Could your gut help clear out toxic “forever chemicals”?

Scientists are beginning to explore the possibility that certain gut bacteria might help remove per- and polyfluoroalkyl substances (PFAS) – colloquially known as forever chemicals – a class of chemicals linked to cancer and other health harms from the body.

A study published in Nature Microbiology found that certain gut bacteria were able to absorb PFAS, allowing mice with these microbes in their gut to excrete the chemicals through faeces. The findings add to growing interest in how gut microbes could influence the body’s handling of environmental pollutants.

What are PFAS and how do they accumulate in the body?

PFAS are a large class of synthetic chemicals often called “forever chemicals” due to their strong carbon-fluorine bonds, which make them highly resistant to degradation in the body or environment.

“These chemicals have been used since the 1940s across everyday products, from nonstick cookware and food packaging to firefighting foams,” said Uday Nagesh Shivagi, senior consultant and clinical lead in medical gastroenterology at Narayana Health, Bengaluru.

These chemicals primarily enter the body through ingestion of tainted water or contaminated food like fish, meat, or eggs. Inhalation of contaminated dust and skin contact with PFAS containing items are also possible, though less prominent.

Once inside, PFAS bind to serum proteins like albumin and accumulate in organs like the liver and kidneys, as well as in the bile staying in the body for years, explained C. Kolandasamy, senior consultant, department of surgical gastroenterology, Rela Hospital, Chennai. The process of enterohepatic circulation in which substances excreted in bile re-enter the intestines and are reabsorbed into the bloodstream can further prolong their half-life in the body. .

“Some of these chemicals, like PFOS or PFOA, can remain with half-lives of over 8 years,” Dr. Shivagi explained.

Can gut bacteria help eliminate PFAS?

In the recent study , researchers observed that mice carrying specific types of gut bacteria were able to excrete PFAS more effectively through faeces, compared to germ-free mice. “This research gives us early clues about how the gut microbiome might influence PFAS elimination,” Dr. Kolandasamy said. “Certain bacteria appear to bind to PFAS molecules, preventing their absorption and helping excrete them via faeces.”

The mechanism is not one of chemical breakdown, but rather of sequestration, where microbes like Lactobacillus or Bacteroides bind to PFAS in the gut and trap them for elimination. Some microbial metabolites, such as bile acid conjugates, may also play a role in promoting excretion.

“Not all microbes do this,” cautioned Kayalavizhi Jayaraman, consultant gastroenterologist, Prashanth Hospitals, Chennai, “Animal studies have shown that strains like Bacteroides can accumulate PFAS within them. While it’s tempting to think of these microbes as filters, much more research is needed before recommending them for PFAS clearance.” The idea is scientifically compelling but still at a preclinical stage.

“So far, the most convincing data comes from lab and animal studies,” said Dr. Kolandasamy. “Mice with a diverse microbiome show reduced PFAS absorption compared to germ-free mice. However, no human clinical trials have conclusively demonstrated that boosting specific gut bacteria reduces PFAS levels.”

Dr. Jayaraman added that human evidence is mostly observational at this point. “We do see associations between PFAS exposure and gut dysbiosis — meaning changes in microbial diversity, but studies on actively changing the human microbiome to eliminate PFAS are still lacking.”

Role of diet and gut health

While there is no specific diet proven to eliminate PFAS, certain dietary strategies could support the gut’s natural filtering functions.

“Dietary fibre has shown potential,” said Dr. Kolandasamy. “Fiber can bind to bile acids, which also carry PFAS, promoting their excretion. Similarly, probiotics, particularly those containing Lactobacillus strains have shown reduced PFAS absorption in rodent models.”

Pilot studies have also explored the use of bile acid sequestrants such as the cholesterol-lowering drug cholestyramine to lower serum PFAS levels. “These findings suggest gut-focused therapies could be promising in the future,” he added.

Dr. Jayaraman emphasised a preventive approach. “While we don’t yet have a diet protocol to clear PFAS, eating wholesome foods, increasing fibre, and limiting processed and packaged food items may support overall gut health and resilience. It is also wise to avoid non-stick cookware and limit known PFAS exposures.”

Future research

With growing awareness of chemical exposures in everyday life, researchers are exploring whether microbiome-based therapies such as designer probiotics or even faecal microbiota transplantation (FMT) could one day help detoxify environmental chemicals like PFAS.

“There is already interest in engineering bacteria that express PFAS-binding proteins,” said Dr. Kolandasamy. “But these are still early-stage concepts, and there are regulatory and scientific challenges to overcome.”

