Antibiotics are reliable killers of dangerous pathogens. And their families. And their friends. And their acquaintances. And distant acquaintances of their acquaintances. That makes them the best weapon against dangerous bacteria—and the most dangerous weapon against good bacteria. But who is it who manufactures most antibiotics? It’s bacteria. Huh?

Antibiotics are the weapons used by both sides in the war between fungi and bacteria.

Ever since researchers discovered all this, pharmaceutical companies have been intensively farming bacteria. Huge tanks with a capacity of up to 26,500 US gallons (100,000 liters) are used to grow so many bacteria that their numbers can hardly be expressed in any meaningful figures. They produce antibiotics, which we purify and press into little tablets. The product sells well, especially in the United States. When researchers were planning a study of the effect of antibiotics on the flora of the gut, they were able to find only two people in the entire San Francisco Bay Area who had not taken antibiotics in the previous two years. In Germany, one person in every four takes antibiotics once a year on average. The main reason for taking them is colds. This is like a knife in the heart of any microbiologist. Colds are often not even caused by bacteria, but by viruses! Antibiotics can work in three different ways: by peppering the bacteria with holes, by poisoning the bacteria, or by rendering the bacteria unable to reproduce. They have no effect on viruses at all.

So taking antibiotics to cure a cold is usually a complete waste of time. If they do bring about an improvement, this is due either to the placebo effect or to the work of the immune system in combating the cold virus. The senseless use of antibiotics does, however, kill many helpful bacteria, which can be harmful in itself. To avoid this, doctors can perform a procalcitonin test, which indicates whether cold-like symptoms are caused by a bacterial or viral infection. The test can be especially helpful to make sure children don’t take antibiotics unnecessarily.

There is no reason not to take antibiotics when it is medically appropriate to do so. The benefits certainly outweigh the disadvantages, for example, in cases of severe pneumonia or for helping children get over a particularly bad infection with no long-term damage. In such cases, those little tablets can save lives. Antibiotics stop bacteria from reproducing, the immune system kills off any remaining pathogens, and we soon start to feel better. We have to pay a price for this, but in the final reckoning, it’s a good deal.

The most common side effect is diarrhea. Even those who don’t get diarrhea may notice that they leave a rather larger deposit in the morning toilet bowl than usual. To tell it like it is: a large portion of that pile is dead gut bacteria. The antibiotic tablet does not travel directly from mouth to blocked-up nose. It descends into the stomach and then on to the gut. Before it graduates from there into the bloodstream—and then to the nose, among other places—it peppers our microbe collection with holes, poisons our gut bacteria, and makes them sterile. The result is a formidable battlefield—you can see the casualties the next time you go to the toilet.

Antibiotics can alter our gut flora significantly. Our microbe collection becomes much less diverse and the abilities of the bacteria in it can change. Changes include the amount of cholesterol they can absorb, their ability to produce vitamins (like skin-friendly vitamin H), and the type of foodstuffs they can help us digest. Preliminary studies carried out at Harvard and in New York have shown that the two antibiotics metronidazole and gentamicin cause particularly hefty changes in the flora of the gut.

Antibiotics can be problematic for children and old people. Their gut flora is already less stable and less able to recover after treatment with antibiotics. Research in Sweden showed that the gut bacteria of children were still significantly altered two months after taking antibiotics. Their guts contained more potentially harmful bacteria and fewer beneficial types like Bifidobacteria and Lactobacilli. The antibiotics used were ampicillin and gentamicin. The study involved only nine children, which means it is not particularly meaningful in scientific terms, but it remains the only study of its kind so far. So the results should be accepted with a degree of caution.

A more recent study of pensioners in Ireland revealed a clear dichotomy. Some gut landscapes recovered very well after a course of antibiotics, while others remained permanently altered. The reasons for this are still completely unclear. The ability to return quickly to a stable state following an extreme experience is described with same word by gut researchers and psychologists: resilience.

Even though antibiotics have been in use for more than fifty years, studies of the long-term effects can still be counted almost on one hand. The reason for this is technological: the equipment necessary for such investigations has only been around for a couple of years. The only long-term effect that has been scientifically proven is drug resistance. For as long as two years after taking antibiotics, bad bacteria are still present in the gut, telling their great-great-great-… -grandchildren stories about the war.

These are the ones that resisted the antibiotics and survived. And with good reason. Bacteria develop resistance strategies. Some install tiny pumps in their cell walls to pump the antibiotic out like emergency workers pumping water out of a flooded cellar. Others prefer to disguise themselves so the antibiotics cannot recognize their surface and so cannot pepper them with holes. Yet others use their ability to split things—they build tools to cut the antibiotics to pieces.

The thing is that antibiotics rarely kill all bacteria. They kill certain communities depending on the toxins they use. There will always be some bacteria that survive and become experienced fighters. In the case of serious illness, these fighters can become a problem. The more resistances the bacteria have developed, the more difficult it is to get them under control again with antibiotics.

