Human beings rarely stop to think about the fact that every single thing they look at which is alive and growing — animal or plant — is absolutely and utterly, completely and irrevocably, dependent on the microbial communities that support it.
If all the microbes on the planet died, or even a significant fraction of them, nearly every life process we are aware of would be disrupted in one way or another. Plants would stop growing; animals would die. Animals have been extraordinarily dependent on microbial communities for survival ever since they developed guts; without the microbes in their guts, they wouldn't make it.
In order to understand this, we have to understand that the gut — a tube in which food substances are broken down into constituent molecular components — has existed since the cambrian explosion, perhaps earlier. Ever since creatures began to eat surrounding organic material — including each other — there has been a need to break down the walls of cells in order to get at the nutrients inside them. In many cases, the walls of cells, which are microscopic, can't be so easily affected by the action of larger structures like teeth — which many creatures, let's remember, don't even have — and the chemistry of the foods inside the cells was bound up by molecular relationships that lock the energy into inaccessible structures — for example, and perhaps most typically, cellulose, the primary form of cell wall in green plants.
In order to avail themselves of these rich reservoirs of nutrient, animals needed microscopic organisms that could act on the structures to break them down. Bacteria, it turns out, are ideally suited for this, for a number of reasons. First of all, they are small enough to act on a microbiotic scale; big things may be able to eat little things, but other little things need to help digest them. Second, due to their short life cycles, they evolve very quickly, so they can quickly develop new responses to new foodstuffs as new evolutionary developments make them available to creatures foraging in new areas. Third, they are capable of one of the most extraordinary acts in the animal world, one that is functionally impossible at larger levels — that is, the inter-species exchange of genes through plasmids. This gives them a developmental edge that has vexed medical scientists for several generations now, since it allows them to rapidly develop resistance to antibiotics across a wide range of species.
But let's get back to what this meant to early life, because it's fun and exciting. A quick trip to the American Museum of Natural History – or any museum, for that matter, that has a good collection of large herbivorous dinosaurs such as apatosaurus— will treat the reader to the sight of creatures that evolved massive bodies with huge guts. These gigantic intestinal reservoirs developed with only one purpose in mind; they were massive housing units for gut bacteria, which fermented and dissolved the huge amounts of plant materials these dinosaurs ingested. Just looking at the skeletons and the shape and size of the guts verifies that by 150 million years ago, the digestion of food stuffs by gut bacteria had been taking place for additional hundreds of millions of years, and had reached what may well be a zenith. It is standard operating procedure in any creature with a gut. The gut is a portable toolkit for microbial digestion, exactly like a set of cookware people bring on camping trips.
Humans aren't any different in this regard. We have skeletal structures, much like the dinosaurs, that support an abdominal cavity that carries around a very neatly organized, species-specific package of bacteria that acts as a bioactive Swiss Army knife. Gut bacteria have been evolving for millennia and are supremely adapted for the diet and lifestyle of the creature that has them. Creatures exist in lockstep with their gut populations; and the gut population itself is a very complex structure that includes both microbiotic creatures such as yeasts, bacteria, and fungi, and macrobiotic creatures such as worms.
These populations, moreover, have existed in such exquisite balance for so many hundreds of millions of years that changing any of it changes the fundamental nature of the organism itself, since all of its inner workings are highly dependent on the balance of these communities.
Anyone who doubts this needs to spend a few hours browsing the articles I've collected at my gut bacteria page. You will come away with a completely new appreciation of what not only human beings, but all species, consist of — a commensal and symbiotic community of organisms that must have one another in order to survive.
We may think we are different than the species of ants who have a parasitic fungus that alters their behavior, causing them to undertake activities that helps the fungus spread; but we are not. The bacteria in us have a direct effect on our psychology, remarkable though that might sound, and the laboratory evidence supporting this contention mounts with every passing day.
There will be more details about this to discuss as we move forward.