All you know about Reflux is WRONG | 5 Surprising Facts

If you are new to this site, you should first read my How I Cured My Silent Reflux article as it explains the underlying root causes of acid reflux, its corresponding treatments, and provides the necessary context to follow some of the concepts in this episode.

Episode Transcript

(Note this is not a word-for-word transcription - it's loosely paraphrased. Alternatively, feel free to watch on YouTube).

Welcome to episode #4 of The Reflux Cycle show. My name is Don, aka The Acid Reflux Guy. In this episode we’re going to cover a few mind-blowing facts about the microbiome. 

The human microbiome is increasingly recognized for its roles in defense against harmful bacteria, viruses and toxins, for its role in nutrition absorption, and modulating our moods and behavior. As, shares it:

  • It defends against harmful microorganisms.
  • It teaches the immune system to tell friends from foes.
  • It degrades toxic compounds.
  • When the gut microbiota breaks down dietary fiber, it produces important molecules (e.g., short-chain fatty acids) 
  • It facilitates absorption of dietary minerals (e.g., magnesium, calcium and iron).
  • It synthesizes some essential vitamins (e.g., vitamin K and folate (B9)) and amino acids (i.e., the building blocks of proteins).
  • It produces and converts hormones that can shape mood and behavior.  

It’s clear that the microbiome is essential for health but, how far reaching is the microbiome and just how essential it is for health? These are precisely the types of questions the Human Microbiome Project aimed to enable scientists to discover.

The Human Microbiome Project was launched by National Institutes of Health with a budget of 5 years $160M, and a remit to create and discover the roles of microorganisms such as bacteria, fungi, protozoa and viruses in human health, nutrition, immunity and disease.

The study characterized 300 healthy volunteers and focused on studying microbial colonies in five body areas: skin, mouth, nose, colon, and vagina. References:

I wanted to open with that info, because similar to the human genome project the human microbiome project has helped to build a foundation that I believe is poised to revolutionize medical science and help people like us who have suffered with digestive and autoimmune diseases that are driven by challenges with gut health.

With that background, I want to cover 5 amazing facts about the human microbiome that I have come across in my ongoing research. I’ve pulled together tidbits from several sources across

  • Medical research:
    • European Society of Neurogastroenterology & Motility
    • Viome
    • US National Library of Medicine
    • Live Science
    • University of Michigan Microbiome Project
    • Book The Microbiome Solution
  • And pop culture such as:
    • Business Insider
    • BBC

As always, links to all the materials in the show notes.

1. Pound for pound, the cells in our body are more than 99% human. Gene for gene, however, our bodies are more than 99% microbial. 

The human genome contains about 23k genes. In contrast, our microbiome encodes more than 3M genes that proces thousands of metabolites essential for our bodies to function

In fact, with trillions of microbes in a single human body there are more microbes in you than there are stars in our own milky way galaxy

So in fact, 99.9% of the unique genes in your body are bacterial, and only about 0.1% are human.

This goes to show you why the microbiome plays such a key role in converting the information found in food into what makes you, you

2. Antibiotics are like a nuclear bomb for your microbiota. Yes, they kill the bad guys, but there is collateral damage

Don’t get me wrong. Antibiotics play a key role in combating serious infections and increasing our life expectancy. That said, if we fully understood the impacts to our metabolism and immunity we would use them as a last resort, and only after natural alternatives proved unsuccessful 

Antibiotics have been implicated in numerous studies to change the microbiomes composition, potentially leading to dysbiosis, which is an imbalance in the gut microorganisms

Consider this: It takes 1 million organisms of salmonella bacteria to infect mice that have normal microbiomes.  After a single dose of antibiotics, it took only 10 organisms to infect them. That is a one hundred thousand-fold difference.

Your own digestive issues may have their roots in antibiotics taken as a child. Ear infections, for example, are usually viral but are often treated with antibiotics just in case. A study published in the journal pediatrics found that pediatricians prescribe antibiotics 62% merely because parents expected it. Consider this:

The highest prescription rates are for children under the age of two: According to The Michigan Microbiome Project an average 1,365 courses per 1,000 babies.  This means that the average American child received nearly 3 courses of antibiotics in his or her first two years of life. They go on to receive, on average, another 8 courses over the next eight years.

According to The Book, The Microbiome Solution “The average American child will receive more than a dozen courses of antibiotics before they reach college, primarily for minor illnesses that require no treatment at all.”

Among other things, this promotes obesity, metabolic abnormalities and/or autoimmune diseases. We see this in farm animals, as antibiotics are routinely given to enhance growth and weight gain

In fact, A 1990 report indicated that 30-90 percent of milk samples had detectable antibiotics, especially sulfa drugs and tetracycline.

So while you may be in the minority that haven’t taken antibiotics, you may be getting a low, albeit regular dose of antibiotics through the food supply

3. Many bacteria traditionally considered bad, can play beneficial roles in our guts

According to, The “bad guys” that aren’t all bad – We were too quick to label certain bacteria like E. coli “bad guys.” Only to find out that we actually need them on some levels and in some locations within our gut.  E. coli actually helps stimulate regeneration of the gut lining, making the digestive tract healthier. The underlying conclusion of gut microbiome research is that it’s all about balance.

