Both diet and micro-bacteria are important. The micro-bacterial community varies by individuals and diseases. The interaction could be existed. If so, evidence is needed for future research and practice.
Look up the GAPS diet by Natasha Cambell McBride. Grain base carbs shift the gut microbiome towards harmful bacteria.
The microbiome can determine your energy extraction from food and therefore body weight.
The microbiome interacts very closely with gut wall permeability and health with onward concequences to liver and immune system.
Dairy and high carb diets alter both gut and skin microbiome exacerbating acne vulgaris
The microbiome in our gastrointestinal tract is essential for our health. It helps us breakdown the food, so that the nutrition in food can be fully utilized. The microbime itself also provides us all the essential nutrients (like amino acids, and some necessary fats) that cannot be produced by our body:
Article Intestinal bacteria modulate the foraging behavior of the or...
The amino acids from microbiome is harvested through autophagy (xenophagy), not by conventional absorption. Although the microbiome in our intestine help us in digestion foods, they are potential pathogens if they have the chance to invade into the interior of our body. So besides food digestion and absorption, our gastrointestinal tract (GIT) mucosa has another very important role as barrier to these microbiome. As an immune effector, autophagy will capture any bacteria, viruses and fungi that touched our epithelial cells of our GIT, degrade them and turn them into amino acids for the use of our body. By this way, autophagy not only helps our immune system in defending pathogen invasion, but also provides extra nutrition to our body by degrading the microbiome in our GIT:
Article Autophagy: roles in intestinal mucosal homeostasis and inflammation
So in order to introduce a great variety of microbiome into our GIT to supply a diversity of essential amino acids and essential fats to our body, the food we eat cannot be too clean. Otherwise no matter how carefully designed nutrition combination is added to our food, we will still be lack of the essential nutrients we need, and fall in sickness inevitably.
Please take a look at these useful RG links.
Article Gut microbiome-Mediterranean diet interactions in improving ...
Article Influence of diet on the gut microbiome and implications for...
Article Interaction between diet composition and gut microbiota and ...
There’s a growing body of work on gut microbiome, it’s influence on local microbiomes eg skin for acne and ocular surface for dry eye disease and blepharitis. It also influences neurotransmitters and inflammation with implications for depression, anxiety, autistic spectrum, Alzheimers and Parkinsons disease. The diet that best supports a healthy microbiome is high in plant fibre, so a plant based, but not plant exclusive of animal products diet. Grains and dairy are less conducive to a good gut microbiome, reference the GAPS diet for autism and ADHD spectrum by Dr. Natasja Cambell-McBride.
I think the interaction between local microbiome like that on skin and respiratory tract with local diseases is more related to the amount of food than what kind foods we eat in the diet. As long as a person eat the food that only enough to support one's life, i.e., no superfluous food are consumed for the local microbiome to develop diseases, then one will stay healthy, no matter what kind food we eat and what diet we adopt.
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