Bacterial swarming is an example of dynamic self-assembly in microbiology in which the collective interaction of a population of bacterial cells leads to emergent behavior. Swarming occurs when cells interact with surfaces, reprogram their physiology and behavior, and adapt to changes in their environment by coordinating their growth and motility with other cells in the colony. This review summarizes the salient biological and biophysical features of this system and describes our current understanding of swarming motility. We have organized this review into four sections: 1) The biophysics and mechanisms of bacterial motility in fluids and its relevance to swarming. 2) The role of cell/molecule, cell/surface, and cell/cell interactions during swarming. 3) The changes in physiology and behavior that accompany swarming motility. 4) A concluding discussion of several interesting, unanswered questions that is particularly relevant to soft matter scientists.

BACKGROUND. l-Carnitine, an abundant nutrient in red meat, accelerates atherosclerosis in mice via gut microbiotadependent formation of trimethylamine (TMA) and trimethylamine N-oxide (TMAO) via a multistep pathway involving an atherogenic intermediate, γ-butyrobetaine (γBB). The contribution of γBB in gut microbiota-dependent l-carnitine metabolism in humans is unknown. METHODS. Omnivores and vegans/vegetarians ingested deuterium-labeled l-carnitine (d 3-l-carnitine) or γBB (d 9-γBB), and both plasma metabolites and fecal polymicrobial transformations were examined at baseline, following oral antibiotics, or following chronic (≥2 months) l-carnitine supplementation. Human fecal commensals capable of performing each step of the l-carnitine→γBB→TMA transformation were identified. RESULTS. Studies with oral d 3-l-carnitine or d 9-γBB before versus after antibiotic exposure revealed gut microbiota contribution to the initial 2 steps in a metaorganismal l-carnitine →γBB→TMA→TMAO pathway in subjects. Moreover, a striking increase in d 3-TMAO generation was observed in omnivores over vegans/vegetarians (>20-fold; P = 0.001) following oral d 3-l-carnitine ingestion, whereas fasting endogenous plasma l-carnitine and γBB levels were similar in vegans/ vegetarians (n = 32) versus omnivores (n = 40). Fecal metabolic transformation studies, and oral isotope tracer studies before versus after chronic l-carnitine supplementation, revealed that omnivores and vegans/vegetarians alike rapidly converted carnitine to γBB, whereas the second gut microbial transformation, γBB→TMA, was diet inducible (l-carnitine, omnivorous). Extensive anaerobic subculturing of human feces identified no single commensal capable of l-carnitine→TMA transformation, multiple community members that converted l-carnitine to γBB, and only 1 Clostridiales bacterium, Emergencia timonensis, that converted γBB to TMA. In coculture, E. timonensis promoted the complete l-carnitine→TMA transformation. CONCLUSION. In humans, dietary l-carnitine is converted into the atherosclerosis-and thrombosis-promoting metabolite TMAO via 2 sequential gut microbiota-dependent transformations: (a) initial rapid generation of the atherogenic intermediate γBB, followed by (b) transformation into TMA via low-abundance microbiota in omnivores, and to a markedly lower extent, in vegans/vegetarians. Gut microbiota γBB→TMA/TMAO transformation is induced by omnivorous dietary patterns and chronic l-carnitine exposure. TRIAL REGISTRATION. ClinicalTrials.gov NCT01731236.

This manuscript describes the high-throughput analysis and isolation of bacterial cells encapsulated in agarose microparticles using fluorescence-activated cell sorting (FACS). Flow-focusing microfluidic systems were used to create monodisperse microparticles that were ~30μm in diameter. The dimensions of these particles made them compatible with flow cytometry and FACS, and the sensitivity of these techniques reduced the incubation time for cell replication before analyses were carried out. The small volume of the microparticles (~1–50 picoliters) minimized the quantity of reagents needed for bacterial studies. This platform made it possible to screen and isolate bacteria, and apply a combination of techniques to rapidly determine the target of biologically active small molecules. As a pilot study, Escherichia coli cells were encapsulated in agarose microparticles, incubated in the presence of varying concentrations of rifampicin, and analyzed using FACS. The minimum inhibitory concentration of rifampicin was determined, and spontaneous mutants that had developed resistance to the antibiotic were isolated via FACS and characterized by DNA sequencing. The β-subunit of RNA polymerase, RpoB, was confirmed as the target of rifampicin, and Q513L was the mutation most frequently observed. Using this approach, the time and quantity of antibiotics required for the isolation of mutants was reduced by 8- and 150-fold, respectively, compared to conventional microbiological techniques using nutrient agar plates. We envision that this technique will have an important impact on research in chemical biology, natural products chemistry, and the discovery and characterization of biologically active secondary metabolites.

