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Review Article

Gut Microbiome: A Potential Modifiable Risk Factor in Biliary Atresia

Jain, Vandana; Alexander, Emma C.; Burford, Charlotte; Verma, Anita; Dhawan, Anil

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Journal of Pediatric Gastroenterology and Nutrition: February 2021 - Volume 72 - Issue 2 - p 184-193
doi: 10.1097/MPG.0000000000002973
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What Is Known

  • An altered gut microbiome (dysbiosis) has been characterised in experimental and adult cirrhotic and cholestatic disease; pathophysiological processes relevant to biliary atresia.
  • Bacterial translocation and the production of bacterial-derived metabolites are key mechanistic host-microbiome pathways in cirrhosis and cholestasis.

What Is New

  • Evidence is emerging for dysbiosis and its potential mechanistic pathways in biliary atresia, although data is limited.
  • This review summarises biliary atresia-microbiome studies, and extrapolates relevant evidence for microbiome pathogenesis in cirrhosis and cholestasis, in order to propose a schematic for biliary atresia-microbiome-pathogenesis, for future research potential.

Biliary atresia (BA) is a disease characterised by fibro-obliteration of the biliary tree, presenting in infancy with obstructive jaundice. The Kasai portoenterostomy (KPE) forms a biloenteric conduit relieving biliary obstruction and re-establishing bile flow. Jaundice clearance is, however, achieved in only 60% of infants and even then, cirrhosis and its complications can occur, necessitating liver transplantation (LT) (1). Despite these serious consequences, mechanisms of BA pathogenesis remain unclear. BA is likely a clinical phenotype with aetiological heterogeneity, incorporating genetic, developmental, and acquired/perinatal variants. In the acquired/perinatal variant, evidence alludes to an unknown exogenous factor (eg, virus/toxin) initiating an exaggerated inflammatory response (predominantly TH1) targeting bile duct epithelium (2,3). Adjuvant therapy (antibiotics, choleretics, and steroids) post-KPE has not convincingly correlated with improved native liver survival (4) and, to date, earlier age at KPE (5) is the only modifiable factor affecting BA outcomes, warranting further research into other potentially modifiable factors including the gut microbiome.

The “gut microbiome” is defined as the genes harboured in the cells of micro-organisms colonising the gastrointestinal tract (gut microbiota) (6). It plays an important role in host metabolism, nutrition, and immune function, and has been implicated in a spectrum of clinical diseases, including liver disease, with the enterohepatic circulation delivering potentially toxic factors from the gut. Liver--gut microbiome exploration has predominated in cirrhosis (mainly alcohol or viral-related), cholestasis [including primary sclerosing cholangitis (PSC)] and nonalcoholic fatty liver disease (NAFLD), mainly in adults, but with emerging paediatric evidence. As cirrhosis and cholestasis share pathogenic similarities to BA, research forums (7,8) have encouraged the exploration of the gut microbiome in BA.

In this review, we summarise existing evidence linking the gut microbiome to BA, and highlight key evidence on gut microbiome involvement in cirrhosis and cholestasis, relevant to BA. We have collated this evidence to propose a schematic for BA-microbiome-pathogenesis, which may have therapeutic implications.


Over the last decade, the development of high-throughput genetic sequencing techniques, particularly 16S sequencing, has facilitated advanced detection and classification of the complex ecosystem that is the human gut microbiome, with faecal sampling being the most common proxy for investigation. The gut microbiome contains over 10 trillion microorganisms from over 2000 species, harbouring 100-fold more genes than the human genome (6). Taxonomic classification is illustrated in Figure 1A.

(A) Taxonomic hierarchy in biologic classification; (B) relevant taxa in cirrhosis, primary sclerosing cholangitis and biliary atresia.

It has been suggested (although debate continues) that the human gut microbiome begins developing antenatally (9). It was previously thought the in-utero environment was sterile but detection of micro-organisms in meconium, amniotic fluid, and human placenta has suggested colonisation of the fetal intestine, raising the possibility of maternal microbiome manipulation.

