Background

Swarming is a unique bacterial property that ensures mass movement across a surface in a collective fashion (Verstraeten et al., 2008; Kearns, 2010). The exact host consequences of bacteria that swarm are not yet fully known; however, recent research has aimed to elucidate such a role in pathogenesis (Barak et al., 2009). It has been theorized that swarming enables bacteria to adhere to and disperse from localized spots of infection (Kearns, 2010), as well as to escape engulfment by macrophages (Amendola, 1998). For instance, the swarming of Proteus mirabilis has been implicated in catheter-associated urinary tract infections (Jones et al., 2004). Moreover, bacteria of many species become resistant to a range of antibiotics when they swarm, in a manner that appears unrelated to normal antibiotic efflux mechanisms (Butler et al., 2010).

More recently, our group has shown for the first time that swarming bacterial activity from human fecal matter is a specific indicator of intestinal inflammation and/or polyp formation (De et al., 2021). This represents a novel advancement since patient feces may now be used to inform clinicians in the assessment of “vague abdominal” symptoms among patients at risk for inflammatory bowel disease, ulcerative colitis, and polyps, among other conditions. This knowledge could help to guide clinical decision-making, such as determining which patients need a colonoscopy and further evaluation versus those who do not, ultimately reducing overall healthcare costs. As a result, the importance of optimizing an assay that detects swarming bacteria from feces is critical to the validation of our findings. Thus far, assays that focus on detecting swarming bacteria have been restricted to the study of cultured single strains of bacteria, namely Pseudomonas (Tremblay et al., 2008; Morris et al., 2011; Ha et al., 2014; Morales-soto et al., 2015). Ha et al., (2014), Morris et al., (2011), and Tremblay et al., (2008) describe thorough protocols for assaying bacterial swarming in Pseudomonas aeruginosa (Tremblay and Deziel, 2008; Morris et al., 2011; Ha et al., 2014); however, little, if any, attention has been focused on designing a protocol for eliciting bacterial swarming from human fecal samples, which are often the most convenient materials from which researchers can learn more about the microbial communities of the human gut. In this protocol, which we used in our group’s recent publication in De et al. (2021), we describe an assay to observe swarming in the shortest amount of time and with the least consumption of laboratory reagents. To the best of our knowledge, this is the first comprehensive description and optimization of an assay protocol that detects swarming bacteria from fecal matter.