirrhosis–point of no return for the liver. As in obesity and type 2 diabetes, the intestinal microbiota plays a frontline role. Hence the hope of countering this overdose of fat through probiotics: an avenue followed with success by research for around ten years.

From animals to humans

The first studies in animal models proved the benefits of using probiotics and prebiotics, and even synbiotics (a combination of the two). By way of example, the addition of fructooligosaccharides to probiotics led to a reduction in inflammation and in fatty particles in the liver, loss of weight and fat mass, and improved insulin sensitivity in some patients. These positive results were confirmed by the decrease in fat content of the liver in Hong Kong patients treated for six months with a mixture of lactobacilli and bifidobacteria. Decreased liver stiffness–a sign of diminished aggression–was observed in Iranian patients after taking synbiotics for twenty-eight weeks.

A convincing trial by the book

on-alcoholic steatohepatitis (the famous NASH¹¹), itself heralding cirrhosis–point of no return for the liver. As in obesity and type 2 diabetes, the intestinal microbiota plays a frontline role. Hence the hope of countering this overdose of fat through probiotics: an avenue followed with success by research for around ten years. From animals to humans The first studies in animal models proved the benefits of using probiotics and prebiotics, and even synbiotics (a combination of the two). By way of example, the addition of fructooligosaccharides to probiotics led to a reduction in inflammation and in fatty particles in the liver, loss of weight and fat mass, and improved insulin sensitivity in some patients. These positive results were confirmed by the decrease in fat content of the liver in Hong Kong patients treated for six months with a mixture of lactobacilli and bifidobacteria. Decreased liver stiffness–a sign of diminished aggression–was observed in Iranian patients after taking synbiotics for twenty-eight weeks. A convincing trial by the book An additional step forward has been taken in establishing probiotics as a valid therapeutic option through a clinical trial conducted in a few dozen Ukrainian patients with non-alcoholic hepatic steatosis. The daily administration of a probiotic containing fourteen living strains over an eight week period produced a clear reduction in hepatic fat, some inflammatory markers and enzymes indicative of a diseased liver. These effects remain to be confirmed in a larger number of patients and over the long-term. But probiotics look very promising in the fight against these overdoses of fat for which our livers pay the price.

Show me your daily menus and I will tell you what your microbiota looks like: our diet has a massive influence on our intestinal flora, and researchers have been able to draw up standard profiles of intestinal microbiotas. You have a sweet tooth? The chances are that your flora contains a predominant amount of Prevotella, which would improve control of glycemia. Fan of animal protein and saturated fats? You will be rather the Bacteroides type, exposed to an increased risk of colon cancer. You prefer brown rice to white rice? You probably harbor fewer proinflammatory enterobacteria. Then, would the recipe for metabolic happiness be to order our intestinal flora through what we eat?

Unpredictable diets

Unfortunately not, as we are not equal in terms of the positive effects of a balanced diet. It is the fault of our intestinal microbiotas, none of which resembles another in all aspects, even in twins. Hence the impossibility of predicting with precision the effects of a dietary intervention on our intestinal bacteria. A flora naturally rich in Lactobacillus will absorb more probiotics after two weeks of consuming fermented milk. Similarly, a microbiota richer in Prevotella before a three day “diet” of barley bread (high in fiber) helps to better control glycemia compared to microbiotas less well endowed with this bacterial species. Taking into account these individual variations, a diet low in FODMAPs⁸ could have more or less success with bloating and abdominal pain depending on the initial composition of the intestinal flora.

Some florae are more resilient than others

Eating more fibers will be all the more beneficial for our level of bifidobacteria if we have already consumed it regularly beforehand. Finally, some microbiotas may show themselves more resistant to a change in diet; a resilience which can prove counterproductive in the context of nutritional regulation. The use of algorithms capable of integrating all of this interconnected data is one of the avenues being studied to direct the remodeling of our flora by means of diet. For the moment, and before researchers manage to simultaneously integrate all these parameters at the level of a single individual (dietary habits, composition and resilience of the intestinal flora), a personalized modulation of the microbiota still remains a challenge.

Hyperglycemia, hyperlipidemia, hypertension: the effects of a diet that is too high in fat are known but they are only the tip of the iceberg. Researchers have thoroughly disclosed the major role of the intestinal microbiota in these metabolic disruptions. They also sorted the good fats from the bad

The same observation is made in laboratory mice given a high fat feed as in patients with metabolic syndrome: their intestinal flora does not resemble that of their healthy counterparts: too much fat on a daily basis reduces the amount of Akkermansia muciniphila, a beneficial bacterium which improves glycemia and insulin sensitivity, and protects against the formation of fatty plaques in the vessels (atherosclerosis). As its name indicates, this bacterium also produces a substance called “mucin”, which strengthens the protective mucus of the intestinal barrier. Another side-effect of excess dietary fat: lactobacilli and bifidobacteria, “good” bacteria which reduce inflammation and formation of adipose tissue, are decreased.

