Microbiota, the intestinal revolution. © INRA

Microbiota, the intestinal revolution

Disease and the microbiota (1)

Diabetes, obesity, cancer, inflammation of the intestines, cirrhosis… all of these disorders are related to imbalances in the intestinal microbiota, called dysbiosis, which have grave consequences for the host. They can be the result of an excess of harmful microorganisms and/or a relative insufficiency of microorganisms that are beneficial to their host. INRA researchers are committed to understanding the role of the intestinal microbiota in these diseases. Their goal? Prevent onset and help find remedies.

Updated on 04/25/2017
Published on 02/16/2017

Inflammatory bowel disease: when genes and microbiota interact

. © Fotolia
© Fotolia

Affecting mostly young adults in developed countries, chronic Inflammatory Bowel Disease (IBD) such as Crohn’s disease and ulcerative colitis is characterised by chronic inflammation of the digestive tract. Scientists have already found that some so-called susceptible genes, but also environmental factors and intestinal microbiota, play a role in the onset and evolution of these ailments. INRA researchers working hand in hand with Inserm, UPMC and AP-HP (the Paris public hospital authority) have shown that the genetic factor alone is not enough to explain the development of these inflammatory diseases. Other studies on the relationships between the immune system, genes and intestinal microbiota have confirmed that all of these mechanisms are inextricably related. The mutation of gene CARD9,the gene that causes susceptibility to IBD, leads to a modification of intestinal microbiota which in turn leads to a dysfunctional immune system. The intestinal microbiota does not produce enough indole derivatives (aromatic chemical compounds), which stimulate a protective immune response to alleviate inflammation. In other words, anomalies in the microbiota of those who suffer from IBD are both the cause and the consequence of inflammation. And that is not all. Researchers have shown that all of these mechanisms are reversible… in mice. By giving certain drugs (that mime indole derivatives) to these tiny mammals, they found that symptoms were allayed. They found the same results when they administered intestinal bacteria that produce the same indole derivatives. But what does this mean for humans? Tests on some 100 patients who suffer from IBD have shown identical deficits as those in patients with a mutant CARD9 gene. Initial findings show that the study of genes that are partially responsible for IBD, combined with analyses of intestinal bacteria, allow doctors to detect disease from one stool sample. Now it’s a question of giving patients supplements of bacteria that produce indole derivatives, or giving the derivatives directly. This is opening broad new avenues for finding effective treatments….

 

Handling specimens under a hood in a lab of the quantitative metagenomic platform, MetaQuant (MICALIS-MetaGenoPolis).. © INRA, NICOLAS Bertrand
Handling specimens under a hood in a lab of the quantitative metagenomic platform, MetaQuant (MICALIS-MetaGenoPolis). © INRA, NICOLAS Bertrand

Diabetes: a promising solution...

Some 4.5% of French people suffer from type 2 diabetes (T2D), representing a whopping annual cost of 12 billion euros! Diabetes is the world’s most common endocrine disease. It is characterised by elevated blood glucose levels and often associated with insulin-resistance*. In healthy people, insulin (secreted by the pancreas) binds to cell receptors, allowing sugar to make its way into the blood. In diabetic people, this process does not work, and glucose accumulates in the bloodstream. The cells of diabetic people are therefore “insulin-resistant”. Many studies have shown that there is a link between T2D and intestinal bacteria. Several types of bacteria present in the microbiota play a major role in T2D. Within the framework of the MetaHIT project, headed by INRA, French and Chinese scientists have unveiled no less than 60,000 bacterial genes associated with T2D. Some of the bacteria that produce butyrate (an anti-inflammatory agent) are generally found in the digestive tract, but less so in diabetics. Inversely, some pathogenic microbes and some microbial functions are amplified. The INRA researchers also studied the intestinal microbiota of diabetics undergoing treatment with metformin, the number one anti-diabetic treatment. By comparing these microbiota with those of healthy people, the scientists concluded that metaformin restores in part the composition of the microbiota in a type 2 diabetic and the production of butyrate. But at the same time, it fosters the growth of Escherichia coli, which may be at the root of digestive disorders. This is a well-known secondary effect of treatment, and some patients do not tolerate metformin well.  

 

... thanks to the microbiota

Also within the scope of the MetaHIT project, scientists have reported that diabetics (or pre-diabetics) have elevated levels of branched-chain amino acids in the blood, which contributes to making human cells resistant to insulin. These amino acids come either from food or bacteria in the microbiota. The scientists set out to find out to what extent food is to blame, and how much the microbiota is the culprit when it comes to elevated BCAA levels among diabetics. Lo and behold, they found that BCAA levels are linked to the microbiota, and not diet. The scientists were even able to identify four microbial species that play an active role in the interactions between the microbiota and insulin-resistance. They are Prevotella copri and Bacteroides vulgatus,which impact the biosynthesis of BCAA, and Butyrivibrio crossolus and Eubacterium siraeum, which are directly involved in the transport and use of amino acids in the colon, curbing the degree to which they pass into the bloodstream. The scientists then turned their undivided attention to one of these four bacteria using experiments with mice. They found that P. copri increases the risk of insulin-resistance in mice since it increases the amount of BCAA in the blood. Now the scientists must tinker with the levels of these bacteria (decreasing those linked to biosynthesis and increasing those that take care of transport) to reach an ideal balance of bacterial species in the microbiota. Once applied to man, this will be a great stride in the right direction.

