Probiotic Choices Shape Gut Recovery After Antibiotics

Different Strains Offer Varying Impacts on Microbiome Resilience

New research reveals that not all probiotics are created equal. Studies show that specific probiotic strains can either hasten or hinder the gut microbiome’s return to normalcy following antibiotic treatment, highlighting the need for strain-specific understanding.

Understanding Strain-Specific Effects

At North Carolina State University, investigations using a mouse model demonstrated that distinct probiotic strains can influence the gut microbiome’s recovery trajectory after antibiotic exposure. This adds to growing evidence suggesting that a probiotic’s effectiveness is highly dependent on the specific strain and the prevailing conditions.

Probiotic supplements are frequently recommended to combat antibiotic-associated diarrhea, often caused by Clostridioides difficile (C. diff). However, the precise influence of individual probiotic strains on the gut’s complex bacterial ecosystem remains an area requiring deeper exploration.

“Colonization resistance, or the ability to prevent pathogen colonization, is a function of a healthy microbiota,” stated Casey Theriot, professor of infectious disease at NC State and co-corresponding author of the study. “This study examined how long it took for resistance against *C. diff* colonization to re-establish after antibiotics and the impact of two commonly used commercial *Lactobacillus* probiotic strains on that recovery.”

The research team administered cefoperazone, a broad-spectrum cephalosporin antibiotic, to three groups of mice. One group received no probiotic. The second group was given L. acidophilus, and the third group received L. Gasseri. Each group was exposed to C. diff weekly for a month, with researchers monitoring bacterial load and resistance.

Mice that did not receive probiotics showed reduced bacterial load and resistance to C. diff infection by four weeks post-antibiotic treatment. In contrast, mice treated with L. acidophilus experienced increased bacterial load in the second and third weeks. However, the L. Gasseri group exhibited no detectable C. diff after just two weeks.

Interestingly, L. Gasseri did not appear to colonize the gut long-term. Instead, its benefits seemed to stem from the production of bacteriocins, which are antimicrobial peptides, and its role in promoting the growth of Muribaculaceae, another bacteria considered potentially beneficial.

Can probiotics help or hinder gut recovery after antibiotic treatment? New @NCState research suggests it depends on the strain. Learn more about how different #probiotics impact gut microbiome resilience. #GutHealth #Antibiotics #Microbiome pic.twitter.com/kLd4yM4L4H

— ScienceDaily (@ScienceDaily) July 23, 2025

“We have always known that understanding the strain-specific impact of probiotic strains is important,” commented Rodolphe Barrangou, Todd R. Klaenhammer Distinguished Professor of Food, Bioprocessing and Nutrition Sciences at NC State and co-corresponding author. “Depending on the condition and composition of an individual’s microbiome, the disease, and the probiotic strain, you will see different effects and outcomes.”

He elaborated, “What’s interesting is that this study indicates it’s more complicated than people think, because probiotics can have transient or indirect effects on the microbiome. *L. Gasseri* doesn’t prevent infection; it transiently promotes microbiome recovery through *Muribaculaceae*, which subsequently could provide resistance. This opens new avenues to inform what we should do next.”

“This is the only study out there that is functionally testing resistance in the microbiome,” Theriot added. “Although this work is in a mouse model, it shows the need for better mechanistic understanding of how probiotics affect the microbiome, because not only can they have effects weeks after they’ve left the body, in certain situations they have the potential to prolong or complicate recovery.”

Implications for Gut Health Strategies

The findings underscore the critical importance of personalized approaches to probiotic use. A study published in Nature Medicine in 2023 found that gut microbiome compositions vary significantly among individuals, influencing how they respond to both probiotics and antibiotics. This variability suggests that a one-size-fits-all approach to probiotics after antibiotic therapy may not be optimal.

The research points to the potential for certain probiotics to indirectly support gut health by fostering the growth of beneficial native bacteria, rather than by directly colonizing the gut themselves. This indirect mechanism is a promising area for future research into targeted gut microbiome restoration therapies.

The study’s reference is: Foley MH, McMillan AS, O’Flaherty S, et al. Differential modulation of post-antibiotic colonization resistance to Clostridioides difficile by two probiotic Lactobacillus strains. Running. 2025; 0 (0): E01468-25.

This article was adapted from materials originally published by NC State University.