cProteus mirabilis is an opportunistic pathogen that is frequently associated with urinary tract infections. In the lab, P. mirabilis cells become long and multinucleate and increase their number of flagella as they colonize agar surfaces during swarming. Swarming has been implicated in pathogenesis; however, it is unclear how energetically costly changes in P. mirabilis cell morphology translate into an advantage for adapting to environmental changes. We investigated two morphological changes that occur during swarming-increases in cell length and flagellum density-and discovered that an increase in the surface density of flagella enabled cells to translate rapidly through fluids of increasing viscosity; in contrast, cell length had a small effect on motility. We found that swarm cells had a surface density of flagella that was ϳ5 times larger than that of vegetative cells and were motile in fluids with a viscosity that inhibits vegetative cell motility. To test the relationship between flagellum density and velocity, we overexpressed FlhD 4 C 2 , the master regulator of the flagellar operon, in vegetative cells of P. mirabilis and found that increased flagellum density produced an increase in cell velocity. Our results establish a relationship between P. mirabilis flagellum density and cell motility in viscous environments that may be relevant to its adaptation during the infection of mammalian urinary tracts and movement in contact with indwelling catheters. Proteus mirabilis is a Gram-negative rod-shaped gammaproteobacterium that is commonly associated with urinary tract infections (1) and the biofouling of catheters (2-4). P. mirabilis may also be present in the human gut microflora (5) and is correlated with the incidence of colitis (6, 7). Broth-grown vegetative cells of P. mirabilis are characteristically ϳ2 m long and have a peritrichous distribution of ϳ4 to 10 flagella. The flagella form a bundle that performs work on the surrounding fluid and propels cells forward via a mechanism that is similar to the motility system of Escherichia coli (8, 9).Broth-grown vegetative cells of P. mirabilis in contact with the surface of agar gels infused with nutrients change their morphology, become "swarmers," and colonize the surface by coordinating the movement of large groups of cells (i.e., "swarming") (see Fig. 1A). P. mirabilis swarm colonies exhibit a terraced pattern of concentric rings (see Fig. S1 in the supplemental material) (10). These rings are produced by alternating phases of consolidation, during which the colony does not expand and cells are dedifferentiated into a vegetative cell-like morphology, and swarming, during which cells are motile and differentiated (11). Motility occurs predominantly at the swarm front and decreases with increasing distance from the front; cells near the center of the swarm are nonmotile. Swarming has several characteristics, including the following: (i) the inhibition of cell division to produce long (10-to 70-m) multinucleate cells, (ii) an increase in the surface dens...

This paper describes a new approach for labeling intact flagella using the biarsenical dyes FlAsH and ReAsH and imaging their spatial and temporal dynamics on live Escherichia coli cells in swarming communities of bacteria by using epifluorescence microscopy. Using this approach, we observed that (i) bundles of flagella on swarmer cells remain cohesive during frequent collisions with neighboring cells, (ii) flagella on nonmotile swarmer cells at the leading edge of the colony protrude in the direction of the uncolonized agar surface and are actively rotated in a thin layer of fluid that extends outward from the colony, and (iii) flagella form transient interactions with the flagella of other swarmer cells that are in close proximity. This approach opens a window for observing the dynamics of cells in communities that are relevant to ecology, industry, and biomedicine.Swimming cells of Escherichia coli are propelled through liquids using flagella that are arranged peritrichously (e.g., uniformly distributed). Each flagellum is rotated by a motor at a rate of ϳ100 Hz using the proton motive force across the cell wall. The balance of torque across the cell results in the counter rotation of the cell body at a frequency of ϳ10 Hz, which biases the movement of cells suspended in fluids and in close contact with surfaces (6,19,24,33,37). The biophysical details of the function and dynamics of the flagella of individual E. coli cells suspended in fluids are well understood (6). In contrast, the role and dynamics of these organelles in cells that are in multicellular communities, where the majority of bacteria arguably reside, are just beginning to emerge (8,9,16,36).Extracellular organelles including flagella, pili, and curli fibers are involved in cell motility and the attachment of cells to surfaces, critical steps in the early formation of multicellular structures (13,22,39,48). In some communities, the dynamic movement of these organelles plays a central role in population-wide behavior. For example, the coordinated movement of individual bacteria in communities, referred to as "swarms," produces cohesive motion over length scales of hundreds of micrometers and provides a mechanism for the migration of colonies across surfaces (20,27,30,41,46,54). Swarming is a phenotype that plays a role in pathogenesis and makes it possible for bacterial colonies to transcend the confines of diffusion-limited growth. Swarming is a mechanism that cells use to replicate, expand rapidly across surfaces, and colonize niches that would be inaccessible to static multicellular structures (3,23,47,52).Swarms of E. coli cells consist of a heterogeneous population of cells with a morphology that ranges from a mononucleate, vegetative state, in which the cells are 2 to 3 m long and have ϳ3 to 7 flagella, to a morphology that is multinucleate, in which the cells are 5 to 20 m long and the density of flagella is ϳ2 to 3 flagella more per unit of surface area than vegetative cells (28). The most "differentiated" cells (e.g., those that are the...