Stanford University School of Medicine scientists explain why two potentially deadly pathogens get a foothold in the forbidding environment of the gut following antibiotic treatment.

The researchers wrote in the journal Nature that their findings may help identify ways to counteract the effects of the depletion of “friendly gut-dwelling bacteria” after antibiotic treatment.

Several gut pathogens can cause serious problems during a course of antibiotics. Senior author, Justin Sonnenburg, PhD, said “Antibiotics open the door for these pathogens to take hold. But how, exactly, that occurs hasn’t been well understood.”

The authors explained that there is a significant rise in carbohydrate availability in the gut twenty-four hours after administering oral antibiotics. This temporary surplus of carbohydrates, plus a reduction of “good bacteria” in the gut, allows at least two potentially life-threatening pathogens to multiply rapidly.

Over the last ten years, scientists have made enormous progress in understanding what goes on in the “complex microbial ecosystem” that exists in the large intestine of every healthy mammal, including humans’.

Approximately 1,000 different types of microbes coexist harmoniously within a typical healthy human’s gut. These bacterial strains that inhabit this challenging but nutrient rich niche have adapted extremely well, so well in fact that we would struggle to survive without them.

Friendly, gut-dwelling bacteria synthesize vitamins, they are key to guiding our immune systems, they are involved in the development and maintenance of our own tissues – they even help regulate blood pressure.

Antibiotic medications devastate this gut-microbe ecosystem. Good bacteria start multiplying rapidly within a few days, and within a month are back to normal numbers. However, according to the authors, “the ecosystem appears to suffer the permanent loss of some of its constituent bacterial strains”.

The scientists liken these friendly bacteria to a kind of lawn which beats the weeds (pathogenic bacteria) to the rich fertilizer that courses through our gut. Previous studies have suggested that our friendly bugs secrete chemicals that prevent the pathogenic bacteria from taking control.

There is a theory that when our inner microbial ecosystem is disrupted, our immune system responsiveness suffers.

Sonnenburg said:

“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.”

When these defenses are weakened, as usually occurs not long after starting on a course of antibiotics, plundering pathogens, such as Clostridium difficile, are able to establish footholds.

As soon as these two parasitic invaders have multiplied to sufficient numbers, they induce inflammation. While inflammation is not a good environment for restoring good bacteria, C. difficile and salmonella thrive in it.

Sonnenburg and colleagues focused on two particular nutrients in the gut – fucose and sialic acid – both members of the sugar family. These are not sugars most people are familiar with, but they are vital for healthy survival and are produced in every cell in the human body. They are also found in dairy products, eggs and meat.