The Gut Microbiome: Symbiosis in Nutrition

Updated: Jan 4

neonatal nutrition and microbiome

An introduction to nutrition from a metabolic perspective

First, a disclaimer. I am not a microbiologist. I am a clinical chemist who seeks to understand our body chemistry (metabolism) through the analysis of essential biochemicals (metabolites) in blood.

Most of my career I used that analysis in the screening of newborns for inherited metabolic disease using a technology known as tandem mass spectrometry. Metabolites such as amino acids, the building blocks of proteins, can be measured from a few drops of blood from newborns using that technology. My years of screening experience showed that one subset of newborns, the very premature infant, had an unusually high rate of false alarms.

Those infants, usually in the neonatal intensive care unit (NICU), were metabolically immature, were treated with high dose nutrition intravenously, and were subject to all kinds of clinical intervention. It became clear that many of the false results were due to the practice of nutrition to encourage health and rapid growth. That led to my interest in the impact of nutrition on metabolism from intravenous amino acids solutions and enteral formulations (human breast milk, infant formulas made from cow’s milk, and human or bovine fortifiers). What became evident was the complexity of how nutrition impacts metabolism.

Very premature infants start out with primarily intravenous administration of nutrition that is maximized by one week of life. There is an important reason for this. Their GI tracts are not fully matured and are at increased risk from problems that could lead disease rather than health growth.

Human breast milk, the preferred source of nutrition, is started at a few days of life for the most premature infants and is increased over time as the infant grows and develops. Intravenous nutrition is reduced after one week while oral feeds continue to increase so that by discharge the premature infants is completely on oral nutrition.

Getting the GI tract to mature rapidly and in a healthy manner so that oral nutrition is absorbed at its maximal rate is the goal. Keep in mind it is ideal to get nutrients from nutrition into the blood whereby those nutrients can then pass into our cells for growth. Therefore, it is critically important to have a healthy, mature GI tract to enable this process to be as efficient as possible.

The role of micro-organisms is believed to be important to this process and is a fascinating aspect of nutrition in general.

A gut check: Nutrition and the gastrointestinal tract

A healthy gastrointestinal tract is full of microorganisms. The cohabitants of our gastrointestinal tract are needed for optimal health and nutrition.

Why are they there? First, our GI tract is an inner tube that is exposed to the environment from intake to outtake. Just as the lungs are the interface for the air we breathe to enable blood to carry oxygen from the lungs to tissues, so is our GI tract an interface of the nutritional building blocks of life to provide growth and energy.

We are surrounded by organisms. Bacteria populate our GI tract in a relationship called symbiosis where one or more organisms are in a close environment to the benefit of each other.

Symbiosis, bacteria, and the microbiome

Humans evolved from a microorganism and in an environment where other microorganisms vastly outnumbered us. We adapted to such a world by developing protections from harmful bacteria while also finding ways to harness the good bacteria for mutual benefit.


Unfortunately, we cannot see symbiotic relationships in our GI tract. However, we can see macro examples in wild animals and birds. Case in point: Birds eat insects that are potentially harmful to the rhinoceros while obtaining an easy source of food.

We are exposed to bacteria in our GI tract through the food we consume. Good bacteria generally thrive in our gut while assisting in the metabolism of undigestible foods and metabolizing certain essential nutrients, so they are more easily absorbed into blood through our intestinal lumen (or cell walls expose to the inside of our gut).

This community of microorganisms in our GI tract is the gut microbiome. It is essential to our health.

Disrupting a thriving community

Consuming harmful bacteria with the food we eat can cause harmful bacteria to outnumber the health symbiotic microflora.

These bad bugs produce toxins as well as metabolites that convert to volatile species producing gas and the pain associated with GI distention. Our systems are designed to eliminate these bugs through increased motility. Unfortunately, this flushing/elimination can cause health problems through dehydration if chronic.

The use of antibiotics may also kill good bacteria and disrupt a healthy microbiome. This decline creates an imbalance of the microflora environment such that GI distress occurs. Furthermore, we may be at higher risk for infection with harmful bacteria upon repopulation once the antibiotic course is completed. Eating foods rich in probiotics can quickly repopulate our GI tract to normal health.

Infants, Nutrition, and the Microbiome

Evidence suggests newborns get their microorganism exposure during the birthing process and from oral contact with the breast and human breast milk. Human milk also contains complex sugars known as oligosaccharides that serve as a source of nutrition and as protection from harmful bacteria and viruses.

