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A new study by researchers at Stanford University School of Medicine published in the September 2013 issue of Nature proposes a mechanism for how disease–causing microbes such as Salmonella and C diff often thrive when people take antibiotics. Soon after someone takes antibiotics two things happen: The number of friendly gut bacteria is dramatically reduced and the amount of available carbohydrates in the gut is dramatically increased. According to the authors, the extra carbs and fewer friendly gut bacteria allows the bad bacteria to take over.

It turns out that friendly gut microbes are able to cleave sugars including fucose and sialic acid from  mucus (mucus is made of a variety of sugars) that cover the entire surface of the gut. With the help of other friendly microbes these sugars are normally broken down and shared. But when people take antibiotics many of the bacteria that cooperate to break down and consume these sugars are lost and bad bacteria (pathogens) can then use these sugars themselves to grow and become established.

I found this paper interesting because it lends support to the idea that fewer excess carbs in the gut leads to more competition which favors indigenous gut microbes over bad or pathogenic bacteria. A good example in the paper likens friendly gut microbes to your lawn. “It is thought that our commensal, or friendly, bacteria serve as a kind of lawn that, in commandeering the rich fertilizer (carbs) that courses through our gut, out-competes the less-well-behaved pathogenic “weeds.” The more healthy grass you have, the fewer weeds will be able to become established.” But if you were to spray your lawn with roundup (like antibiotics) and continue to add fertilizer, soon you will have a weed-filled yard. According to the authors: “Resident microbes hold pathogens at bay by competing for nutrients.”

While we may not be able to control the amount of sugar chains comprising our gut mucous supply, there are two things we can do: 1. Take antibiotics only when they are absolutely necessary. 2. Limit the overall amount of difficult-to-digest but fermentable carbohydrates in our diet. That’s the strategy of the Fast Tract Digestion book series for control of SIBO-related conditions such as IBS, GERD, Rosacea and many others. One day, this diet strategy may prove to be supportive of people who need to take an antibiotic. Clearly excess fermentable carbs is not something you want when you are about to drastically inhibit a large number of your friendly gut microbes – which is what happens when you take antibiotics.

Update: Here is an interesting report on how another bad bug, enterohaemorrhagic Escherichia coli (EHEC), uses a chemical sensing system to manipulate a friendly gut microbe (Bacteroides thetaiotaomicron, also the subject of  this blog) to serve it up a nice meal of fucose sugar.