Your microbiome (microorganisms such as bacteria, fungi, and viruses) is solely governed by what you eat. If you, for example, stop eating harmful fiber and starches, the bacteria that feed off it will die and be replaced by other bacteria that enjoy what you are now eating. The only reason you have a specific strain of bacteria is because that strain is taking advantage of what you are feeding them by your current food choices. And truth is, you don’t need them.
In fact, your microbiome will always adapt to your diet and no matter what you eat, it will be able to ferment some of the foodstuff and supply you with short-chain fatty acids and probiotics.

In other words, the popular talk about consuming a varied diet to accomplish a diverse microbiome, which is believed to make ‘the whole system more stable’, is mostly nonsense. Funny thing is, a strict carnivore diet (eating only meat and organ meat), will score you an 8 out of 10 on a microbiome diversity test.
Simply adding other foods on top of that will only accomplish more bacteria, and mostly of the bad kind that feed on starches/sugar.
Actually, too much gut bacteria can be very harmful to your intestines, especially if your intestine walls have been damaged by consumption of insoluble fiber, lectins (grains and legumes) and saponins (soybeans, beans, garlic, oats, quinoa, etc.).

To put it simple. If you follow our natural animal-based diet, your gut microbiome will take care of itself. You will have all the good bacteria needed for optimal health. In fact, people with inflammatory bowel diseases, metabolic disorders, and those who have taken antibiotics, show less bacterial diversity than healthy people. And those diseases are caused by nutritional deficiencies and toxins from a poor diet that is high in plant based foods – and especially starches and fiber.
In other words, the more animal-based foods you consume, the better and healthier your gut microbiome will be – and going fully animal based will always be the healthiest option.