A Gut Feeling: The Roles of Digestion and the Microbiome in Health and Disease

January 28, 2022 5 min read

A Gut Feeling: The Roles of Digestion and the Microbiome in Health and Disease - Layer Origin Nutrition

After decades of most doctors and scientists virtually ignoring the gut microbiome’s role in our health, we are now practically bombarded with people discussing “the gut” all over Instagram, YouTube and pretty much everywhere else you look.

But do you know the basics when it comes to your “gut”?

Let’s take a moment to make sure you do before we dive deeper.

The gut is comprised of three major parts: the stomach, the small intestines and the large intestines (colon), with each performing a unique function in the body. Together, they are responsible for digesting and assimilating nutrients from food and eliminating waste in the form of stool.

The small intestines and the colon possess a combined length of 15 feet or more. This remarkable length provides a high amount of surface area and increases transit time to maximize nutrient absorption from food.


Any complex carbohydrates (e.g. resistant starches, soluble fibers, insoluble fibers, unique oligosaccharides like human milk oligosaccharides) that are unable to be enzymatically digested, traverse the small intestine intact and ultimately enter into the colon.

Although there are bacteria in all the regions of the gut, the colon is home to the highest density of microbes. In fact, each individual’s colon contains upwards of 100 trillion bacteria.

However, the species that constitute this vast biome change rapidly in response to different dietary inputs. Shifts in microbiome composition can occur in response to a single meal, with even more dramatic changes occurring over 1-3 days of introducing new foods into the diet.

Strikingly, not only does the food we eat directly influence the composition of our microbiome, but the composition of our microbiome also influences our cravings for particular foods.

In this way, eating a fast-food diet begets cravings for more fast food, whereas a diet based around whole foods facilitates healthier cravings.


In addition to the interplay between the microbiome and diet, there is also an important relationship between the microbiome and gut health. Specifically, microbes within two genera, Bifidobacteria and Akkermansia, play critical roles in supporting the energy metabolism and structural integrity of the colon.

Bifidobacteria  are largely responsible for digesting soluble fibers, resistant starches, and oligosaccharides like fructooligosaccharides, galactooligosaccharides, human milk oligosaccharides (e.g.2-fucosyllactose) into small molecules that feed butyrate-producing bacteria in the colon.

Butyrate is a short chain fatty acid that supports gut barrier function, exerts anti-inflammatory effects via immunomodulation, and serves as the primary fuel source for colonocytes (colon cells).


In addition to their role in supporting butyrate production, Bifidobacteria also synthesize B vitamins, which are critical cofactors for energy metabolism, effectively protect against and treat colon cancer, and prevent the colonization of pathogenic bacteria in the gut. Dietary polyphenol intake is associated with increased abundance of Bifidobacteria.

Additionally, the intake of soluble fiber, resistant starches, and 2-fucosyllactose directly feed Bifidobacteria and support their growth.

  • Foods containing soluble fiber include apples, pears, oats, barley, turnips, broccoli, avocado, chicory root, artichoke, and beans.
  • Foods containing resistant starches include green or semi-green bananas, cooked and cooled potatoes, cooked and cooled rice, beans, and legumes. Interestingly, cooking potatoes or rice with a fat source like ghee or butter dramatically increases the fraction of resistant starches formed upon cooling.

Finally, 2-Fucosyllactose, an oligosaccharide abundant in human breast milk, is highly bifidogenic and can be found in Layer Origin’s PureHMO® product line.

Strikingly, breast-fed infants have a gut microbiome composed of up to 90% Bifidobacteria thanks to the unique nutrient profile of breast milk. Declines in populations of Bifidobacteria in the gut occur in response to aging and are associated with the development of age-related diseases.

On the flipside, both Bifidobacteria and Akkermansia are more abundant in the guts of healthy aged populations compared to aged populations with comorbidities.


