It is thought that our commensal, or friendly, bacteria serve as a kind of lawn that, in commandeering the rich fertilizer that courses through our gut, outcompetes the less-well-behaved pathogenic “weeds.” It has also been suggested that our commensal bugs secrete pathogen-killing factors. Another theory holds that the disruption of our inner microbial ecosystem somehow impairs our immune responsiveness.
“While these hypotheses are by no means mutually exclusive, our work specifically supports the suggestion that our resident microbes hold pathogens at bay by competing for nutrients,” Sonnenburg said.
When that defense falters, as it does shortly after a course of antibiotics begins, marauding micro-organisms such as salmonella or Clostridium difficile can establish beachheads. Once they reach sufficient numbers, these two parasitic invaders can mount intentional campaigns to induce inflammation, a condition that impairs the restoration of our normal gut ecosystem but in which salmonella and C. difficile have learned to prosper.