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Persons with cystic fibrosis (CF), starting in early life, show intestinal microbiome dysbiosis characterized in part by a decreasedrelative abundance of the genus Bacteroides. Bacteroides is a major producer of the intestinal short chain fatty acid propionate. Wdemonstrate here that cystic fibrosis transmembrane conductance regulator-defective (CFTR−/−) Caco-2 intestinal epithelial cellsresponsive to the anti-inflammatory effects of propionate. Furthermore, Bacteroides isolates inhibit the IL-1β-induced inflammatorresponse of CFTR−/− Caco-2 intestinal epithelial cells and do so in a propionate-dependent manner. The introduction of Bacteroisupplemented stool from infants with cystic fibrosis into the gut of CftrF508del mice results in higher propionate in the stool as wethe reduction in several systemic pro-inflammatory cytokines. Bacteroides supplementation also reduced the fecal relativeabundance of Escherichia coli, indicating a potential interaction between these two microbes, consistent with previous clinicalstudies. For a Bacteroides propionate mutant in the mouse model, pro-inflammatory cytokine KC is higher in the airway and serucompared with the wild-type (WT) strain, with no significant difference in the absolute abundance of these two strains. Takentogether, our data indicate the potential multiple roles of Bacteroides-derived propionate in the modulation of systemic and airwayinflammation and mediating the intestinal ecology of infants and children with CF. The roles of Bacteroides and the propionate itproduces may help explain the observed gut-lung axis in CF and could guide the development of probiotics to mitigate systemic aairway inflammation for persons with CF. 

Abstract Particulate organic carbon settling through the marine water column is a key process that regulates the global climate by sequestering atmospheric carbon. The initial colonization of marine particles by heterotrophic bacteria represents the first step in recycling this carbon back to inorganic constituents—setting the magnitude of vertical carbon transport to the abyss. Here, we demonstrate experimentally using millifluidic devices that, although bacterial motility is essential for effective colonization of a particle leaking organic nutrients into the water column, chemotaxis specifically benefits at intermediate and higher settling velocities to navigate the particle boundary layer during the brief window of opportunity provided by a passing particle. We develop an individual-based model that simulates the encounter and attachment of bacterial cells with leaking marine particles to systematically evaluate the role of different parameters associated with bacterial run-and-tumble motility. We further use this model to explore the role of particle microstructure on the colonization efficiency of bacteria with different motility traits. We find that the porous microstructure facilitates additional colonization by chemotactic and motile bacteria, and fundamentally alters the way nonmotile cells interact with particles due to streamlines intersecting with the particle surface. 

Bacterial biofilms are communities of bacteria that exist as aggregates that can adhere to surfaces or be free-standing. This complex, social mode of cellular organization is fundamental to the physiology of microbes and often exhibits surprising behaviour. Bacterial biofilms are more than the sum of their parts: Single cell behaviour has a complex relation to collective community behaviour, in a manner perhaps cognate to the complex relation between atomic physics and condensed matter physics. Biofilm microbiology is a relatively young field by biology standards, but it has already attracted intense attention from physicists. Sometimes, this attention takes the form of seeing biofilms as inspiration for new physics. In this roadmap, we highlight the work of those who have taken the opposite strategy: We highlight work of physicists and physical scientists who use physics to engage fundamental concepts in bacterial biofilm microbiology, including adhesion, sensing, motility, signalling, memory, energy flow, community formation and cooperativity. These contributions are juxtaposed with microbiologists who have made recent important discoveries on bacterial biofilms using state-of-the-art physical methods. The contributions to this roadmap exemplify how well physics and biology can be combined to achieve a new synthesis, rather than just a division of labour.