Measuring bacterial composition is relatively straightforward with currently available tools, but scientists so far understand little about the factors contributing to successful colonization and a stable microbiota composition at any point in time.

Researchers from the University of Oregon in Eugene (USA) recently published a study that used zebrafish as a vertebrate model for investigating bacterial competition in the gut. They colonized zebrafish with a microbiota consisting of two species native to the zebrafish gut, Aeromonas veronii and Vibrio cholerae, with the aim of studying how these two species fluctuated in abundance over time. The group used light sheet fluorescence microscopy (LSFM) to examine the population dynamics, collecting data (3-D images) at 20-minute intervals for 12 to 15 hours.

In normal zebrafish hosts, the bacterial species were in direct competition: Vibrio cholerae was dominant, while a large and sudden drop occurred in the Aeromonas veronii population. Next, the researchers asked whether direct bacterial competition fully explained the dynamics of the competing populations, or whether host factors might have contributed to the observed fluctuations. To investigate this, they repeated the experiment with a different kind of host: zebrafish that had enteric nervous system (ENS) dysfunction and reduced gut motility—a model which may have applicability to humans with a condition called Hirschsprung’s disease or other digestive diseases such as (mechanical) ileus or pseudo-obstruction.

When fish with dysfunctional peristalsis were colonized with Aeromonas veronii and Vibrio cholerae, the bacterial species showed robust coexistence in the gut. That is, in the absence of the mechanical contractions that move contents through the intestines, the Aeromonas population stabilized, becoming less susceptible to competitive exclusion by Vibrio.

Researchers concluded that both host motility and competitive bacterial species were required to explain Aeromonas populations in the zebrafish gut, and that Aeromonas and Vibrio seem to be affected in different ways by intestinal motility.

The study highlighted the idea that perturbation of bacterial communities in the gut by host peristalsis can drive bacterial population dynamics. On a broader scale, this suggests that the ENS may have a top-down influence on microbiota composition. A better understanding of the factors involved in bacterial colonization may eventually help scientists learn to manipulate gut microbiota for better health.

Says Raghuveer Parthasarathy, University of Oregon professor of physics and the paper’s corresponding author: “This research shows that the physical environment and activity of the host intestine can be a major determinant of the bacterial makeup of the gut – an idea that we think should very generally influence how we tackle issues of health and disease.”




Wiles TJ, Jemielita M, Baker RP, et al. Host Gut Motility Promotes Competitive Exclusion within a Model Intestinal Microbiota. PLOS Biology. 2016.