There are many different oligosaccharides in human breast milk that are largely undigested compared to the milk sugar lactose that is converted to galactose and glucose by lactase in the gut. Glucose is the sugar that we require for energy and storage as glycogen. Oligosaccharides are specialty sugars that play a role in the character of our gut microbiome and health. We are still learning a great deal about these complex sugars.

One role besides food for bacteria is that some microorganisms stick to these sugars, sort of like two pieces of Velcro (or sticky fly paper, if you prefer) where the flies are the microbes, and the "fly paper" is the oligosaccharide. The cells lining the intestine have sticky molecules on the surface where microbes and viruses can attach, representing a potential site of infection. Oligosaccharides may mop up these microorganisms and eliminate in them in feces. Therefore, oligosaccharides may have an immunological role.

A healthy gut means optimum absorption of food for metabolism and energy. A premature infant has an immature GI tract that is not efficient in metabolism or absorption of the building blocks of proteins required for growth, as well as the source of molecules that produce energy needed for metabolism.

It is a major reason why infants who are born very prematurely require intravenous nutrition while the GI tract matures. During such time, the GI tract is at high risk for disease and exposure to bad bacteria. Human breast milk contains components that help ensure this optimum growth and protection and is a key reason why it is recommended as the major source of nutrition and is introduced as early as possible when it can be done safely.

Neurological Connections

The role of the GI tract in our health is still being discovered and better understood. What is most fascinating is how our gut impacts our brain. It reminds me of a joke that all parts of the body argued who is the boss. Basically, the brain argued he was the boss compared to all the other organ systems, but this was not to be outdone by example where the GI tract showed that it was the boss. With stomach pain and the usual symptoms associated with gastric distress, the brain couldn’t think straight, and the pain was excruciating. The legs knew where they had to go, and the eyes looked for the nearest restroom. Therefore, the GI tract proved that it was, indeed, the boss. This joke and its variations suggest a strong link between the GI tract and the brain. How does the gut direct our behavior and what is the mechanism?

The most obvious first role is that the gut provides the means to absorb nutrients which are a source of growth as well as energy. We know that after we eat our blood flow changes so we pick up nutrients in the gut (we often feel sleepy). We also know that the mediators of these responses are hormonal, as well as the importance of insulin in the process. When the stomach is upset and distended, we experience pain that reduces our intake of food but also increases the outflow to get rid of the source of pain. Pain impacts our behavior. There are more subtle roles, however, in impacting our brain – and that relates to development.

The gut is the mediator of all the important biochemicals needed for proper growth and function in the brain. Lack of the correct mixture of absorbed metabolites, vitamins, and minerals can result in a dysfunctional brain and neurological disease. This may be a long-term chronic process due to a deficiency of an essential nutrient.

Back to the Future - Metabolism

Bacteria are single-celled organisms. Like our own cells, they require energy-producing molecules and building blocks to grow and survive. Some bacteria require oxygen (aerobic) and some do not (anaerobic). Aerobic bacteria are generally known as the good bacteria. Bacteria have their own biochemistry or body chemistry (metabolism) and can digest, or break down, molecules we cannot. The products of these metabolites can be volatile (for a gas), many can be absorbed into blood. All can be eliminated in urine, respiration or from the GI tract. Many of these metabolites are unique to bacteria and not to human biochemistry. Their detection can provide information that identifies their presence and perhaps concentration.

Furthermore, the concentration of endogenous metabolites in blood may reflect our functioning GI tract and may help identify deficiencies in important substrates or toxic levels of compounds both endogenous or exogenous.

As a host to microorganisms, our nutrition and metabolism is affected by the make-up of this population and their interaction with our own biochemistry.

We are not alone. And that is a good thing.

Looking for more on this topic? Read An Exclusive Human Milk Diet Improves Premature Infant Gut Health and Feeding Tolerance

About the Author

Donald H. Chace, PhD, MSFS, FACB is the Chief Scientific Officer for Medolac, a public benefit corporation. He is one of the primary developers of newborn metabolic screening using tandem Mass Spectrometry. Developed 25 years ago with the first screening publication in Clinical Chemistry that describes the MS-based newborn screening of PKU, the method is now used to screen millions of infants per year, worldwide. Dr. Chace is an expert in metabolism and clinical chemistry using mass spectrometry as well as microsample analysis, e.g. the dried blood spot. Learn more about Dr. Chace by visiting his LinkedIn profile.