Findings could lead to new therapies and clinical laboratory biomarkers for detecting and defeating antibiotic-resistant bacteria
Once again, new research shows that human gut bacteria (microbiota) may be useful in fighting antibiotic-resistant bacterial infections. The study findings could provide new therapeutics and clinical laboratory biomarkers for diagnosing and treating severe gastrointestinal disorders.
Antibiotic-resistant bacterial infections often appear in patients with chronic intestinal conditions and in those with long-term antibiotic use. Enterobacteriaceae is a large family of gram-negative bacteria that includes more than 30 genera and over 100 species.
“Despite two decades of microbiome research, we are just beginning to understand how to define health-promoting features of the gut microbiome,” said Marie-Madlen Pust, PhD, a computational postdoctoral researcher at the Broad Institute and co-first author of the paper, in the news release.
“Part of the challenge is that each person’s microbiome is unique. This collaborative effort allowed us to functionally characterize the different mechanisms of action these bacteria use to reduce pathogen load and gut inflammation,” she added.
The researchers identified a way to treat patients infected by antibiotic-resistant strains of bacteria that does not involve antibiotics. Should further research validate these early findings, this could be a viable approach to treating patients with this condition.
“Microbiome studies can often consist of analyzing collections of genetic sequences, without understanding what each gene does or why certain microbes are beneficial,” said Ramnik Xavier, MD (above), director of Broad Institute’s immunology program, co-director of the infectious disease and microbiome program, and co-senior author on the study, in a news release. “Trying to uncover that function is the next frontier, and this is a nice first step towards figuring out how microbial metabolites influence health and inflammation.” Clinical laboratories that test for intestinal conditions caused by antibiotic resistance will want to follow the Broad Institute’s research. (Photo copyright: Broad Institute.)
Suppressing Growth of Antibiotic-resistant Bacteria
To perform their research, the scientists isolated about 40 strains of bacteria from the stools of five healthy fecal donors. They then used those stool samples in fecal microbiota transplants to treat mice that had been infected with either Escherichia coli (E. coli) or Klebsiella, both forms of Enterobacteriaceae. The scientists tested different combinations of the 40 strains and identified 18 that suppressed the growth of Enterobacteriaceae.
“Antibiotic-resistant Enterobacteriaceae such as E. coli and Klebsiella bacteria are common in hospitals, where they can proliferate in the gut of patients and cause dangerous systemic infections that are difficult to treat. Some research suggests that Enterobacteriaceae also perpetuates inflammation in the intestine and infection by other microbes,” the Broad Institute news release notes.
The researchers discovered that Klebsiella changed the gene expression in carbohydrate uptake and metabolism in the Klebsiella-infected mice that were treated with the 18 beneficial strains. The gene expression included the downregulating of gluconate kinase and transporter genes, which revealed there is increased competition among gut bacteria for nutrients.
When combined, these 18 strains alleviated inflammation in the guts of the treated mice by depriving the harmful gut bacteria of carbohydrates. This non-antibiotic approach also prevented harmful bacteria from colonizing in the gut.
“In partnership with the Broad’s Metabolomics Platform, led by senior director and study co-author Clary Clish, PhD, they analyzed samples from pediatric patients with ulcerative colitis, looking for the presence of alternate gluconate pathway genes of gut microbes and fecal gluconate levels. They found higher levels of gluconate linked to more gluconate-consuming Enterobacteriaceae in samples from pediatric patients with ongoing inflammation, indicated by high levels of the protein calprotectin,” the study authors wrote in Nature.
“Together, the findings suggest that Enterobacteriaceae processes gluconate as a key nutrient and contributes to inflammation in patients. But when a gut microbiome includes the 18 helpful strains, they likely compete with Enterobacteriaceae for gluconate and other nutrient sources, limiting the proliferation of the harmful bacteria,” the scientists concluded.
Promising New Bacterial Therapies
This research could ultimately lead to the development of fecal microbiota transplants for individuals to eradicate antibiotic-resistant bacteria in a more objective and specific manner, with fewer side effects than current treatments.
“Harnessing these activities in the form of live bacterial therapies may represent a promising solution to combat the growing threat of proinflammatory, antimicrobial-resistant Enterobacteriaceae infection,” the scientists wrote in Nature.
According to the news release, they plan to continue research to “uncover the identity and function of unknown metabolites that contribute to gut health and inflammation.” The team hopes to discover how different bacteria compete with each other, and to develop microbial therapeutics that improve gut microbiome and curb bacterial infections.
More studies are needed to prove the efficacy of this type of fecal bacterial treatment. However, this research demonstrates how using nano processes enabled by new technologies to identify the actual work of proteins, RNA, and DNA in the body cheaply, faster, and with greater precision, will open doors to both therapeutic and diagnostic clinical laboratory biomarkers.
