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10 Microbiome Basics-- A Primer For The Beginner Looking To Optimize Gut Health

Guy Daniels

You hear the buzz word “microbiome” in the news regularly, but you don’t know what it is and why it matters to your health. Look no further! This brief primer is an easy read to get you updated on the latest well-known information about a vital aspect of our body—the gut microbiome.

1. The gut microbiome is loaded with bacteria!

Although we have bacteria and other microscopic critters all over and in our bodies when you hear the term microbiome, it’s typically referring to the bacteria in our gastrointestinal tracts, and even more specifically in the distal ileum (the end of the small intestine) and the colon (the large intestine). Their count is estimated to outnumber our cells by a factor of 10, and their genome by a factor of 100.

The reason why the term “microbiome” may be unfamiliar to you is that it’s a relatively new one, both in the general community and with conventional medical practitioners. However, within the world of scientific research, the term is nothing new, but due to relatively recent technological advances, our knowledge has exploded in the past dozen or so years. 

2. It’s all about balance.

“And why are the bacteria (and others) in my belly so important to my health?” you ask. Simply put, there is a tremendous amount of data linking the microbiome to both disease and health, depending on the balance. 

Here’s an example that seems to resonate with people: When researchers take the human microbiome from someone who has autism, depression, obesity, IBS, dementia, or just about any condition you can imagine, and they transfer it into an animal model-- usually a rodent-- the animals invariably develop those conditions! So, what is going on?

3. Your future starts at birth!

Our future health is, in part, determined at birth. Two-thirds of babies born today are delivered via vaginal delivery, and assuming the mother is in good health, the baby gets a healthy initial inoculation of bacteria in this process. However, one third aren’t as fortunate and are delivered via cesarean (C-section) delivery. Their gut inoculation is quite different, which predominantly includes bacteria from the skin and hospital rooms. Research shows a C-section delivery is associated with an increased future risk of many adverse conditions, directly or indirectly and to different degrees, including autism, obesity, asthma, allergies, celiac, gastroenteritis, systemic connective tissue disorders, juvenile arthritis, inflammatory bowel disease, immune deficiencies, leukemia, and type 1 diabetes.

Now we consider breastfeeding. Breastfeeding is so important that the American Academy of Pediatrics recommends exclusive breastfeeding for at least the first six months of life no other foods. The reasons for this are that it’s the ideal food for an infant, it’s better to delay the introduction of potentially problematic foreign proteins into an immature gut, and the infant's microbiome needs to be established. 

The best way to illustrate the importance that nature places on our microbiome is the fact that the third-largest solid component of breast milk, called human milk oligosaccharides (HMOs), is exclusive fuel for the microbiome. We cannot digest HMOs, as we do not possess the enzymes to utilize them, but the good bacteria in our guts do. Think about what nature is telling us: in times of feast or famine, the mother is dedicating an enormous amount of her energy to producing fuel, not for her baby, but the bacteria inside her baby’s belly. If that doesn’t illustrate the importance, I don’t know what does. 

4. Our microbiome is continually reshaping.

As we live our lives, the bacteria in our guts take a hit. The two biggest offenders are poor diet and antibiotics. Antibiotics are important and essential, but their overuse is harmful to our microbiome. Data shows that following antibiotics, especially multiple rounds, bad bacteria thrive more so than good bacteria. 

This leads to perhaps the most important concept when it comes to the microbiome: the opportunistic pathogen. We define opportunistic pathogen as, “although a normal inhabitant of the healthy human gut microbiome, when given the right environment, it thrives; by its troublesome nature, it can promote health problems for the host (us).”

Let’s take the best example we can use, that of a C. diff infection—not a diagnosis you want. So why is a C. diff infection a good example of an opportunistic pathogen? Well, the word “infection” is a bit of a misnomer. It leads you to believe that you acquired this “infection” from someplace. However, data shows that virtually 100% of all healthy adults have detectable levels of C. diff in their gastrointestinal tracts. So, it’s already there. And even the CDC states that “most cases of C. diff occur when you’ve been taking antibiotics.” When we change the environment in the gut, bad bugs have an opportunity to thrive and create havoc. 

