Although it is a non-specific procedure that does not identify specific health conditions, it could lead to new biomarkers that clinical laboratories could use for predictive healthcare
Researchers from the Mayo Clinic recently used artificial intelligence (AI) to develop a predictive computational tool that analyzes an individual’s gut microbiome to identify how a person may experience improvement or deterioration in health.
Dubbed the Gut Microbiome Wellness Index 2 (GMWI2), Mayo’s new tool does not identify the presence of specific health conditions but can detect even minor changes in overall gut health.
Built on an earlier prototype, GMWI2 “demonstrated at least 80% accuracy in differentiating healthy individuals from those with any disease,” according to a Mayo news release. “The researchers used bioinformatics and machine learning methods to analyze gut microbiome profiles in stool samples gathered from 54 published studies spanning 26 countries and six continents. This approach produced a diverse and comprehensive dataset.”
“Our tool is not intended to diagnose specific diseases but rather to serve as a proactive health indicator,” said senior study author Jaeyun Sung, PhD (above), a computational biologist at the Mayo Clinic Center for Individualized Medicine: Microbiomics Program in the news release ease. “By identifying adverse changes in gut health before serious symptoms arise, the tool could potentially inform dietary or lifestyle modifications to prevent mild issues from escalating into more severe health conditions, or prompt further diagnostic testing.” For microbiologists and clinical laboratory managers, this area of new knowledge about the human microbiome may lead to multiplex diagnostic assays. (Photo copyright: Mayo Clinic.)
Connecting Specific Diseases with Gut Microbiome
Gut bacteria that resides in the gastrointestinal tract consists of trillions of microbes that help regulate various bodily functions and may provide insights regarding the overall health of an individual. An imbalance in the gut microbiome is associated with an assortment of illnesses and chronic diseases, including cardiovascular issues, digestive problems, and some cancers and autoimmune diseases.
To develop GMWI2, the Mayo scientists provided the machine-learning algorithm with data on microbes found in stool samples from approximately 8,000 people collected from 54 published studies. They looked for the presence of 11 diseases, including colorectal cancer and inflammatory bowel disease (IBS). About 5,500 of the subjects had been previously diagnosed with one of the 11 diseases, and the remaining people did not have a diagnosis of the conditions.
The scientists then tested the efficacy of GMWI2 on an additional 1,140 stool samples from individuals who were diagnosed with conditions such as pancreatic cancer and Parkinson’s disease, compared with those who did not have those illnesses.
The algorithm gives subjects a score between -6 and +6. People with a higher GMWI2 score have a healthier microbiome that more closely resembles individuals who do not have certain diseases.
Likewise, a low GMWI2 score suggests the individual has a gut microbiome that is similar to those who have specific illnesses.
Highly Accurate Results
According to their study, the researchers determined that “GMWI2 achieves a cross-validation balanced accuracy of 80% in distinguishing healthy (no disease) from non-healthy (diseased) individuals and surpasses 90% accuracy for samples with higher confidence,” they wrote in Nature Communications.
Launched in 2020, the original GMWI (Gut Microbiome Wellness Index) was trained on a much smaller number of samples but still showed similar results.
The researchers tested the enhanced GMWI2 algorithm across various clinical schemes to determine if the results were similar. These scenarios included individuals who had previous fecal microbiota transplants and people who had made dietary changes or who had exposure to antibiotics. They found that their improved tool detected changes in gut health in those scenarios as well.
“By being able to answer whether a person’s gut is healthy or trending toward a diseased state, we ultimately aim to empower individuals to take proactive steps in managing their own health,” Sung said in the news release.
The Mayo Clinic team is developing the next version of their tool, which will be known as the Gut Microbiome Wellness Index 3. They plan to train it on at least 12,000 stool samples and use more sophisticated algorithms to decipher the data.
More research and studies are needed to determine the overall usefulness of Mayo’s Gut Microbiome Wellness Index and its marketability. Here is a world-class health institution disclosing a pathway/tool that analyzes the human microbiome to identify how an individual may be experiencing either an improvement in health or a deterioration in health.
The developers believe it will eventually help physicians determine how patients’ conditions are improving or worsening by comparing the patients’ microbiomes to the profiles of other healthy and unhealthy microbiomes. As this happens, it would create a new opportunity for clinical laboratories to perform the studies on the microbiomes of patients being assayed in this way by their physicians.
