Powered by flagella, many bacterial species exhibit collective motion on a solid surface commonly known as swarming. As a natural example of active matter, swarming is also an essential biological phenotype associated with virulence, chemotaxis, and host pathogenesis. Physical changes like cell elongation and hyper flagellation have been shown to accompany the swarming phenotype. Less studied, however, are the contrasts of collective motion between the swarming cells and their counterpart planktonic cells of comparable cell density. Here, we show that confining bacterial movement in circular microwells allows distinguishing bacterial swarming from collective swimming. On a soft agar plate, a novel bacterial strain Enterobacter sp. SM3 in swarming and planktonic states exhibited different motion patterns when confined to circular microwells of a specific range of sizes. When the confinement diameter was between 40 μm and 90 μm, swarming SM3 formed a single swirl motion pattern in the microwells whereas planktonic SM3 formed multiple swirls. Similar differential behavior is observed across several other species of gram-negative bacteria. We also observed 'rafting behavior' of swarming bacteria upon dilution. We hypothesize that the rafting behavior might account for the motion pattern difference. We were able to predict these experimental features via numerical simulations where swarming cells are modeled with stronger cell-cell alignment interaction. Our experimental design using PDMS microchip disk arrays enabled us to observe bacterial swarming on murine intestinal surface suggesting a new method for characterizing bacterial swarming under complex environments, such as in polymicrobial niches, and for in vivo swarming exploration.

Bacterial swarming is a conserved and distinct form of bacterial motility that allows for 29 rapid migration over a surface. Swarming motility is often oppositely regulated and 30 antagonistic to biofilm formation 1 . To-date, while bacterial biofilms have been associated 31 with pathogenesis and pathobiology of human diseases (e.g., infections, inflammation and 32 cancer) 2-4 , there are very few examples of swarming behaviors that uniquely define or align 33 with human pathophysiology (e.g., antibiotic resistance) 5,6,7 . Here we report that bacterial 34 swarming is highly predictive of the presence of intestinal stress in mice, pigs and humans. 35 Using a modified agar plate assay, we isolated from murine feces a novel Enterobacter 36 hyperswarming strain, SM3 that demonstrated significant protection from intestinal 37 inflammation and promoted restitution in a mouse model of colitis. As opposed to bacterial 38 biofilms 8 , we report that the swarming phenotype protects against intestinal inflammation 39 in mice. Mechanistically, commensal swarming strains rapidly consume oxygen in vitro and 40 in vivo, leading to a favorable anaerobic environment conducive to the growth of beneficial 41 anaerobes. The swarming property of bacteria rather than the individual strains 42 themselves, independently lends the ability to protect and heal from intestinal 43 inflammation. This work identifies a new paradigm in which intestinal stress, specifically 44 inflammation, allows for emergence of swarming bacteria, which in turn act to suppress 45 inflammation via mechanisms that are associated in part with oxygen depletion and bloom 46 of beneficial anaerobes. 47