By Katarina Zimmer
The revelation that our commensal bacteria play important roles in health and disease has turned the microbiome into one of the most active frontiers of biomedicine. Yet our efforts to turn our “inner bugs” into drugs have long been limited to investigational fecal microbiota transplantation (FMT) procedures, which are meant to resolve dysbioses, or harmful microbiome imbalances, by taking gut bacteria of various and sundry types from healthy donors and infusing them into ailing recipients.
FMT has shown considerable success in treating Clostridioides difficile infections of the gut, and it has shown promise in certain other conditions. But many scientists see a need for more targeted microbiome-based therapeutics. Introducing an inconsistent hodgepodge of bacteria isn’t a reproducible method, and it can carry safety risks—an issue highlighted in a 2019 FDA warning following one patient death linked to the presence of antibiotic-resistant bacteria in donors.1
But armed with new technologies, and a growing understanding of the mechanisms by which the human microbiome influences health, researchers are finding more refined methods of harnessing the microbiome to treat disease. Such methods were discussed at the 6th Microbiome Movement Drug Development Summit Europe, a digital event that took place January 25–27, 2022.
Topics of discussion included the identification of specific consortia of beneficial bacteria; the development of novel approaches of correcting gut flora activity; and the use of microbial signatures to rescue drugs that failed in clinical trials. Overall, the event emphasized that microbiome-derived therapies are more targeted and better defined than ever.
Restoring lost functions in metabolic disease
The approach of Switzerland-based BEO Therapeutics is to identify gut bacteria that can correct metabolic disturbances in certain conditions, which can then be cultured and administered to patients orally. In essence, “we supply missing functions to the microbiome,” said Rikke C. Nielsen, PhD, the company’s founder and CEO.
One focus of the company is gout, a form of arthritis caused by hyperuricemia, that is, an excess of uric acid—a metabolic waste product—in the blood. Previous research has found distinct differences in the composition of gut microbiota between gout patients and healthy people,2 including changes associated with dysregulated urate metabolism,3 suggesting that gut bacteria could play a role in driving the disease.
Nielsen and her colleagues hypothesized that the gut microbiota of gout patients might be deficient in genes with a urate-lowering effect, and that the condition could be treated by introducing bacteria with the lost functionalities. To find candidate microbes, the team sifted through genetic sequencing data from the gut bacteria of gout patients, screening for “missing” functions, such as those for reducing urate production or boosting urate excretion.
The researchers identified two promising bacterial strains with a urate-lowering effect. These were administered orally in mouse models of hyperuricemia in as-of-yet unpublished experiments. In animal studies, the effects of the bacteria were compared to those of a small-molecule drug called allopurinol, a standard treatment for gout.
“The bacteria act like a long-acting biologic,” Nielsen observed. “[They] can keep lowering the serum urate over a duration of 23 hours, in contrast to the small molecule that’s washed out.” Nielsen hopes that bacteria could eventually complement existing treatments in people with elevated serum urate, including gout patients.
Boosting responses to immunotherapy
Meanwhile, other companies like Cambridge, U.K.-based Microbiotica are working to find gut bacteria that can improve patients’ responses to existing therapeutics. That’s the goal in advanced melanoma, where treatment with anti-PD-1 immunotherapy can substantially improve survival,4 but not in all patients. Several studies5,6 suggest that the success of anti-PD-1 treatment in these patients depends on the initial composition of their gut microbiome, yet they disagree over specifically which bacteria are associated with a clinical response, said Mat Robinson, PhD, the vice president of translational biology at Microbiotica.
His team conducted another analysis of the gut microbiota of advanced melanoma patients, this time employing Microbiotica’s comprehensive flagship genomic sequencing approach. This revealed nine bacteria that were enriched in patients who responded to the immunotherapy.7 What’s more, this signature could predict patient responses in four independent cohorts with 91% accuracy. According to Robinson, the abundance of these bacteria “seems to make a big difference in whether or not the patients respond.”