Following birth, the human intestine is rapidly colonised. Bacterial diversity is low in the infant microbiome, with Proteobacteria and Actinobacteria dominating at a phyla level. It gradually increases, and by approximately 2 years of age, the microbiome resembles that of an adult, with Firmicutes and Bacteroidetes becoming prominent phyla (10,11). Environmental factors throughout life continually influence the microbiome (6). Diet and pharmacotherapy play a particular role, such that any microbiome study should incorporate age, diet, and medications (especially antibiotics) (12) in their design. Furthermore, disruption to the taxa diversity, abundance and composition of the gut microbiome, known as “dysbiosis” (6), is increasingly associated with disease states. Research is ongoing into mechanistic pathways for dysbiosis and disease pathogenesis, in order to understand avenues for therapeutic microbiome-modulation.


There is increasing evidence characterising dysbiosis in cirrhosis and cholestasis, with evidence for BA in its infancy. Despite inter-study variation, affected by geography and methodological heterogeneity, reduced bacterial diversity has been associated with disease, and microbial signatures are becoming apparent. Figure 1B lists the most relevant taxa associated with cirrhosis, cholestasis and BA.


Experimental models, in particular germ-free (microbial-free) mouse models for biliary disease, have highlighted an association between the gut microbiota and cholestasis (13,14). Clinical studies exploring the role of the gut microbiome in cholestatic liver diseases, such as PSC and Primary Biliary Cirrhosis (PBC) are also relevant for BA. The striking association between PSC and inflammatory bowel disease (IBD) and the biochemical/histological improvement seen, in both adults and children, with antibiotic administration, allude to a microbiome-driven pathogenesis (15–17). Furthermore, recent large microbiome-PSC adult studies (18–20) demonstrated reduced bacterial diversity and global changes in bacterial composition between PSC and healthy controls; an enrichment of the following genera; Veillonella, Enterococcus, Lactobacillus, Streptococcus, and Fusobacterium; and a positive correlation between Veillonella and Enterococcus and markers of PSC disease severity [Mayo PSC Risk Score (18) and alkaline phosphatase (20)]. A small paediatric PSC study (21) showed reduced bacterial diversity, and increased abundance of Veillonella and Enterococcus genera. Interestingly, significant microbiome differences are described between PSC and IBD alone, but not between PSC and PSC-IBD, highlighting a key concept, that biliary rather than gut disease, could be the predominant factor driving dysbiosis in PSC. There are fewer microbiome-PBC studies (22,23) but Lv et al (23) identified higher numbers of opportunistic pathogens, such as Proteobacteria and Enterobacteriaceae in early PBC, compared with healthy controls. Together this evidence points to a strong case for gut microbiome involvement in BA.


Cirrhosis is the final histological pathway for a broad range of liver diseases, including BA, and is characterised by loss of liver cells, thick fibrous scars, and regenerating nodules. Adult microbiome-cirrhosis studies have demonstrated reduced bacterial diversity and distinct microbiome patterns (including increased Staphylococcaceae, Streptococcaceae, Enterobacteriaecae, Enterococcaceae, and decreased Lachnospiraceae and Ruminococcaceae) (24,25) with worsening overall dysbiosis, as well as individual taxa (including Clostridiae from Lachnospiraceae family), correlating positively with disease severity (25,26). Interestingly, hepatic encephalopathy, a complication of cirrhosis contributed to by ammonia production from gut microbiota, has its own dysbiotic pattern with a higher abundance of Ruminococcaceae and Lachnospiraceae, compared with cirrhotic patients without hepatic encephalopathy (27). As cirrhosis is a disease end-point in BA, the aforementioned taxa could be relevant for BA, although caution should be taken when extrapolating from studies in alcoholic liver cirrhosis, as alcohol itself impacts the microbiome (28).