With further research, clinical laboratories may soon be performing macrobiotic testing to measure certain bacterial levels in patients’ gut bacteria
New insights from the University of Chicago (UChicago) into how human microbiota (aka, gut bacteria) play a role in food allergies has the potential to change the way a number of gastrointestinal health conditions are diagnosed and treated. This would give microbiologists and clinical laboratories a greater role in helping physicians diagnose, treat, and monitor patients with these health issues.
Past research has shown that certain gut bacteria can prevent antigens that trigger allergic reactions from entering the bloodstream. For example, Clostridium bacteria in the stomach produce a short-chain fatty acid known as butyrate, a metabolite that promotes the growth of healthy bacteria in the gut. This helps keep the microbiome in balance.
One way butyrate is created in the gut is through the fermentation of fiber. However, a lack of fiber in the diet can deplete the production of butyrate and cause the microbiome to be out of balance. When this happens, a state known as dysbiosis occurs that disrupts the microbiome and can lead to food allergies.
Without butyrate, the gut lining can become permeable and allow food to leak out of the gastrointestinal tract and into the body’s circulatory system. This reaction can trigger a potentially fatal anaphylactic response in the form of a food allergy. Thus, eating enough fiber is critical to the production of butyrate and to maintaining a balanced microbiome.
But today’s western diet can be dangerously low in soluble fiber. Therefore, the scientists at the University of Chicago have developed “a special type of polymeric molecule to deliver a crucial metabolite produced by these bacteria directly to the gut, where it helps restore the intestinal lining and allows the beneficial bacteria to flourish. … these polymers, called micelles, can be designed to release a payload of butyrate, a molecule that is known to help prevent food allergies, directly in the small and large intestines,” according to a UChicago news release.
This will be of interest to microbiologists, in particular. It’s another example of researchers connecting a specific species of bacteria in the human microbiome to a specific benefit.
“It’s very unlikely that butyrate is the only relevant metabolite, but the beauty of this platform is that we can make polymers with other microbial metabolites that could be administered in conjunction with butyrate or other therapies,” said Cathryn Nagler, PhD (above), Bunning Family Professor in the Biological Sciences Division and Pritzker School of Molecular Engineering at UChicago and a senior author of the study. “So, the potential for the polymer platform is pretty much wide open.” As further research validates these findings, clinical labs are likely to be doing microbiomic testing to monitor these therapies. (Photo copyright: University of Chicago.)
Restoring Butyrate in the Gut
One way to treat this anomaly has been through a microbiota transplant—also called a fecal biota transplant—where the administration of a solution of fecal matter is transplanted from a donor into the intestinal tract of the recipient. This transplant alters the recipient’s gut microbial composition to a healthier state, but it has had mixed results.
So, the UChicago researchers went in another direction (literally). They created an oral solution of butyrate and administered it to mice in the lab. The purpose of the solution was to thwart an allergic reaction when the mice were exposed to peanuts.
But there was a problem with their oral solution. It was repulsive.
“Butyrate has a very bad smell, like dog poop and rancid butter, and it also tastes bad, so people wouldn’t want to swallow it,” Shijie Cao, PhD, Postdoctoral Scientist at the Pritzker School of Molecular Engineering at UChicago and one of the researchers who worked on the project, told Medical News Today.
The researchers developed a new configuration of polymers that masked the butyrate. They then delivered these polymer micelles directly into the digestive systems of mice that lacked healthy gut bacteria or a proper gut linings.
The treatment restored the microbiome by increasing the production of peptides that obliterate harmful bacteria. This allowed more of the beneficial butyrate-producing bacteria to emerge, which protected the mice from an anaphylactic reaction to peanuts and even reduced the symptom severity in an ulcerative colitis model.
“We were delighted to see that our drug both replenished the levels of butyrate present in the gut and helped the population of butyrate-producing bacteria to expand,” said Cathryn Nagler, PhD, Bunning Family Professor in the Biological Sciences Division and Pritzker School of Molecular Engineering at the University of Chicago and a senior author of the study, in the press release. “That will likely have implications not only for food allergy and inflammatory bowel disease (IBD), but also for the whole set of non-communicable chronic diseases that have been rising over the last 30 years, in response to lifestyle changes and overuse of antibiotics in our society.”
