Answered Dec 12, 2017
Continued work on drug discovery in the long-standing “arms race” with antibiotic resistant bacteria. This is the potentially the largest public health issue in modern history, and in the coming decades. A related concern is finding more ways to get drugs into Gram-negative species.
The worst-case scenario is (no-joke, no-exaggeration) a replay of the medieval plagues, when more then half the population of Europe died. There is actually a real risk that humanity could be brought to its collective knees again. We could be exterminated within a few hundred years. But don’t worry – the microbes will continue to thrive just nicely, on their planet.
CRISPR / Cas9 originated as an immune system that bacteria use to defend themselves from bacteriophages, but may be a viable tool for gene-editing in humans. This has the potential for major ethical and legal implications. Do you have enough money to buy a better genome (for you or your child)?
Phage therapy to treat infections. Lots of technical problems, and not likely for prophylactic use.
Microbiomes, for humans and also other animals. Right across the road from me, people are working on trying to get cows to stop belching so much methane (which is generated by microbes in the cows’ gut).
Pharming, which is using microbes to produce drugs. This is where antibiotics were originally discovered (although that was by accident). Synthetic insulin is already manufactured using microbes, and there will be more drugs in the future, including both peptides and small molecules.
Bioremediation, for things like oil spills. Also, there are microbes that are able to eat a certain kind of plastic.
Plant diseases. This has very large economic implications for agriculture, and human implications involving famines.
Synthetic biology. Some of this is cool, like, “what is the simplest organism that we can make, and it will still be able to survive?” However, there are issues involving efforts to legally patent life forms, along with other ethical and economic risks.
If life is ever found on another planet or moon, it will be a microbe.
Biological weapons. Unfortunately, science isn’t always nice or helpful.