Yes, the gut microbiome or the gut flora is essential to digestion, assimilation and elimination processes! It may actually inconspicuously be one of the couple of pillars in the domain. The mechanical aspect, or the peristalsis and other movements isn’t alone sufficient, though indispensable. The chemical aspect through the mixing of different secretions by organs such as bile along the way are also instrumental.

The colonizing bacteria remain essential, and from the instant the body of the infant passes through the birth canal! Babies' gut bacteria affected by delivery method

In addition we hear that food has consciousness. Well, clinically it has been shown that the gut flora as a direct influence on the state of mind: Gut Microbiome and Depression: How Microbes Affect the Way We Think

Maintaining a healthy gut microbiota is a major contribution to good and sound overall health. I think it is very important to pay attention to this aspect of food/nutrients processing, assimilation and elimination, it does take sensitivity and a balancing act. 

I haven’t researched this aspect, but I can sense and would posit that it is also a major contributor to a good immune system as well. Already, the poop pills have been sold since the past  few years, to be used by individuals who appear incapable to create an adequate gut flora, and from the stool of those doing great. 

With serious digestive issues, one can be miserable enough to gladly use an extreme measure like that, after trying all other types of friendly bacterias on the shelves produced from fermentation of different foodstuffs from Kombucha to Kimchi. Bacteria predates humans by a long shot, and they had to be here for us to be facilitated as bigger organisms.

The minute the flora is disturbed there will be signs of disturbance in the process, it is a very delicate internal condition. They differ from species, and in the case of humans or omnivores, diet or whatever is ingested overall makes a big difference.

A critical aspect that is rudimentary along with the bacteria life form, is the environment they want for the whole implicated system to be an efficient ecosystem. Prebiotics constitute the environment that will allow the probiotic or the friendly symbiotic bacteria to thrive, and that is a certain diet, one that favors a natural and balanced diet along with adequate enzymatic reactions.