Not all fats are the same

But incidentally, which fats are we talking about? Saturated fatty acids like palm oil are indeed to be avoided, as is hammered home by public health messages: they are associated with lowered bacterial diversity and weight gain. Conversely, the oleic acid contained in olive oil, a monounsaturated fatty acid of the omega-9 family, is thought capable of restoring bacterial diversity and of reducing weight –in mice at least. We should also rely on omega-3 polyunsaturated fatty acids, such as fish oil, which promote the presence of Akkermansia muciniphila, lactobacilli and bifidobacteria. These omega-3-containing foods should moreover take precedence over those containing omega-6, which are also essential to the organism but are to be consumed with moderation as they cause inflammation and a reduction in bifidobacteria

“First and foremost, eat your fiber”

And as fat doesn’t do everything, good or bad, another food category also carries weight with respect to metabolism: fibers. Those indigestible sugars present in cereals, tubers, nuts, seeds, fruits and vegetables. Without fibers to ferment to extract their energy in the form of SCFA, bacteria begin to snack on the protective mucus which lines our intestinal cells, exposing them to bacterial invasion. Moreover, fibers enable better control of glycemia, probably through the presence of Prevotella in our intestines. Conclusion: for your microbiota, eat fat without excess–but good fat–and don’t forget your fibers!

It has been known for a long time that diabetes is associated with sugars. However, it is also associated with intestinal bacteria which enable us to digest slow sugars (starch and other dietary fibers) by breaking them down into simple sugars which ferment into short chain fatty acids (SCFA) and, inevitably, gas. However, individuals with type 2 diabetes are thought to have a microbiota less rich in bacteria that produce these famous SCFA. Other bacteria have less beneficial effects: they cause chronic inflammation of the liver through accumulation of fats (the famous “NASH”, or non-alcoholic steatohepatitis). Some also release toxic substances when they die, whose presence in the blood is associated with an increased risk of diabetes. Furthermore, as 90 to 95 % of diabetics are also obese, they suffer from the chronic inflammation found in obesity, partly generated via the intestinal microbiota.

Bacteria which tilt the balance

In type I diabetes, where the immune system turns against the pancreatic cells responsible for insulin production (beta cells), the composition of the microbiota changes: a flora less rich in Proteobacteria and overabundance of Firmicutes relative to Bacteroidetes are thought to be some of the risk factors. Conversely, some bacteria (lactobacilli, bifidobacteria, bacteria that produce butyric acid) could provide protection against autoimmunity, a deregulation which forces us to fight against our own immune defenses. Finally, there are also other members of the microbiota– i.e. viruses–such as Coxsackie viruses⁴ that are capable of infecting the insulin-producing cells of the pancreas.

On the track of elucidating treatment mechanisms

To complicate matters, bacteria are also thought to influence the actions of metformin. This drug used in first line treatment of type 2 diabetes is thought to reduce the inflammation caused by toxic bacterial substances while reducing the absorption of fats… via the intestinal flora. This might shed light on its mode of action which is still unclear, but could also bias the results of studies conducted in these patients. These are all mechanisms among many others which link diabetes and the intestinal microbiota, whose vast and complex field of action we are barely beginning to discern

If our cells require the right fuel to carry out their various functions, this is also the case for our intestinal bacteria: the multiple essential roles they play in our great metabolic symphony have only recently been discovered. Watch out for harmful effects in the event of wrong notes…

Our intestines are home to a common base of bacteria mainly divided into two large groups: the Bacteroidetes and Firmicutes; the former being more abundant than the latter when we are healthy. However, in obese individuals, the balance tilts towards the Firmicutes. These bacterial species are thought to extract more calories from the food that we ingest–in particular complex sugars–than the Bacteroidetes, leading to excess weight.

A vicious circle of inflammation

Then, an entire cascade of “bad” reactions of the organism is activated by a diet that is too high in fat which unbalances the intestinal microbiota. The barrier function of the intestines is no longer as effective; they are less resistant and let through molecules produced by the bacteria. This triggers an abnormally persistent and silent response from the immune system. The pancreas is impacted by this chronic inflammation and produces less insulin, which in turn is less well used by our cells leading to insulin resistance, a characteristic of type 2 diabetes. Storage of fats in the tissues and their transport in the blood are also disrupted. The blood vessels are not just obstructed by fat, but also dilate less effectively. Finally, a cardiovascular bomb made up of abdominal fat, elevated blood lipids, high blood pressure and hyperglycemia leads straight to what is called metabolic syndrome.

