How to Improve Gut Microbiome Health: Development from Infant to Adult

June 7, 2023

The first bacteria you take on as an infant can have a lasting impact on your health, and could make the difference between you contracting a chronic illness or not.  

The human microbiome remains, for the most part, a huge mystery to doctors and scientists. The sheer amount of microbial material in our bodies far outnumber the human cells, meaning there is still a lot to be uncovered about the composition of the microbiome.

As it turns out, some of the biggest clues might lie in the development of the infant microbiome. And thanks to researchers, led by Dr. Jens Walter, at the University of Alberta, there is new insight into how the microbiome is developed. The team at U of A found that the first bacteria to colonize our bodies have a lasting impact on our microbiomes and how they are structured, and may be an early factor in whether one develops a chronic illness or not.

How the microbiome develops and how that can lead to chronic illness is complicated, but we’ve outlined the main things you need to know below:

  • The first bug runs the deepest: infant microbiome development
  • How microbiome health can cause chronic illness
  • How to improve gut microbiome health
  • Other great resources for learning about the Microbiome and FMT treatments

The First Bug Runs the Deepest: Infant Microbiome Development

Our microbiome, not unlike our fingerprint, is unique to us. It is made up of millions of bacteria, fungi, protozoa, and viruses, and no one in the world has a combination that is one in the same - not even identical twins. Our microbiomes are not easily duplicated, and as it turns out, not easily changed.

Research has already determined that our microbiome doesn’t develop much beyond the first years of our life, and that lifestyle and environment factor for less than 30% of microbiome makeup; what you start with is more or less what you have for life.

The microbiome begins its development at birth. A child is brought through the birth canal, exposing them to vaginal microbiota that will become their first bacteria. As their exposure to the world outside continues, they collect more bacteria, gradually building what will become their microbiome.

There is new insight into exactly how the microbiome is developed, and what impact that has on us later in life:

How and When the Microbiome is Developed

The development of the microbiome in humans is mostly complete within the first few years of life, and it is now thought that how it is formed has long-lasting effects. The 2013 University of Alberta study performed on mice found that the first microbes introduced into the gut were consistently the most prominent later on. The study outlines that the order in which microbes enter the gut directly correlates to how they survive and thrive in the body.

This means that your whole life could be impacted by one single bacteria entering your system mere days earlier than another. For instance, if the first microbe that enters you is the one found to be associated with weight gain, you are more likely to become obese than someone who is introduced to that same microbe later in the process of their microbiome development. The same goes for the multitude of bacteria that scientists suspect have strong associations with certain chronic illnesses.

So how exactly do these microbes get into the body in the first place? Where are our first microbes coming from?

From Birth to Beyond

We inherit a lot of our initial bacteria from our mother through vaginal childbirth. The importance of this inheritance has been shown in an NYU study looking at the effects of brushing newborns born through C-section with the birthing fluids from their mothers to provide them with the bacteria their vaginally birthed counterparts would get.

The many benefits of vaginal birth have long been appreciated; research has shown that babies born by c-sections were found to have less bacteroids than those birthed vaginally, and were more often found to be colonized with the deadly bacteria Clostridium Difficile. Additionally, Babies fed exclusively with formula were also found to be more likely colonized by C. difficile and E. coli microbes over those who were breastfed.

The immediacy of colonization of an infant's microbiome has been known to be important, but until now, the long term impacts of our earliest microbial exposures have not. So, if the bacteria you receive first has the highest likelihood of thriving and multiplying in your body, then being colonized by C-diff early on is probably a good predictor of gut issues down the line. This development of early microbes goes for any other potentially harmful bacteria as well, this is why our infant microbiome might be at the core of chronic illnesses people develop later in life.

How microbiome health can cause chronic illness

Stomach bacteria

When it comes to chronic illnesses it’s hard to know how or when you contracted it. In fact, it’s one of the most frustrating things for those with chronic disease, and those who treat it.

It is widely appreciated that there is a connection between the microbiome and chronic inflammatory diseases, but the specifics of how or why the microbiome is affecting the body in such a way is still to be determined. The discovery that these microbes might set in very early in life, is a step in the direction of cracking the code. This is the main research that has already been completed:

Microbiome and Disease: how improving microbiome health cures illness

The connection between the microbiome and health is still being researched. Many of these studies are attempting the manipulate the microbiome, using FMT (explained below) and other methods. So far, it is working to treat diseases such as Colitis, Autism and Parkinson’s Disease. In fact, Dr. Majdi Osman, from OpenBiome, says that they are currently “supporting trials looking at Inflammatory Bowel Disease, Metabolic Syndrome, peanut allergy, and even looking at things such as Multiple Sclerosis and Anorexia.”