Biliary Atresia

In the 1980s, faecal culture-based methodology highlighted a role for dysbiosis in BA, showing significantly reduced Bifidobacteria (dominant in the gut of healthy infants) in BA (2.4% vs 75% in controls) (29). Nonculture-based exploration of the gut microbiome in BA is currently in its infancy. A higher Proteobacteria to Firmicutes ratio was seen in a rhesus rotavirus mouse model of BA, with the species Anaerococcus lactolyticus from the Clostridiales order (30), significantly associated with improved biliary outcomes. Maternal exposure to antibiotics shifted the mouse pup microbiome to a higher Firmicutes to Proteobacteria ratio, and improved jaundice and native liver survival outcomes, highlighting not only the potential to manipulate BA outcomes via the infant microbiome but also via the maternal microbiome. Two molecular studies demonstrated reduced bacterial diversity at KPE, compared with healthy controls, and further reduction in diversity post-KPE (31,32). Moreover, diversity inversely correlated with the degree of cholestasis. At KPE, increased Streptococcus, Klebsiella and Enterococcus, and reduced Bifidobacteria, Faecalibacterium, Lachnospiraceae, Clostridium XIVa, and Blautia were revealed, consistent with adult cirrhosis studies. Higher Bifidobacteria levels 1-month post-KPE were associated with jaundice clearance by 3 months. Furthermore, even pre-KPE, increased diversity was associated with improved bile flow, and different microbiome structures correlated with bile flow outcomes. This finding, although requiring corroboration, raises the possibility of modulating the microbiome at diagnosis to improve outcomes. We must also understand more about the long-lasting effects of disruption to the evolution and developmental milestones of the microbiome in the crucial first 2 years of life, and whether replication of a “normal” pattern could be beneficial. Bifidobacteria consistently reveals positive correlation to improved BA outcomes but whether it has a protective role or is a consequence of a beneficial hepatic phenotype/increased bile flow (ie, chicken or egg), warrants further interrogation.


Studies characterising the gut microbiome in liver disease are largely associational. Recent research has, therefore, focused on microbiome-mechanistic pathways in liver disease. Translocation of bacteria and bacterial components, and the production of microbiome-specific metabolites, have been identified as key microbiome-mechanistic pathways. We will summarise relevant aspects of these mechanisms in cirrhosis and cholestasis, pulling together evidence within BA literature. Figure 2 proposes a hypothetical schematic for gut microbiome linkage in BA pathogenesis. Table 1 summarises dysbiosis-related and microbiome-mechanistic studies in BA.

