Probing metabolomic and microbiomic perturbations driven by antimicrobial exposure to infant and adult gut microbial consortia via phenotypic array

In this work, we explored the use of the Biolog GEN-III phenotypic array to characterise the composition and metabolomic functionality of faecal microbial communities obtained from 19 healthy donors (6 infants and 13 adults). This plate allowed the screening of 71 carbon sources and 23 chemicals, including antimicrobial compounds, against each donor faecal sample. However, we focused this manuscript on comprehensive analysis and modelling of the information obtained from the chemical sensitivity assays that were available on the plate. Incubated plate cultures were analysed by 1H NMR spectroscopy at 600 MHz, allowing for the comprehensive identification and quantification of metabolomic fluctuations within the microbial consortia. Additionally, microbiomes under all antimicrobial treatment conditions were characterised via 16S ribosomal RNA sequencing using long-read PacBio sequencing.