Impaired mucosal homeostasis in short-term fiber deprivation

The gut mucosal environment plays a key role in host health by protecting against pathogens and harmful substances and providing a niche for beneficial bacteria, thereby facilitating a mutualistic balance between host and microbiome. Lack of dietary fibers, crucial for this balance, results in erosion of the mucosal layer, which has been suggested to be due to a bloom of mucus-degrading gut bacteria. The aim of this study was to use quantitative analyses to deepen insights into the diet-induced imbalance of mucosal homeostasis. A general loss of bacterial taxa with fiber-degrading and butyrate-producing capabilities was observed. Most importantly, there was little change in the absolute abundances of known mucus-degrading bacteria, although, due to the loss of many abundant taxa, the analysis of relative abundances would erroneously indicate an increase in mucus degraders. These findings underscore the importance of using quantitative methods in microbiome research, and suggest that erosion of the mucus layer during fiber deprivation is due to diminished mucus production rather than overgrowth of mucus degraders. Sequencing was performed at the Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna under the project IDs JMF-1904-2 and JMF-2009-3.