Okay I've already made a previous post but to get into more, we can talk about the gut microbiome, though it's too nebulous to say anything for certain.
There's been studies (at least in other species) that suggest the gut microbiome is dynamic (obviously) and regulates absorption of certain things.
Here's one such study:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3517662/they basically showed a certain type of ubiquitous gut bacteria greatly increased the absorption of lipids into the enterocytes and increased number/size of subsequent lipid droplets. This implies actually MORE absorption of the same fats occurring which would clearly lead to an increase in the # of calories.
Furthermore, this bacteria in particular has been found in many obese patients and is more proliferative in times of food abundance. They've shown there's a shift in the major phylum of gut bacteria when food is more scarce.. and that also means less lipid absorption.
I have no idea how/why the bacteria would actually be augmenting lipid absorption. One possibility is that they produce a large amount of short chain fatty acids and that's where a bulk of it comes from. Perhaps it's a specific phylum (ie the ones that are more present in food abundance) that produce more of them? Probably something else to do with a majority of this noted effect though.
Corroborating these findings and thoughts, it's been shown elsewhere, such as here (and others actually, I just remembered the title to this one exactly):
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC524219/ --- that germ free mice lacking a gut microbiome were actually leaner than their counterparts. And that introducing a canonical flora to these animals, they became obese. Interesting thought. I believe this would imply the gut microbiota is negative in any sense, it just happens that there are "lesser evils" down there.
You know I love intermittent fasting / time-restricted feeding, so here's a recent study exploring some of the complex dynamics of the microbiome under certain conditions:
http://www.sciencedirect.com/science/article/pii/S1550413114005051And what do you know.. as I said above about diff types of bacteria, this found something similar: "TRF Decreases Relative Amounts of Presumed Obesogenic Microflora and Increases Relative Amounts of Presumed Obesity-Protective Microflora"
Going back to the first study I cited, they did propose a few mechanisms by which the gut microbiome affected lipid absorption:
"We propose four nonexclusive mechanisms by which microbes might stimulate FA absorption and LD accumulation in enterocytes. First, microbes might increase bioavailability of FAs by modifying the production or composition of bile salts (Swann et al., 2011). Second, microbes could directly contribute to luminal lipolytic activity that promotes FA availability for potential absorption in the intestinal epithelium (Ringø et al., 1995). Third, microbes might enhance FA absorption indirectly by evoking physiologic responses in the intestinal epithelium that stimulate its inherent absorptive capabilities. Finally, the microbiota might reduce rates of fatty acid oxidation in intestinal epithelial cells permitting increased storage of FA in LDs."
I won't go too much further. The gut microbiome is one of the most interesting topics to me and I've love to keep discussing it.. but in terms of how it actually affects ABSORPTION? I have no idea. I've really only seen that 1-2 studies on that specifically.
So I'll end with an incredible figure from a very recently published paper. This should give some of you others that aren't up on the research behind it how exactly the gut microbiome could impact our body to promote obesity, diabetes, inflammation, etc.
http://i.imgur.com/9oqRYsm.png