10 Key Terms to Help Understand Gut Health

The human gut microbiome can be a tricky topic to navigate. Yet, as a human, the state of your gut microbiome plays an integral role in managing overall health and well-being, and can provide relief of symptoms of certain health conditions , such as Crohn’s disease and irritable bowel syndrome (IBS). A well-balanced gut microbiome has been linked to improving immune function, metabolic processes and also mental wellbeing.

So, if you don’t know your gut flora from your gut microbiota, or the difference between probiotics and prebiotic fibres, we’re here to help you understand 10 key terms associated with ‘gut health’.


A microorganism – often abbreviated to ‘microbe’ – is a tiny living thing that can only be seen with a microscope. Most microorganisms are so tiny that millions can fit into the eye of a single needle. Microorganisms include bacteria, archaea, fungi, protozoa, and viruses.

Microbiome and gut microbiome

The microbiome is the collective term for the community of microbes living in a biological environment. So, the gut microbiome is the community of microbes that inhabit the gastrointestinal tract and it includes trillions of bacteria, fungi, parasites, and viruses.

The gut microbiome can impact many aspects of human health, including digestion, immunity, and metabolism. Disruptions to the gut microbiome have been linked to disease severity of a wide range of health conditions, including heart health, Type 2 Diabetes, and inflammatory bowel disease (IBD). Therefore, maintaining a healthy gut microbiome is essential for overall health.

Gut microbiota

The gut microbiota is the community of microorganisms living in the gastrointestinal tract. The composition of the gut microbiota varies from person to person, but certain types of bacteria are generally more abundant than others.

Specific strains of gut bacteria have been linked with various health benefits, including weight control, lower blood sugar levels, and improved digestion. However, more research is needed to confirm these potential benefits.

It is important to note that the gut microbiota is complex and dynamic, meaning that it is constantly changing in response to various factors, including diet, lifestyle, and medications, such as antibiotics (drugs used to treat bacterial infections).

Although ‘microbiome’ and ‘microbiota’ are now used interchangeably, originally there were subtle differences between the terms.


Bacteria are tiny, single-celled organisms that are classified as ‘prokaryotes’, meaning they have no membrane-bound nucleus or other organelles. Their genetic material is organised into a single, circular DNA molecule that is not enclosed within a membrane.

Despite their small size, they are one of the most diverse groups of organisms on earth. Bacteria live in one of three types of relations with humans, animals, and plants:

Symbiotic relationships

Symbiotic relationships are mutually beneficial, or necessary for the survival of both parties.

Commensal relationships

Commensal relationships neither harm nor hinder either of the parties.

Parasitic relationships

Parasitic relationships involve an organism living in or on another orgasm and benefitting from that ‘host’.

While most people think of bacteria as being harmful, the majority of species are harmless or even beneficial for the human body. For example, beneficial bacteria in the gut help to break down food, synthesise vitamins, and protect against harmful microorganisms.

>Gut flora

Gut flora is the collection of microorganisms inhabiting the digestive tract. These microorganisms play an important role in digestion, nutrient absorption, and immune function. Imbalance in the gut flora has been linked to a variety of health problems, including inflammatory bowel disease, immune response, and allergies.

Starting to sound repetitive?

That’s because gut flora was once the preferred term over gut microbiota. However, scientists and researchers have moved away from using the term ‘gut flora’ as they believe it incorrectly suggests there are communities of microscopic plant-based organisms in the human gut, rather than microbes.


Gastrointestinal – or G.I. – refers to the stomach and intestines. However, the term often refers to the digestive system as a whole, which includes the mouth, oesophagus, stomach, small intestine, large intestine, rectum, and anus.

The gastrointestinal tract – or G.I.T – is responsible for processing foods and liquids that travel through the body.  Its main functions are to digest food, absorb nutrients, and eliminate waste from the body. It is lined with a layer of mucus that protects humans from the corrosive effects of stomach acids and enzymes. The mucus also contains beneficial gut bacteria that help with digestion.

Disorders of the gastrointestinal tract can be caused by infections, inflammation, or other conditions. Common gastrointestinal disorders include Crohn’s disease, ulcerative colitis (UC), irritable bowel syndrome (IBS), and gastroesophageal reflux disease (GERD).


Digestion is the term we use to describe the breakdown of food into smaller components that can be easily absorbed into the bloodstream. A person digests food mechanically in the mouth, and chemically in the gastrointestinal tract where digestive enzymes break the food down into smaller molecules.

How digestion occurs

The digestive process begins in the mouth, where food is chewed and combined with saliva. Saliva contains key enzymes that begin to break down food before it travels down the oesophagus and into the stomach.

In the stomach, acids and enzymes continue to break down the food. The partially digested food then moves into the small intestine, where most of the nutrient absorption takes place. The indigestible part of the food (chyme) is then pushed through to the large intestine where it uses gut bacteria to break it down further.  This process “feeds” the good gut bacteria, creates vitamins, absorbs any remaining water, vitamins and electrolytes and lastly, forms the waste product into a stool which is eliminated through the rectum and anus.


Stemming from Greek and meaning “for life”, probiotics are living microorganisms that have a beneficial effect on the health of the host. They can be found in the human digestive system, fermented foods, and dietary probiotic supplements.

Probiotics are thought to provide a range of benefits related to digestive health, including:

  • modulating gut microbiota composition imbalance by allowing good bacteria to thrive and reducing the number of harmful bacteria
  • reducing the risk of gastrointestinal infections
  • improving gut barrier function
  • supporting the immune system by improving inflammation

There are many probiotic strains, with Lactobacillus and Bifidobacterium being the most prominent. Although it can be beneficial to choose a multi-strain probiotic supplement, there is usually more benefit in choosing a probiotic supplement containing the specific strains that target the specific health issue you are experiencing.

Prebiotics fibre

Prebiotics are non-digestible carbohydrates, or dietary fibres, that serve as food for helpful gut bacteria. They can be found in certain foods, such as resistant starch, which is an indigestible fibre found in cooked and cooled potatoes.

When Prebiotic fibres are digested in the large intestine, several whole body health benefits occur. Some of these benefits are:

  • Short-chain fatty acids (SCFA) are produced which help improve immunity, aid in digestive health and even assist in balancing cholesterol levels.
  • Current research is now indicating prebiotics may help regulate blood sugar levels (glycaemic control) to support diseases such as Type 2 Diabetes.
  • Calcium bioavailability and absorption are increased in the large intestine, benefiting healthy bone density and reducing conditions such as osteoporosis.
  • Good microbial diversity reduces allergy-type conditions (eczema, allergic reactions etc.) by regulating the inflammatory response.
  • Dietary fibre is important for bowel health and function.  Prebiotics encourage healthy stools, in both form and regularity.
  • Prebiotics slow down the digestive process and support appetite control by helping to feel fuller for longer.  This can be helpful for weight control and management.


Metagenomic sequencing

Metagenomic sequencing is a highly advanced method of sequencing DNA from an entire community of microorganisms in a sample. Most commonly used to analyse the diversity of bacteria living in a unique microbiome, metagenomic sequencing can identify what species of bacteria are present in a sample, what they’re capable of, and how they interact with each other.


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