Background: The gastrointestinal tract microbiome has significant functional roles in maintaining host health, maintained through a delicate balance. Disruptions to this balance may lead to diseases such as antibiotic-associated diarrhoea and Clostridioides difficile infection. Taxonomic analyses can only partially explain this dysbiotic states due to the inter-individual microbiome variability. Functional and metabolic analyses may provide more a unified description of the microbiome and dysbiosis.
Aims: Identify bacterial markers of antibiotic induced dysbiosis utilising in-vitro gut models.
Methods: In-vitro gut models (Leeds Human Gut Model, MiGut) were used to simulate antibiotic-induced dysbiosis using three clinically reflective broad spectrum antibiotic dosing regimens (Amoxicillin, Ciprofloxacin, Piperacillin/Tazobactam). Gut models were challenged with two pathogens (Clostridioides difficile (027), KPC-positive Klebsiella pneumoniae) to demonstrate post-antibiotic functional dysbiosis. Shotgun metagenomic analysis was used to taxonomically and functionally profile the microbiome. Liquid Chromatography-Mass Spectrometry was used to identify metabolic markers of dysbiosis.
Results: Cultural analysis: Antibiotic instillation resulted in wide scale disruptions to the microbiome coinciding with antibiotic therapy. This resolved post-antibiotic instillation with monitored taxa returning to similar abundance and composition pre-antibiotic instillation. However, functional dysbiosis was demonstrated by the colonisation and proliferation of Clostridioides difficile and Klebsiella pneumoniae within the models.
Metagenomic analysis: Reductions in species diversity and a loss of key genera was associated with short chain fatty acid (SCFA) production. KEGG pathway analysis identified changes in abundance to pathways associated with SCFA metabolism for acetate, propanoate and butyrate. SCFA producers Faecalibacterium and Coprococcus were reduced in abundance following antibiotic instillation.
Metabolomic analysis: Reduced SCFA levels within the metabolome coincided with antibiotic instillation that persisted beyond recovery of key microbial genera. Putative Metabolic Markers; Butyrate, Valerate, Lactate, 2-Hydroxyglutarate, 2-Oxoglutarate. Acetate and Propanoate.
Conclusions: A putative panel of nine biomarkers of dysbiosis, consisting of 2 taxonomic species and 7 metabolites, were identified. In vitro models are effective tools to screen for marker of antibiotic induced dysbiosis.
