Druglike molecules produced by gut bacteria can affect gut immune health

Druglike molecules produced by gut bacteria can affect gut immune health

Stanford researchers found that manipulating the gut microbe Clostridium sporogenes changed levels of molecules in the bloodstreams of mice and, in turn, affected their health.

Here’s some food for thought: When you lick your Thanksgiving plate clean this week, you’re not just feeding yourself; you’re also providing meals to the trillions of microbes that live in your gut. And if your dinner includes turkey, a notoriously rich source of the amino acid tryptophan, the gut bacterium Clostridium sporogenes will have the job of breaking down that tryptophan. Then the molecules that are produced by the microbe will flow into your bloodstream in the same way a prescription drug might, interacting with your immune system and changing the biology of the intestines.

Stanford University School of Medicine researchers have used mice to demonstrate how gut bugs could be bioengineered to produce possibly therapeutic changes in the body.

A paper describing their efforts was published online Nov. 22 in Nature. Justin Sonnenburg, PhD, associate professor of microbiology and immunology, and Michael Fischbach, PhD, associate professor of bioengineering, share senior authorship. The lead author is Dylan Dodd, MD, PhD, instructor in pathology.

When the researchers blocked the ability of C. sporogenes to break down tryptophan in mice, levels of certain molecules in their bloodstreams changed. Moreover, the researchers saw physiological changes to the mice’s immune systems and intestines.

“This is a vivid example of not only how the microbiome is affecting things all over your body, but of how we can leverage that to improve health,” said Sonnenburg, using a term for the collection of microbes living on or inside an animal, or in a particular part.

Improving health from the inside

Over the past 15 years, researchers have shown that the composition of a person’s gut microbiome can alter their risk for all sorts of health problems, from diabetes and heart disease to allergies and depression. One reason these tiny microbes have such an outsized effect: They can produce molecules known as metabolites that enter the bloodstream and circulate throughout the body. Pinning down exactly which molecules are produced by which bacteria, however, and how to alter their levels to change health, has been challenging.

Previous studies have shown that just a few bacteria, including C. sporogenes, can break down tryptophan and produce the metabolite known as indolepropionic acid. Studies have also hinted that IPA helps fortify the intestinal wall, letting fewer molecules leak through.

In the new work, the researchers first detailed exactly how C. sporogenes produces IPA from tryptophan. They identified a handful of other compounds also produced in the process — 12 metabolites in total, nine of which can accumulate in the blood and three of which are produced only by bacteria. Then, the researchers pinpointed for the first time the genes that C. sporogenes requires for the breakdown of tryptophan and metabolism of the resulting molecules. A gene called fldC, they showed, is required for the production of IPA.

Next, the team gave germ-free mice either wild-type C. sporogenes—with the ability to produce IPA—or a version of the bacteria that lacked fldC. In mice that received the wild-type bacteria, levels of IPA in the bloodstream were around 80 micromolar; in mice that received the engineered version of the bacteria, IPA was undetectable.

Finally, they looked at how altering the levels of IPA affected the mice. Mice with undetectable IPA, they found, had higher levels of immune cells, including neutrophils, classical monocytes and memory T cells. This suggested activation of two branches of the immune system—the innate and adaptive immune system. In addition, the mice with the engineered version of C. sporogenes had more permeable intestines, a defect which is often seen in gut diseases, including inflammatory bowel disease.

Targeting microbes

If the results hold true in humans, said Sonnenburg, it could point toward a new paradigm for treating some diseases: rather than give a compound, such as IPA, physicians may one day be able to tweak levels of bacteria to affect levels of metabolites. For instance, it might be possible to treat inflammatory bowel disease by boosting levels of C. sporogenes and ensuring patients eat enough tryptophan.

“This gives us a specific example of how we can target individual microbes and pathways in the gut to change a person’s health,” Dodd said. “And this is just one example of hundreds or thousands that are likely out there.”

The group next plans to study C. sporogenes and IPA levels in mice with more complex gut microbiomes—rather than germ-free mice—and begin tracking down other metabolites produced by the gut microbes that may have health effects.

“While providing a stunning example of how a single gut microbe, and a single gene within that microbe, can impact host health, IPA is just the tip of the iceberg,” said Fischbach, “The possibility to positively impact human health through microbiome-produced chemicals is tremendous, and we are poised to take big strides and make this a reality.”

Other Stanford authors are Matthew Spitzer, PhD, a former graduate student; graduate students William Van Treuren and Bryan Merrill; postdoctoral scholar Andrew Hryckowian, PhD; life science researcher Steven Higginbottom, PhD; Gary Nolan, PhD, professor of microbiology and immunology; adjunct faculty member Anthony Le; and Tina Cowan, PhD, professor of pathology.