Future Benefits of UChicago Treatment
According to data from the Asthma and Allergy Foundation of America, about 20 million Americans suffered from food allergies in 2021. This includes approximately 16 million (6.2%) of adults and four million (5.8%) of children. The most common allergens for adults are shellfish, peanuts, and tree nuts, while the most common allergens for children are milk, eggs, and peanuts.
The best way to prevent an allergic reaction to a trigger food is strict avoidance. But this can be difficult to ensure outside of the home. Therefore, scientists are searching for ways to prevent food allergies from happening in the first place. The micelle technology could be adapted to deliver other metabolites and molecules which may make it a potential platform for treating allergies as well as other inflammatory gastrointestinal diseases.
“It’s a very flexible chemistry that allows us to target different parts of the gut,” said Jeffrey Hubbell, PhD, Eugene Bell Professor in Tissue Engineering and Vice Dean and Executive Officer at UChicago’s Pritzker School of Molecular Engineering and one of the project’s principal investigators, in the UChicago news release. “And because we’re delivering a metabolite like butyrate, it’s antigen-agnostic. It’s one agent for many different allergic indications, such as peanut or milk allergies. Once we begin working on clinical trials, that will be a huge benefit.”
Nagler and Hubbell have co-founded a company called ClostraBio to further the development of butyrate micelles into a commercially available treatment for peanut and other food allergies. They hope to begin clinical trials within the next 18 months and expand the technology to other applications as well.
Further research and clinical trials are needed to prove the validity of using polymer micelles in the treatment of diseases. But it is possible that clinical laboratories will be performing microbiomic testing in the future to help alleviate allergic reactions to food and other substances.
Biobattery might one day power clinical laboratory testing devices designed to function in vivo to measure and wirelessly report certain biomarkers
Clinical laboratories may one day regularly process biomarker data sent by ingested medical devices from inside the human body, such as the colon and intestines. But powering such devices remains a challenge for developers. Now, researchers at Binghamton University in New York have developed a biobattery that derives its power based on pH reactions when it comes in contact with acids inside the gut.
The battery uses “bacteria to create low levels of electricity that can power sensors and Wi-Fi connections as part of the Internet of Things,” according to a Binghamton University news release.
The biobattery uses microbial fuel cells with spore-forming bacteria for power and it remains inactive until it reaches the small intestine.
Ingestible devices, such as wireless micro cameras, are being utilized more frequently to investigate a myriad of activities that occur in vivo. But traditional batteries that power ingestible diagnostic gadgets can be potentially harmful and are less reliable.
In addition, the small intestine in humans is typically between 10 and 18 feet in length and it folds several times to fit the abdomen. Thus, the inside area can be very difficult to reach for diagnostic purposes.
“There are some regions in the small intestine that are not reachable, and that is why ingestible cameras have been developed to solve this issue,” said Seokheun “Sean” Choi, PhD (above), Professor of Electrical and Computer Engineering at Binghamton University, in a news release. “They can do many things, such as imaging and physical sensing, even drug delivery. The problem is power. So far, the electronics are using primary batteries that have a finite energy budget and cannot function for the long term.” As these technologies develop, clinical laboratories may play a role in collecting biomarker data from these devices interpretation by physicians. (Photo copyright: Binghamton University/Jonathan Cohen.)
How Binghamton Researchers Developed Their Biobattery
The dime-sized fuel cell assembly is then sealed with a piece of Kapton tape, which can withstand temperatures from -500 to 750 degrees Fahrenheit. When the tape is removed, moisture mixes with a chemical germinant that causes the bacteria to begin manufacturing spores.
The biobattery generates around 100 microwatts per square centimeter of power density, but it can take up to an hour to germinate completely. After one hour, the energy generated from the device can power an LED light, a small clock, or a digital hygrometer, as well as a micro camera for in vivo use.
“We wanted to make these bio-batteries for portable, storable, and on-demand power generation capabilities,” Choi said in the news release.
“The problem is, how can we provide the long-term storage of bacteria until used? And if that is possible, then how would you provide on-demand battery activation for rapid and easy power generation? And how would you improve the power?” Choi added.
Heating the fuel cell decreased the time it took to reach full power to 20 minutes, and increasing the humidity resulted in higher electrical output.