C. diff is not the only opportunistic pathogen. E. coli is another recognizable example, but there are many others. It’s not just one bad bug at play, but an overall balance. When more bad bugs are thriving than good bugs working for us, the environment is considered dysbiosis

6. The environment of your gut dictates what survives and thrives. 

Good bugs have two basic benefits, direct and indirect. A direct benefit is when they “plugin” to our cells, and drive healthy responses, such as dampening inflammation, which is at the center of so many conditions. The indirect benefit is a result of the byproducts of the fermentation of their favorite foods, which is generally a plant fiber (from here on prebiotic). They produce short-chain fatty acids (SCFAs), which are highly beneficial, particularly butyrate, but also propionate. These SCFAs, in turn, make the pH of the gut more acidic, thereby reducing bad-bug activity and proportionately increasing good-bug activity. 

The fuels that make it past our absorptive capacity in the upper GI are fuels for the bacteria down lower. And their fuel depends on what you eat and what you digest. Bad bugs tend to like a higher pH, higher animal protein and fat diet, whereas good bugs prefer a lower pH (acidic) and a diet rich in plant fiber. 

7. Prebiotics are the best choice to rebalance your gut.

You’re familiar with probiotics, and you may be thinking that they should do the trick to rebalance your gut. They can help, but it’s not that simple. 

First, you can drive numerical change far better with appropriate doses of prebiotics than you can with the mere counts in these probiotic products. Second, lactobacillus, as a genus, is not always a good idea, and the data shows that, often, it’s associated with a variety of unhealthy conditions. Third, and possibly most important, the available probiotics represent species from only three genera within the gut. There are many other bugs in the gut that are highly beneficial, which are not available in probiotic products. However, these highly beneficial species can be significantly increased when you feed the lower gut with their favorite fuels: prebiotics.  Not only can that correct dysbiosis, but more importantly, it can support the antiinflammation process and fix leaky gut.

8. Dysbiosis can affect your whole body- not just your gut. 

Our incredibly complex GI tract covers a surface area of about 400 square meters, requires about 40% of our energy, and is lined by only a single layer of cells, which turn over about every five days. This enormous single-celled border is connected by what is called tight junctions. However, bad bacteria possess the ability to adhere to and invade the cells themselves and disrupt these connections. When that happens, 70% of our immune system, which lines our gut goes into high alert. 

Whole bad bacteria and their inflammatory components like endotoxin (LPS) can go systemic in the body, and with a subsequent series of immune-mediated inflammatory events, bad things can happen. The scientific literature has shown dysbiosis to be one common underlying factor associated with many conditions, including autism, metabolic syndrome, obesity, autoimmune disease, heart disease, dementia, anxiety and depression, non-alcoholic fatty liver disease, non-alcoholic steatohepatitis, and other conditions. This means dysbiosis goes far beyond the apparent connections to irritable bowel syndrome (IBS), Crohn’s Disease, and Ulcerative Colitis--  all of which there are plenty of data. 

9. Gut microbiome sequencing technology advancement has allowed for more precise health intervention. 

Historically, practitioners may not have been aware of these concepts until more recently, when the research and technology have progressed enough to identify the core taxonomy and principles of the gut. However, up until now, even the professional approach to solving gut health has been a bit of trial and error, combining the art and science of medicine, tests with general identification, dietary restrictions, and some pre- and probiotics. This combination can work, but it often takes a few doctor’s visits, additional tests, food restrictions, and re-evaluation of symptoms. 

The advanced metagenomic sequencing technology of whole-genome shotgun sequencing can identify every microorganism to pattern a patient’s gut composition; this is the same technology Onegevity uses. 

As a team of scientists, we at Onegevity are focused on healing the gut-- and fast! We’ve learned many customers are tired of trying and failing, fed-up with unnecessary food restrictions, and have exhausted their options with undetectable tests and a plethora of professional specialists. We are here to help save time, money, and effort so you can go back to being the best you.  

10. Microbiome testing has extended beyond the doctor’s office or research lab-- You can do it at home!

Microbiome analysis is extremely complex, but Onegevity can make it simple. A convenient Gutbio at-home kit can yield remarkable insight into one’s microbiome. Although our microbiomes are all unique, there are roughly 40 taxa, both good and bad, to keep your eyes on. And although the total microbiome possesses thousands of enzymes in total, each species may only have the genetic capability to snip one or a few bonds. Diversity of the microbiome means diversity in the choice of prebiotics. And knowing exactly which pre or probiotic to choose is key--as the wrong one could worsen constipation or other symptoms. 

As this science is rapidly evolving, we learn something every day. We feel confident we’ve combined the right technology, all the research, and using artificial intelligence, have designed the best recommendations to make drastic improvements in people’s lives.