The educational content in this post, elaborated in collaboration with Lesaffre, was independently developed and approved by the GMFH publishing team and editorial board.

Why the bacterial and fungal intestinal microbiome are relevant in the development of irritable bowel syndrome

Irritable bowel syndrome (IBS) is the most common disorder of gut-brain interaction seen by primary care physicians and diagnosed by gastroenterologists. Despite it being a heterogeneous disease, changes in the gut microbiome have recently been associated with IBS symptoms.

There are three clinical scenarios that link IBS to the gut microbiome (also available for review elsewhere). First, while the majority of patients suffering from a bout of gastroenteritis recover, 10% will develop IBS symptoms. Second, the administration of systemic antibiotics may increase the risk of IBS by altering the gastrointestinal environment. Last, interventions that target the gut microbiome, such as probiotics and non-absorbable antibiotics, may lead to symptoms improvement.

While studies on the role of the gut microbiome in IBS have focused primarily on bacteria, intestinal fungi (known collectively as gut mycobiome) have been largely overlooked. Nevertheless, the fecal mycobiome may help with differentiating patients with IBS from healthy controls and may contribute to IBS-related visceral hypersensitivity.

Indeed, aside from bacteria, the gut mycobiome may participate to the known mechanisms of IBS, which include low-grade inflammation, fungal-bacterial interactions in the gut mucosa, visceral hypersensitivity, gut-brain interactions, intestinal barrier dysfunction and impaired gastrointestinal motility. These findings highlight the relevance of an altered microbiota-gut-brain axis in IBS development and suggest the potential of targeting not only bacteria, but the fungal component of the gut microbiome for diagnosing or managing IBS.


Can bacteria and yeast probiotics help patients with IBS?

A recent systematic review has reported that specific probiotics can benefit patients with IBS through alleviating abdominal pain and improving bowel movement frequency.

When choosing the right probiotic for IBS management, it should be remembered that within species strain differences may affect clinical outcomes. While core effects for probiotics have been described (e.g., a healthy gastrointestinal tract), strain-specific effects include immune modulation, anti-inflammatory properties and production of specific bioactives, which are worth considering when managing gastrointestinal disorders.

Particular species and strains of bacteria (belonging to the Lactobacillus, Bifidobacterium, Escherichia coli and Streptococcus genera) or yeast (i.e., Saccharomyces cerevisiae and S. boulardii) or a combination (i.e., Lactobacillus and Bifidobacterium strains) have been shown to be effective for improving overall IBS symptoms and abdominal pain (here; here).


Advantages of yeast probiotics versus bacterial probiotics

While yeast probiotics share health benefits with bacterial probiotics, important advantages of yeast probiotics (here; here) are that:

  • They are resistant against gastrointestinal enzymes, bile salts and variations in pH and temperature. That ensures yeast probiotics can reach the colon almost intact.
  • They continue to work during antibiotic use due to yeast’s intrinsic resistance to antibiotics, which means yeast probiotics can be co-administered with antibiotics.
  • The modification of the host immune response is considered an important mechanism of action that explains some of the positive health benefits of yeast probiotics.

Pierre Desreumaux, Professor of Gastroenterology at the University and Hospital of Lille France and founder of the European Charity Foundation DigestScience, explained to GMFH editors that yeast probiotics have several advantages compared to bacteria probiotics. “Yeast have higher natural resistance and robustness compared to bacteria particularly toward the aggressive environment encountered in the intestinal tract, but also against bacteriophages and antibiotics. Microbial driven world in the human intestinal flora is tempered by bacteriophages which are 10 times more numerous than bacteria and have the ability to kill bacteria and bacteria probiotics. With more than 44 million antibiotic prescriptions in 2020 in France having the ability to inactivate bacteria probiotics, the better robustness of yeast give a superiority of yeast probiotic compared to bacteria probiotic if we consider that the ability of the probiotic to remain alive in the digestive tract is important”, acknowledged Prof. Desreumaux.


Clinical evidence on the effect of probiotic yeasts on gastrointestinal symptoms in patients with IBS

“Modifying gut microbiota can be a potential strategy for treating IBS”, according to Professor Magnus Simrén. Saccharomyces has been the most widely studied genera as yeast probiotics for IBS management and more specifically the fungal strains S. boulardii and S. cerevisiae.

Three randomized clinical trials have shown the efficacy of S. boulardii in IBS. Since 2015, four prospective randomized placebo-controlled studies (here; here; here; and here) have shown that the Saccharomyces cerevisiae CNCM I-3856 strain can reduce abdominal pain—as demonstrated by the significant and clinically relevant response observed in 45 to 63% of volunteers—with a good level of tolerance in adult patients with IBS. In particular, it seems that S. cerevisiae CNCM I-3856 works better in patients who have IBS with constipation, compared to patients with IBS mixed or IBS with diarrhea.

The studied dose included one or two capsules (one capsule equals 500 mg, 8 x 109 colony forming units/g) for 8 to 12 weeks, which showed efficacy both when administered alone or when administered together with the standard treatment of IBS (i.e., antidiarrheal and/or antispasmodic). “The most recent study published in 2022 including a total of 456 subjects demonstrates also that S. cerevisiae CNCM I-3856 improves significantly the quality of life of patients restoring particularly their body image, health worry, food avoidance and dysphoria”, explains Prof. Desreumaux.

The putative mechanisms of action of S. cerevisiae CNCM I-3856 in IBS include immune-modulating properties and an interaction by the resident gut microbiota and a shift towards an increase in the production of short-chain fatty acids.

Regarding when probiotics fit within the patient with IBS’ journey, Prof. Desreumaux states that “The British Society of Gastroenterology Guidelines on the management of patients with IBS recommend in 2021 in first line therapy the practice of regular exercise, dietary and relaxation advice, and the use of probiotics. The use of probiotics therefore comes very early in the therapeutic arsenal offered to IBS patients, especially if these patients wish to have this type of treatment. Probiotic efficacy must be evaluated after 12 weeks and discontinues in absence of improvement. Depending on the activity of the disease, long-term or fractioned maintenance treatment may be proposed.”


Take-home messages

  • While IBS is a heterogeneous disorder of the interaction between gut and brain, the bacterial and yeast components of the human gut microbiome are gaining attention as a potential therapeutic target.
  • Particular species and strains of bacteria or yeast or a combination of the two have been shown to be effective for improving overall IBS symptoms and abdominal pain.
  • Yeast probiotics have some advantages compared to bacterial probiotics, such as their resistance to the gastrointestinal tract’s harsh conditions and the possibility to be co-administered at the same time with antibiotics.
  • The cerevisiae I-3856 strain has been shown to be effective and safe for reducing abdominal pain in patients with IBS, in particular for the subset of patients who have IBS with constipation.



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