A hypothetical schematic for gut microbiome linkage in biliary atresia pathogenesis. (A) In health, gut microbiota and related PAMPs are locally regulated by an intact intestinal barrier and intestinal immune system. In BA, dysbiosis favours increased production of bacterial LPS. Intestinal barrier integrity is compromised by dysbiosis-mediated dysregulation of bile acids, SCFAs (particularly butyrate) and intestinal innate immunity as well as cirrhosis-mediated intestinal barrier structural changes. This “leaky gut” facilitates translocation of bacteria/LPS from gut-mesenteric lymph node-portal circulation-liver. (B) Cholestasis and cirrhosis in BA leads to a reduced production and secretion of primary bile acids to the gut influencing dysbiosis. Dysbiosis, in turn (i) creates a pro-inflammatory state (increased LPS-mediation inflammation), which reduces primary bile acid production via CYP7A1 inhibition; (ii) reduces the conversion of primary to secondary bile acids through reduction of 7a-hydroxylating bacteria (Lachnospiraceae, Blautia, Clostridium). Reduction in secondary bile acids can influence FXR-stimulation and further affect dysbiosis (via reduction in antimicrobial peptide production) and bile acid structure. (C) Bacterial PAMPs, in particular LPS, reaches the liver via the portal circulation, and forms a complex with LBP and CD14 to promoting an inflammatory cascade via TLR4 signalling. Dysbiosis-mediated dysregulation of SCFAs promotes the inflammatory milieu in BA. (D) Reflux of bacteria and associated PAMPS via the bilioenteric conduit, from the gut to the liver, contributing to cholangitis pathogenesis. BA = biliary atresia; LPS = lipopolysaccharides; PAMPs = pathogen-associated molecular patterns; SCFAs = short-chain fatty acids.
TABLE 1 - Summary of clinical biliary atresia studies exploring gut microbiota structure (culture and nonculture-based methodology) and bacterial translocation
First author (Ref. No.) (date) Study population Gut microbiota-related parameter (s) Diagnostic method Findings
Tessier (32) (2020) BA (n = 8) newly diagnosedLongitudinal samples (pre-KPE and 1, 3, 6 months post-KPE) Gut microbiome diversity and taxonomy Faecal 16S sequencing and whole genome sequencing Microbial diversity inversely proportional to degree of cholestasisMicrobial diversity pre-KPE associated with good bile flow at 6 months post-KPE (total serum bile acid <40 μmol/L)Bifidobacterium at 1 month post-KPE significantly associated with good bile flow at 6 months post-KPEBifidobacterium breve pre-KPE, higher in successful KPE (bilirubin <2 mg/dL at 3 months post-KPE) and good bile flow groups.
Wang (31) (2020) BA (n = 34) newly diagnosed versus age-matched HC (n = 34)Longitudinal BA samples (n = 16) at 2 weeks post-KPE Gut microbiome diversity and taxonomy Faecal bile acid Faecal 16S sequencing and metagenomics Ultra-high performance liquid chromatography Microbial diversity reduced BA versus HCIncrease in Streptococcus, Klebsiella, Enterococcus in BA versus HCDecrease in Bifidobacterium, Faecalibacterium, Lachnospiraceae, Clostridium XIVa and Blautia.Reduced total bile acids in BANo reduction of primary: secondary bile acid ratioClostridium XIVa positively correlated with the ratio of primary/secondary bile acids
Kobayashi (29) (1988) BA (n = 9) <3 months old versus age matched HC (n = 16) Gut microbiota composition Faecal culture Bifidobacteria, lecithinase-negative Clostridia, Streptococci and Staphylococci reduced in BA
Urao (84) (1999) BA (n = 5) mean age 5.1 monthsAll patients administered probiotic Gut microbiota compositionSerum endotoxin Faecal culture Toxicolor and endospecyPre-and postprobiotic Bifidobacterium increased and E-coli, Streptococcus, Klebsiella decreased post probioticSerum endotoxin decreased post probiotic
Lien (85) (2015) BA jaundice-free (n = 20)Randomised to 6-month course of neomycin (n = 10; mean 0.88 +/− 0.75 years age) or Lactobacillus casei rhamnosus (n = 10; mean 1 +/−0.74 years age) Gut microbiota compositionCholangitis frequency Faecal cultureClinical diagnosis Escherichia coli decreased in antibiotic and probiotic groupsLactobacillus increased in probiotic groupCholangitis frequency same (20%) in antibiotic and probiotic groups
Chou (63) (2010) BA (n = 115), choledochal cyst (n = 9), HC (n = 7) LPS, soluble CD14 hepatic CD14 expression Limulus amebocyte lysate (LAL) test, ELISA immunohistochemistry Hepatic CD14 and soluble CD14 increased in early stage BA versus late stage BA. LPS higher in BA versus controls. LPS not significantly different between early and late stage BA
Faddan (67) (2017) Cholestatic infants (n = 53)NH (n = 32) BA (n = 21)HC (n = 29) Intestinal epithelial damageIntestinal permeability Serum levels of I-FABP, I-BABP; D-lactate Cholestatic infants have higher levels of I-FABP and I-BABP than controls.No difference in I-FABP, I-BABP between NH and BANo differences in D-lactate in any group
Luo (61) (2015) BA (n = 110) Cholangitis frequencySystemic bacterial DNA (bactDNA) Clinical diagnosis16S rDNA-based technique Seventy-seven of 110 had an episode of cholangitis; 14.3% positive blood culture versus 58.4% bactDNA (P < 0.0001)39.4% cholangitis-free patients show presence of bactDNA
BA = biliary atresia; KPE = Kasai portoenterostomy; LPS = lipopolysaccharides.

Bacterial Translocation

Bacterial translocation describes the migration of live microorganisms or pathogen-associated molecular patterns (PAMPs), such as lipopolysaccharides (LPS), from the intestinal lumen, across an anatomically intact intestinal barrier, to the mesenteric lymph nodes and extra-intestinal sites. In healthy individuals, this is a regulated physiological process, but in liver disease, pathological bacterial translocation develops. Dysbiosis (and associated altered PAMPs), increased intestinal permeability, and disrupted intestinal innate immunity are known contributory risk factors for bacterial translocation. Interruption of structural (mucin, intestinal epithelial cells, tight junction proteins), biochemical (bile acids, short-chain fatty acids, anti-microbial peptides) and/or immunological components (secretory IgA, dendritic cells, neutrophils, and lymphoid follicles) of the intestinal barrier, contribute to increased intestinal permeability (33,34). The gut microbiome also influences intestinal permeability through interaction with intestinal immune system and metabolism of bile acids and short-chain fatty acids. LPS, the main component of the outer membrane of Gram-negative bacteria, is often studied as a surrogate marker for bacterial translocation, because of the challenges of accessing mesenteric lymph nodes. LPS bind to LPS-binding protein (LBP), which is produced in hepatocytes, and this LPS-LBP complex then binds to the cell receptor CD14, a macrophage cell surface glycoprotein, promoting an inflammatory cascade via Toll-Like Receptor-4 (TLR-4) activation (35).

