A comprehensive review published in the World Journal of Pediatric Surgery has identified the gut microbiome as a critical factor in the progression of biliary atresia (BA), the leading cause of liver transplantation in children. The analysis, conducted by Dr. Vandana Jain and published on January 7, 2026 (DOI: 10.1136/wjps-2025-001068), synthesizes evidence showing that infants with BA harbor a strikingly imbalanced gut microbial ecosystem, characterized by an overgrowth of harmful bacteria and a severe depletion of beneficial microbes like Bifidobacterium.
Biliary atresia affects approximately one in 10,000 to 15,000 infants worldwide. The standard surgical treatment, the Kasai portoenterostomy, aims to restore bile flow by connecting the liver directly to the small intestine. However, only about 60% of infants achieve adequate bile drainage, and ongoing liver injury often persists. Despite decades of research, most patients eventually require liver transplantation by early adulthood.
The review reveals a consistent microbial signature across multiple studies. Before surgery, infants with BA show a pronounced shift in gut bacteria compared to healthy babies, with pathobionts such as Streptococcus, Enterococcus, Veillonella, Klebsiella, and Clostridium dominating, while beneficial commensals like Bifidobacterium, Faecalibacterium, and Blautia are severely depleted. This pattern persists and worsens after the Kasai procedure, driven by ongoing cholestasis and clinical practices such as reduced breastfeeding rates and routine use of broad-spectrum prophylactic antibiotics, which suppress beneficial bacteria.
Critically, depletion of Bifidobacterium has been linked to worse jaundice clearance, increased liver fibrosis, and a higher risk of post-surgical cholangitis, a serious complication that further damages the liver. The review also highlights emerging evidence that microbial metabolites, particularly short-chain fatty acids like acetate and butyrate, may play protective roles, with butyrate showing anti-fibrotic effects in experimental models. Disruptions in bile acid metabolism, driven by gut bacteria through enzymes like bile salt hydrolase, compound the problem, creating a vicious cycle of liver injury and microbial imbalance.
“The gut microbiome is not just a bystander in BA — it appears to be an active participant in disease progression,” the authors said. “We’re seeing consistent patterns where harmful bacteria expand and beneficial ones like Bifidobacterium are lost, and these changes correlate with how well patients do after surgery. The exciting part is that the microbiome is modifiable.”
The findings open the door to new therapeutic approaches. Microbiome-modulating strategies — including probiotics, prebiotics, and potentially fecal microbiota transplantation — have shown promise in adult liver diseases and could be adapted for infants. Early studies with Lactobacillus rhamnosus GG have yielded mixed results, suggesting that strain selection, timing, and combination approaches will be critical. The review calls for a re-evaluation of current clinical practices, such as the widespread use of prophylactic antibiotics immediately after the Kasai procedure, which may inadvertently disrupt the developing microbiome. By integrating microbiome science into clinical care, researchers hope to improve native liver survival and reduce the need for liver transplantation in these vulnerable infants.
