Try Total Gut Health for free! Try Total Gut Health for free! LEARN MORE
Gut Health – It All Starts with Gut Bacteria

Gut Health – It All Starts with Gut Bacteria

August 15, 2016
Updated October 1, 2019
Category: Nutrition
Tags: Digestion

In the last year I’ve been on over 50 planes, traveled 30,000 miles, visited traditional villages and cultures around the world and sat in on several of the latest medical research seminars.

It’s fascinating to me how often the philosophies and practices that I have encountered ultimately come full circle.

Case in point, gut bacteria.

While many different schools of health and performance have unique philosophies about how to reestablish harmony and ideal function in the human system, most modern practitioners of the health sciences are shifting some of their focus to ancient views – namely, that a healthy gut is the foundation of longevity and vitality.

For many this sounds pretty simple and straightforward, however this was overlooked in my Western medical schooling and was further neglected during my secondary psychiatric training.

The idea of the brain-gut bacteria connection has only been medically validated in the last couple of decades (huge props to Michael Gershon and his landmark book, The Second Brain), and many in the field are touting it as the “latest medical discovery.“

Ask most practitioners of alternative disciplines like Naturopathic, Ayurvedic or Chinese medicines (founded in thousands of years of evolutionary data and successful practice) and most will laugh at how long it has took for the Allopathic – aka Western medical – to catch on.

As a culture on the whole, we tend to think of gut bacteria as being responsible for “food in and food out.” While this is certainly true, the human gut is a bit more complicated and interwoven than that.

The Gut’s Role in a Healthy Body

One of its primary roles is the intake and digestion of food, as well as metabolizing and assimilating nutrients.

Additionally, research in modern medicine is now pointing to the idea that the Gut (aka the Gastrointestinal System) is integrally connected to most other systems – most notably the nervous, hormonal and immune systems.

For example, most of the immune system is located in the gut – about 70% of it – through something called the Gut Associated Lymphoid Tissue (GALT).

Many of the building blocks for neurotransmitters that drive mood, focus and mindset are processed and modulated in the gut, later to be transferred to the brain.

Similarly, the endocrine system – whose hormones govern metabolism, energy and reproduction – are also built through the digestive network in association with the liver.

When opening up the topic of the gut, there are tons of ways to go about discussing it and many associated factors.

We could talk about diet and idealized nutritional typing for each person at each stage of life, we could talk about Nutrigenomics – essentially the use of nutrition [in diet or supplement form] to address specific genetic weaknesses We could talk about food allergy markers and the potential association with a growing cadre of inflammatory conditions from autism to ulcerative Colitis.

We could talk about the process of detoxification of the whole GI system and the research supporting the health benefits… suffice it to say, there are plenty of topics related to the gut.

An Overview of the Primary Functions of the Gut

Gut Health – It All Starts with Gut Bacteria

Here, in the interest of covering the basics, we will focus on function and an overview of the main parts. To break it down, the gut has 3 major areas – the stomach, the small intestine and the large intestine – and it’s important to optimize each for the best overall function.

The stomach acts as the furnace of the GI system. It’s the “fire in the belly” that helps break down proteins, while also serving as the primary defense mechanism for the GI system through adequate hydrochloric acid (HCL) production.

This acid level helps to kill off the unwanted bugs we eat and drink through an acid potency, that when ideal can eat through steel.

It’s the associated burning sensation after food in the form of acid reflux that leads so many people to take antacids – which incidentally are in the top 3 medications on the market behind cholesterol meds and antidepressants.

However, for most people with acid reflux it’s not high acid that is the culprit, it’s low. The reason for the lowered acid levels in the stomach can vary widely, often ranging from infection (like H. pylori) to low “stomach chi” (chi means energy in Chinese medicine) to lower HCL production as we age.

In the second phase, the small intestine acts as the workhorse by taking care of 90% of digestion and assimilation of the food taken in.

It does this by receiving the food (aka chime) from the stomach, mixing in enzymes and bile salts to break down the carbohydrates and fats and churning it all through about 22 feet of intestinal tubing, whose surface area if stretched out would cover a full double’s tennis court.

When carbs and fats can’t be digested well, it leads to the undesirable and rather unfashionable gas that makes riding on airplanes and any other tight-quartered scenario less than joyous.

Lastly, the large intestine acts as the train depot, constantly receiving and dynamically balancing beneficial bacteria for the incredibly complex interplay with all other systems in the body, while absorbing water in order to bulk up the stool and ship it out of the body.

This microbiome (the population of all the microorganisms and their genetics in the large intestine) consists of more bacteria than stars in the sky and grains of sand on the beaches, and is the hottest topic in the fields of functional medicine, integrative psychiatry and peak performance right now.

How to Optimize a Healthy Gut

In just the last year we’ve seen the University of Leiden show that supplementing with probiotics (good bacteria for the gut) can decrease reactivity to low moods, i.e. improve depressive tendencies, and at Oxford University the use of prebiotics (the non-digestible fiber that serves as food for the good bacteria) lessening anxiety by lowering the reactivity to negative stimuli.

Who in the arena of modern medicine (and especially psychiatry) would have predicted twenty years ago we would be talking about gut support supplements as a potential adjunct or even alternative to medications?

It’s a testament to the rapid explosion in the arena of gut research that the word’s getting out and the various fields are coming together in consensus when it comes to healing… start with the gut and take it from there.


1. Probiotics: Leiden University

2. Prebiotics: Oxford University

3. Intestine as sensory organ – neural, endocrine and immune responses

The Onnit Research Team is comprised of medical professionals, researchers, and scientists interested in providing data-driven, actionable information.
Free shipping is offered on orders with a minimum subtotal of $100 less discounts. Free shipping is only available in the contiguous U.S. and excludes Fitness and Digital items.
For media inquiries please contact us at
With a subscription, you'll get your favorite Onnit products whenever you want at 15% off MSRP unless otherwise noted. All automatic, worry free, and with our same great money back guarantee.
Cancel or adjust your order at any time, hassle free. Your payment method will only be charged right before your order ships. The discount applied every time is 15% off MSRP (unless otherwise noted) or the current sale discount, whichever is greater. For more information, see the complete Onnit Subscription Terms & Conditions and Frequently Asked Questions.

Secure Shopping

We implement a variety of security measures to maintain the safety of your personal information when you place an order or enter, submit, or access any information on our website. We incorporate physical, electronic, and administrative procedures to safeguard the confidentiality of your personal information, including Secure Sockets Layer (SSL) for the encryption of all financial transactions through the website. We use industry-standard, 256bit SSL encryption to protect your personal information online, and we also take several steps to protect your personal information in our facilities. For example, when you visit the website, you access servers that are kept in a secure physical environment, behind a locked cage and a hardware firewall. After a transaction, your credit card information is not stored on our servers.