Within this section, we will focus on evidence for LPS and intestinal permeability in cirrhosis, cholestasis, and specific to BA.


Numerous experimental studies in biliary obstruction have demonstrated increased systemic and portal LPS, with a profound pro-inflammatory response demonstrated following an LPS challenge (36,37). Human cholangiocytes express TLRs, which under normal circumstances, recognise PAMPs, and respond by secreting immunoglobulin A and antibacterial agents (lactoferrin, lysozyme, and defensins) (38). In PSC, TLR4 and TLR9 (both bacterial receptors) are upregulated (39), and cholangiocytes have been shown to accumulate LPS (40), and exhibit persistent hypersensitivity to LPS (41), suggesting a microbiome-translocation-PSC pathway. Furthermore, bacteria and bacterial components have been detected in the bile of PSC patients (42,43). Clinical bacterial translocation-PSC studies, however, are limited and inconclusive (44,45). A recent large clinical study revealed an increase in circulating CD14 and LPS in PSC, which negatively correlated with transplantation-free survival, irrespective of concomitant IBD (46). On the other hand, urinary excretion of lactulose/ l-rhamnose (47) and serum zonulin (46), a physiological regulator of intercellular tight junctions, have not revealed increased intestinal permeability in PSC or PSC-IBD patients. Further studies using more robust techniques are required.


Bacterial translocation to mesenteric lymph nodes has been demonstrated in experimental (48) and clinical (49) cirrhotic studies. Systemic LPS/LBP levels (endotoxemia) are higher in cirrhotic patients (50), and positively correlate to liver disease severity markers and specific complications of cirrhosis, such as spontaneous bacterial peritonitis and portal hypertension. Positive correlation between LBP levels and soluble CD14 in cirrhotic patients has been demonstrated, suggesting a pathophysiological pathway for LPS-LBP (50). Spontaneous bacterial peritonitis provides the most striking correlation between bacterial translocation and cirrhosis, with gut-derived bacteria, commonly Enterobacteriaceae, being isolated from ascitic fluid, in adults and children (51). Fluorescent-labelled Escherichia coli administered orally to cirrhotic ascitic rats was subsequently detected in mesenteric lymph nodes and ascitic fluid (52). Moreover, LBP has been detected in nonneutrocytic culture-negative ascitic fluid (53), highlighting the limitations of culture-based investigations, and emphasizing a role for sub-clinical bacterial translocation in ascites. Histological staining for tight junction proteins, urinary analysis of enteral nondigestible markers, and serum zonulin (54), have revealed increased intestinal permeability in cirrhosis, with correlation to disease severity, in particular, ascites and spontaneous bacterial peritonitis (55,56). Assimakopoulos et al (56) showed reduced expression of tight junction proteins (occludin and claudin-1) in the duodenal mucosa of cirrhotic patients, was associated with ascites, LPS, and cirrhosis severity. Known structural changes of the intestinal mucosa seen in cirrhosis, including widening of intercellular spaces, vascular congestion, and oedema, will contribute to permeability. It is important to highlight that although bacterial translocation is a key mechanistic pathway, it is not a pre-requisite for cirrhosis, not only because of the diagnostic challenges of bacterial translocation, but also the complexity and interplay of multiple factors in cirrhosis.