Potential for Long-term Power Storage
In addition, after a week of being stored at room temperature, the activated battery had only lost 2% of its power. The researchers also believe that the device could function properly in an inactivate state for up to 100 years, provided there is enough moisture to activate the bacteria after the Kapton tape is removed.
“The overall objective is to develop a microbial fuel cell that can be stored for a relatively long period without degradation of bio-catalytic activity, and also can be rapidly activated by absorbing moisture from the air,” said Choi in the news release.
More research and studies are needed to confirm the biobattery performs properly and is feasible for general use. This experimentation would require both animal and human testing, along with biocompatibility studies.
“I think this is a good start,” Choi added. “Hopefully, we can make a commercial product using these ideas.”
If the biobattery can power an ingestible medical device for a reasonable period of time, then this invention may be able to power a clinical laboratory testing device that could function in vivo to measure and wirelessly report certain biomarkers inside the body.
GI pathologists will be interested in how the Endoculus device uses tank-like treads to traverse the gastrointestinal tract, where it can capture images and perform biopsies
Gastroenterologists (GI) may soon gain a useful new tool for use in gathering both biopsies and diagnostic information when examining the gastrointestinal tract. Ongoing development of a new robotic device promises both capabilities using technology that will be of interest to GI pathologists and clinical laboratory scientists.
The minute robotic device uses tank-like treads to traverse the colon. While there, it can capture live images and perform biopsies under the control of a gastroenterologist. The researchers believe the robotic technology will benefit GIs performing the colonoscopies as well as the pathologists called upon to analyze biopsies.
“Currently, endoscopy consists of a gastroenterologist using a semi-rigid, long rope-like device and endoscope to propel through your colon manually,” Gregory Formosa, PhD (above) a member of the AMTL team that developed Endoculus, said in a YouTube video describing the device. “We think that a robotic capsule endoscope can replace conventional endoscopes by making them faster, safer, and more robust than a human operator can do currently with traditional techniques,” he added. (Photo copyright: University of Colorado.)
AMTL researcher Gregory Formosa, PhD, said the team’s goal is to “have a capsule-sized robot that can actively traverse [a patient’s] entire gastrointestinal tract and send out diagnostics in real time, as well as autonomously navigate itself to localize problematic areas within [the] intestinal tract.”
Formosa noted that colorectal cancer is “the third-most fatal and diagnosed cancer in the United States.” But if caught at an early stage, these cancers are “95% treatable,” he added. “So, if we can get people screened early, we definitely can reduce the fatality rate of colorectal cancers significantly.”
Currently about the size of a C battery, Endoculus (above) is a “fully packed medical device, complete with a camera, an air pump for inflating the colon, a water pump for cleaning, and a tool port for holding biopsy snares,” states a University of Colorado news story, titled, “A Robot May One Day Perform Your Colonoscopy.” (Photo copyright: University of Colorado.)
How Endoculus Works
One key to the device are the four treads, which are designed for traction on digestive tissue.
“You have to forget about everything you know from a locomotion standpoint because driving around inside the body is very different than driving around in a car,” said Rentschler in the University of Colorado news story. “The environment is highly deformable. It’s very slick. There are sharp peaks that you have to go over.”
The university news story noted the current availability of ingestible “pill cams” that can take photos as they travel through the digestive system. But once swallowed, their movements cannot be controlled.
“For our robots to be able to reach those regions that [can be] reached with a pill-cam—but also be able to stop and look around—that could be a big paradigm shift in the way we view these procedures,” said Micah Prendergast, PhD, an AMTL research team member.
Could Biopsies Be Diagnosed In Situ with Endoculus?
The researchers currently view Endoculus as a potentially better way to perform conventional biopsies. But could it lead to bigger advancements?
“Researchers continue to develop devices to help various specialist physicians—in this case GIs—do more when treating patients,” said Dark Daily Publisher and Editor-in-Chief Robert Michel. “This device fits that description. It is designed to improve the ability of GIs to evaluate the colon. Not only does this device do that, but it can also collect a biopsy at sites of interest. In this way, it is a device that can be a benefit to pathologists who will analyze the biopsy.
“With improvements in digital cameras and associated AI-powered analytical tools, the day might not be far off when a device like this can use the camera and artificial intelligence to diagnose the tissue of interest in situ,” he added. “This might create the opportunity for pathologists to be present in the exam room during the procedure, or even viewing the images remotely.
