Clinical application of microbial therapy in infectious digestive diseases

1. Introduction

The digestive tract is one of the organs in which the human body is in closest contact with the external environment. Under the mucous membrane with a surface area of 300 square meters, there are 70% of human immune cells stationed to prevent pathogens that enter the body with food from infecting the host. At the same time, they monitor the thousands of microorganisms that live in the digestive tract, including bacteria, molds and viruses, forming a complex symbiotic system between the human body and the microflora. In addition to the immune system used to defend against microorganisms, the gastrointestinal mucosal barrier against pathogens also includes gastric acid, bile salts, digestive juices, mucus layer and antimicrobial peptides. However, the first-line soldiers facing foreign pathogens are not the human immune cells, but the trillions of symbiotic bacteria that reside in the digestive tract. These intestinal microorganisms that coexist peacefully with humans are actually the body's first line of defense against diseases that enter the body through the mouth.

2. Colonization resistance

Once pathogens enter the body through ingestion and pass the test of gastric acid and bile salts, they may further colonize, proliferate, release toxins, and even become dominant bacteria that invade mucosal epithelial cells, leading to gastrointestinal infection and inflammation. At this time, the symbiotic bacteria in the intestine play an important role in preventing gastrointestinal infections by maintaining the stability of the intestinal ecology and exerting colonization resistance against pathogens. Intestinal microflora can block the expansion of pathogens in the intestine through direct and indirect colonization resistance mechanisms. Direct ways to exert colonization resistance include (1) competing with pathogens for nutrients and space. (2) Killing invading pathogens through the production of bacteriocin and the Type VI Secretory System (T6SS). (3) Forming special small molecule metabolites such as short-chain fatty acids, indoles and secondary bile acids to inhibit the growth of pathogens. The indirect colonization resistance mechanisms of intestinal microflora against pathogens include (1) promoting goblet cells to produce mucus to form a mucosal barrier. (2) Stimulate intestinal epithelial cells to consume oxygen and maintain an absolutely anaerobic environment that is unfavorable to the proliferation of pathogens. (3) Induce intestinal immune response. If the microflora enters an imbalanced state (dysbiosis), it will lead to the inability or defect of colonization resistance, greatly increasing the chances of pathogen invasion and infection. Therefore, maintaining the health and balance of intestinal microflora plays an important role in the prevention and treatment of infectious digestive diseases. The following selects several of the more promising microbiome-based therapeutics for infectious digestive diseases and introduces their current development status and future prospects.

3. Clostridioides difficile infection (CDI)

Clostridioides difficile is a bacterium that causes serious intestinal infections, often following antibiotic use for other infections. The pathogenesis is therefore believed to be related to the imbalance of the microflora caused by antibiotics. Symptoms of CDI include severe diarrhea, abdominal pain, and potentially life-threatening inflammation and intestinal damage. Microbial treatment of CDI has developed rapidly in the past decade. Initially, the treatment of Clostridium difficile infection (CDI) relied mainly on antibiotics, including the broad-spectrum vancomycin, metronidazole, and the newer fidoximycin. However, because antibiotics also destroy intestinal microflora and reduce colonization resistance, making patients susceptible to reinfection (recurrent CDI, rCDI), better treatments are needed. In recent years, fecal microbiota transplantation (FMT) has been proven to be an effective treatment for rCDI. By transplanting stool samples from healthy people into the intestines of patients, FMT can help patients restore healthy intestinal microflora and reduce the recurrence rate of CDI after treatment. Many clinical evidences have shown that the therapeutic effect of FMT after a course of antibiotics is significantly better than traditional antibiotic treatment. Despite the striking success of FMT in treating rCDI, its specific mechanisms are still under investigation. It is generally believed that the introduction of highly diverse healthy microflora through FMT can compete with Clostridium difficile for nutrients and living space, thereby inhibiting its growth. Some studies also believe that the therapeutic effect of FMT on rCDI comes from the metabolites of bacteriophages and microflora. In the past decade, clinical trials using FMT to treat rCDI have flourished around the world. The routes of implementation include administration from the upper gastrointestinal tract through nasogastric tubes and gastroscopy, or administration from the lower gastrointestinal tract through enema and colonoscopy. These routes have shown significant therapeutic effects. In the United States, FMT was previously performed under the FDA's IND experimental regulatory approach, but it has been included in many medical guidelines as a standard treatment for rCDI and has even been included in federal Medicare reimbursement items. It was not until 2022 that the US FDA approved the first new FMT drug Rebyota (Rebiotix) for the treatment of rCDI. It was administered through enema and achieved an improvement of 70.6% in the Phase III clinical trial of rCDI, an increase of 14.1% compared to the 57.5% in the placebo group. In 2023, the FDA approved the first oral FMT new drug VOWST (Seres Therapeutics), which processed healthy human feces to leave spores of Firmicutes and made them into oral capsules for a three-day course of treatment. In the Phase III clinical trial of rCDI, it achieved a therapeutic effect of 88%, an increase of 28% compared to the 60% effect of the placebo group. In addition, the adverse reactions of Rebyota and VOWST in the short and medium term were not significantly different from those of the placebo group, and the long-term safety needs further follow-up. However, it is worth noting that the current FDA-approved indications for Rebyota and VOWST are limited to the treatment of rCDI and are not applicable to primary CDI. Although studies have shown that FMT treatment for the first CDI infection can maintain better treatment results than Vancomycin alone, more clinical evidence is still needed to support this.