Aditya Kulkarni, consultant, Paediatric Gastroenterology and Hepatology, Narayana Health SRCC children’s Hospital, Mumbai said “While it’s exciting to imagine a future where a probiotic capsule could help clear toxins, we need years, if not decades of research, to reach that point. Until then, the focus should remain on minimising exposure and supporting gut health naturally.”

This is a field worth watching,” said Dr. Kolandasamy, “but for now, prevention and awareness remain the best defense.”

Published – July 31, 2025 03:16 pm IST

Many tiny organisms including bacteria, fungi and viruses normally live on our bodies, and even inside us. These are called the microbiome. The large number of these organisms living in the gastrointestinal tract are collectively known as the gut microbiome.

Increasingly the gut microbiome is recognised as playing a large part in health and disease, particularly relating to human physiology, metabolism and immune function.

There are now more than 700 published papers looking at the interaction between COVID and the gut microbiome. Many of these studies demonstrate the possible contribution of gut bacteria to COVID infection and severity, as well as the effect COVID (and its treatment) potentially has on our gut bacteria.

Now, a new study has found severe COVID may be related to fungal bugs in our gut microbiome. This could be through a variety of changes to the immune system in response to specific fungal species.

Also Read | Humans evolved with their microbiomes – like genes, your gut microbes pass from one generation to the next

What the study did

Fungal organisms in the microbiome are referred to as the fungal microbiota, or mycobiota. While it’s normal to have a range of fungal organisms in the gut, changes in the types or amount can be linked to disease, just like with variations in gut bacteria.

In the study published in Nature Immunology, the researchers investigated the possible relationship between mycobiota and COVID in a few different ways.

First, they compared patients with and without COVID, looking at the levels of certain fungal organisms in samples from their gastrointestinal tracts. This included 66 people with severe COVID, 25 with moderate COVID and 36 without COVID.

The researchers also measured antibodies in the participants’ blood against these same organisms, which lets us know that they triggered an immune response.

Explained | How does the gut microbiome link to autism spectrum disorders?

To investigate further, the researchers conducted experiments in mice. They gave the mice some of the fungal organisms taken from COVID patients and measured some of the same outcomes, including antibodies in the blood. They also looked to see if certain treatments, such as antifungals, would make a difference.

While this isn’t the first study looking at gut mycobiota and COVID, it’s very comprehensive and reports some interesting findings.

What the study found

The researchers detected a greater amount of fungal organisms in patients who had COVID compared with controls who did not.

Antibodies to certain fungi were also heightened in the blood of COVID patients. In other words, the presence of these fungal organisms and an associated immune response seems to be linked to a more severe COVID infection. In particular, two Candida species and S. cerevisiae were linked to disease severity.

When the researchers isolated live fungi from fecal samples of COVID patients, Candida albicans was common in the gut of patients with COVID, and its growth correlated with more severe disease.

Also Read | COVID and your gut: How a healthy microbiome can reduce the severity of infection – and vice versa

To look at the impact of these fungal species on immune responses, mice were colonised with Candida strains isolated from the COVID patients.

The researchers found older mice who were colonised with C. albicans and then infected with COVID showed a very different immune response compared to mice that weren’t given the Candida fungus. This included having more immune cells called neutrophils in the blood and increases in other markers of inflammation including in the lungs.

Some of these changes were partially resolved with anti-fungal treatment or other specific anti-inflammatory medications that have shown benefit in COVID patients.

Some limitations

All of this suggests variations in the mycobiota may contribute to the excessive inflammatory immune response seen in severe cases of COVID. A link between the fungal microbiome and inflammation isn’t completely new – other studies have shown an impact on inflammatory conditions linked to similar changes in the mycobiota.

As with all studies, there are some limitations to consider here. First, the number of human participants was relatively low, with only 91 patients with COVID included, and 36 in the control group. Many parts of the study analysed even smaller groups of patients or patient samples.

Also Read | Are you sure you contain 10x as many microbes as human cells? 

Second, the study was conducted in 2020 during the first wave of COVID infections. A lot has changed since then including the virus itself. And most people have now not only been vaccinated but also previously exposed to the virus.

Nonetheless, this study raises many possibilities including perhaps being able to look at who might be a greater risk of more severe COVID based on their mycobiota. There may even be a possibility of trying to change the mycobiota to reduce the risks from COVID infection. But to get to these points we need a lot more research.

There are multiple factors that determine the make-up of our microbiome, including mycobiota. These are likely to include diet and lifestyle factors alongside other factors like medical conditions and treatments, such as antibiotics.

At this stage there are fewer proposed interventions for influencing mycobiota than for gut bacteria. But studies such as this one demonstrating the importance of the fungal bugs in our gut will hopefully lead to more research in the area.