Akkermansia, specifically Akkermansia muciniphila, is a species of bacteria that lives in the mucosal layer of the gut lumen. This species is an important regulator of intestinal permeability, and its presence is negatively associated with obesity and type II diabetes.

In other words, the more Akkermansia are present in the gut, the less likely an individual is to develop type II diabetes or obesity. Additionally, by increasing the strength and integrity of the tight junctions between cells of the colon, the presence of Akkermansia effectively prevent and treats leaky gut, a major driver of food allergies and systemic inflammation, and also reduces total macronutrient extraction from food, thereby decreasing caloric load and supporting weight loss.

By ameliorating or preventing leaky gut and its downstream consequences, Akkermansia play an important role in decreasing the likelihood of diseases driven by inflammation including cancer, insulin resistance/type II diabetes, Alzheimer’s disease, and autoimmunity.

  • Akkermansia thrive on dietary polyphenols like those found in red apple peels, cranberries, pomegranate, raspberries, blueberries, blackberries, black grapes, and tea.
  • Additionally, studies suggest that populations of both Akkermansia and Bifidobacteria can increase in response to consumption of fructooligosaccharides (FOS), like those found in Layer Origin Nutrition's PureHMO® tri-prebiotic powder. These oligosaccharides are also naturally found in bananas, asparagus, and onion.


In summary, the gut is a multifaceted term to describe the tissues responsible for the extraction of nutrients from food and the elimination of wastes from the body via stool. In addition to the physical and chemical breakdown of food by our bodies, gut bacteria also play a critical role in the breakdown of indigestible polysaccharides into key molecules that support the health of our guts, immune systems, and bodies as a whole.

Bifidobacteria and Akkermansia are key genera within the microbiome that facilitate a range of beneficial effects which include decreased risk of chronic disease and cancer, decreased inflammation, and weight loss.

Finally, the introduction of specific foods into the diet, such as those containing resistant starches, polyphenols, and soluble fibers, or supplementation with unique oligosaccharides like 2-fucosyllactose, HMO, and red polyphenols, can successfully bolster populations of Bifidobacteria and Akkermansia and, in doing so, improve overall health and wellbeing in both the short and long term.


Written by: Dr. Alexis Cowan, a Princeton-trained PhD specializing in the metabolic physiology of nutritional and exercise interventions. Follow Dr. Cowan on Instagram: @dralexisjazmyn



 Hui S, Cowan AJ, et al. Quantitative Fluxomics of Circulating Metabolites. Cell Metab. 2020;32(4):676-688.e4. doi:10.1016/j.cmet.2020.07.013

Chelakkot C, Choi Y, Kim DK, et al. Akkermansia muciniphila-derived extracellular vesicles influence gut permeability through the regulation of tight junctions. Exp Mol Med. 2018;50(2):e450. Published 2018 Feb 23. doi:10.1038/emm.2017.282

Rivière A, Selak M, Lantin D, Leroy F, De Vuyst L. Bifidobacteria and Butyrate-Producing Colon Bacteria: Importance and Strategies for Their Stimulation in the Human Gut. Front Microbiol. 2016;7:979. Published 2016 Jun 28. doi:10.3389/fmicb.2016.00979

Kumar Singh A, Cabral C, Kumar R, et al. Beneficial Effects of Dietary Polyphenols on Gut Microbiota and Strategies to Improve Delivery Efficiency. Nutrients. 2019;11(9):2216. Published 2019 Sep 13. doi:10.3390/nu11092216

Hasani A, Ebrahimzadeh S, et al. The role of Akkermansia muciniphila in obesity, diabetes and atherosclerosis. J Med Microbiol. 2021 Oct;70(10). doi: 10.1099/jmm.0.001435.

Longhi G, van Sinderen D, Ventura M, Turroni F. Microbiota and Cancer: The Emerging Beneficial Role of Bifidobacteria in Cancer Immunotherapy. Front Microbiol. 2020;11:575072. Published 2020 Sep 8. doi:10.3389/fmicb.2020.575072



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