In severe cirrhosis, RFX profoundly alters gut microbial composition by reducing pathobiont abundance while promoting rifampicin resistance in E. coli, and microbiota-derived signatures were associated with Child-Pugh scores, highlighting their potential to improve patient stratification.
Rifaximin treatment reduced microbial richness in patients with severe cirrhosis over 12 months.
Rifaximin decreased the abundance of taxa typically enriched in advanced cirrhosis.
Rifaximin treatment increased the proportion of Escherichia coli isolates exhibiting phenotypic resistance to rifampicin.
In exploratory analyses, a decrease in Child-Pugh scores was correlated with enrichment of commensal taxa.
Higher abundance of Ruminococcus bromii at inclusion was associated with improved 12-month survival.
Higher abundance of Blautia obeum at inclusion was associated with a lower incidence of spontaneous bacterial peritonitis (SBP).
The study population consisted of patients with severe cirrhosis enrolled in the ProPILA-Rifax randomized trial.
This research examined how a commonly used antibiotic called rifaximin (RFX) — prescribed to people with severe liver scarring (cirrhosis) to prevent serious complications — affects the community of bacteria living in the gut. Using stool samples from 42 patients collected over 12 months, the researchers compared those who received rifaximin to those who received a placebo. They found that rifaximin significantly changed gut bacterial communities: it reduced the overall variety of bacteria and lowered the levels of certain harmful bacteria (such as Escherichia, Streptococcus, and Veillonella) that tend to overgrow in severe cirrhosis. However, rifaximin also caused more E. coli bacteria in the gut to become resistant to a related antibiotic, rifampicin, though this resistance did not extend to other commonly used antibiotics like ciprofloxacin or cefotaxime. The study also found that the makeup of gut bacteria at the start of the study was linked to patient outcomes. Patients who had higher levels of certain 'good' bacteria — specifically Ruminococcus bromii and Blautia obeum — at the beginning of the study had better 12-month survival rates and lower risk of a dangerous complication called spontaneous bacterial peritonitis (SBP), respectively. Additionally, patients whose liver disease scores improved over time tended to have more beneficial, commensal bacteria in their guts. This research suggests that the gut microbiome in cirrhosis patients is deeply connected to disease severity and clinical outcomes, and that rifaximin has a complex dual role: it reduces potentially harmful bacteria but also selects for antibiotic-resistant strains. The bacterial signatures identified here — particularly Ruminococcus bromii and Blautia obeum — may eventually help doctors identify which cirrhosis patients are at higher risk of complications, though further larger studies are needed to confirm these findings.
Ladeira R, Biguenet A, Meunier A, Gonthier M, Di Martino V, Pitta A, et al.. (2026). Gut microbial dynamics and antibiotic resistance during rifaximin therapy in severe cirrhosis: a ProPILA-Rifax ancillary study.. Frontiers in cellular and infection microbiology. https://doi.org/10.3389/fcimb.2026.1930709