You don't really need full organisms to test the conditions of the planet and nanotechnology doesn't have to be the counter-measure either. Bioengineering could do all the work.
Since the colonists would be arriving in space-ships, the ship could have scanners/sensors that would measure and gather the air/soil/water of the planet before the colonists even got out. Then, batches of human tissue (or organs or organ systems or even just cells!) could be grown in labs to act as test cases against the planetary conditions.
Even today, researchers are able to grow tissue in labs without it ever being actually attached to living humans (which has a lot less ethical implications).
Then data about the exposure could be gathered, and the ship could then grow human-friendly m-o's designed to counteract the conditions of the planet, combine them with a new batch of human tissue, gather new data, and then continue iterating until any negative effects were either eliminated or negligible.
These m-o's would then be administered to the colonists and act as an immune system upgrade. Or you could go with gene therapy to change the behavior of white blood cells etc, so that the human immune system could handle the environment with as little change as possible.
Computers could even do simulations based on the data from the new planet and formulate a workable solution based only on those simulations. This would be much faster than the grow/test cycle. Real tissue testing would take place only once the simulations had come up with something, and just to make absolutely sure nothing bad happens.
And if it didn't work with the first iteration, you still have a faster process with simulate/grow/test since the simulate step gets you at least close before you bother growing anything.
All of this could be automated by the ships computer, which would use machine learning algorithms to iterate on the immune solutions.
These ways of doing things are less intrusive, faster, cheaper, more ethical, more "natural" (whatever that means), and less dangerous than using crew members or animals as test subjects or augmenting the crew with "synthetic" technology.