A bit more meddling, anyone?

Admit to being a navel-gazer. Who hasn't become caught in the obsession these days with yoghurt and little bottles of 'friendly bacteria'? In the first edition of the Times' eureka science magazine I found a great overview of the current known microbiota of the gut.
But having sufficient 'friendly bacteria' is not the sole important factor in gut health. It has been discovered only within the last ten years that our long term health, our weight, even our mental condition, are affected by the range of microbes in our gut.
Unfortunately we have been meddling with the microbiota for 60 years now.
Jeremy Nicholson, Professor of Biological Chemistry at Imperial College London, is quoted in eureka:"Since the Second World War we've been using lots of antibiotics. Well, guess what? They've killed the good bugs as well. A lot of diseases have become more common in the West since the Second World War, such as Type 2 diabetes and obesity. Now that the Far East is westernising, you're seeing the same thing there. You've got more western diets, which can change your bugs, and antibiotic use is going up as well."

Antibiotics, initially penicillin, were originally life-saving medicines that brought injured soldiers back from the frontline field hospitals when they would otherwise have succumbed to infection. Today a short course (or two) has become everyone's drug treatment of choice and health managers are trying to put the brakes on antibiotic use.
But chronic illness had already mushroomed before this consensus for change was realised.
Far from being a decisive weapon against infection, unmonitored antibiotic use can promote the growth of the worst kinds of resistant, spore-carrying bacteria; hence the emergence of the hospital superbug C.diff.

Now some microbiologists are suggesting we should help patients by altering their personal gut bacteria - surely the ultimate in individualised care. Not by using probiotics - they don't seem to work, despite what the ads say - but possibly by tampering with the current balance of gut flora in some way.
Professor Nicholson enthuses: "We may be able to modulate drug metabolism and toxicity. It's interventional personalisation: this is the way you are, this is what you need and we can change you to make it work. Nobody's ever done that before."

Woah!
So let's get this straight.
1) Sixty years of an intervention which has tried to beat bacteria at their own game through overwhelming antibiotic force has led to an unpredicted increase in chronic conditions in the general population.
2)We have just discovered a few more complex facts about the microbiota of the human body.
3) Excited scientists want to rush ahead and intervene by forcing our microbial balance back to roughly where they think it should be.
Has no one learned any lessons from the past? Do we have to recklessly hurtle on? Or shall we pause for a public debate about this?
Hands up all those in favour of more meddling?
Personally, I prefer to be sure my own immune system is working effectively, so it can do the job of fighting infection that it was well designed to do.