“Not only would that eliminate the need to collect a tissue specimen that must then be sent to a pathology lab, but it would create a new opportunity for pathologists to add value to patient care while shortening the time to diagnosis for the tissue of interest during these procedures,” Michel noted.
Researchers found that early in life intestinal microorganisms “educate” the thymus to develop T cells; findings could lead to improved immune system therapeutics and associated clinical laboratory tests
The researchers published their findings in Nature. They used engineered mice as the test subjects and say the study could lead to a greater understanding of human conditions such as Type 1 and Type 2 diabetes and inflammatory bowel disease (IBD). In turn, this new knowledge could lead to new diagnostic tests for clinical laboratories.
“From the time we are born, our immune system is set up so that it can learn as much as it can to distinguish the good from the bad,” Matthew Bettini, PhD, Associate Professor of Pathology said in a University of Utah news release.
Does Gut Bacteria ‘Educate’ the Immune System?
The researchers were attempting to learn how the body develops T cells specific to intestinal microorganisms. T cells, they noted, are “educated” in the thymus, an organ in the upper chest that is key to the adaptive immune system.
“Humans and their microbiota have coevolved a mutually beneficial relationship in which the human host provides a hospitable environment for the microorganisms and the microbiota provides many advantages for the host, including nutritional benefits and protection from pathogen infection,” they wrote in their study. “Maintaining this relationship requires a careful immune balance to contain commensal microorganisms within the lumen, while limiting inflammatory anti-commensal responses.”
Matthew Bettini, PhD (left), Associate Professor of Pathology at the University of Utah, co-authored the study along with Gretchen Diehl, PhD (right), an immunologist at Sloan Kettering Institute. The team also included researchers from the Baylor College of Medicine in Houston and the Washington University School of Medicine in St. Louis. “Our studies make clear that there is a window in which gut microbiota have access to the immune education process. This opens up possibilities for designing therapeutics that can influence the trajectory of the immune system during this early time point,” Bettini said in the University of Utah news release. (Photo copyright: University of Utah/Sloan Kettering Institute.)
Findings Challenge Earlier Assumptions about Microbiota’s Influence on Immunity
The researchers began by seeding the intestines of mice with segmented filamentous bacteria (SFB), which they described as “one of the few commensal microorganisms for which a microorganism-specific T-cell receptor has been identified.” In addition, SFB-specific T cells can be tracked using a magnetic enrichment technique, they wrote in Nature.
They discovered that in young mice, microbial antigens from the intestines migrated to the thymus, resulting in an expansion of T cells specific to SFB. But they did not see an expansion of T cells in adult mice, suggesting that the process of adapting to microbiota happens early.
“Our study challenges previous assumptions that potential pathogens have no influence on immune cells that are developing in the thymus,” Bettini said in the news release. “Instead, we see that there is a window of opportunity for the thymus to learn from these bacteria. Even though these events that shape which T cells are present happen early in life, they can have a greater impact later in life.”
For example, T cells specific to microbiota can also protect against closely related harmful bacteria, the researchers found. “Mice populated with E. coli at a young age were more than six times as likely to survive a lethal dose of Salmonella later in life,” the news release noted. “The results suggest that building immunity to microbiota also builds protection against harmful bacteria the body has yet to encounter.”
According to the researchers, in addition to protecting against pathogens, “microbiota-specific T cells have pathogenic potential.” For example, “defects in these mechanisms could help explain why the immune system sometimes attacks good bacteria in the wrong place, causing the chronic inflammation that’s responsible for inflammatory bowel disease,” they suggested.
Other Clinical Laboratory Research into the Human Microbiome
All of this suggests the potential in the future “for clinical laboratories and microbiologists to do microbiome testing in support of clinical care,” said Robert Michel, Editor-in-Chief of Dark Daily and its sister publication The Dark Report. Of course, more research is needed in these areas.
“We believe that our findings may be extended to areas of research where certain bacteria have been found to be either protective or pathogenic for other conditions, such as Type 1 and Type 2 diabetes,” Bettini said in the University of Utah news release. “Now we’re wondering, will this window of bacterial exposure and T cell development also be important in initiating these diseases?”
