A comprehensive review of emerging evidence points to the gut microbiome as a critical factor in biliary atresia (BA), the leading cause of liver transplantation in children. The findings, published in the World Journal of Pediatric Surgery (DOI: 10.1136/wjps-2025-001068), reveal that infants with BA harbor a strikingly imbalanced gut microbial ecosystem, marked by an overgrowth of harmful bacteria and a severe depletion of beneficial microbes like Bifidobacterium. These disturbances are present even before surgery and are strongly linked to poorer outcomes, including failure to clear jaundice and more rapid disease progression.
BA is a progressive fibro-obliterative disease of the bile ducts that affects approximately one in 10,000 to 15,000 infants worldwide. The Kasai portoenterostomy, the standard surgical intervention, attempts to restore bile drainage by connecting the liver directly to the small intestine. However, only about 60% of infants achieve adequate bile flow, and even among those who do, ongoing liver injury often persists. Despite decades of research and various post-surgical therapies, the majority of patients still require liver transplantation by early adulthood. The gut microbiome has emerged as a major player in liver diseases, but its role in neonatal and infant liver conditions has remained largely unexplored.
The review, conducted by Dr. Vandana Jain, synthesizes current evidence on the gut microbiome in BA, examining microbial composition in patients before and after the Kasai procedure. It identifies consistent patterns of dysbiosis, with pathobionts such as Streptococcus, Enterococcus, Veillonella, Klebsiella, and Clostridium taking over, while beneficial commensals like Bifidobacterium, Faecalibacterium, and Blautia are severely depleted. This pattern persists and worsens after surgery, driven by ongoing cholestasis and clinical practices such as reduced breastfeeding rates and the routine use of broad-spectrum prophylactic antibiotics. Critically, the depletion of Bifidobacterium has been linked to worse jaundice clearance, increased liver fibrosis, and a higher risk of post-surgical cholangitis.
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 potential anti-fibrotic effects in experimental models. Disruptions in bile acid metabolism, driven by gut bacteria, further 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 for BA, where treatment options have remained limited for decades. 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 also calls for a re-evaluation of current clinical practices, such as the widespread use of prophylactic antibiotics immediately after 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.
