Science of Cacao: Gut Microbes — What Happens After Digestion
Updated: Oct 21
What Happens After Digestion
Cacao’s chemistry continues to change after you swallow it.
Some of its compounds are absorbed and transformed early in digestion. Others reach the large intestine, where resident microbes can break them down into smaller molecules. Some of those newly formed compounds can then enter circulation.
This interaction runs in both directions: microbes transform cacao compounds, and cacao flavanols can influence certain microbial populations. [1, 2]
At a glance
Gut microbes can transform cacao compounds into smaller metabolites.
Researchers also study how cacao flavanols affect microbial populations.
A change in bacterial counts alone does not establish a health benefit.
A second stage of transformation
The microorganisms living in the intestine possess enzymes that can act on food compounds reaching them.
For cacao flavanols, this can involve breaking apart their chemical ring structures and producing smaller substances called metabolites. Researchers have identified products including phenyl-γ-valerolactones and various phenolic acids.
The names are complicated, but the principle is straightforward: a compound in cacao can become several different compounds as the body and its microbes process it. [1]
Following one flavanol through the body
In a 2016 human study, researchers used a labeled form of epicatechin to track what happened after ingestion.
They found that gut microbial activity played a major role in its metabolism. Much of the absorbed material appeared after microbial breakdown in the lower intestine.
This helps explain why measuring the original flavanol alone gives an incomplete picture. Researchers also need to identify its metabolites, establish when they appear, and investigate what they do at the concentrations actually present in people. Finding a metabolite demonstrates exposure; establishing its effects requires further experiments. [1]
Can cacao change the microbial community?
A small human trial published in 2011 investigated that question.
Twenty-two healthy adults consumed cacao drinks providing either 494 milligrams or 23 milligrams of flavanols daily for four weeks. After a break, participants switched to the other drink, allowing researchers to compare both conditions within the same people.
The higher-flavanol drink increased the measured populations of bifidobacteria and lactobacilli relative to the lower-flavanol drink. Researchers assessed these changes using stool samples.
The result supports the idea that cacao flavanols can influence selected gut bacteria. Its scope remains specific: a small group of healthy adults, particular drinks, measured flavanol amounts and four-week treatment periods. It does not establish that every cacao serving produces the same changes or treats digestive symptoms. [2]
Does that make cacao a prebiotic?
Prebiotic has a specific scientific meaning. A substance must be selectively used by microorganisms in the body and provide a demonstrated health benefit.
Changing bacterial counts is one piece of that evidence. Researchers also need to establish the benefit and its connection to microbial activity.
That is why prebiotic potential is useful wording for this area of cacao research. It recognizes the findings while leaving room to determine which preparations, amounts and outcomes meet the full definition. [3]
Two questions worth keeping separate
When reading research about cacao and the gut, look for which question the experiment addresses:
What do microbes do to cacao compounds? This concerns chemical transformation and the metabolites produced.
What do cacao compounds do to microbes? This concerns changes in microbial populations or their activity.
Both help explain cacao’s journey through the body. Together, they show why understanding a food involves studying the interactions that begin after we eat it.
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