Zizzle,
FWIW, after my last surgery (which resulted in an ileostomy), I had virtually no residual gut bacteria (and no colon). Since the surgery was done on an emergency basis (with no time to clean out), the remaining part of my small intestine was flooded with antibiotics for days.
Trust me, nothing allows you to check out your gut output like an ileostomy.
When I left the hospital, my gut output was absolutely odorless (due to a lack of bacteria), and pretty much free of gas (only air that I swallowed while eating). I never took any probiotics, and it remained that way (odorless) for a period of 6 to 8 weeks (as best I can recall), and then the odor began to return (as the bacteria became re-established). With the return of the bacteria, I had to reduce the amount of fiber and certain carbs in my diet, in order to minimize the gas problem (because with a pouch, an exhaust system is no longer readily available).
During that time when I had no established colonies of gut bacteria, I had absolutely no problem digesting my food (and gaining weight). The claim that gut bacteria are needed for good digestion is a myth, with absolutely no data to substantiate it. The only changes that I could see as the bacteria became established, were that I found it necessary to modify my diet, in order to minimize the generation of gas. IOW, my menu was reduced, not expanded.
IMO, gut bacteria definitely affect digestion (and a lot of other body systems), but their advantages are highly overrated. As far as I can tell, researchers haven't even scratched the surface, when it comes to actually understanding how gut bacteria affect our digestion and most other body systems, so it's difficult to put much faith in their tentative conclusions at this early stage of the game.
Tex