When we spoke to Dr. Thomas Borody, he told us about his successes treating both autism and Parkinson’s using FMT. “We've done a couple of patients whose Parkinson's markedly disappeared with FMT,” said Dr. Borody. He added, “People have been asking what the connection is between Parkinson's disease and the microbiome and the flat simple answer is, we don't know. But there are lots of clues.” Though, the connection is not concrete yet, there has been success in treating patients using microbiome manipulation techniques. However anecdotal, it shows that the connection is far beyond speculation at this point. While we are trying to figure out how to manipulate the microbiome for the better, through practices like FMT, there are factors that can disrupt it for the worse.  

Dysbiosis of microbiome and later life disruptions

A healthy microbiome provides many benefits and can help stave off bad bacteria to keep you from getting sick. As studies have shown, there are many early life factors that can cause you to have an unreliable microbiome, but there are also circumstances later in life that can put your microbiome into a bad state.

When the microbiome becomes unbalanced and the good bacteria that normally keep it balanced dissipate, something known as dysbiosis happens. Dysbiosis is what happens when the microbiome is disrupted by something environmental. Diet, stress, pollution, and antibiotics for example can all affect your microbiota and send your microbiome into dysbiosis, which could onset chronic illness and other serious health issues.

The effects of this have been seen in people who have taken Accutane in their teens to treat acne, only to report severe repercussions of such heavy antibiotic use later on. There is a class action lawsuit of people who have taken the antibiotic medication and, as they claim, later developed Ulcerative Colitis as a result of its use. There seems to be a correlation between the overuse of antibiotics and the rise of Chronic Diseases as a whole.

In an interview with Mark Smith, OpenBiome CEO,  he noted that “As japan started to adopt … western dietary practices, and antibiotic use, you suddenly saw this massive epidemic of ulcerative colitis in a population that previously hadn't really experienced it.” Associations like are are leading experts to view the overprescription of antibiotics as a major public health threat.

So, the microbiome can be placed out of whack, but does that mean you become a lost cause if this happens? There are some ways in which scientists and medical practitioners are trying to reverse some of this dysbiosis, and put the microbiome back in good standing.

How to improve gut microbiome health

The research into microbiome development has furthered interest in the manipulation of the microbiome and how we might be able to use manipulation tactics to ward off illnesses associated with it. In the future, manipulating the microbiome may not just be used for treatment of chronic illnesses, but also for prevention of chronic illness, whose bacterial associates might become easier to pinpoint and eradicate - potentially allowing scientists to adjust the microbiome for optimal bacterial composition, straight out of the womb.

“Having long-term persistence of microbes when they colonize in the gut early in life means that a health-promoting biome could potentially be established by introducing beneficial bacteria straight after birth,” says Dr Jens Walter. The later life manipulation of the microbiome through practices like FMT is already gaining popularity for treatment of chronic illness.

What is FMT and how does it treat chronic illness?

Fecal Microbiota Transplants (FMT) involves the insertion of stool from a healthy individual into the gut of an ill patient, in order to improve gut microbiome health and diversity. The idea is that the healthy bacteria will be able to stave off the bad bacteria in the gut.

The gut altering practice is beginning to be explored as a treatment for chronic illnesses associated with the microbiome, but it has its limits. Though it might work as a treatment to fight off invasive and bad bacteria, it’s not likely to be a complete cure. “I like to think of it more like a band-aid approach where you're providing functions to allow the body to work properly, to recover,” says Dr. Emma Allen-Vercoe, a professor and researcher of molecular and cellular biology at the University of Guelph. The best hope still might be starting early and practicing preventative medicine, rather than treating a disease once it is in full swing. And for that, targeting further research on the development of the microbiome will be key.

Other great resources for learning about The Microbiome and FMT treatments

For now, understanding the microbiome better in all aspects and treating it with procedures such as FMT is the best science has to offer. There is still a lot of work to be done to build the perfect microbiome. Dr Jens Walter says “I think in 30 or 40 years we’ll be able to colonize infants with specific bacteria we know are health-promoting and shape the microbiome in a beneficial way” - setting up peoples microbiomes to be resilient and balanced for life.

If you’re interested in learning more about this process, these great articles can help you along the way:

Fecal Transplant Treatment for C Diff: Successes, Risks, and Rewards

Fecal transplants are an incredibly safe and effective treatment for C Diff infections. Learn more about how this treatment works.

Three Distinct Stages in Infant Microbiome Development Identified

Scientists reveal  three stages in the development of the microbiome of infants, and how that can affect long-term health development.

How Long Does it Take for Your Gut to Recover After Antibiotics?

Parts of the microbiome might not fully recover after the use of heavy antibiotics. Learn about how long this period lasts, and how you might be affecting your body with antibiotics in unexpected ways.