Biliary Atresia

Cholangitis, the inflammation of the biliary system, post-KPE, provides the most convincing evidence for bacterial translocation in BA. It is reported in 40% to 60% of BA infants within the first 2 years following KPE, and is associated with higher rates of LT (57). The enteric origin of culturable systemic bacteria in cholangitis, both in adults and children (eg, Klebsiella spp, E coli), strongly support gut microbiota-related pathogenesis. Proposed mechanisms include reflux of gut microbiota/PAMPs via the bilioenteric conduit into the biliary system and/or bacterial translocation via the enterohepatic circulation. Porcine BA models post-KPE have supported the hypothesis of ascending infection via the bilioenteric conduit, demonstrating bacterial colonisation of the bilioenteric conduit as promptly as 1-week postprocedure, with subsequent bacterial translocation to the liver (58–60). In human BA, bacterial DNA has been detected systemically in cholangitis, where culture-based techniques have been negative (58.4% vs 14.3% P < 0.001) (61). Furthermore, bacterial DNA was detected in 39% patients without clinical cholangitis, highlighting a role for subclinical bacterial translocation in BA. Sepsis is a frequently reported cause of death for nontransplanted patients with BA (62), further stressing the importance of understanding the relationship between bacterial translocation and BA progression. Increased circulating and hepatic concentrations of LPS and CD14 (63,64) have been described in experimental and clinical BA, with a likely protective role for CD14 in early endotoxemia. Genomic DNA analysis from 90 BA patients revealed a higher prevalence of a CD14 promoter polymorphism, correlating with poorer outcome, possibly through an exaggerated activation of macrophages (65). Unpublished data from our centre (BA, n = 24), suggests an association between LBP and post-KPE short-term outcome (see Fig. 3). Interestingly, TLRs expressed in cholangiocytes lining the remnants of the extrahepatic bile ducts favour viral (TLR3, TLR7) (38), not bacterial, PAMP signalling. Despite some progress in understanding bacterial translocation mechanisms in BA, there remain many unanswered questions, and in particular, data is limited in paediatrics. Urinary excretion of melibiose/rhamnose did suggest increased intestinal permeability in children with cirrhotic portal hypertension but details on disease aetiology were limited (66). One paediatric study revealed an increase in serum markers for intestinal wall integrity in cholestatic versus healthy infants, but could not differentiate BA versus non-BA cholestatic subgroups, suggesting infant cholestasis, indiscriminate of cause, may be associated with intestinal epithelial damage (67).

Association between lipopolysaccharide-binding protein and post-Kasai portoenterostomy short-term outcome (unpublished data).

Gut Microbiome-derived Metabolites

The gut microbiome is known to communicate with host metabolism, to produce an array of metabolites with downstream functions. Metabolomic analyses have permitted the identification of microbiome-associated metabolites, which, in combination with gut microbiome sequencing, help elucidate potential microbiome-mechanistic pathways. In this section, we focus on relevant evidence for microbiome-associated bile acid and short-chain fatty acid metabolism in cirrhosis, highlighting BA-specific evidence.

Gut Microbiome-Bile Acid Interaction

The liver-bile acid-microbiome axis is emerging as an important pathway, particularly in cirrhosis pathogenesis. In health, primary bile acids (cholic acid and chenodeoxycholic acid), are produced in the liver, and are conjugated to glycine or taurine, before being secreted to solubilise fats and fat-soluble vitamins (68). Approximately 95% of bile salts are actively transported across the ileum, to the liver, via the enterohepatic circulation. The remaining 5% enter the colon and are subjected to enzymatic processes of deconjugation and 7α-dehydroxylation by gut microbiota, producing the secondary bile acids (lithocholic acid and deoxycholic acid). Hence, cirrhosis and cholestatic liver disease can influence bile acid composition (eg, primary vs secondary ratios) through dysbiosis-mediated alteration of these enzymatic processes. In turn, the reduction in total bile acid production, and its secretion, in liver disease, can impact the gut microbiome milieu. Furthermore, both the gut microbiota- and liver disease-mediated transformation of the bile acid pool can alter the activation of the intestinal bile acid receptor, farnesoid X receptor, which amongst many roles, promotes the synthesis of antimicrobial agents, although to what extent this affects the gut microbiome composition is unknown (69). In a landmark study by Kakiyama et al (70), this microbiome-bile acid interplay was illustrated by a reduction of faecal total and secondary : primary bile acid ratio in cirrhotic adults, associated with a reduction in 7α-dehydroxylating bacteria (eg, Lachnospiraceae, Ruminococcaceae, and Blautia from the Clostridiales order). Ruminococcaceae and deoxycholic acid were positively correlated, further highlighting a mechanistic role between gut microbiota and the bile acid pool. The metabolic and immune effects of secondary bile acids in liver disease require further investigation. In BA, serum bile acid profiles have been used as a diagnostic tool to discriminate between BA and non-BA infantile cholestasis, but increasingly studies have described a reduction in total and primary faecal bile acids (71,72). Molecular analysis has demonstrated a reduction in 7α-dehydroxylating bacteria, Lachnospiraceae, Blautia, and Clostridium XIVa in BA, although a concomitant reduction in secondary bile acids has yet to be described. A comprehensive study of the liver-bile acid-microbiome axis in BA could establish important mechanistic pathways for therapeutic interventions.

