FISH–Flow Cytometry Reveals Microbiome-Wide Changes in Post-Translational Modification and Altered Microbial Abundance Among Children with Inflammatory Bowel Disease

Metaproteomic analysis of microbiome post-translation modifications (PTMm) is challenging, and little is known about the effects of inflammation on the bacterial PTM landscape in IBD. Here, we adapted and optimised fluorescence in situ hybridisation–flow cytometry (FISH-FC) to study microbiome-wide tyrosine phosphorylation (p-Tyr) in children with and without inflammatory bowel disease (IBD). Microbial p-Tyr signal was significantly higher in children with IBD, compared to those without. Faecalibacterium prausnitzii, Bacteroidota, Gammaproteobacteria and Bifidobacteria tended to be more abundant in IBD than in non-IBD control children but there were only minor differences in p-Tyr among these bacterial communities in those with and without IBD. p-Tyr was significantly lower in non-IBD children older than 9 yrs compared with those less than 9 yrs, and the effect was seen in all four bacterial subgroups studied. The opposite trend was seen in patients with IBD. p-Tyr overall is higher in children with IBD but the effects of inflammation on p-Tyr vary according to the bacterial community. The overall microbiome p-Tyr signal changes with age in healthy children. FISH-FC can be used to study the microbiome-wide PTM landscape.