Despite what Wikipedia says, the microbiome is neither new nor recently discovered. It has, however, become the hot topic in medicine as the scientific community rediscovers the intimate relationship between ourselves and our "little masters" the gastrointestinal flora known as the microbiome.
Why the fuss? Yes, these bacteria outnumber us 10 to 1 if you just count the cells, and 150 to 1 if you count the genes. But there's less than a kilo of them and they're, well, kind of dirty. They make poo! How important can they be?
The answer seems to be, "more important than we ever could have imagined". We depend upon them for nutrients that we cannot make or absorb from our diet. They control energy harvesting and obesity, especially when provided with loads of sugar. They are very involved in inflammation, and our immune system is hugely influenced by their numbers and diversity. They manipulate our autonomic nervous system and affect mental functioning very profound ways. When the balance is distorted by antibiotics in drugs or foods the proportions change and they can turn feral very quickly. They were around before we were born, and if we are buried rather than cremated they will recycle us and continue on well beyond our death.
The microbes in your gut have never died. We can trace their lineage back over many billions of generations to the primitive bacteria and archaea. In many ways, we are just temporary housing for them, and there is a good case that we live healthily when we meet the needs of our microbiome optimally.
Managing gastrointestinal ecology and gut biodiversity requires a deep appreciation of the value of fresh organic food in season, avoidance of antiseptics and unnecessary antibiotics, a reduction in simple carbohydrates, and avoidance of preservatives and antiseptics in foods that blunt the genetic and species diversity within us.
The art of managing digestion, nutrition and the gastrointestinal tract is arguably the most difficult task for a health-care practitioner. When it works, however, it is among the most rewarding outcomes, as food becomes the friend rather than the enemy and the microbes work to give us rewards and keep us healthy.