Intestinal bacteriomes of patients with recurrent enteritis Functional restoration with fecal transplantation treatment Clarification of mechanisms by Osaka City University, etc.

Professor Satoshi Uematsu and Assistant Professor Kosuke Fujimoto of Osaka City University's Graduate School of Medicine, Professor Seiya Imoto and his colleagues in the Human Genome Center of the Institute of Medical Science, the University of Tokyo, and Brigham and Women's Hospital in the U.S., have announced that they have jointly clarified the mechanisms by which intestinal bacteriomes recover their functions when a patient with recurrent enteritis associated with Clostridioides difficile (C. difficile) is treated with a fecal transplant. Researchers carried out whole genome analysis of the intestinal bacteriomes and viromes in the feces of patients in whom fecal transplantation treatment had demonstrated effectiveness, and analyzed their functions and interactions. They found that before and after the transplant, intestinal bacteriomes were replaced, and intestinal bacteriomes and viromes interacted and recovered their functions. It is expected that this outcome will lead to the development of effective treatment methods. The findings were published in the February 9 edition of the international science journal Gastroenterology.

Intestinal bacteriomes and viromes differ between individuals, and fluctuate according to environments and stress. It has been reported that compositional abnormalities are associated with a variety of illnesses, including obesity and type 2 diabetes.

Enteritis associated with C. difficile also appears when antibiotics are used to treat infectious diseases and normal intestinal bacteriomes are destroyed. C. difficile is a bacterium normally present in the digestive tract of a healthy person, but in the case of above enteritis, C. difficile proliferates and produces a toxin, causing symptoms of abdominal pain, fever, and diarrhea. In Japan, stopping administration of the antibiotics used for treatment means that in many cases these symptoms improve, but in Europe and the U.S. a highly virulent strain of C. difficile that is resistant to antibiotics has appeared, affecting between 200,000 to 300,000 people each year, and leading to tens of thousands of deaths. The effectiveness of fecal transplantation treatment in these cases has been confirmed, and is being incorporated into treatment guidelines.

Fecal transplantation treatment is a treatment method in which feces from a healthy person (a donor) is suspended in normal saline solution and, after being filtered, is transplanted into the intestines of a patient using an endoscope. There are reports that it has a success rate of over 90% against enteritis associated with the C. difficile that is caused by the virulent strains in Europe and the U.S. On the other hand, one death has been reported, which was the result of the presence of multidrug-resistant E. coli in the donor's feces. Thus, clarifying the mechanisms of action for safety and effectiveness became the next challenge.

The research group was provided with donor fecal samples and samples before and after treatment from nine patients with enteritis associated with C. difficile in whom fecal transplantation had demonstrated effectiveness, and aimed to clarify the mechanisms through which the fecal transplantation was effective. The samples came from Brigham and Women's Hospital, which is leading fecal transplantation treatments in the U.S. Prior to this, the research group had established a way of analyzing large amounts of genome information on intestinal bacteriomes and viromes, and shed light on their classifications and symbiotic relationships.

The group carried out genome analysis on intestinal bacteriomes and viromes from the patients with enteritis associated with C. difficile before the fecal transplant and eight weeks after the fecal transplant, and from the donor fecal samples. They analyzed the changes in the composition ratio before and after treatment using an original analysis technique that they had previously developed.

The results showed that among the patients, there were a certain number of cases before the transplant in which there were Gammaproteobacteria and Caudovirales , which are thought to have an adverse effect and were almost entirely absent from the donors. After the transplant, the Gammaproteobacteria and Caudovirales declined, and Bacteroidetes and Clostridial bacteria and Microviridae, which are thought to have a comparatively positive effect, increased and replaced them, meaning that the patients' intestinal bacteriomes and viromes became similar to those of the donors.

Moreover, the group analyzed the functions of intestinal bacteriomes using the genome data they had obtained. When they did this, fluorobenzoic acid pathways associated with inflammation of the digestive tract were characteristically discovered before the transplant, and secondary bile acid synthetic pathways, arginine and ornithine metabolic pathways that inhibit the pathogenicity of C. difficile were characteristically discovered after the transplant. By carrying out a detailed investigation of bacteriomes associated with inflammation in the digestive tract, the group clarified that there is a connection with Gammaproteobacteria. An increase of Gammaproteobacteria within patients' intestines had been confirmed previously, and their involvement was considered likely, but this was the first time that involvement was proved.

C. difficile is a bacterium that produces two types of toxin, but the bacterium itself cannot be detected with existing technology. It is thought that for treatment, both the normalization of intestinal bacteriomes and viromes and the selective sterilization of C. difficile are necessary. Applying the knowledge that has been obtained will make safer and more effective fecal transplantation treatments possible.

Moreover, this research has obtained knowledge about interactions between bacteria and viruses, and so there are expectations that it will lead to the realization of phage therapy that will use viruses that infect bacteria to remove only specific bacteria.

Uematsu stated, "Japan's C. difficile is a weak strain; it occurs by administering antibiotics, but we have not yet reached any case in which a fecal transplant is necessary. However, it is highly prevalent overseas, and if there is a resurgence of people into Japan when the novel coronavirus disease (COVID-19) ends, there is a high possibility that it will be brought in from overseas, making this an urgent issue. On top of this, if pneumonia increases due to COVID-19, we will not be able to avoid prescribing antibiotics, and so I believe that the risk is increasing, and that Japan must also deal with this danger."