Profiling gut microbiota and bile acid metabolism in critically ill children

• Published in: Scientific reports Vol. 12; no. 1; p. 10432
• Main Authors: Kean, Iain Robert Louis, Wagner, Joseph, Wijeyesekera, Anisha, De Goffau, Marcus, Thurston, Sarah, Clark, John A, White, Deborah K, Ridout, Jenna, Agrawal, Shruti, Kayani, Riaz, O'Donnell, Roddy, Ramnarayan, Padmanabhan, Peters, Mark J, Klein, Nigel, Holmes, Elaine, Parkhill, Julian, Baker, Stephen, Pathan, Nazima
• Format: Journal Article
• Language: English
• Published: England Nature Publishing Group 21.06.2022; Nature Publishing Group UK; Nature Portfolio
• Subjects: Acids; Bile; Bile acids; Bile Acids and Salts - analysis; Child; Children; Clostridiales - genetics; Critical Illness; Digestive system; Digestive tract; Disseminated infection; Feces; Feces - chemistry; Fermentation; Gastrointestinal Microbiome - physiology; Humans; Immune response; Intestinal microflora; Keystone species; Lachnospiraceae; Liquid chromatography; Mass spectrometry; Mass spectroscopy; Microbiomes; Microbiota; Patients; Respiratory failure; RNA, Ribosomal, 16S - analysis; RNA, Ribosomal, 16S - genetics; rRNA 16S
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-022-13640-0

Broad-spectrum antimicrobial use during the treatment of critical illness influences gastrointestinal fermentation endpoints, host immune response and metabolic activity including the conversion of primary to secondary bile acids. We previously observed reduced fermentation capacity in the faecal microbiota of critically ill children upon hospital admission. Here, we further explore the timecourse of the relationship between the microbiome and bile acid profile in faecal samples collected from critically ill children. The microbiome was assayed by sequencing of the 16S rRNA gene, and faecal water bile acids were measured by liquid chromatography mass spectrometry. In comparison to admission faecal samples, members of the Lachnospiraceae recovered during the late-acute phase (days 8-10) of hospitalisation. Patients with infections had a lower proportion of Lachnospiraceae in their gut microbiota than controls and patients with primary admitting diagnoses. Keystone species linked to ecological recovery were observed to decline with the length of PICU admission. These species were further suppressed in patients with systemic infection, respiratory failure, and undergoing surgery. Bile acid composition recovers quickly after intervention for critical illness which may be aided by the compositional shift in Lachnospiraceae. Our findings suggest gut microbiota recovery can be readily assessed via measurement of faecal bile acids.