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About the human gut microbiome

The human body (ecosystem) comprises 90% non-human cells. Most of the ‘life’ taking place in and on our bodies involves microbial organisms, collectively known as the human microbiome.

This human microbiome is a collection of all the trillions of microorganisms that live on and in the human body – on our skin, in our mouths, throughout our digestive tract and in the genito-urinary tract. These microbes include bacteria, viruses and fungi and they are essential for a wide variety of bodily functions, including helping to digest foods, absorb nutrients and protect the body from disease-causing pathogens.

The key to a healthy microbiome is diversity of species and strains, which is impacted by diet and lifestyle choices.

Composition of the gut microbiome

The gut microbiome refers to the microbes that live in our gastrointestinal (GI) tract – there are trillions of them and the two main groups of bacteria are known as Firmicutes and Bacteroidetes.

Firmicutes are the single largest grouping of bacteria in the microbiome and play a role in energy metabolism through the production of short chain fatty acids (SCFAs). They also help to regulate hunger and satiety. They include more than 200 different species (genera) of bacteria, including Lactobacillus, Bacillus, Clostridium, Enterococcus and Ruminococcus.

As the Clostridium strains represent around 95% of the Firmicutes bacteria classification, this grouping is less diverse than other main bacteria groups.

Bacteroidetes include around 7,000 identified species of bacteria that are predominantly from the Bacteroides, Alistipes, Parabacteroides and Prevotella groups. They are associated with immunity and the production of immune cells throughout the body.

The ratio of Firmicutes to Bacteroidetes has become widely accepted as influencing normal intestinal homeostasis and an increased or decreased F/B ratio has become known as ‘dysbiosis’. An increased ratio has been linked to obesity and a decreased ratio associated with inflammatory bowel disease (IBD).

Proteobacteria are a third group of bacteria found in the human microbiome. This group contains the widest variety of different species, currently known to be more than 100 ‘families’ of bacteria. Proteobacteria are thought to help metabolize oxygen to maintain anaerobic environments in the body and some of the strains (including Escherichia coli, Salmonella and Campylobacter) have the potential to become pathogenic and contribute to dysbiosis. Variations in this group are also correlated with a decline in Firmicutes.

How and when is the gut microbiome formed?

Recent studies have found evidence that our gut microbiome begins to form in the womb. Commensal microbes have been discovered in amniotic fluid, umbilical cord blood, fetal membranes and the placenta, as well as in the meconium first passed by babies. Whilst this pre-natal microbial transfer is now evident, the largest bacterial colonization occurs at birth as the baby acquires his or her first microbial bacteria from the environment they are born into.

For babies born vaginally, the first colonization is from their mother’s vaginal, skin and rectal bacteria. For those born via Cesarean section, these bacteria come from skin and the hospital environment.

A few hours following birth, a mucosal layer starts to form on the baby’s GI tract to act as a barrier to prevent pathogens from crossing into the gut. This mucosal layer is where the beneficial bacteria colonize, helping to reinforce the barrier and support developing immunity.

The development of the baby’s microbiome is then influenced by their diet. Breast milk contains the mother’s bacteria (known as ‘mammary microbes’) and prebiotic oligosaccharides. These are the fibers that feed the bacteria and help them to colonize as part of the baby’s microbiome.

If the baby is formula fed, he or she will not receive the ‘mammary microbiota’, and many formula milks now contain prebiotic fiber, which helps to feed the existing bacteria in the baby’s microbiome.

When the baby is weaned onto solid foods, the microbiome development will continue based upon the foods that are introduced. Fruits and vegetables help provide prebiotics, which feed the good bacteria and help them to grow, and plain yogurt and fermented foods contain probiotic bacteria, which can support the development of the microbiome in these early years.

Can the composition of the microbiome change throughout our lives?

By the time we are three years old, the intestinal microbiome has acquired adult characteristics and is fully formed. Its composition depends upon the factors already discussed – maternal diet during pregnancy and breastfeeding, mode of birth and diet during infancy and the first three years of life. An excessive intake of sugar will potentially lead to the development of a less diverse microbiome, while a diet high in vegetables will help to encourage diversity.

Whilst the basic structure of our microbiome is established by three years of age, the specific composition will change almost daily throughout our lives. Bacteria forms around half of the fecal mass (poop) we excrete every day and replenishing this bacteria with beneficial species depends upon what we eat and drink and any medications and supplements we take on a daily basis.

Like the rest of our body, our gut microbiome is designed to reset back to its ‘normal’ structure following any challenges, such as illness or medications, but vegetables and a healthy diet are required to enable this to happen.

Before refrigeration was invented, we ate lots of fermented and cultured foods (such as sauerkraut and pickled vegetables), which gave us an ongoing supply of bacteria and helped to maintain balance in the microbiome. Today’s standard American diet lacks these foods and, whilst they are once again becoming more popular, probiotic supplements have been developed to help provide additional bacteria to enhance our modern diets and support the structure and function of our gut microbiome.

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