Gut Microbiome-Short-chain Fatty Acid Interaction

Short chain fatty acids, predominantly butyric acid, acetic acid, and propionic acid, are produced by the microbiome, after metabolising polysaccharides and dietary starches, that are otherwise indigestible (73). They have multiple downstream effects on host cells, including dietary energy extraction, maintenance of gut barrier function, and interaction with host innate and adaptive immune pathways. Experimental studies have shown that administration of butyrate, an important energy source and regulatory molecule for colonocytes, in LPS-induced liver injury, can reduce the inflammatory component (74). The circulating short-chain fatty acid butyrate is reduced in cirrhosis, and inversely correlated to liver disease severity and LPS (75). Furthermore, Ruminococcaceae, Blautia, and Lachnospiraceae, known butyrate-producing taxa, are all reduced in adult cirrhosis and BA (70,72). A conference abstract showed reduced faecal acetate, propionate, and butyrate in BA infants <4 months post-KPE (76) compared with healthy controls. Unpublished data from our centre showed a significantly lower abundance of faecal acetate and propionate pre-KPE, compared with age-matched cholestatic controls, suggesting BA-specific, rather than cholestasis-induced microbiome mechanisms. Hence, data is suggesting a potential role for short-chain fatty acid supplementation in BA, warranting further exploration.


Understanding the role of the gut microbiome in BA pathogenesis opens avenues for microbiome modulatory therapy. Whilst in its infancy in BA, there is evidence of success in adult cirrhosis with outcomes for hepatic encephalopathy improved by rifampicin, probiotics (77,78), and faecal microbiota transplantation (79). Current adjuvant therapy (antibiotics, steroids, and choleretics) for BA, as well as dietary manipulation, are likely to shape the microbiome.

There is no global consensus on antibiotic regimes for post-KPE cholangitis prophylaxis (80) but the use of broad-spectrum antibiotics will indiscriminately inhibit pathogenic and commensal bacteria. Ciprofloxacin has been shown to indefinitely alter taxonomic composition and diversity, and negatively impact production of microbial-related metabolites, including butyrate (81,82). Antibiotic use, however, has been associated with increased transplant-free survival in a large retrospective BA cohort (83) and remains the only microbiome-modulating therapy to have shown positive effects in PSC (15–17). Given these findings, probiotics may offer an alternative/addition to antibiotics via supplementation of “beneficial” bacteria. One study showed an increase in Bifidobacteria, and a decrease in pathogenic bacteria (eg, E coli, Streptococcus, and Klebsiella) after administering a 2-week probiotic course to 5 BA infants (84). Subsequently, a small open-label cross-sectional Taiwanese study in 20 jaundice-free patients (0–3 years old), returned identical cholangitis rates (20%) between the probiotic (Lactobacillus casei rhamnosus) and antibiotic (neomycin) arm following 6 months of treatment (85), suggesting probiotic equivalence to antibiotics.

Other adjuvants, including steroids and choleretics, such as ursodeoxycholic acid, may also modulate the microbiome. Ursodeoxycholic acid and corticosteroids are administered in BA despite evidence questioning clinical benefits (4,86). Ursodeoxycholic acid has been convincingly shown to improve outcomes in PBC and PSC (87,88). In PBC, the microbiome differed between patients who responded to ursodeoxycholic acid versus those that did not, indicating a potential role for patient pre-selection (22). Meanwhile, animal studies have shown a steroid-mediated effect with a reduction in Bacteriodetes and increase in Firmicutes after 14 days of prednisolone in liver-transplanted mice (89).

There is more striking evidence for dietary modulation with medium-chain triglyceride-enriched formulas or supplements, used in the management of fat malabsorption in BA, demonstrating significant shifts in gut bacterial populations and beneficial effects of this remodelling, including reduced LPS-related liver injury (90).

We appreciate the difficulty in conducting randomised controlled trials on therapeutics in BA, but large, longitudinal observational studies, controlled for confounders, are essential to enhance our understanding of therapeutic-dietary-microbiome interactions, and if, and how, to best optimise this relationship.


There is currently no effective therapy post-KPE to improve BA outcomes; BA remains the leading indication for LT in paediatrics. Evidence for gut microbiome pathogenesis in BA is emerging, together with encouraging evidence from experimental and adult cirrhotic and cholestatic microbiome studies. It is imperative for BA researchers to further investigate the microbiome-host interactions, together with the effects of current modulatory therapy, in order to optimise and develop microbiome-targeted therapeutics, which could potentially improve BA outcomes and reduce the need for LT.


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biliary atresia; cholestasis; cirrhosis; microbiome; microbiota

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