When Antibiotics Deplete Our Gut Microbiome, a Human Gut Pathogen Takes Advantage

Photo of Ophelia S. Venturelli

University of Wisconsin–Madison researchers have made strides toward understanding how interactions within bacterial communities in the human gut impact our ability to treat a deleterious bacterial infection with antibiotics.

Ophelia Venturelli, Associate Professor in the Department of Biochemistry, is investigating how pathogenic bacteria respond to antibiotic treatments in the presence of other bacteria found in the pathogen’s ecosystem.

“A lot of antibiotic studies look at how the antibiotic effects the pathogen. But pathogens aren’t living in our bodies in isolation,” explains Venturelli.

The human intestine is home to a diverse ecosystem of bacteria — often referred to as the gut microbiome — that, among many other things, helps to ward off infection. Disruptions to this delicate ecosystem can make way for pathogenic bacteria to proliferate, which can lead to infection or illness.

Venturelli and Susan Hromada, a recent graduate of the Microbiology Doctoral Training Program and former member of the Venturelli Lab, have been exploring interactions among antibiotics, bacteria found in the gut microbiome, and the bacterial pathogen Clostridioides difficile. The pathogen infects the human gastrointestinal system and can be notoriously difficult to treat effectively with antibiotics. In fact, C. difficile (often called C. diff for short) has been known to proliferate with greater intensity after treatment with some antibiotics.

“There have been many studies demonstrating how interspecies interactions among bacteria alter C. diff’s growth,” says Hromada, “but almost nothing was known about how these interactions alter C. diff’s susceptibility to antibiotics. Doctors treat C. diff infections while the pathogen is living among other microbes, so understanding these interactions could be useful information for designing effective treatments.”

In 2021, the Venturelli Lab explored how C. diff grows in the presence of human gut bacteria. They found that C. diff growth is greatly inhibited by other bacteria. “Bacteria aren’t always inhibited by each other,” says Venturelli, “but it seems as though C. diff doesn’t compete well with other bacteria. That really impacts C. diff’s ability to secure an ecological niche in the gut and cause severe infection.”

Venturelli believes this is due, in part, to resource competition. A healthy gut microbiome contains many different bacteria, each with their own niche. Pathogens like C. diff must outcompete well-established bacterial communities in order to survive and thrive.

An infectious bacterium that doesn’t compete well for resources may sound like good news. But if C. diff competes so poorly with other bacteria, why is it so difficult to treat?

The answer to this question lies in what happens when the balance of the gut’s ecosystem is disrupted.

One reason that C. diff may stand a better chance of survival after a course of antibiotics is that the antibiotics themselves inhibit the growth of a critical mass of bacteria competing with C. diff — a concept known as competitive release. While antibiotics can help to control bacterial infections, they may also inhibit other bacteria in the gut, making the environment more beneficial for C. diff to thrive.

This is what Venturelli and Hromada found in their most recent study, published in PLOS Biology. The researchers examined how C. diff responds to two different clinically relevant antibiotics, metronidazole and vancomycin, in the presence of other gut bacteria. They used a combination of computational modeling and high-throughput laboratory experiments to identify C. diff’s response to combinations of gut microbiome bacteria and antibiotic presence or absence.

“In the presence of bacteria that are both sensitive to the antibiotic and compete with C. diff, we generally see an increase in C. diff growth when the competing bacteria are inhibited by the antibiotic,” Venturelli says.

“The general pattern we see is that most bacterial interspecies interactions seem to promote C. diff growth in response to antibiotics instead of sensitizing it,” says Venturelli. “We looked at this with a lot of different bacteria. Based on our results, we believe that it’s going to be challenging to find interactions that sensitize C. diff to antibiotics.”

Venturelli and Hromada also looked more closely at how one specific bacterium, Desulfovibrio piger (D. piger), impacts C. diff’s susceptibility to antibiotic.

In their analysis of how interspecies interactions impact C. diff’s response to antibiotics, “the largest effect we saw was the extent that D. piger decreases C. diff’s susceptibility to metronidazole,” Hromada explains. “When D. piger was present, C. diff could withstand substantially higher concentrations of the antibiotic than when C. diff was on its own.”

This response can be attributed to unique properties of both the antibiotic and D. piger.

“Metronidazole is a unique antibiotic. It enters the bacterial cell as a pro-drug, or a drug that is inactive,” says Venturelli. “The bacterial cell has to import the antibiotic, and enzymes inside the cell activate the antibiotic.”

But antibiotic activation is inhibited by the presence of D. piger, which depletes key bioavailable metals in the gut environment, resulting in a metal starvation response in C. diff. Without access to these necessary metals, C. diff is not able to produce the enzymes needed to activate metronidazole.

The researchers took a two-pronged approach to exploring the metal starvation theory: looking at changes in gene expression when C. diff is grown in the presence of D. piger, and quantifying C. diff’s susceptibility to metronidazole in the presence of D. piger when key metals are added in abundance to the environment.

Their findings supported the theory: C. diff’s genes associated with activating metronidazole were down-regulated, and genes associated with metal acquisition were up-regulated. When Hromada and Venturelli supplemented C. diff and D. piger’s environment with metals in excess of what D. piger depletes, this restored C. diff’s sensitivity to metronidazole and reversed the changes in gene expression seen under metal-starved conditions.

The Venturelli Lab’s research points to how crucial it is to study C. diff in the context of the gut ecosystem.

“All of our findings suggest that it’s important to consider the ecological context when designing antibiotics because in the presence of certain bacteria, the medication just won’t be as effective at treating C. diff infection,” Venturelli notes.

Venturelli hopes that this research will contribute to a deeper understand of the microbial interactions that inhibit C. diff treatment and, eventually, will lead to new discoveries about interactions that can suppress C. diff infection.

“That’s the ultimate goal,” Venturelli says. “Some day, we may be able to tailor antimicrobial treatments to be specific to the pathogen. We’d be able to look at someone’s gut microbiome and know what they need to be able to treat the infection.”

Written by Renata Solan.