Fecal microbiota transplant allows patients to receive approximatively 10¹¹ bacteria per gram of stool, but also fungi, viruses and archaea. Its objective is to correct gut dysbiosis. The number of necessary attempts and results vary according to the individuals and their pathology, and the protocol requires seamless controls.¹³

Gut microbiota modulation is a potential treatment for IBD. In practice, this strategy could be carried out through fecal microbiota transplant (FMT). The fecal matter comes from one or several healthy donors and is then transplanted into the distal gastrointestinal tract of the patient thanks to a nasogastric tube, during a colonoscopic enema, or more recently through oral capsules. This protocol is already being successfully used in case of recurrent Clostridium difficile infections. But what about IBD?

Ulcerative Colitis

Although safety conditions of the first tests were satisfying and the therapy led to partial or total remission in some patients with ulcerative colitis (UC), other attempts were more controversial.¹⁴ The donor’s fecal composition quality, the number of transplants and early therapeutic care, could modulate the chances of success and appear as a post-hoc explanation of heterogeneity of results.

Crohn's disease (CD)

Studies conducted on Crohn’s disease (CD), although fewer in number, produced either positive (clinical and endoscopic remission) or neutral results.In the only study that did not show a significant disease reduction, patients still reported an improvement in their quality of life.¹⁴ To confirm the clinical efficacy of fecal transplant in Crohn’s disease, additional studies are still necessary.

Many pending issues

Whatever the disease, several questions remain unanswered regarding: FMT engraftment, which could require several fecal transplants; the quality of the transplanted microbiota often obtained from donors living in countries where IBD prevalence rate is high; the restoration of microbiota altered functions after the transplant (for instance, production of protective short-chain fatty acids such as butyrate); and of course, the role of inflammation, either as a cause or consequence of dysbiosis.¹⁴

Defensins play a major role in innate immunity. Ten defensins have been identified in humans: six α-defensins that are mainly secreted by Paneth cells, neutrophils and some populations of small intestine macrophages; and four β-defensins that are secreted by epithelial cells.⁵

Mechanisms of action

Mechanisms of action of antimicrobial peptides are variable:⁸ some puncture bacterial membranes and cause ion and nutrient efflux, loss of structure, or even bacterial lysis; other “bind” to bacteria and limit they passage through the gut epithelium without killing them; in other words, they reduce pathogen colonization and change the composition and density of bacterial communities in the intestinal lumen.

Crohn's disease and decrease in defensins

When CD affects the ileum, the production of some α-defensins decreases, which reduces antibacterial activity and promotes pathogenic bacteria penetration⁵. Among possible explanations there is NOD² gene mutation, involved in the recognition of bacterial surface and onset of defensin production; and impaired signaling pathways, whose dysregulation is involved in the development of many human cancers. Some researchers believe that the decrease in α defensin content is not the cause but the consequence of inflammation.⁴ In colonic CD, only β-defensin rates are disrupted5: increase in secretion of β-defensin type 2 and decrease in type 1. Some scientists believe that the smaller number of copies of the gene located on chromosome 8 in affected patients (3 instead of 4) is at fault.

The alteration of the intestinal barrier observed in patients with IBD could explain the pathophysiology of dysbiosis: not only would this mechanical frontier be altered, but also its first line of immune defense.

Besides its role in the absorption of ions, water and other nutrients, the intestinal barrier serves as a wall and prevents the entry of bacteria into the gut lumen. But its permeability increases in acute phases of Crohn’s disease (CD), which promotes translocation of bacteria through the mucus as well as local inflammation.⁵

The role of the instestinal barrier

Potential causes: alteration of the tight junctions of intestinal epithelial cadherins (glycoproteins playing a key role in intracellular adherence); involvement of some transcription factors¹¹ related to epithelial regeneration. Other mechanisms under discussion involve the gut mucus, whose thickness keeps pathogenic bacteria at bay, but which is considerably decreased in patients with IBD. This phenomenon could be explained by the alteration of mucus- producing goblet cells whose disruption induces the development of colitis in murine models. It could also be explained in patients with CD by the impairment of Paneth cells located at the bottom of small intestinal crypts, known to be involved in homeostasis and with a defensive role of the gut mucus through antimicrobial secretion.^5,11

