Spatial Sorting of Soft and Stiff Bacteria in the Human Colon

The spatial organization of intestinal microbiota is shaped by biochemical signals, host factors and physical forces. While chemical gradients and host immunity are well studied, the influence of mechanical properties is underexplored. Drawing on soft matter physics and microbiome research, we combined atomic force microscopy data with gut-like flow simulations to investigate whether bacterial stiffness influences spatial organization and mechanical/hydrodynamic responses. Indeed, colonic bacteria differ markedly in stiffness: soft species like Bacteroides fragilis, Escherichia coli and Akkermansia muciniphila display thin peptidoglycan layers and flexible outer membranes, while stiff species like Clostridium difficile, Lactobacillus rhamnosus, Enterococcus faecalis and Faecalibacterium prausnitzii display greater rigidity linked to thick Gram-positive cell walls. Our simulations showed that mechanical compliance can drive spatial partitioning under laminar shear, with soft bacteria localizing near the mucosal surfaces and stiff bacteria aligning along central flow paths. Further, soft bacteria aligned more quickly with shear flow, migrated more efficiently toward the lumen center, dissipated more energy during collisions and detached more readily from mucosal surfaces. Soft bacteria also formed slower, more diffuse biofilms and exhibited greater displacement under peristaltic compression. This suggests that stiffness, independent of chemical signalling, may shape microbial localization, interaction, organization and persistence in gut-like environments. Stiffness may serve as non-chemical, precision tool for microbiome modulation, paving the way for targeted, mechanically informed interventions. This approach could enable applications like stiffness-guided drug delivery to specific gut regions, selective removal of stiff pathogenic bacteria using mechanical cues and mechanical pre-sorting of microbial populations for diagnostic and therapeutic purposes.