It was a strange idea that popped into my head. Could wild infectious microbes be bred (directed evolution) by some mechanism (such as through hypothetical drug therapies) to "domesticate" them and reduce their infectious qualities? Can we transform infectious microbes into innocuous ones rather than fighting against their antimicrobial resistance?

  • Naturally it often goes in the opposite direction, bacteria "want" to be more virulent (cause disease more easily). This can be done by transferring genetic information among them. You might find this interesting: en.wikipedia.org/wiki/Griffith%27s_experiment.
    – Lucky
    Jul 16, 2015 at 23:30
  • Couldn't they instead become more commensalic or symbiotic? Jul 16, 2015 at 23:38
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    To be honest, I don't know for sure. But my reasoning is this: evolution is about the survival of the fittest. And in bacterial species where some strains are virulent/pathogenic the most tough bacteria are usually the ones that make you sick (because it's not easy to kill them, they overpopulate the host, so to speak). If you used antimicrobial agents (such as antibiotics) - the resistant ones would prevail. On the other hand, there are extremophile bacteria that are quite tough, and are not pathogenic. All in all this is a very interesting question.
    – Lucky
    Jul 16, 2015 at 23:56
  • Well definitely bacteria want to be more virulent. But they don't want to kill their host( at least not so fast) that's why the most successful bacteria infects nearly every human, but do not cause disease. So they can spread more , not trigger immune defense and we don't research how to kill them. HIV is a example of top of my head of a virus that is getting weaker and less lethal
    – Freedo
    Jul 16, 2015 at 23:57
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    I guess we could surround ourselves by human cell cultures that microbes will then find easier to infect than the cells in our bodies. Farmers use a similar technique: by planting weed near to crops they make the pests go to the weed. Insects like weed better than crop, also by using pesticides selectively on crops the weed will become a lot more attractive, you only need a small amount of pesticides, resistance is less likely to develop. Jul 17, 2015 at 18:42

2 Answers 2


You have three separate issues here; I'll focus on how they affect bacteria in the gut. First, are different yet similar bacteria better or worse for people? Clearly yes; with various types of Escherichia coli being common and usually benign inhabitants, but E. coli O157:H7 causing severe problems.

Second, can directed evolution coax a bad type of bacteria into being a less harmful type? Also clearly yes: this is being done all the time in the biofuels industry to create bacteria with specific abilities to break down and reform materials into fuel.

Third, can such improved bacteria be used to crowd out the bad bacteria? Again, yes: Clostridium difficile is (see the name) a difficult-to-control gut inhabitant. Classic treatment with antibiotics has not been very effective, but transplanting good gut flora with fecal microbiota transplantation (FMT) seems to be very effective in the limited studies so far.

The trouble is when you want to combine them all. FMT is still controversial, because it's difficult to control exactly what gets transplanted, and we don't completely (or even mostly) understand the functionality of the gut biota. What if a transplant recipient goes downhill in an unexpected way: was it the fault of the transplant? It may be tough to tell, but lawyers could make enormous amounts of money on the question. Now, if you're working with a designed bacteria, the consequences could be even harder to predict, and the legal fault could be even clearer. (Plus there's the "ick" factor of poop transplantation.)

To summarize, the basic idea is good, but the proof is in the implementation.

  • It should be noted that people have developed synthetic gut cultures. See the RePoopulate study.
    – Fomite
    Jul 17, 2015 at 19:55
  • There was an interesting case recently in the news linking FMT to obesity post-transplant. I think Hopkins now disallows obese donors. Jul 18, 2015 at 1:19


In principle, this is what happens with any vaccine using an "attenuated" virus or bacteria - they have been directed through essentially forced evolution to lose some of their properties that effect virulence - how sick they make you when you get infected.

Some examples of this include the influenza nasal spray vaccine or the type of polio vaccine used in developing countries. These are both viral examples, but bacterial examples exist, including tuberculosis.

In a grander sense outside vaccination research, this is theoretically possible, but has some complications. The first is whether or not you can actually get attenuation. There are some microbes (norovirus and C. difficile come to mind) that are very hard to culture, so this kind of directed evolution is difficult. And, if successful, you'd have to reintroduce them in a setting where the "full strength" microbes exist, and if those full strength microbes have a selective advantage in the environment, the engineered strains are unlikely to be successful in the long term.

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