First line of defense of the immune system

The scientific literature also mentions several mechanisms involving innate immunity, and more precisely dendritic cells, macrophages, innate lymphoid cells and neutrophils. These cells, which complete the previously described system, act as the first line of defense of the immune system. In the intestines of healthy subjects, macrophages are hyporeactive (reduced proliferation and activity) and can produce anti-inflammatory cytokines.¹¹ On the contrary, in patients with IBD, the imbalance in innate immunity cell populations could be associated to several phenomena:¹¹ bacteria crossing the mucus which became permeable due to macrophage activity decrease and defective neutrophil recruitment; inflammation induced by the production of large quantities of pro-inflammatory cytokines (TNF-α and IL-6) by specific macrophages; and inflammatory T-cell recruitment through the accumulation of dendritic cells which induce an adaptive immune response.

It appears that the bacterial and viral components of the microbiota are not the only ones to be affected in patients with IBD. The mycobiota, i.e. all fungi present in the gut ecosystem, also seems to be disrupted.

Disrupted microbiota

A study conducted in 235 patients with IBD and 38 healthy controls brought to light the presence of a fungal dysbiosis in affected patients: increase of the Basidiomycetes/Ascomycetes ratio, decrease in the proportion of Saccharomyces cerevisiae, and increase in that of Candida albicans.⁹ In patients with CD, it is believed that the development of fungi occurs to the detriment of bacteria, triggering a loss of diversity. Moreover, interactions between these two kingdoms (bacteria and fungi) also seem to be degraded compared to those observed in healthy subjects, thus revealing inter-kingdom alterations specific to IBD. Although data on the fungal portion of the microbiota are still very fragmented, these initial results suggest that the mycobiota plays a role in the pathogenesis of IBD. This dysbiosis, characterized by alterations in biodiversity and composition, adds itself to the bacterial dysbiosis.

Urbanization as a cause of this dysbiosis?

Meanwhile, some research teams focused on the link observed between rapid urbanization and increased incidence of autoimmune diseases, including IBD.⁷ Several hypotheses were suggested, including one involving the mycobiota: the Western diet, rich in carbohydrates, which promotes the development of Candida in the intestines; the impact of atmospheric pollution in urban areas which could reduce fungal biodiversity; and quality of urban air, less rich in some spores (Actinomyces, Botrytis…) than rural air. It seems that urbanization does not only impact the mycobiota but could also be related to the dysbiosis of other microorganism communities (bacteria, viruses, parasites...).

The second microbiota component that could be involved in IBD is the virome (viral component of the microbiota), made up of both eukaryote-infecting viruses and bacteriophages infecting bacterial cells, which are the most studied. In patients with IBD, a dysbiosis of this virome has been observed: loss of diversity in addition to a greater variability of gut viruses in patients with CD. A study conducted in the United States and United Kingdom in 2015 also revealed an increased abundance and diversity of the enteric virome in patients with CD or UC.⁷

Impact of bacteriophages on the bacterial microbiota

Bacteriophages are ten times more numerous than bacteria and are involved in the microbiota mechanism through the control of bacterial abundance and diversity, which leads to an either protective or harmful effect: in patients with CD, the expansion of Caudovirales bacteriophages is associated to a loss in bacterial diversity and could be involved in the bacterial dysbiosis and gut inflammation.⁸

Virome signature

While studies on the virome are rare, those focusing specifically on eukaryotic viruses are even more so. One of them compared the gut mucosa of healthy controls to that of treatment- naive young patients whose IBD had been diagnosed early,⁸ and suggested that some eukaryote-infecting viruses could be involved in the onset of gut inflammation and contribute to IBD pathogenesis, with a specific signature depending on the disease: more viruses from the Hepadnaviridae family compared to controls and patients with CD, and less Polydnaviridae and Tymoviridae in patients with UC; increased abundance of Hepeviridae (a family of viruses including HEV for instance) and less Virgaviridae in patients with CD compared to controls. These virome signatures could be acquired early in life (for instance through diet) and later increase host susceptibility to IBD.⁸

A double bacterial gut dysbiosis, characterized by a decrease in some beneficial strains and an increase in pathogenic strains, is associated to IBD. These composition abnormalities could be both the cause and the consequence of these disorders, thus inducing a vicious circle.