Clinical laboratory scientists and microbiologists could play a role in helping doctors explain to patients the potential dangers of do-it-yourself medical treatments
Be careful what you wish for when you perform do-it-yourself (DIY) medical treatments. That’s the lesson learned by a woman who was seeking relief for irritable bowel syndrome (IBS). When college student Daniell Koepke did her own fecal transplant using poop from her brother and her boyfriend as donors her IBS symptoms improved, but she began to experience medical conditions that afflicted both fecal donors.
“It’s possible that the bacteria in the stool can influence inflammation in the recipient’s body, by affecting their metabolism and activating their immune response,” microbial ecologist Jack Gilbert, PhD, Professor and Associate Vice Chancellor at University of California San Diego (UC San Diego) told Business Insider. “This would cause shifts in their hormonal activity, which could promote the bacteria that can cause acne on the skin. We nearly all have this bacterium on skin, but it is often dormant,” he added.
A Fecal Microbiota Transplant (FMT) is a procedure where stool from a healthy donor is transplanted into the microbiome of a patient plagued by a certain medical condition.
Our guts are home to trillions of microorganisms (aka, microbes), known as the gut microbiota, that serve many important functions in the body. The microbiome is a delicate ecosystem which can be pushed out of balance when advantageous microbes are outnumbered by unfavorable ones. An FMT is an uncomplicated and powerful method of repopulating the microbiome with beneficial microbes.
“With fecal microbiome transplants there is really compelling evidence, but the science is still developing. We’re still working on if it actually has benefits for wider populations and if the benefit is long-lasting,” said Gilbert in a Netflix documentary titled, “Hack Your Health: The Secrets of Your Gut.”
“The microbial community inside our gut can have surprising influences on different parts of our body,” microbial ecologist Jack Gilbert, PhD (above), of the Gilbert Lab at University of California San Diego told Business Insider. “Stools are screened before clinical FMTs, and anything that could cause major problems, such as certain pathogens, would be detected. When you do this at home, you don’t get that kind of screening.” Doctors and clinical laboratories screening patients for IBS understand the dangers of DIY medical treatments. (Photo copyright: University of California San Diego.)
Changing Poop Donors
When Koepke began experiencing symptoms of IBS including indigestion, stabbing pains from trapped gas and severe constipation, she initially turned to physicians for help.
In the Netflix documentary, Koepke stated that she was being prescribed antibiotics “like candy.” Over the course of five years, she completed six rounds of antibiotics per year, but to no avail.
She also changed her diet, removing foods that were making her symptoms worse. This caused her to lose weight and she eventually reached a point where she could only eat 10 to 15 foods.
“It’s really hard for me to remember what it was like to eat food before it became associated with anxiety and pain and discomfort,” she said.
In an attempt to relieve her IBS symptoms, Koepke made her own homemade fecal transplant pills using donated stool from her brother. After taking them her IBS symptoms subsided and she slowly gained weight. But she developed hormonal acne just like her brother.
Koepke then changed donors, using her boyfriend’s poop to make new fecal transplant pills. After she took the new pills, her acne dissipated but she developed depression, just like her boyfriend.
“Over time, I realized my depression was worse than it’s ever been in my life,” Koepke stated in the documentary.
She believes the microbes that were contributing to her boyfriend’s depression were also transplanted into her via the fecal transplant pills. When she reverted to using her brother’s poop, her depression abated within a week.
Gilbert told Business Insider his research illustrates that people who suffer from depression are lacking certain bacteria in their gut microbiome.
“She may have had the ‘anti-depressant’ bacteria in her gut, but when she swapped her microbiome with his, her anti-depressant bacteria got wiped out,” he said.
FDA Approves FMT Therapy for Certain Conditions
Typically, the fecal material for an FMT procedure performed by a doctor comes from fecal donors who have been rigorously screened for infections and diseases. The donations are mixed with a sterile saline solution and filtered which produces a liquid solution. That solution is then administered to a recipient or frozen for later use.
On November 30, 2022, the US Food and Drug Administration (FDA) approved the first FMT therapy, called Rebyota, for the prevention of Clostridioides difficile (C. diff.) in adults whose symptoms do not respond to antibiotic therapies. Rebyota is a single-dose treatment that is administered rectally into the gut microbiome at a doctor’s office.
Then, in April of 2023, the FDA approved the use of a medicine called Vowst, which is the first oral FMT approved by the FDA.
According to the Cleveland Clinic, scientists are exploring the possibility that fecal transplants may be used as a possible treatment for many health conditions, including:
Doctors and clinical laboratories know that do-it-yourself medicine is typically not a good idea for obvious reasons. Patients seldom appreciate all the implications of the symptoms of an illness, nor do they fully understand the potentially dangerous consequences of self-treatment. Scientists are still researching the benefits of fecal microbiota transplants and hope to discover more uses for this treatment.
