I generally find dichotomies, whilst reassuring (because they imply everything is clear-cut), rarely representative of real life. Fat/thin, rich/poor, right/wrong, good/bad, ethical/unethical, nice/nasty, healthy/unhealthy - they invariably grossly oversimplify the complexity that is humanity. The same is true about references to "good" and "bad" bacteria. I try very hard to avoid referring to bacteria in these terms.
It is seductive to dumb down scientific findings to a level which makes it clear-cut for the rest of us. I think this happens because we are all so keen on simply wanting to know the bottom line, the "so what". But the dumbing down process can result in inaccuracy and mis-information. And this is a particular risk in an area that is so new and so complex, with so many moving parts - the gut microbiome.
Defining bacteria as either good or bad grossly oversimplifies what science is discovering. Bacteria can alter function depending on their environment, on the nutrition that is available to them, on the competitors around them. Bacteria can take DNA from other microbes, thereby altering their genetic make-up in their own lifetimes. This inevitably means that black and white distinctions make us a bit blinkered, risk us missing the true picture. The truly complex picture.
Helicobacter pylori is a very good example. In Martin Blaser's book Missing Microbes, he explains how, after initially thinking the only good Helicobacter pylori is a dead one because of its link with stomach ulcers, they found that this bacteria was actually protective against gastro-oesophageal reflux disease (GORD). So indiscriminately destroying them to avoid stomach ulcers resulted in a rise in the incidence of GORD.
This interview, between Kristina Campbell and Catherine Lozupone of the University of Colorado, beautifully illustrates how we need to take great care not to compartmentalise bacteria. Catherine raises the possibility that, through a dynamic interaction involving our diet, our immune system and our microbes, some interactions result in optimal adjustments in our microbial population and their function to best deal with the particular food we eat in a way that optimises our health. And others do not. Roughly translated as - some people can eat sub-optimal diets and remain fit and well because, via immune interaction, their microbes adapt successfully in a way that optimises the health of the host (that's you and me).
We don't yet know precisely how we can help to maximise our microbial agility in our favour in the face of a range of diets. In the meantime then, it makes sense to try to do whatever we can to move our dietary intake towards diets that minimise the strain on our immune system. The specifics will differ from individual to individual but in general, this usually means reducing reliance on highly processed foods.