The Microbiota Don’t Like Antibiotics — Of Course!


A healthy microbiome, like a healthy brain, makes good decisions for both itself and the fleshy vehicle that carries it around. It does its best to send helpful signals, and if we ignore its messages it makes its objections known in uncomfortable and sometimes spectacular ways. Feeding the bugs what they don’t want, or not feeding them what they do want, can inspire them to act out, like the unstable ex who pulls out a chisel to give your car racing stripes.

It seems that variety and diversity are important for the microbiome, which has actually been referred to as a distinct organ. Researchers want to understand the microbiota — a difficult task because half the creatures that live inside us are not amenable to laboratory cultivation. About what they are doing inside us, we are clueless.

The trillions of individual residents live mostly in the colon, and display intriguing connections with obesity or the lack of it. They belong to different tribes. Scientists have hazarded a guess that the ideal balance would be 80% good bacteria holding out against over-colonization by 20% bad bacteria.

Dr. N. Campbell-McBride wrote:

One of the major functions of the good bacteria in the gut flora is controlling about 500 different known to science species of pathogenic (bad) and opportunistic microbes. When the beneficial bacteria get destroyed the opportunists get a special opportunity to grow into large colonies and occupy large areas of the digestive tract.

However, such statements must be accompanied by a caveat. Further investigation suggests that any given species is able to play more than one role, and can be “good” or “bad” depending on what else is going on.

Americans who never have antibiotics prescribed manage to take in plenty of them, through meat and even through drinking water. Even a small amount of the antibiotic ciprofloxacin has “significant effects on roughly one-third of the bacterial species.” A study that followed people six months post antibiotic therapy found that a lot of microbial species do not just bounce back.

Even with help, they may not regenerate. Chris Kresser wrote:

Unfortunately, even a single course of antibiotics can permanently alter the gut flora. One study found that after a single treatment of intravenous antibiotics, fecal bacteria tests demonstrated a significant change in the variety of bacterial strains, and the development of the pathogen Clostridium difficile.

Anyone who has ever had C. diff, as it is affectionately known, advises others not to catch it. Apparently, it is one of the bad neighbors that moves in when the neighborhood has already started to deteriorate; when the microbiome is already wounded.

In a related discussion about probiotics, we find this:

A study on 135 hospital patients taking antibiotics found that only 12% of the probiotic-receiving group developed antibiotic-associated diarrhea, compared with 34% of the placebo group. Additionally, while 17% of the placebo group developed diarrhea specifically from C. difficile, nobody in the probiotic group did.

The notion that the ferocious C. diff can be so easily averted is impressive. Kresser goes on to say:

If antibiotics must be used (and there are certainly situations where this is the case), special care should be taken to not only restore their gut flora using probiotic foods and supplements, but to eat a diet that supports healthy gut microbiota with plenty of fermentable fibers from starch and the removal of food toxins.

In the future, saving stool specimens for an auto-FMT (Fecal Microbiota Transplant) might be routine, just like setting aside a patient’s own blood is now.

Your responses and feedback are welcome!

Source: “Gut and Psychology Syndrome (GAP Syndrome or GAPS),”, undated
Source: “The high price of antibiotic use: can our guts ever fully recover?,”, 02/10/12
Source: “What To Do If You Need To Take Antibiotics,”, 01/10/14
Photo credit: Torsten Scholz (ViewPix69) via Visualhunt/CC BY

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