In patients with IBD, structural and functional alterations of the gut microbiota have been observed. The composition is also different in patient undergoing an acute episode compared to those in remission.²

Decrease in beneficial bacteria and increase in pathogens

First feature: decreased Firmicutes/ Bacteroidetes ratio. A decrease in somebeneficial bacteria from the Firmicutes phylum is observed, for instance, lower abundance of Faecalibacterium prausnitzii, a commensal bacterium with anti-inflammatory properties and whose decrease seems to be a marker of CD;³ reduced rate of Firmicutes, commonly observed in patients with IBD;⁴ significant decrease in Bacteroides fragilis (Bacteroidetes), a bacterium with proven protective effects in murine models of induced colitis.⁵ In patients undergoing an acute phase of IBD, there is also a lower abundance of Clostridium coccoides, Clostridium leptum, Faecalibacterium prausnitzii and Bifidobacterium.² Second feature: excess of potentially harmful microorganisms, especially Gammaproteobacteria and Actinobacteria. In one out of three patients with CD, the mucosa is invaded by a strain of Escherichia coli called AIEC (Adherent-invasive Escherichia coli).³ Contrary to other infectious agents, these strains are able to cross the intestinal mucus barrier, adhere to it, then invade the gut epithelial cells, and survive and replicate in macrophages. This leads to the secretion of large quantities of TNFα, which in turn causes inflammation.

Dysbiosis: cause or consequence of ibd?

This bacterial gut dysbiosis, which seems to be a marker of IBD, is suspected to play a role in its pathogenesis. A study conducted in mice genetically predisposed to UC revealed a two-way relation between this disease and gut dysbiosis.⁶ Bacterial dysbiosis could thus not only contribute to the onset of IBD, but also be a secondary consequence of gut inflammation. Different hypotheses were suggested to explain this dual phenomenon: some species from the Firmicutes phylum have anti-inflammatory properties and are major producers of short-chain fatty acids (SCFA)–especially butyrate–, which represent the main energy-producing substrate for colonocytes. Moreover, a decrease in the number of Firmicutes could trigger or intensify a local inflammation by decreasing the levels of anti-inflammatory cytokines (key regulators of mucosal immunity) and/ or by altering the colon barrier function through a deficit of SCFA.⁴

Why is the psychiatric field interested in the microbiota?

This interest is relatively new. It stems from studies published less than 10 years ago showing that some stress factors have an impact on the digestive barrier, making it more permeable, thus allowing gut bacteria to cross into the bloodstream. This phenomenon leads to the production of inflammatory molecules at the intestinal level, that would then travel to the brain and disrupt it. This inflammation impairs the synthesis of serotonin, a chemical messenger produced in the intestines and the central nervous system and involved in depression. Instead of producing serotonin, the body produces a toxic substance which destroys neurons and neural connections. We believe that the gut microbiota imbalance could trigger this cascade of events.

What is the link between microbiota and mood disorders?

Depressed individuals have an overrepresentation of some bacterial families, the presence of bacteria that are not found in healthy people, as well as bacterial species associated to an increase in the severity of the depressive episode. We also know that some gut bacteria synthesize dopamine and serotonin, two molecules responsible for regulating mood, among others. An imbalance of these bacteria would thus have an impact on the functioning of the brain. The disruption of the gut microbiota could thus be related to the onset of a depressive illness and/or symptom severity. This is why, my team and I are about to study the interest of the use of probiotics in depressed patients: we want to see if we can improve depression symptoms by modulating the microbiota.

From depression to addiction, is there only one step?

The link between gut microbiota and addiction should be studied. Nowadays, the research focus is mainly on alcohol dependency, which is known to alter the digestive barrier. A few years ago, in Belgium, scientists demonstrated that there is a correlation between alcohol consumption, dependency and microbiota: dependent patients who have a strong disruption of the digestive barrier are those who present the most severe anxiety and depression disorders and the strongest desire to drink. They are also the patients who are most at risk to relapse. Their intestinal flora is different from that of patients who are at low risk of relapsing French researchers have shown that apple pectin (a type of carbohydrate mainly found in the skin and seeds of apples) restores the digestive barrier in alcohol dependent rodents. This promising study is the first to demonstrate that diet can be a protective factor against addiction, although results are not yet applicable to humans.