Robinson suggested that administering MB097, a consortium of the nine bacteria, could make the microbiome of nonresponding patients more permissive to anti-PD-1 therapy. Indeed, administering MB097 could be more tailored and efficacious than FMT-based methods that have already shown promise. (Two small trials in 2021 showed that using FMT to introduce bacteria from responding patients helped overcome resistance to anti-PD-1 therapy in melanoma patients.8,9)
Unlike FMT procedures, which are conducted over a short period, MB097 could be given daily over extended periods, ensuring high concentrations of the beneficial bacteria, Robinson asserted. His team is planning a Phase I study in 2023 that will administer MB097 alongside anti-PD-1 therapy to advanced melanoma patients who have failed to respond to the immunotherapy within six months. Robinson said that for these patients, the team hopes to “change the trajectory of their disease.”
CRISPR meets the microbiome
Others prefer to avoid actions that could disrupt the gut microbiome’s delicately balanced ecosystem—actions that include the introduction (or removal) of bacterial groups. A company interested in gentler alternatives is Paris-based Eligo Bioscience. It specializes in gene therapy applications that deliver DNA payloads to gut microbes via engineered bacteriophage capsids. Once the therapeutic payloads are delivered, they may disable deleterious genes or enable the expression of therapeutic proteins.
The company’s lead program is EB003, a phage-derived particle engineered to attach to Escherichia coli bacteria of the O157:H7 serotype, which express Shiga toxins. These can damage the gut lining and cause bloody diarrhea. Children under five are particularly vulnerable to such infections; up to 15% develop the potentially life-threatening hemolytic uremic syndrome.10
Once attached to the O157:H7 serotype, the engineered particle delivers a batch of DNA encoding the CRISPR-Cas nuclease and corresponding guide RNA designed to disable two Shiga toxin–expressing genes, thereby killing the bacteria.
EB003 was tested in a rabbit model of infection with Shiga toxin–producing E. coli. The duration of infection was significantly shorter in rabbits that received EB003 than in rabbits that received buffer. “We can then alleviate the [diarrhea] symptoms, dramatically speed up the restoration of the epithelium, and [abolish] the toxin release,” explained Edith Hessel, PhD, chief scientific officer at Eligo Bioscience.
To Hessel, EB003 demonstrates the advantages of a selective approach to modifying the microbiome. In this case, the approach relies on gene editing. “[You want to] kill off the [harmful] bacteria,” she explained, “but you want to do it in a very specific manner and leave the rest of the E. coli intact.”
Tinkering with microbiome activity
Enterome is pursuing a similarly “soft” approach in modifying the gut microbiome. One arm of the Paris-based company focuses on finding small proteins that are secreted by gut bacteria and that—like human cytokines or hormones—influence physiological processes in the gut and elsewhere.
One of Enterome’s programs addresses ulcerative colitis, an inflammation of the inner walls of the colon and rectum. To advance this program, the company’s scientists decided to look for proteins that naturally induce gut-dwelling immune cells to secrete interleukin-10, a potent immunoregulating cytokine that has an inflammation-dampening effect.
The scientists turned to the company’s library of gut-bacteria-secreted small proteins. This library, which includes around 20,000 small proteins, was derived from sequencing data from the gut microbiota of thousands of people. The database was screened for proteins that could coax human monocytes in vitro to secrete interleukin-10, explained Grégoire Chevalier, PhD, Enterome’s scientific affairs manager.
The most effective protein, the scientists found, was EB1010. In models of ulcerative colitis in which rats or mice received EB1010 either directly in the colon or orally, the team observed decreases in inflammatory markers and intestinal sores compared to animals that received standard-of-care treatment. “In both models,” Chevalier said, “we were able to see a very nice efficacy.”
Enterome plans to trial the efficacy of EB1010 in a Phase I study in mild to moderate ulcerative colitis by 2023. Chevalier suggested that administering EB1010 directly into the gut through an oral pill may overcome the limited success of previous efforts to treat certain inflammatory bowel diseases by injecting patients with interleukin-10, as the short-lived cytokine needs to be present locally at high concentrations to have an effect. He added, “We just try to use a natural crosstalk that already exists between our microbiome and our physiology.”
Saving failed drugs
The microbiome could be a partner in drug development. That is, it could provide biomarkers that would distinguish between high responders and low responders in clinical trials. Such biomarkers could even identify patient subpopulations that benefitted from drugs that failed most clinical trial participants. In short, close attention to the microbiome could rescue supposedly failed drugs.
