| Fecal microbiome profiles in infants with biliary atresia versus nonbiliary atresia cholestasis: a pilot study |
Nur Azizah1 
, Fadilah Fadilah2
, Silvia Werdhy Lestari4
, Muzal Kadim5
, Fithriyah Sjatha6
, Hanifah Oswari5
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1Doctoral Program in Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
2Bioinformatics Core Facilities, Institute of Medical Education and Research Indonesia (IMERI), Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
3Department of Medical Chemistry, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
4Department of Medical Biology, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
5Department of Child Health, Gastrohepatology Division, Cipto Mangunkusumo Hospital, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
6Department of Microbiology, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia |
Correspondence:
Hanifah Oswari, Email: hanifah.oswari@ui.ac.id
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Received: 8 March 2025 • Revised: 25 May 2025 • Accepted: 20 June 2025 |
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| Abstract |
Background
Cholestasis is characterized by disrupted bile flow and can lead to severe liver disease in newborns, of which biliary atresia (BA) is a common cause. The gut microbiome plays a crucial role in aggravating liver injury in BA and non-BA cholestasis. However, information is lacking regarding the differences in gut microbiome composition between patients with BA and non-BA cholestasis.
Purpose
This study aimed to assess the gut microbiome profile of infants with BA versus those with non-BA cholestasis and healthy controls in an Indonesian population.
Methods
We investigated the changes in the microbial composition of fecal samples from 12 infants with BA and 8 with non-BA cholestasis and compared them with those of 8 age-matched healthy controls (HCs). Fecal DNA from all the participants was subjected to 16S rRNA amplicon sequencing.
Results
The fecal microbiome at the phylum level differed between the BA and non-BA cholestasis groups with increased Proteobacteria and decreased Firmicutes. At the genus level, the BA group was enriched with Bacteroides, unclassified Enterobacteriaceae, and Dialister (P<0.05), whereas the non-BA group was enriched with Klebsiella, Chryseobacterium, Acinetobacter, and Pseudomonas (P<0.05). Parabacteroides, unclassified Lachnospiraceae, Actinomyces, Anaerococcus, Clostridium innocuum group, Collinsella, Gemella, and Peptostreptococcaceae (P<0.05) were more enriched in the HC than in the other 2 groups. Detected cytomegalovirus in fecal samples was associated with significant microbial shifts, including increased Lactobacillus, decreased Escherichia-Shigella, and altered Faith’s phylogenetic diversity, highlighting its potential role in gut microbiome modulation. Microbial alterations in patients with BA versus non-BA cholestasis were significantly correlated with liver function indicators.
Conclusion
The BA and non-BA groups showed specific genus enrichment, highlighting the urgent need to identify potential treatments to inhibit the progression of liver injury in infants with cholestasis. |
| Key Words:
Biliary atresia, Cholestasis, Cytomegalovirus infections, Fecal microbiota, Infant |
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