Meet Your Second Brain: The Gut Microbiome and Your Digestion

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If you’re an avid reader of the Viome blog, you might have read some interesting news about the gut-brain axis and mental health and behavior, but you might not realize how connected it is to normal digestion, too. The gut-brain axis is “bidirectional” which means messages and signals are sent both from the gut to the brain via the vagus nerve, and from the brain to the gut. That means, your gut microbes might be telling your brain what to eat, but your brain is also telling your gut when to start digesting and how quickly it occurs.1 The messages being sent to your GI tract are just as important as the ones being sent from it – but these interactions may affect you in several different ways.

From the tip of your tongue…

The moment you put food in your mouth, your body immediately, and rapidly, responds by releasing enzymes, a type of digestive protein that degrades starch and sugar. As soon as you start chewing, a series of mechanical and biological processes begin breaking down your food. Your teeth grind together to tear each component into small pieces, ripping apart difficult to digest proteins and carbohydrates until they pass down into our stomach through our esophagus. From there, our stomach makes up the brute force of digestion by sensing food that enters it and releasing the hormone gastrin, used to communicate to parietal cells in our stomach lining to release highly acidic gastric juice supported by the powerful aid of hydrochloric acid.2 Man, that’s a mouthful – pun intended.

Our stomach produces over 6 cups of gastric acid per day, which is at the same pH as lemon juice (putting it at a pH of 2!).2 Imagine everything you’ve eaten in a day soaked in a giant bowl of pure lemon juice: that is some potent degradation power. (If you can’t, consider this: lemon juice contains only about 8% citric acid, which 10,000 – 100,000 times more acidic than water!3

That is a miracle of biology in itself – something I bet you never thought of before – and yet it doesn’t break our insides down. How is that? Because our body performs amazing balancing acts to help neutralize this acidic pH. When it comes to digestion, this balancing trick takes the form of bicarbonate produced in our pancreas  – the basic counterpart to our gastric juices that immediately neutralizes the acidic, digested food entering our small intestine after the stomach has done its work.

Once our food is neutralized, then we can begin the process of absorption : this is where our digestive tract shines and the gut-brain axis takes over. Our liver begins secreting bile acids, and in conjunction with the pancreatic juices and bicarbonate – our body begins subtly finishing the digestion process and switching to absorbing whatever has been broken down and passing into our bloodstream and lymphatic system for energy, building blocks, and everything else our food gets turned into. Our digestive tract motility – or the movement of our gut that helps pass digested food through it for absorption – is controlled by the gut-brain axis. With a perfectly healthy connection – this whole process from your mouth to the end of your colon can take around 24-72 hours.4

But… what about our gut microbiome? Where does that come in?

Gut Microbes: they've got your digestion’s back

No matter how efficient our body is, and what a natural, physiological miracle it is, we can’t digest everything we eat. Whatever finally gets passed down to our large intestine is fair game for our gut microbes. In many ways, their activity helps provide beneficial nutrients we couldn’t gain access to through normal digestion. This remaining food also feeds and supports many gut microbes that have beneficial activity influencing our immune system, intestinal lining health, and fighting against foreign invaders. That is, assuming, you’re eating the kinds of foods that support a healthy gut microbiome.

But sometimes, we end up consuming foods that not only do we find difficult to digest, but they support opportunistic microbes lying in wait, or disrupt and harm beneficial microbes we rely on. Sometimes, they can take microbes that normally function to help us, and switch them to doing activities that actually harm us. What’s more – without the proper digestion pathway mediated by a healthy gut-brain axis, food components we should have been able to break down find their way into our large intestine intact, potentially wreaking havoc on our gut health.

The disruption of normal functions from our gut-brain axis have been incriminated in several gastrointestinal issues.5 Conditions such as Inflammatory Bowel Syndrome may have their cause in a disrupted gut-brain axis. Historically, IBS has been termed the vague category of gastrointestinal dysfunction, meaning, “We aren’t sure why you’re having GI upset, but it’s certainly there.”

“But you don’t look sick”

There can be a number of factors that impact a diagnosis of IBS, including environmental factors, stress, diet, and food sensitivities.6 Some scientists have even determined that microflora imbalance may be influencing how well messages are being sent via the gut-brain axis by causing our intestinal lining to become more permeable.6

Some researchers even suggest that these factors inducing gut flora imbalance may be muddling the messages between the gut and the brain by changing the length of time of our digestive motility.6 This means more foods may be entering the large intestine undigested, leaving our gut microbes a feast that can result in painful consequences like occasional gas, diarrhea, constipation, bloating, or even just GI discomfort. It also seems that IBS diagnosis is on the rise with 12% of Americans having received a diagnosis of IBS at least once in their lives.7 Unfortunately, determining the exact source of the issue is a clinical nightmare for patients and their healthcare practitioners alike. The cause could be just about anything which translates to a trial-and-error type of dietary assessment which often results in a level of frustration, coupled with truly uncomfortable issues, that can disrupt even the simplest aspects of daily life.

IBS can be the difference between leading a free and happy lifestyle and someone closing themselves off from the rest of the world, living in fear of their next meal.

No person living with IBS has the same cause, nor should they be treated the same. Changes in how we assess our gut health can mean more than just cleaning up your diet – it can mean the freedom to go back to living. It means feeling confident about your body, traveling, socializing, and eating. It means regaining control of your life.


1. Carabotti M, Scirocco A, Maselli MA, Severi C. (2015). Annals of Gastroenterology. PubMed Central.
2. Ma T, Verkman AS. (1999). The Journal of Physiology. PubMed.
3. Penniston KL, Nakada SY, Holmes RP, Assimos DG. (2008). Journal of Endourology. PubMed Central.
4. Metcalf AM, Phillips SF, Zinsmeister AR, MacCarty RL, Beart RW, Wolff BG. Gastroenterology. PubMed.
5. Martin CR, Osadchiy V, Kalani A, Mayer EA. (2018). Cell Mol Gastroenterol Hepatol. PubMed Central.
6. Menees S, Chey W. (2018). F1000Research. PubMed Central.
7. Weaver KR, Melkus GD, Henderson WA. (2017). The American Journal of Nursing. PubMed.