4. Graft versus Host Disease (GvHD)

In addition to the important breakthroughs in treating recurrent Clostridium difficile infection, another disease related to gastrointestinal infection with potential for development is graft versus host disease (GvHD) following hematopoietic stem cell transplantation (HSCT). HSCT patients usually receive high-dose chemotherapy and/or whole-body radiation therapy (Conditioning regimen), and use strong broad-spectrum antibiotics to prevent infections caused by low white blood cells. Therefore, in addition to causing intestinal mucosal inflammation, HSCT will also severely damage the intestinal microflora, resulting in a decrease in diversity and an increase in the proportion of pathogens (dysbiosis). In this case, damage associated molecular patterns (DAMPs) and pathogen associated molecular patterns (PAMPs) in the intestine can easily enter the body through the damaged intestinal mucosal barrier, activating the transplanted T cells to produce an excessive immune response, which in turn attacks the host's intestinal mucosal cells (GvHD), further exacerbating intestinal inflammation and bacterial translocation, leading to a vicious cycle. Since microbial imbalance is closely related to GvHD, infection and mortality after HSCT, microbial therapy has great potential in this field, especially when traditional immunosuppressive drugs are ineffective. Some small-scale clinical trials have shown that FMT can help alleviate the symptoms of GvHD, but the actual clinical benefits and safety issues need further research to clarify.

5. Gastric Helicobacter pylori infection

Helicobacter pylori (H. pylori) is one of the most common infectious digestive diseases and may cause serious digestive system diseases such as gastric ulcer, duodenal ulcer, and gastric cancer. Traditionally, H. pylori eradication therapy involves the use of two or more antibiotics and a proton pump inhibitor. However, as H. pylori becomes increasingly resistant to antibiotics, the effectiveness of antibiotic treatment is gradually decreasing, and there is a need to develop new adjuvant treatment methods. In addition, antibiotics used in H. pylori eradication therapy can disrupt the microflora, leading to side effects such as gastrointestinal discomfort and diarrhea. Therefore, the use of probiotics has become one of the options to increase the eradication rate of H. pylori and improve side effects. A lot of research has been done on the use of probiotics as an adjuvant therapy for H. pylori in the past, but most of them are small and medium-sized clinical trials. Systematic reviews and meta-analyses have shown that probiotics may improve the eradication rate and side effects of H. pylori, but this may also be due to reporting bias, and large-scale randomized studies are still needed to support its clinical benefits. In addition, which probiotic strain, dosage and mechanism are effective in the adjuvant treatment of H. pylori infection also need to be further clarified. Although clinical evidence is not yet clear, probiotics still provide a new possibility for improving H. pylori eradication rates and reducing side effects.

6. Necrotizing enterocolitis

Necrotizing enterocolitis (NEC) is a major intestinal disease that occurs in newborns, especially premature infants. It is characterized by necrosis of parts of the intestinal wall and is one of the important causes of sepsis and even death in premature infants. The etiology of NEC is not yet fully understood, but it is generally believed to be related to the following four mechanisms: (1) excessive expression of TLR4 receptors; (2) imbalance of intestinal microflora; (3) mesenteric ischemia; and (4) interruption of amniotic fluid signaling leading to intestinal dysplasia.