Every year, many thousands of people die because they are infected with bacteria that have developed resistances that no drug can counter. When their immune system is compromised—for example, after an operation—or if the resistant bacteria have got out of hand after a long course of treatment with antibiotics, the patient can be in real danger. Very few new drugs are in development, for the simple reason that it is not very profitable for pharmaceutical companies to do so.

SO HERE ARE four pieces of advice for anyone who wants to keep out of unnecessary antibiotic gut wars.

  1. Do not take antibiotics unless it is really necessary. And if you do have to take them, then always complete the course. This is because resistance fighters who are less skilled will eventually give up the cause and succumb to the drug. So the only ones that remain are those that would never have been killed by the antibiotics anyway. But at least the rest will have been well and truly done in.
  2. Choose organically farmed meat. Drug resistances differ from country to country. It is shocking to see how often these resistances correspond to the antibiotics used in large-scale animal farming. In countries like India or Spain, for example, there is almost no regulation of the amount of antibiotics given to animals. This turns the animals’ guts into giant breeding zoos for resistant bacteria. And people in such regions have significantly more infections with multi-drug-resistant strains. In other countries, regulations do exist, but even here the rules are ridiculously vague. This allows many vets to make a lot of money in the semi-legal antibiotics trade.

It was not until 2006 that the European Union banned the use of antibiotics in animal feed as performance enhancers. The kind of performance being enhanced here is the ability of an animal to not die of infections in a crowded and dirty pen. Antibiotics are a great way to “enhance” this “performance.” In the United States, the Food and Drug Administration is working on a voluntary plan to phase out the use of some of these antibiotics in regular farming. In organic farming, the Department of Agriculture forbids the use of any antibiotics, and an animal given antibiotics—for example, to relieve suffering—must be removed from organic production.

If possible, it is worth spending that little extra—to prevent resistance-breeding zoos and for your peace of mind… and peace of gut. The dividends are not immediate, but it is an investment in a better future for us all.

  1. Wash fruit and vegetables thoroughly. Animal feces are a popular fertilizer, and liquid manure is used in vegetable fields. In many countries, fruit and vegetables are not routinely tested for residues of antibiotics—and certainly not for multi-drug-resistant gut bacteria. Milk, eggs, and meat are usually tested to make sure they don’t exceed certain limits. So err on the side of caution and wash your fruit and vegetables one extra time if you are not sure. Even tiny amounts of antibiotics can help bacteria develop resistances.
  2. Take care abroad. One traveler in four returns home carrying highly resistant bacteria. Most disappear in a few months, but some lurk around for much longer. Special care should be taken in bacterial problem countries like India. In Asia and the Middle East, you should wash your hands regularly, and clean fruit and vegetables thoroughly—if necessary with boiled water. Southern Europe also has its problems. “Cook it, peel it, or leave it” is not only a good rule for avoiding diarrhea, it also protects against unwanted resistant souvenirs for you and your family.

Are There Alternatives to Antibiotics?
Plants produce antibiotics that have functioned for centuries without causing resistances. (Fungi, such as the penicillin fungus, are not plants but opisthokonts, like animals.) When parts of plants snap off or become perforated, they need to produce antimicrobial substances at the location of the damage. If they did not do this, they would immediately become a feast for any bacteria in the vicinity. Pharmacies sell concentrated plant antibiotics to treat developing cold symptoms, urinary infections, and inflammations in the mouth and throat. Some products contain mustard seed or radish seed oil, for example, or chamomile and sage extract. Some can reduce the numbers of viruses as well as bacteria. That leaves our immune system with less to contend with, giving it a better chance of dealing with pathogens.

Such plant-based remedies are not the solution for serious illnesses or for illnesses that drag on with no noticeable improvement. In such cases, they can even be harmful because they encourage us to wait too long before turning to powerful antibiotics. In recent years, the incidence of heart and ear damage in children has increased. This is often due to the behavior of parents who want to protect their children from too much exposure to antibiotics. Such a decision can have damaging consequences. A well-informed doctor will not prescribe antibiotics for every little thing—but will tell you in no uncertain terms when they are really necessary.

Our relationship with antibiotics is an arms race: we use them to arm ourselves to the hilt when faced with dangerous bacteria, and they respond by arming themselves with even more dangerous resistances. Medical researchers should really be developing the next generation of weapons in this race. Every one of us accepts a trade-off when we take these drugs. We agree to sacrifice our good bacteria in the hope of getting rid of the bad. In the case of a minor cold, that’s not a good deal; for serious illnesses, it’s a trade that pays off.

There is no species protection program for gut bacteria. We can be pretty certain that we have annihilated many family heirlooms since the discovery of antibiotics. The places they leave vacant should be colonized by the best candidates possible—probiotics, for example. They help the gut to return to a state of healthy equilibrium after danger has been averted.

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