Story Source: medicalxpress.com

More information: A gut bacterial pathway metabolizes aromatic amino acids into nine circulating metabolites, Nature (2017). nature.com/articles/doi:10.1038/nature24661

 


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Bacteria in the gut modulates response to immunotherapy in melanoma

Bacteria in the gut modulates response to immunotherapy in melanoma

Bacteria that live in the human digestive tract can influence how cancer responds to immunotherapy, opening a new avenue for research to improve treatment, a team led by researchers at The University of Texas MD Anderson Cancer Center reports in the journal Science.

Patients with metastatic melanoma treated with anti-PD1 checkpoint blockade have their disease controlled longer if they have a more diverse population of bacteria in the gut or an abundance of certain types of bacteria, according to the team’s analysis of fecal samples to assess patients’ gut microbiomes.

“You can change your microbiome, it’s really not that difficult, so we think these findings open up huge new opportunities,” said study leader Jennifer Wargo, M.D., associate professor of Surgical Oncology and Genomic Medicine. “Our studies in patients and subsequent mouse research really drive home that our gut microbiomes modulate both systemic and anti-tumor immunity.”

Wargo and colleagues are working with the Parker Institute for Cancer Immunotherapy to develop a clinical trial that combines checkpoint blockade with microbiome modulation.

Research has shown that a person’s microbiome is a modifiable risk factor that can be targeted by diet, exercise, antibiotic or probiotic use or transplantation of fecal material, said lead co-first author Vancheswaran Gopalakrishnan, Ph.D.

Immune checkpoint blockade drugs that free the body’s own immune system to attack cancer cells help around 25 percent of metastatic melanoma patients, and those responses are not always durable. Research focuses on extending the impact of these drugs.

To assess the impact of the microbiome, Wargo and colleagues analyzed buccal swabs — tissue samples from inside the cheek — and fecal samples of patients treated with anti-PD1 therapy that blocks the PD1 protein on T cells, which acts as a brake on the immune system. They conducted 16S rRNA and whole genome sequencing to determine diversity, composition and functional potential of the buccal and fecal microbiomes.

While the team found no substantial differences in response or progression based on buccal samples, analysis of fecal samples of 30 patients who responded to treatment and 13 who did not told a different story.

  • Patients with higher diversity of bacteria in their digestive tract had longer median progression-free survival (PFS), defined at the time point where half of studied patients have their disease progress. While the patient group with high diversity had not reached median PFS (more than half had not progressed), those with intermediate and low diversity had median PFS of 232 and 188 days respectively.
  • Notable compositional differences existed in the gut microbiome of patients who responded versus those who did not, with the Ruminococcaceae family enriched in responders and the Bacteroidales order enriched in non-responders. Patients who had a high abundance of the genus Faecalibacterium (of the Ruminococcaceae family and Clostridiales order) in their gut had significantly prolonged PFS (median not reached), compared to patients who had a low abundance (median PFS of 242 days)
  • Abundance of Bacteroidales was associated with more rapid disease progression, with high abundance within the gut microbiome associated with significantly reduced PFS (median 188 days), compared to low abundance (median PFS of 393 days).

Additional analysis showed that responding patients with high levels of the beneficial Clostridiales/Ruminococcaceae had greater T cell penetration into tumors and higher levels of circulating T cells that kill abnormal cells. Those with abundant Bacteriodales had higher levels of circulating regulatory T cells, myeloid derived suppressor cells and a blunted cytokine response, resulting in dampening of anti-tumor immunity.

A favorable microbiome also was associated with increased antigen processing and presentation by the immune system at the tumor site.

To investigate causal mechanisms, the team transplanted fecal microbiomes from responding patients and non-responding patients via fecal microbiome transplant (FMT) into germ-free mice. Those receiving transplants from responding patients had significantly reduced tumor growth as well as higher densities of beneficial T cells and lower levels of immune suppressive cells. They also had better outcomes when treated with immune checkpoint blockade.

Wargo and colleagues note that there is still much to learn about the relationship between the microbiome and cancer treatment, so they urge people not to attempt self-medication with probiotics or other methods.

Story Source: sciencedaily

Gut microbiome modulates response to anti–PD-1 immunotherapy in melanoma patients. Science (2017). Gopalakrishnan, V., Spencer, C. N., Nezi, L., Reuben, A., Andrews, M. C., Karpinets, T. V., et al.

http://doi.org/10.1126/science.aan4236


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