I want to read an interesting excerpt from

”Consider Helicobacter pylori, the bacteria responsible for causing stomach ulcers. The bacteria were once found in the majority of the population, but their prevalence has steadily been decreasing, and today only about half of the world’s population has it. Most of them do not have symptoms, but a small number develop painful ulcers in an acidic part of the digestive tract (a finding that earned a Nobel Prize in Medicine in 2005). Helicobacter infections are treatable with antibiotics, but there’s a twist: Blaser and colleagues have found the absence of Helicobacter appears to be associated with diseases of the esophagus, such as reflux esophagitis and certain cancers of the esophagus. In other words, Helicobacter may be bad for our stomachs, but good for our throats. Though not all scientists agree, “There’s a big body of evidence that Helicobacter has both biological costs and biological benefits”

Again, it’s all about balance:

Feel like you've done all the things and are just not seeing progress? I've helped a lot of people over the years that felt the same way. Perhaps an at home microbiome test can help break the cycle and provide the insights you need to move froward. With it, you can test your gut microbiome and receive actionable recommendations on how to optimize your digestive health with the BIOHM Gut Report.

I have arranged a 20% discount if you use the code THEACIDREFLUXGUY at checkout!

4. Humans are 99% similar in their DNA, but not in their microbiomes

While your DNA is 99% similar to any random person you pass on the street, your microbiome isn’t. It most closely resembles your mothers and other individuals you spend the most time with, such as siblings going up

“This is because the initial colonization of gut microbes comes from birth. Long before we enter the world our mother’s microbiome starts to prepare for our arrival. Just prior to birth, pregnancy cells in the birth canal ramp up production of a carbohydrate called glycogen, sending glycogen loving Lactobacillus bacteria into a feeding frenzy and increasing their numbers.” – The Microbiome Solution

Subsequently, the baby drops into the birth canal and turns so that it gets a mouth full of this slurry on the way out. So in early life, the infant born vaginally acquires bacteria resembling its own mother’s vaginal and fecal microbiota. 

Afterwards, breast milk delivers live bacteria and a variety of complex carbohydrates that cannot be digested by babies. Instead, these carbohydrates act as prebiotics by nurturing the bacterial composition in the baby’s gut.

It is truly amazing to me that people believe this incredibly complex symphony of interactions is a result of anything but God’s design.

In contrast, babies that are born via c-section are bathed in skin microbes from the doctors hands or in whatever is lingering in the hospital room. Similarly, those that are bottle fed have an entirely different gut microbial composition.

Sadly, the rate of C-sections in the United States increased from one in five births in 1996 to one in three births in 2011–a 50% increase. It’s just a matter of convenience for the doctor.

To make matters worse, 40% of women are given antibiotics during childbirth. At a minimum, American babies receive an antibiotic immediately after birth in the form of eye drops to prevent a very rare infection called gonococcal ophthalmitis.

5. Like tree rings, the microbial community in your gut can tell scientists if you are overweight

Looking at the composition of your gut microbiome, researchers can tell with 90% accuracy whether you’re overweight or lean. This has fascinating implications because we know that the microbiome is essential to metabolism through harvesting and storing energy.

In fact, up to 15 percent of the calories present in your food are extracted by bacteria in your colon and used to feed you.

In one study, researchers analysed the blood plasma and stool samples of 600 obese and non-obese people, and found 19 different metabolites linked to four types of gut bacteria that could lead to weight gain, including glutamate, linked to obesity, and branched chain amino acids, associated with higher insulin secretion and risk of type 2 diabetes and cardiovascular disease.

In another study, participants went on a lower-calorie diet high in fruit and vegetables, and some didn’t lose as much weight as others. Analysis of their gut bacteria found participants had different levels of two particular types of bacteria. In those unable to lose weight, certain bacteria were able to break down carbohydrates and use their energy more effectively. That higher energy extraction translates into weight gain and retention

Of course, we covered in episode 001 that fecal microbiota transplant research shows that transferring microbial communities from one host to another can cause a thin recipient to gain weight and a heavy recipient to lose weight

I have seen first hand the positive effects of a balanced gut on my own weight. If you want to get a good laugh, go to my youtube channel and compare my weight just after healing my reflux (from my early videos) to now, more than a year and a half later. I have lost some serious weight, just by healing my gut. This, despite already being pretty thin. 

Disclosure: This is a free website so I do advertise to cover the costs of website hosting and other services. If you find the information on this site useful, please consider making a purchase using the following links as I will earn a small commission at no cost to you.

Wrap Up

I hope the material we have covered has been eye opening to you and can perhaps provide some clues as to the risk factors that contributed to your gut health challenges

Links to all the materials I referenced are available in the show notes or by going to

Remember, before you try any reflux remedy, be sure that you can explain how it helps to get you off of the reflux cycle, by addressing the underlying causes of reflux. If you can’t, consider looking into it further, before putting it in your body.

If you want to know more about ways that I addressed my reflux then you can go to or check out my book, ‘How I Cured My Silent Reflux

My name is Don Daniels aka The Acid Reflux Guy and this was another episode of The Reflux Cycle show. Signing off.

I do need to remind you that the information included in this show is for educational purposes only and is not intended to be a substitute for medical treatment by a healthcare professional. Because of unique individual needs, listeners should consult their physician to determine the appropriateness of the information for their situation.

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Don is a best selling author of 'How I Cured My Silent Reflux,' and a former acid reflux sufferer for more than 15 years. With several family members with the disease, and a medically diagnosed hiatal hernia he resigned to the fact that he would take acid blockers for the rest of his life. Dissatisfied with medical advice, he researched the root causes of acid reflux and by solving them was able to eliminate his acid reflux for good!
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