Premature infants have high TLR4 expression in intestinal epithelial cells and respond more strongly to stimulation by PAMPs of intestinal microflora. In addition, the anaerobic environment of the neonatal intestine is not yet stable and the diversity of early intestinal microflora is low. Therefore, they are easily colonized by facultative anaerobic Gram-negative bacteria. Excessive lipopolysaccharide (LPS) in the intestine can easily induce TLR4 downstream reactions in intestinal epithelial cells, leading to inflammation and necrosis of intestinal mucosal cells and destruction of the intestinal mucosal barrier. Intestinal bacteria migrate into the body and cause sepsis. Currently, there are not many known ways to prevent NEC in premature infants. Giving human milk oligosaccharides and probiotics is a method supported by more clinical studies. Human milk oligosaccharides can act as prebiotics to help infants establish and regulate immunity through microflora. Some human milk oligosaccharides can act as TLR4 inhibitors, reducing intestinal inflammation in premature infants and stimulating intestinal epithelial cells to secrete mucus. Giving probiotics to premature infants is the approach with the most clinical trials for preventing NEC. The results of many systematic reviews and comprehensive analyses have shown the preventive effect of probiotics on NEC in premature infants (RR 0.54, 95% CI 0.46 to 0.65). However, due to the different probiotic strains and formulas used in each trial and the lack of description of blinded procedures in most trials, the credibility is still rated as medium to low by Cochrane Review. Therefore, whether premature infants should be routinely given probiotics to prevent NEC still requires more large-scale, high-quality clinical trials to determine the most suitable type of probiotics, the best time and dosage of administration, as well as possible side effects and long-term effects.

7. Acute gastroenteritis

Acute gastroenteritis (AGE) is one of the most common clinical diseases. Most of them are caused by viral infection, which leads to inflammation of intestinal mucosal cells and symptoms such as abdominal pain, vomiting and diarrhea. Gastroenteritis in adults usually lasts 3-5 days and usually improves after taking symptom-relieving medications. In contrast, infants and young children suffer from more severe symptoms of acute gastroenteritis and may even suffer from dehydration and electrolyte imbalance, and are more likely to require hospitalization, thus creating a heavy care burden. Supplementation with probiotics is often believed to reduce the incidence of AGE in infants and young children, but there has been a lack of large-scale, high-quality clinical trials to confirm this. In 2017, a double-blind, randomized clinical trial involving 4,556 people in India was published in the journal Nature, showing that taking Lactobacillus plantarum ATCC-202195 and fructooligosaccharides can effectively prevent sepsis in infants and young children in rural areas of India. This study attracted the attention of European and American scholars, and two multicenter double-blind, randomized clinical trials were launched in the United States and Canada respectively to study whether probiotics can prevent the progression of AGE to moderate or severe cases in infants and young children. However, two large clinical trials published in NEJM, using single (Lactobacillus rhamnosus GG) and combined (Lactobacillus rhamnosus R0011 and L. helveticus R0052) probiotics, respectively, showed that probiotic intervention could not reduce the incidence of AGE progression to moderate or severe disease and hospitalization in infants and young children. However, the probiotic strains and dosages used in the three large studies in India and North America were different, and the trial locations, experimental designs and clinical observation results were also different. Therefore, if relevant trials are to be conducted in the future, it may be necessary to conduct more complete research on mechanisms and indications when screening probiotic strains for clinical trials to increase the chances of success.

8. Conclusion

The concept that bacteria can not only cause disease but also be used to treat disease is no longer a fantasy. In recent years, microbial therapy for infectious digestive diseases has developed rapidly, especially the clinical application of FMT in rCDI, which has reached the milestone of FDA approval. As the definition and mechanism of microbial imbalance in various diseases become clearer, I believe that more microbial treatment methods will be put into clinical use in the future.

Experts and scholars: Wu Weikai / Co-founder of Leeuwenhoek, attending physician of the Department of Medical Research, National Taiwan University Medical School Hospital

The original article was published in the 44th Educational Symposium of the Society of Digestive Medicine

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