This possibility is being explored by Micronoma, a California-based company that specializes in developing cancer diagnostic tools. The company’s “microbiome-driven liquid biopsy” technology screens blood for unique signatures of microbial genetic material that have been found to be associated with different cancer types.11 Many of these signatures stem from microbes that populate tumor tissue and are naturally shed into the blood during tissue renewal—although curiously, some of them originate from elsewhere in the body, noted Sandrine Miller-Montgomery, PharmD, PhD, Micronoma’s CEO.
Micronoma’s scientists are also investigating the utility of this approach to characterize cancer patients’ responses to treatments. Effective drugs likely alter the tumor microenvironment, in turn affecting its microbial community—producing signatures in the blood that could distinguish responding from nonresponding patients.
Those signatures could be used to parse out groups of patients in unsuccessful clinical trials who in fact responded to a given treatment, although the collective cohort did not. To that end, the company is planning studies that retroactively analyze blood samples collected prior to clinical trials, to search for early signals of response. These studies could lead to “failed” drugs being put to use for patient subgroups.
According to Miller-Montgomery, Micronoma’s technology may serve as a “precision clinical trial design tool.” That is, it may detect microbial signatures that could serve as companion diagnostics. In general, understanding such microbial signatures, and the mechanisms behind them, may also eventually lead to the development of new therapies. “We need to remind everyone that microbes didn’t adapt to us,” Miller-Montgomery stressed. “We adapted to microbes. [Consequently, much] of our health is linked to microbes.”
1. U.S. Food and Drug Administration. Important safety alert regarding use of fecal microbiota for transplantation and risk of serious adverse reactions due to transmission of multi-drug resistant organisms. Published June 13, 2019. Updated December 4, 2020. Accessed March 1, 2022.
2. Guo Z, Zhang J, Wang Z, et al. Intestinal microbiota distinguish gout patients from healthy humans. Sci. Rep. 2016; 6: 20602. DOI: 10.1038/srep20602.
3. Chu Y, Sun S, Huang Y, et al. Metagenomic analysis revealed the potential role of gut microbiome in gout. NPJ Biofilms Microbiomes 2021; 7: 66. DOI: 10.1038/s41522-021-00235-2.
4. Larkin J, Chiarion-Sileni V, Gonzalez R, et al. Five-Year Survival with Combined Nivolumab and Ipilimumab in Advanced Melanoma. N. Engl. J. Med. 2019; 381: 1535–1546. DOI: 10.1056/NEJMoa1910836.
5. Matson V, Fessler J, Bao R, et al. The commensal microbiome is associated with anti-PD-1 efficacy in metastatic melanoma patients. Science 2018; 359(6371): 104–108. DOI: 10.1126/science.aao3290.
6. Frankel AE, Coughlin LA, Kim J, et al. Metagenomic Shotgun Sequencing and Unbiased Metabolomic Profiling Identify Specific Human Gut Microbiota and Metabolites Associated with Immune Checkpoint Therapy Efficacy in Melanoma Patients. Neoplasia 2017; 19(10): 848–855. DOI: 10.1016/j.neo.2017.08.004.
7. Robinson MJ, Vervier K, Harris S, et al. Precision microbiome profiling identifies a novel biomarker predictive of Immune Checkpoint Inhibitor response in multiple cohorts and a potent therapeutic consortium of bacteria. Abstract presented at: American Association for Cancer Research Annual Meeting; Apr 10–15 and May 17–21, 2021; Philadelphia, PA. Cancer Res. 2021; 81(13_Suppl.): Abstract 1783. DOI: 10.1158/1538-7445.AM2021-1783.
8. Baruch EN, Youngster I, Ben-Betzalel G, et al. Fecal microbiota transplant promotes response in immunotherapy-refractory melanoma patients. Science 2021; 371(6529): 602–609. DOI: 10.1126/science.abb5920.
9. Davar D, Dzutsev AK, McCulloch JA, et al. Fecal microbiota transplant overcomes resistance to anti-PD-1 therapy in melanoma patients. Science 2021; 371(6529): 595–602. DOI: 10.1126/science.abf3363.
10. National Organization for Rare Disorders. STEC Hemolytic Uremic Syndrome. Accessed March 1, 2022.
11. Poore GD, Kopylova E, Zhu Q, et al. Microbiome analyses of blood and tissues suggest cancer diagnostic approach. Nature 2020; 579(7800): 567–574. DOI: 10.1038/s41586-020-2095-1.