Bipolar patients (as well as schizophrenics) have increased levels of antibodies against fungi (Saccharomyces cerevisiae and Candida albicans) that are naturally present in the gastrointestinal tract. The presence of a specific protein in the blood indicates that bacteria usually located in the intestines were able to migrate. Moreover, concentrations of anti- Saccharomyces cerevisiae antibodies are higher in treatment-naive patients than in those who are treated with antipsychotics. These observations strengthen the hypothesis of a link between disease and inflammation²⁶.

Is nutrition education an avenue to pursue?

Yes, without a doubt, according to some psychiatrists who rely on diet to reduce inflammation and restore gut microbiota balance²⁷. Actually, a link between Western diet (high intake of carbohydrates and fat) and a disruption of neural and inflammation activity has been demonstrated. On the contrary, Mediterranean diet is the example to follow: it could have a protective effect against bipolar disorders as well as depression. The same could be said of omega-3 intake.

It manifests itself by unusual sadness, loss of interest, inability to perform daily tasks, greater fatigue and is accompanied by an increase of cortisol levels²², and thus a disruption of stress response.

In animals, the absence of gut microbiota(or its disruption) is associated to depressive symptoms and to an imbalance of neurotransmitters (serotonin, dopamine, GABA...). Furthermore, inflammation-inducing molecules that are present in excess in the blood and produced by gut bacteria, seem directly related to the development of depression²³. Although there are few, studies made in humans seem to have brought to light a bacterial signature: very recently, researchers discovered for instance that low levels of some bacterial genera in the intestines (Coprococcus and Faecalibacterium) are related to a feeling of poor quality of life in depressed patients.

Balanced gut, balanced mind

The administration of some psychobiotics, such as Lactobacillus and Bifidobacteria (bacteria from the Firmicutes phylum that are present at low levels in affected people) could be beneficial and be used as a supplement to antidepressant and anxiolytic treatments currently used. Initial results are encouraging: prolonged use can relieve depressive symptoms and psychological distress, without causing adverse events²⁴.

Change your shopping list

It would seem that high-glucose transformed products could increase predisposition to depression. In depressed patients, prebiotics (mainly galacto-oligosaccharides found in red beans, chickpeas, artichokes...) could act positively by stimulating the increase of bifidobacteria²⁵. Opting for fruits, vegetables, fish (rich in omega-3 fatty acids) could restore the microbiota, regulate pro-inflammatory processes, and thus favorably impact mood. Turmeric could decrease cortisol levels in the saliva and increase gut flora diversity, resulting in positive effects on the state of mind and behavior

Among other factors is, once again, gut dysbiosis! It leads to an increase of intestinal permeability and a disruption of stress response, as well as an increase in inflammatory activity.

All roads lead to the microbiota¹⁵

Scientists agree that gut bacteria play a role in this process. But according to scientific studies, the microbiota could either have an anxiety-inducing effect or an anxiolytic effect¹⁶. The use of antibiotics– that disrupt and impoverish the gastrointestinal flora–could be associated to the onset of anxiety disorders, or conversely, to a decrease in anxiety in animals.

The flora is being explored “blindly”

In animal models, antibiotics seem to decrease anxiety during the treatment period. The drawback is that an early disruption of the gut microbiota by antibiotics could lead to behavioral changes that persist into adulthood^17,18. Some probiotic strains could also have an anxiolytic effect. Finally, fecal microbiota transplant could reduce anxiety levels¹⁹. All these results still have to be confirmed in humans.

What to eat to stay zen?

Fermented foods such as cheese, yogurts, kefir, kombucha or soy sauce are excellent sources of probiotics and prebiotics. They act as anti-inflammatory agents by strengthening the integrity of the intestinal barrier, improving the composition and function of gut bacteria, and stimulating immune cells in the digestive tract. Probiotics decrease frequency and severity of anxiety symptoms in rat models. In humans, they decrease cortisol levels in urine²¹. In healthy people with no psychiatric disorders, consumption of fermented milk leads to changes in brain activity in regions that are responsible for emotions and pain.

Healing - Body and mind²⁰

Psychobiotics are live microorganisms (bacteria, for instance) which, once ingested, produce a beneficial effect on the health of patients with psychiatric, psychological or neurological disorders.

In brief, they are probiotics that could have psychotropic properties and regulate the gut-brain axis by: