You can't really selectively kill different bacteria unfortunately. And it's also not as simple as 'good' and 'bad'. We probably need all of them for various reasons, and without the trillions of them in our bodies we would die. They perform all kinds of essential tasks, from digesting and delivering nutrients, regulating the immune system, to producing various functional hormones and even controlling our fat cells - but only when in the 'correct' ratios.
Too much of one can cause, for example, inflammation and a massive immune response, making you very unwell, bloated, causing diarrhoea; or could cause leaking of the intestines, causing all kinds of bacteria to enter the bloodstream and settle in joints or anywhere else, possibly causing trouble like joint inflammation and early onset osteoarthritis and even heart attacks. Many diseases (eg Crohns, IBS etc) are thought to possibly erupt as a result of these bacterial imbalances.
Now if you take an anti-biotic, for example, it kills most bacteria unselectively. The trouble with this is that as the bacteria populations recover, it's often the invasive 'bad' ones (think weeds in a flower bed) that recover fastest. They basically outcompete the rest, overgrow everywhere, and cause you intestinal hell.
Clostridium difficile is a very potent example of this - it ends up killing a lot of people after treatment with strong antibiotics kills all the other bacteria that were competing with it for resources (the food we eat). It's so difficult to treat once it's taken over that most antibiotics simply cannot kill it, and so the fairly recent innovation of fecal (shit) transplants direct to the guts was thus invented to rapidly restore a *balanced* bacterial flora. All the other bacteria do what antibiotics fail to do - control the clostridium and out-compete it for food.
Now most of us don't really want a shit tranplant though lol, so the only other way to really get the less desirable bacteria back under control and create balance is to flood the system with bacteria that are known to have positive effects in the body - hence the explosion in the use of pro and pre biotics over the last 10-15 years.
Frequent, consistent consumption has been shown repeatedly to help restore normal intestinal function, improve immune function, even prevent the development of obesity. Other things can help it too, including things like water soluble and insoluble fibres and glutamine. Generally speaking if you have a lot of intestinal troubles, you need to sort out what it is in your diet that's causing trouble and foster a nice healthy playground for all the bacteria to grow ;-)
