Fundamentals of the Gut Microbiome, Fermented Foods, and Biotics

Reading Time: 12 minutes

Key Takeaways:

Unique and Dynamic Microbiomes: Each person's gut microbiome is unique and adapts throughout life, influenced by factors like diet, lifestyle, and environment.
Role of Biotics: Biotics, including probiotics and prebiotics, can modulate the gut microbiota and support health. However, not all fermented foods contain probiotics or meet the International Scientific Association for Probiotics and Prebiotics (ISAPP) clinical definition.
Microbial Diversity: A diverse gut microbiome is associated with better health outcomes, whilst reduced diversity can often be linked to poorer health outcomes.
Diet and Lifestyle: A varied diet rich in plant-based foods, fermented foods, regular exercise, good sleep, and stress reduction can be beneficial for good gut health

Intro to the gut

The gut plays a key role in our health and well-being.

Whilst digestion is perhaps its most well-known function, the gut also plays a fundamental role as part of the immune system. In fact, up to 70% of immune cells are found within the gut[1]. Both of these functions are supported, shaped and influenced by the diverse ecosystem of trillions of living microbes that live within us.

Gut Microbiota

Microbiota (historically called ‘flora’)[2] is the term used to describe the trillions of living microorganisms both on us and in us. The gut microbiota refers to the community of microorganisms living specifically within the gut, including bacteria, fungi, yeast and viruses.

Gut microbiome

The microbiome is the combination of the genetic material of the living microorganisms, their genomes, functions, and the metabolites they produce. If the gut microbiome was a factory, the gut microbiota are the people who work there, the machinery they use and the products they make.[3]

Microbiomes are located all along the interfaces between the inside and the outside of our body.[4-6] The body’s richest microbiome community lives along the mucosa in our gut, and most predominantly in the colon[7] – this is the gut microbiome.

No two people have the same gut microbiome,[8] it is unique to each individual, just like fingerprints. It adapts throughout the various stages of life, from gestation to old age and in most people is highly resilient.

What are biotics?

The word ‘biotics’ is derived from the Ancient Greek word ‘biōtikós’ referring to life. Biotics can modulate the gut microbiota (either directly by forming part of the microbiota, or indirectly through other mechanisms) and they can also support human health.

In 2013, the International Scientific Association for Probiotics and Prebiotics (ISAPP) established an expert panel to explore the field of prebiotics and probiotics, including defining various types of biotics[9].

Prebiotics

They are normally non-digestible food components such as fibres and oligosaccharides which promote the growth and activity of beneficial bacteria. Found in foods such as chicory, garlic, onions and wholegrains.[39]

Probiotics

Live microorganisms, which when administered in adequate amounts, confer a health benefit to the host. Found in foods such as some specific yogurts and some supplements. Probiotic foods must have clinical evidence to demonstrate survival and specific health outcomes.9

Synbiotics

A combination of prebiotics and probiotics that work synergistically

Postbiotics

Compounds beneficial for health, which are either produced by live microorganisms within the microbiota, or derived from dead microorganisms. These may include , short chain fatty acids, vitamins, amino acids, antimicrobial peptides.[10] These can have several health benefits and have been linked to supporting gut health and reducing inflammation[11]

What are fermented foods?

Fermented foods – such as, kimchi, kombucha or sauerkraut – typically deliver a wide variety of live cultures but may not always contain probiotics or a consistent level or amount of probiotics. Fermented foods are an important component of a gut-friendly diet, but the live cultures within them may not meet the specific ISAPP definition of a ‘probiotic’. Probiotics work in a strain specific manner, survive to the gut alive and have clinical evidence to show benefits for specific health outcomes. These key criteria are not always met for the live cultures within fermented foods. Learn more about the health benefits of fermented foods in one of our blogs or the importance of strain specificity within Activia

Gut microbiota dysbiosis

There is no set definition of an ‘optimal’ or ‘healthy’ gut microbiota composition since it is different to individuals. But evidence points to microbial diversity, balance and stability being associated with better gut health and overall wellbeing. Sometimes, the gut microbiota and subsequently, the gut microbiome can be disturbed; an imbalanced or disordered gut microbiota is often referred to as “dysbiosis” [1-2].

Dysbiosis is thought to contribute to the pathophysiology of many health conditions, including poor digestion, metabolic functions and decreased immunity.

