Some Gut Microbes Sequester PFAS Internally

Gut bacteria intracellularly accumulate some PFAS compounds.

Image credit:Peter Northrup/MRC Toxicology Unit

Environmental pollutants pose issues for ecosystems and human health alike. One class of problematic chemicals are per- and polyfluoroalkyl substrates (PFAS), a large family of compounds with many uses but that are notoriously difficult to break down. Scientists have found the “forever chemicals” in almost every part of the world and even in human blood.¹

“These chemicals are really, really hard to break down because that (carbon-fluorine) bond is so strong,” said Matt Simcikan environmental chemist who studies PFAS and other pollutants at the University of Minnesota Twin Cities. He added that organic compounds with fluorine are uncommon in nature. As a result, he said, “Biology doesn’t see them, so they don’t really know what to do with them. They can’t break them down. They tend to behave strangely within an organism.”

Researchers showed that some PFAS molecules caused toxicity in birds and fish, and some human studies have shown that PFAS exposure was associated with altered levels of cholesterol and hormones as well as altered liver and immune functions.^2-4 However, these effects are still poorly understood.

Kiran Patila systems biologist studying the gut microbiome at the University of Cambridge, started exploring the interactions between environmental pollutants and these bacteria in 2020. Around this time, he watched the movie Dark Waters which featured a lawsuit arising from PFAS chemical exposures. This sparked his interest in the compounds and prompted him and his team to look for interactions between PFAS and gut microbes in their data. “And there it was,” he recalled. “We said, ‘this is very important, and we have to follow this up.’”

In a recent study published in NaturePatil and his team showed that bacteria living in the guts of mice bioaccumulate PFAS intracellularly. This process helps remove these compounds from the body via the feces. The findings offer important insights into the effects of PFAS on the gut microbiome and the bacteria’s response to them.⁵

From an initial screen of several chemical pollutants, the team selected perfluorononanoic acid (PFNA) as a representative PFAS to study because its longer carbon chain length increased the likelihood that it would reach the gut for excretion and thus come in contact with the gut microbiome. They exposed 89 microbial strains to PFNA and assessed which of these accumulated the chemical. The team saw that members of the Bacteroidota phyla accumulated the most PFNA.

The researchers further selected Bacteroides uniformis as a representative of high PFNA-accumulating gut bacteria to study the effects of the molecule further. They showed that the bacteria accumulated PFNA across a range of concentrations, which told them that the sequestration was not concentration dependent. Additionally, B. uniformis and other gut bacteria grew unimpeded in the presence of high concentrations of PFNA and other similar length PFAS.

One species that did not accumulate PFAS was They exhibited chill. Using efflux pump mutants, the researchers showed that the gene Tolc promoted the removal of PFAS from the cell.

The team used this E. coli mutant and B. uniformis to study the accumulation of a mixture of PFAS compounds, which is more representative of how organisms encounter these molecules in nature. The PFAS chemicals ranged in carbon chain length from four to 14 carbons. The researchers saw that both bacterial species only accumulated PFAS with eight or more carbons. The bacteria sequestered these compounds similarly whether there were multiple different chemicals present at once or not.

Previous research only showed that the PFAS compounds associated with the lipid membrane of cells. However, if this were the case in these microbes, their high accumulation of PFAS could be detrimental to cellular processes.⁶ Using focused ion beam time-of-flight secondary ion mass spectrometry (FIB-SIMS), the team showed that PFNA aggregated in the cytoplasm of Tolc-deficient E. coli. “That’s a fantastic use of that (technique),” said Simcik, who wasn’t involved in the study, adding that it was a great way to prove the chemicals were not just on the surface of the bacteria.

This confirmation also impressed Patil and his team. “The real moment, I can recall, that we were super excited (was) when we got these FIB-SIMS images where we could see PFAS molecules inside the cells,” he said.

To assess how intracellular PFAS affects cellular processes, the researchers profiled the proteome and metabolites produced by Tolc-deficient E. coli and B. uniformis. They saw the largest increases in membrane proteins, in particular efflux pumps. PFNA exposure only altered metabolites in B. uniformiswhere it caused a decrease in amino acids related to acid stress.

Finally, the team studied PFAS accumulation in a mouse model of chemical exposure. After colonizing mice with either five high- or low-accumulating bacterial strains, the team orally administered one dose of PFNA. In the two days after this treatment, the researchers detected more PFNA in the feces from mice colonized with high-accumulating bacteria. Patil said that the results are “implying that these bacteria actually do this job of PFAS cleaning up or soaking up also in the gut environment.”

Simcik said, “I’m not surprised that it’s being taken up by the bacteria. I really would like to see what it’s doing to the microbial community and what that change in microbial community might have on the organism, or the digestive health of the organism.” He added that looking at the effects of PFAS on the gut microbiome is interesting. “This really does open up a new area of research that is certainly worthy of investigation and needed.”

Patil said that his team is interested in investigating how these molecules aggregate in the bacteria and the mechanisms that lead to differences in PFAS accumulation.

“This study gives a bit of a glimmer of hope that our microbiome already might be helping us in some ways,” Patil said. From these results, he cofounded and serves as the board member of a company, Cambiotics, that aims to develop and test probiotics as interventions for PFAS exposure.