Microbiota and metabolome dynamics induced by Shiga toxin-producing E. coli in an in vitro model of an infant’s colon
Authors:Mariana Izquierdo1,a, Deborah O’Sullivan2,a, Ophélie Uriot2, Morgane Brun2, Claude Durif2, Sylvain Denis2, Pablo Gallardo1, Cormac G M Gahan3-5, Lucie Etienne-Mesmin2, Stéphanie Blanquet-Diot2,b and Mauricio J. Farfan1.b
1 Departamento de Pediatría y Cirugía Infantil Oriente, CICA Hospital Dr. Luis Calvo Mackenna, Facultad de Medicina, Universidad de Chile, 7500539 Santiago, Chile. 2 UMR 454 INRAe, Microbiology, Digestive Environment and Health (MEDIS), Université Clermont Auvergne, F-63000 Clermont-Ferrand, France. 3 APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland. 4 School of Microbiology, University College Cork, T12 K8AF Cork, Ireland. 5 School of Pharmacy, University College Cork, T12 K8AF Cork, Ireland.
a Equal contribution as first authors.
b Co-last authors.
Keywords:
Shiga toxin-producing Escherichia coli (STEC), diarrhea, gut microbiota, gut metabolome, Toddler artificial colon model (T-ARCOL).
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Conflict of interest statement:
The authors declare no conflicts of interest. The funders had no role in the study’s design, in the data collection, analyses, or interpretation, in the writing of the manuscript, or in the decision to publish the results.
Please cite this article as:
Mariana Izquierdo, Deborah O’Sullivan, Ophélie Uriot, Morgane Brun, Claude Durif, Sylvain Denis, Pablo Gallardo, Cormac G M Gahan, Lucie Etienne-Mesmin, Stéphanie Blanquet-Diot and Mauricio J. Farfan (2025). Microbiota and metabolome dynamics induced by Shiga toxin-producing E. coli in an in vitro model of an infant's colon. Microbial Cell 12: 65-83. doi: 10.15698/mic2025.03.846
© 2025 Izquierdo et al. This is an open-access article released under the terms of the Creative Commons Attribution (CC BY) license, which allows the unrestricted use, distribution, and reproduction in any medium, provided the original author and source are acknowledged.
Abstract:
Shiga toxin-producing Escherichia coli (STEC) is a major food-borne pathogen causing human diseases ranging from diarrhea to life-threatening complications, mainly in young children. Colonization, virulence, and interactions of STEC strains with human gut microbiota are pivotal during infection but remain poorly described, particularly in children, the most affected population. In this work, we evaluated changes in the microbiota and metabolome composition in the in vitro gut model: Toddler ARtificial COLon (T-ARCOL) infected with EHEC O157:H7 strain EDL 933. Stool samples collected from children with STEC-positive diarrhea and stool from the same children after recovery from the diarrheal episode (n=5) were used to inoculate the T-ARCOL model. STEC colonization was progressively reduced throughout fermentation in T-ARCOL with diarrhea or recovery fecal samples. Beta diversity showed that the diarrhea-associated microbiota was significantly distinct from the recovery microbiota and exhibited a lower α-diversity. In contrast to recovery conditions, diarrheal conditions were characterized by an increased abundance of potential pathobionts such as members of the Clostridiaceae family and higher acetate, succinate, and N-acetylneuraminic acid levels. Our results provide new evidence of the impact of EHEC in the microbiota and metabolome dynamics in an in vitro gut model that could be useful in understanding their physiopathology in this at-risk population, considering inter-individual variabilities in gut microbiota.
doi: 10.15698/mic2025.04.847
Volume 12, pp. 76 to 92, published 14/04/2025.