Is gut microbiota the fabled fountain of youth? Researchers at Valenzano Research Lab in Germany found it works for killifish. Could it work for other vertebrates as well?
Research into the microbiomes of humans and other animals is uncovering tantalizing insights as to how different microbes can be beneficial or destructive to the host. It is reasonable to expect ongoing research will eventually give microbiologists and clinical laboratories useful new medical laboratory tests that assess an individual’s microbiome for diagnostic and therapeutic purposes.
Human microbiota (AKA, microbiome) have been identified as having a key role in several different health conditions. In previous ebriefings, Dark Daily reported on several breakthroughs involving the microbiome that bring the promise of precision medicine ever closer. Research and clinical studies are contributing to more accurate diagnoses, identification of best drugs for specific patients, and, enhanced information for physician decision-making, to name just a few benefits.
Valenzano Lab published its study online in August. The team of scientists and researchers led by Dario Valenzano, PhD, focused on the longevity of the turquoise killifish (Nothobranchius furzeri), a tiny fish native to the African countries of Mozambique and Zimbabwe. They found that when older killifish ate the fecal matter of younger killifish they lived longer. The fecal matter carried the microbiota to the older fish and extended their lifespans.
Moving Microbiome from One Gut to Another
To perform the research, Valenzano and his team first treated killifish that were nine and a half weeks old (considered middle-aged) with antibiotics to cleanse their gut flora. The fish were then placed in a sterile aquarium containing the gut contents of young adult killifish that were just six weeks old. Although killifish won’t typically eat feces, they would nip at the gut contents in the water and swallow some of the microbes from the younger fish in the process. The researchers discovered that the transplanted microbes were able to successfully colonize the stomachs of the older fish.
Dario Valenzano, PhD (above), gazes at an older Killifish, the subject in his research into increased aging at the Valenzano Research Lab in Cologne, Germany. Studies of the microbiomes of different species is expected to eventually give microbiologists new and useful clinical laboratory tests. (Photo copyright: Max Planck Institute for Biology of Aging.)
When the middle-aged killifish reached the age of 16 weeks—considered elderly—their gut microbiomes were still similar to that of a six-week-old fish. The process had a noticeable effect on the lifespan of the killifish that received the microbiome transplants from the young fish. They lived 41% longer than killifish that received microbes from middle-aged fish and their longevity increased by 37% over fish that were not exposed to any treatment at all. In addition, at 16 weeks, the killifish who had received the transplants were much more active than fish of the same age who had not received the transplants.
“These results suggest that controlling the composition of the gut microbes can improve health and increase life span,” the study paper noted. “The model system used in this study could provide new ways to manipulate the gut microbial community and gain key insights into how the gut microbes affect aging. Manipulating gut microbes to resemble a community found in young individuals could be a strategy to delay the onset of age-related diseases.”
Transferring Fecal Microbiota to Save/Extend Human Lives
Previous research has indicated there may be a connection between microbiomes and aging in some animals, and that the diversity of gut microbes decreases with age. This study proved that this same pattern is true in turquoise killifish.
However, Valenzano does not know how the microbes are affecting the lifespans of the older killifish. “It is possible that an aging immune system is less effective at protecting the micro-organisms in the intestines, with the result that there is a higher prevalence of pathogens in older guts. The gut microbiota in a young organism could help to counter this and therefore support the immune system and prevent inflammation. This could lead to longer life expectancy and better health,” he stated in a press release.
“You can really tell whether a fish is young or old based on its gut microbiota,” Valenzano told Nature. He noted, however, that it is too early to determine if fecal transplants can be used in humans to extend life. “I wouldn’t go that far. This is really early evidence that this has a potential positive effect.”
There is, however, a similar procedure used in humans called Fecal Microbiota Transplant or FMT that has demonstrated promising results in treating certain illnesses.
In a fecal transplant, fecal matter is collected from an approved donor, treated, and placed in a patient during a colonoscopy, endoscopy, sigmoidoscopy, or enema. The purpose of the transplant is to replace good bacteria in a colon that has undergone an event that caused the colon to be inundated with bad bacteria, such as Clostridium difficile, resulting in C. diff. infection, a life-threatening illness that, according to the Centers for Disease Control and Prevention (CDC), kills tens of thousands of people each year.
“The challenge with all of these experiments is going to be to dissect the mechanism. I expect it will be very complex,” stated Heinrich Jasper, PhD, in the Nature article. Jasper is a professor at the Buck Institute for Research on Aging in Novato, California. His lab is working on similar research with microbiome transplants in fruit flies. He predicts this type of longevity research will be performed on other animals in the future.
Valenzano’s and Jasper’s research may eventually create new diagnostic tools for microbiologists to assess the microbiome of individual patients. This technology may also enable microbiologists to advise pathologists and clinical laboratories regarding what specific microbes may be harmful and what microbes may be therapeutically beneficial to patients.