Microscope view of a histological section of the intestinal epithelium of a mouse. Cells secreting mucosa are tinted blue.. © INRA
Microscope view of a histological section of the intestinal epithelium of a mouse. Cells secreting mucosa are tinted blue. © INRA

Tracking down obesity

Some 700 million people the world over suffer from obesity. The primary causes of this epidemic are a sedentary lifestyle, a high-calorie, readily-available diet, and some genetic causes. Several studies have shown that people who have a deficit of intestinal bacteria (poor diversity) run a greater risk of developing complications linked to obesity. The bacterial species that are missing may well play a role against weigh gain. A study was recently carried out on patients in France. It recommended a low-calorie diet rich in protein and fibre.  After six weeks, most patients lost weight, trimmed fat, and found their metabolism altered, but in those whose intestinal bacteria were less diverse, the results were less impressive or non-existent. And it was predictable with analyses of their microbiota. With the microbiota in the limelight, it is now possible to diagnose people who risk becoming obese.

Fungus and yeast of the microbiota and IBD

Histological sections of the colon of axenic mice that received the microbiota of genetically normal mice (left) and Card9-/- mice (right), 12 days after induced colitis. The severity of colitis is largely superior in the mouse with the microbiota of the Card9-/- mouse.. © Inserm
Histological sections of the colon of axenic mice that received the microbiota of genetically normal mice (left) and Card9-/- mice (right), 12 days after induced colitis. The severity of colitis is largely superior in the mouse with the microbiota of the Card9-/- mouse. © Inserm

In patients who suffer from IBD, studies have shown that their microbiota is in a state of imbalance. The proportion of some pro-inflammatory bacteria is high, while that of anti-inflammatory bacteria (like those that produce indole derivatives) is low. Thanks to high throughput sequencing, studies have also shown that the network of connections between bacteria and microscopic fungi inside the intestine is out of whack. An increase in the diversity of fungal microbiota is, for example, a sign of Crohn’s disease. One solution would be to lower the quantity of pro-inflammatory fungi, or, conversely, boost levels of protective fungi in the microbiota. A study on the complex relationship between intestinal bacteria and fungi could accelerate science’s understanding of a number of diseases that plague man.

Cirrhosis of the liver: a diagnostic test with a + 90% reliability rate

Liver sections of mice with microbiota presenting metabolic disorders (left) or with no metabolic disorder (right). Only the mice associated with the “bad” microbiota (left) developed massive hepatic steatosis in response to a high-fat diet (the lipid droplets are clearly distinguishable in white).. © INRA, Stephan Bouet, GABI
Liver sections of mice with microbiota presenting metabolic disorders (left) or with no metabolic disorder (right). Only the mice associated with the “bad” microbiota (left) developed massive hepatic steatosis in response to a high-fat diet (the lipid droplets are clearly distinguishable in white). © INRA, Stephan Bouet, GABI

Alcohol, hepatitis, obesity... the risk factors of cirrhosis of the liver are no strangers to science. More than 700,000 cases have been reported in France, leading to between 10 and 15,000 deaths per year. To better understand the development of cirrhosis, INRA researchers teamed up with their Chinese counterparts to launch a large-scale study. The microbiota of 237 individuals (of which 50% suffered from cirrhosis) were closely examined. No less than 2.7 million bacterial genes were analysed - of which 800,000 were as yet unknown - and 75,000 of them were unevenly distributed between healthy and sick patients. In the end, the researchers found that more than 40% of the microbiota of a person suffering from cirrhosis can be made up of bacteria that are near-absent from the intestines of healthy individuals. Most of those bacteria come from none other than… the mouth! The malfunctioning of bile, which is common with cirrhosis, explains this migration of mouth bacteria to the intestine. The researchers then developed a test based on the presence of only seven bacterial species found in the stool of patients. The test’s reliability rate is nearly 95%. The quantity of these mouth bacteria that end up in the intestine is also proportional to the severity of liver insufficiency. Going forward, doctors will be able not only to detect cirrhosis but also determine the stage of the disease. Moreover, the researchers showed that these bacteria produce ammonia and γ-aminobutyric acid (chief inhibitory neurotransmitter of the central nervous system in mammals). These substances may explain one of the complications of cirrhosis: hepatic encephalopathy. And as it happens, this complication is treated with antibiotics, enemas and probiotics. In other words, treatments that target - you guessed it - bacteria. The next step will be to inhibit the bacteria present in the intestines of people who suffer from cirrhosis, and to tackle the problem of bile dysfunction (to prevent bacteria from migrating from the mouth to the intestine).