The guardians of our metabolism

Conversely, in the case of a diet that is beneficial for our intestinal flora like the Mediterranean diet (diet rich in fruit, vegetables and olive oil, and low in meat), a virtuous mechanism is set in motion: our bacteria produce shortchain fatty acids (SCFA), a source of energy for our cells. These SCFA are involved in the regulation of appetite, bowel movements and the formation of fats. They can act on insulin production and blood pressure. Some, like butyric acid, protect the cells of our intestines from inflammation and help them fight against aggressive microbes. They are even thought to have anti-cancer properties. Not to mention the fact that bacteria produce vitamins (K, H and B) and help us to absorb calcium, magnesium, vitamin D and iron. Some researchers no longer hold back from stating that the intestinal microbiota is an organ in its own right.

THE INTESTINAL MICROBIOTA IN FIGURES¹

The list of environmental damages caused by plastic waste polluting our oceans on the surface as well as at great depths keeps getting longer as research on this “seventh continent” has been advancing. An Australian team has just added another item to this sad list: plastic leachates, i.e. liquid pollutants produced by plastic waste under the effect of rainwater, among others, that carry solvents, metals, dyes, UV filters or fire retardants into the oceans.

A cocktail of bacteria and plastics

To assess the impact of these “leaching juices” on aquatic organisms, the researchers focused on the second lungs of our planet: Prochlorococcus, the most abundant bacteria in the oceans, which play a key role: they produce a large part of the oxygen we breathe. Prochlorococcus were cultured in a water medium for 72 hours with two types of common plastics, HDPE (high-density polyethylene) found in shopping bags, and PVC (polyvinyl chloride) frequently used in packages and construction.

PVC is more harmful than HDPE

Result: not only was the growth of bacteria lowered by plastic leachates, but their capacity to produce oxygen from water and light (photosynthesis) was also impaired, starting after only 24 hours. PVC turned out to be more detrimental. Its harmful effects appear at much lower doses than with HDPE. This could be explained by the quantity (almost twice as much) of substances released by PVC (more than 10,000 vs. near 6,000 for HDPE). Among them, there are metals such as zinc, which are used to make PVC fire-resistant, but also other “organic components” (made of carbon) that may be harmful to Prochlorococcus. Other studies are necessary to assess the havoc caused by this suffocating liquid plastic cover which keeps on growing: the mass of our plastic waste should be multiplied by ten in the next ten years.

Modulation of the gut microbiota: prevention and treatment at the same time?

It is highly probable: beyond standard hygiene and dietary measures and especially rehydration, two probiotics (Saccharomyces boulardii yeast and Lactobacillus rhamnosus GG bacterium (LGG)) seem to prevent antibiotic-associated diarrhea in high risk patients (newborns, children with concomitant diseases…) and are recommended for this purpose by experts of the European Society for Pediatric Gastroenterology Hepatology and Nutrition (ESPGHAN). They could also prevent the onset of nosocomial diarrhea in hospitalized children or in community facilities: according to encouraging data which still needs to be confirmed, they could reduce the risk by 15%, in some studies. As add-on treatment for gastroenteritis, S. boulardii, and some concentrations of Lactobacillus rhamnosus GG (LGG), could reduce the duration of diarrhea by a day and decrease the risk that it lasts more than four days. As for fecal microbiota transplant, it is only indicated in cases of Clostridium difficile drug-resistant or recurrent infection, which is rare in children.

Is the microbiota of a child treated with antibiotics impacted in the long term?

It is difficult to say at the moment since there is currently no scientific evidence of this. But the question needs to be asked: after an antibiotic treatment, the gut microbiota is disrupted for two to three months. Then a normalization process, that tends to give the patient its previous microbiota back, although the restored version is not the exact copy of the original microbiota. Because the repeated and/ or prolonged intake of these molecules in young children compromises the organization of intestinal microbiota and the immune system, it could very well have long-term consequences on the intestinal flora and increase vulnerability to some diseases later in life.

What is the outlook in terms of prevention and treatment?

Oral vaccination, undoubtedly. It has allowed to considerably reduce the number and severity of cases of rotavirus-induced diarrhea. In this area, one of the perspectives is to extend this vaccination to all babies under 6 weeks old (for the first injection). Beyond this age, its efficacy seems to decrease. Researchers are also trying to develop more effective vaccines and identifying more effective probiotic strains: according to some scientific data, our body’s immune response seems to depend, among others, on our “bacterial profile”. Our gut microbiota, when modulated and/ or boosted by probiotics, could allow us to better respond to vaccination against rotavirus.

