John,
I'm not quite getting how you're making the jump from this:
"Gut flora have a continuous and dynamic effect on the host's gut and systemic immune systems. The bacteria are key in promoting the early development of the gut's mucosal immune system both in terms of its physical components and function and continue to play a role later in life in its operation. The bacteria stimulate the lymphoid tissue associated with the gut mucosa to produce antibodies to pathogens. The immune system recognizes and fights harmful bacteria, but leaves the helpful species alone, a tolerance developed in infancy.[2][11][4][5]
As soon as an infant is born, bacteria begin colonizing its digestive tract. The first bacteria to settle in are able to affect the immune response, making it more favorable to their own survival and less so to competing species; thus the first bacteria to colonize the gut are important in determining the person's lifelong gut flora makeup."
to this:
No matter how long, be it millions of years\billions of years these organisms were just as they are from the very beginning.
Nowhere in your cited example was there any suggestion that these bacteria couldn't change.
"Recent findings have shown that gut bacteria play a role in the expression of Toll-like receptors (TLRs) in the intestines, molecules that help the host repair damage due to injury. TLRs cause parts of the immune system to repair injury caused for example by radiation"
There is no doubt of their function and this cannot be disputed, just as i said without there would not be one life, no humans, no fish - NOTHING.
In modernity, for modern organisms.
Now, in ages past, when the gut was first evolving, what then? Your argument only holds true if you presume that modern organisms were identical 600 million years ago. They were most definitely not.
No you are wrong. Without these beneficial organisms that had to be present from the very beginning nothing with a stomach can survive adn if you think that the fundamental organisms that need to be present have changed then you dont even know the basics of life and its requirements.
http://pruned.blogspot.com/2006/12/gut-flora.html
Way back, there were some bacteria, and some worms.
The bacteria did their thing where they ate food where they could find it. Of course, being so tiny, they had trouble dispersing to other places where they could find more food.
The worms had recently developed a specialized organ that allowed them to digest food- the gut. It excreted acid into a compartment where it put its food. Specialized cells would then absorb the nutrients. Previously, it has just excreted acidic mucous directly into the environment, but this worked much better.
Now, a worm gains a mutation that allows some bacteria to live in its stomach, and some bacteria gains the ability to live in the worm. The bacteria produce novel enzymes that greatly increase what foods the worm can eat; the bacteria gain a place to live and all the food they need. There are, of course, problems, at first. Gut flora ends up eating the host. The host kills the gut flora.
But if having bacteria in the gut outweigh the costs (there are always costs), then they stayed. And since those worms with the bacteria, and the bacteria with the worms did so well, they passed their genes down to the next generation.
When those worms later became bigger, more complex organisms, the benefit of having gut flora was retained. All the way to people.