Modulation of the gut microbiome and resistome by antibiotic use, but not by subsequent 2'-fucosyllactose intake, in adults with overweight or obesity.
Vliex L, Godinho Mimoso I, et al. • Gut microbes • 2026
Seven-day vancomycin use disrupted microbial richness and diversity and affected the resistome, but eight-week 2'-fucosyllactose supplementation showed no detectable improvements in microbial recovery or differential impact on the resistome compared to placebo.
Key Findings
Results
Seven-day vancomycin use significantly disrupted gut microbial richness and diversity in adults with overweight or obesity.
Microbial richness and diversity were disrupted by vancomycin use (p < 0.001)
Study involved 18 adults with overweight or obesity as a subset from a double-blind placebo-controlled randomized intervention
Whole-metagenome shotgun sequencing was used to characterize the gut microbiome at baseline, after vancomycin use, and after supplementation
Microbial composition also changed following seven-day vancomycin use
Results
Eight-week 2'-fucosyllactose (2'-FL) supplementation did not improve microbial recovery compared to placebo after vancomycin use.
No improvements in microbial recovery were detected after eight-week 2'-FL supplementation compared to placebo
2'-FL was administered after seven days of vancomycin use
The study was designed as a double-blind placebo-controlled randomized intervention
The detectable effects of 2'-FL supplementation were described as 'limited'
Results
Vancomycin use did not affect overall resistome richness and diversity, although the presence of specific antibiotic resistance genes (ARGs) changed.
Resistome richness and diversity were not significantly affected by vancomycin use
Despite stable overall richness and diversity metrics, the presence of specific ARGs changed following vancomycin use
Whole-metagenome shotgun sequencing was used to characterize the gut resistome at baseline, after vancomycin use, and after supplementation
Presence of ARGs was noted as a potential determinant of the response to antibiotics
Results
2'-FL supplementation had no differential impact on resistome richness, diversity, or composition compared to placebo.
No differential impact of 2'-FL supplementation on resistome richness, diversity, and composition was detected
The supplementation period lasted eight weeks following vancomycin use
Resistome outcomes were assessed using whole-metagenome shotgun sequencing
Whether prebiotic supplementation results in changes in the gut resistome remained unclear prior to this study
Methods
The study population consisted of adults with overweight or obesity, representing a subset of a larger randomized controlled trial.
18 adults with overweight or obesity were included in this sub-study
Participants were drawn from a double-blind placebo-controlled randomized intervention
The study assessed three time points: baseline, after vancomycin use, and after 2'-FL or placebo supplementation
The intervention included seven days of vancomycin use followed by eight weeks of 2'-FL or placebo supplementation
What This Means
This research suggests that taking the antibiotic vancomycin for seven days significantly disrupts the community of bacteria living in the gut, reducing their variety and changing their composition. The study also found that vancomycin changed which specific antibiotic resistance genes — genetic elements that allow bacteria to survive antibiotic treatment — were present in the gut, even though the overall number and diversity of these resistance genes did not change substantially. These findings were observed in 18 adults with overweight or obesity who underwent gut microbiome and resistome analysis using advanced DNA sequencing at three time points.
The study also tested whether taking a prebiotic supplement called 2'-fucosyllactose (2'-FL) — a compound naturally found in human breast milk — for eight weeks after antibiotic use could help the gut bacteria recover or alter the antibiotic resistance genes present. The results showed that 2'-FL supplementation had no detectable benefit in restoring gut microbial diversity compared to a placebo, and it also had no meaningful effect on the antibiotic resistance gene profile of the gut.
This research suggests that while antibiotics like vancomycin cause notable disruptions to the gut microbiome and affect which antibiotic resistance genes are present, a common prebiotic supplement (2'-FL) may not be sufficient to reverse these effects in people with overweight or obesity. The authors call for more detailed future research on how antibiotics and prebiotics interact with antibiotic resistance genes in the gut, which is an important public health concern given the global rise of antibiotic-resistant bacteria.
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Vliex L, Godinho Mimoso I, Le G, Blaak E, Penders J. (2026). Modulation of the gut microbiome and resistome by antibiotic use, but not by subsequent 2'-fucosyllactose intake, in adults with overweight or obesity.. Gut microbes. https://doi.org/10.1080/19490976.2026.2746814