Antibiotics not only eradicate pathogenic microorganisms responsible for infection, but they can also destroy some bacteria that are beneficial to the gut microbiota. They always cause a more or less significant imbalance within this ecosystem. This ecosystem becomes less rich and less diversified, and is no longer able to properly carry out its protective functions².

Antibiotics are not automatic anymore¹⁵  !

Between 10 and 30% of patients treated with antibiotics experience a change in their intestinal transit within 3-5 days of treatment, most often in the form of diarrhea¹⁶. Most of the time, this diarrhea is purely functional, caused by the antibiotic-induced dysbiosis. It usually presents without fever, it is short lived, not severe, and in most cases, it regresses once antibiotics are discontinued, or in the following weeks. However, dysbiosis starts in the first 24 hours of antibiotic treatment and lasts up to six weeks after its conclusion. New microorganisms, close to the initial strains but not necessarily identical, slowly re-colonize the intestines and create a new balance, although it often remains incomplete.

A new route for pathogens

But sometimes, the mucus layer, true line of defense of our intestines, has been so weakened that the body becomes more vulnerable to pathogens. In 10 to 20% of cases, diarrhea results from the colonization of the microbiota by Clostridium difficile. This bacterium is very widespread in hospitals and nursing homes, and elderly people are particularly vulnerable: in these facilities, up to 20% of residents (50% in cases of long-term stay) can host this bacterium in their intestines without showing any symptom (asymptomatic carriers). Although most cases of C. difficile diarrhea resolve once the antibiotics are discontinued, most severe forms could occur (pseudomembranous colitis and fulminant colitis, especially in people over 65 years old¹⁷). In the US, for instance, this infection is responsible for around 30,000 deaths/year18. The families of antibiotics that are often blamed are penicillins, some generations of cephalosporins, fluoroquinolones and clindamycins. To stop this vicious circle, stool transplant (transplant of healthy microbiota into the GI tract of a patient) could be a therapeutic alternative to antibiotics in order to repopulate the microbiota and restore the gut barrier.

Why are some people particularly sensitive when others are more resistant? “It depends on the microbiota”, answer the researchers, whose studies underline the impact of interactions between invasive pathogens and microorganism living in our intestines.

An uphill battle

To understand the infectious process of enteropathogenic bacteria, researchers reviewed the mechanisms employed by the body to fight the colonization of the digestive tract by Salmonella typhimurium¹⁴, a bacterium causing food poisoning with diarrhea, that is sometimes severe although short-lived. The first mechanism comes into play in the stomach where the acid environment destroys between 95 and 99% of ingested bacteria (through food). For bacteria that are able to reach the intestines, it is too early to claim victory: they can only grow if the level of resistance to colonization allows it. But the latter depends on the composition of the gut microbiota, specific to each person, that has an arsenal of tools to fight this colonization: secretion of components blocking the invader’s growth and virulence, competition for the same binding sites, creation of an oxygen-poor environment that is unfavorable to its growth…

A fierce fight

And our defenses have not said their last word: bacteria must be present in sufficient amounts to trigger diarrhea, and it only happens between 12 to 36 hours (sometimes 72 hours, depending on the number of ingested bacteria) after they cross the intestiWhen bacteria and parasites attack the gut microbiota nal barrier. Based on animal models, S. typhimurium accomplishes this by secreting toxic substances, thus allowing it to reach the mucosa and then the submucosa. The body reacts by expelling infected intestinal cells thus dividing the number of pathogenic bacteria in the tissues by 100– and sets off a massive inflammatory response which affects the enemy in two ways: by reducing the bacterial load in the body, while serving as fuel to the remaining bacteria.

Long-term consequences

There is another enemy: Giardia lamblia. This protozoan infects humans through the consumption of contaminated water or food. Although the frequency of giardiasis does not exceed 7% in developed countries, it can reach 30% in developing countries. In most cases, the infection takes a few weeks to resolve but it can sometimes last several months and become chronic. There is currently no vaccine and available treatments have different levels of effectiveness. Giardiasis is often asymptomatic, but it can cause diarrhea, cramps and nausea. In newborns, disease severity hinges on its long-term consequences: at the age of two, they show a significant growth deficit. And some people may develop post-infectious syndromes several years after the elimination of the parasite, such as irritable bowel syndrome or chronic fatigue. According to several papers, Giardia lamblia could act by decreasing the immune response and causing dysbiosis.