Diversity in the gut microbiome

One of the most important characteristics of a gut microbiome is its diversity: the number of different microorganisms it holds.[8] It is predicted that the gut microbiome encodes over 3 million genes that can lead to the production of thousands of metabolites. To put into perspective, the human genome consists of approximately 23,000 genes.[12]

Interestingly, researchers have found a possible connection between reduced diversity in the gut microbiome and various diseases, including autoimmune disorders (such as Crohn's disease and Type 1 diabetes), metabolic conditions (like obesity and Type 2 diabetes), and certain cancers. While the exact role of the gut microbiome in these diseases is not fully understood, it seems that a diverse gut microbiome may play a beneficial role.[3-4]

Gut microbiome through the years [12,5,6]

The gut microbiota diversity is ever evolving and gradually changes from gestation right through to old age. Early life is an important stage for shaping the gut microbiome and the composition throughout the first period of life is influenced by factors such as birth gestational date, delivery method, feeding methods and weaning. External factors will also come into play, such as the living environment or presence of pets.

During adulthood, the core native microbiota remains relatively stable but can differ between individuals, dependent on factors like dietary habits, lifestyle, exercise, geographical areas and antibiotic and medication usage. However, certain life events such as bariatric surgery, illness, infection or use of antibiotics can profoundly influence the composition of the microbiota in adulthood.

Various factors affect the gut microbiota including [7]

Key functions of the gut microbiome:

Helps digestion

Non-digestible carbohydrates, like dietary fibre, cannot be digested due to the lack of human enzymes able to break them down

Production of short-chain fatty acids (SCFAs)

SCFAs like butyrate and acetate can:

Provide energy [9]
Promote a thicker protective mucus layer lining in the intestine which prevents harmful pathogens from attaching to the intestinal lining and entering the blood stream
Provide a more acidic environment which increases the growth of beneficial bacteria, and can compete with pathogenic bacteria for gut adhesion [10]
Maintain a low pH level in the gut, thus limiting the growth of bacteria like pathogens [11]
Improved glucose homeostasis [12]
May play a role in supporting immunity, as expression of SCFA’s receptors have been found on immune cells [22]

Synthesis of key vitamins

Contributes to the synthesis of key vitamins like vitamin K, vitamins B5, B8, B9 and B12 [24-31]

Helps with neurotransmitter synthesis

May be involved in some neurotransmitter synthesis, such as gamma-aminobutyric acid (GABA) and serotonin - 95% of the body's serotonin is produced in the gastrointestinal tract [32,33]

Defends against harmful pathogens

The gut favours good bacteria, thus limiting pathogens [23]
Production of antimicrobial molecules [24]
Directly prevent the proliferation of competing bacteria, without being affected themselves [25]
Modulation of immune cells

Helps maintain the integrity of the gut epithelial barrier

Helping to prevent a ‘leaky gut’ which prevents harmful substances from entering the bloodstream

How do pre and probiotics influence gut microbiome functions?[26-31]

Supporting gut health through dietary choices

Our food choices play an important role in determining the wellbeing of our digestive system and consequently, our health.

Having a diverse and varied diet rich in plants (aiming for 30 different plant-based foods a week) can help increase the amount and diversity of fibres and other nutrients which are important for achieving an enhanced gut microbiome. In addition, consumption of fermented foods, like yogurts, kefir and kombucha, can also be beneficial for good gut health along with regular exercise, good sleep quality and reducing stress.[32]

Finally, consumption of products containing specific probiotics, which are backed by clinical evidence may help in supporting specific health outcomes. For example, Activia has over 40 years of scientific evidence showing it’s role in supporting digestive comfort in both healthy adults and in IBS-C patients.[33-34].To learn more about the specific evidence behind Activia, visit Activia Research

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[13] EFSA, Scientific Opinion on the substantiation of health claims related to vitamin K and maintenance of bones (ID 123, 127, 128 and 2879), blood coagulation (ID 124 and 126), and function of the heart and blood vessels (ID 124, 125 and 2880) pursuant to Article 13(1) of Regulation (EC) No 1924/2006 on request from the European Commission. EFSA Journal, 2009. 7(9), 1228. DOI:

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[16] EFSA, Scientific opinion on the substantiation of health claims related to biotin and energy-yielding metabolism (ID 114, 117), macronutrient metabolism (ID 113, 114, 117), maintenance of skin and mucous membranes (ID 115), maintenance of hair (ID 118, 2876) and function of the nervous system (ID 116) pursuant to Article 13(1) of Regulation (EC) No 1924/2006 on request from the European Commission. EFSA Journal, 2009. 7(9),1209.v

[17] EFSA, Scientific Opinion on the substantiation of health claims related to biotin and maintenance of normal skin and mucous membranes (ID 121), maintenance of normal hair (ID 121), maintenance of normal bone (ID 121), maintenance of normal teeth (ID 121), maintenance of normal nails (ID 121, 2877), reduction of tiredness and fatigue (ID 119), contribution to normal psychological functions (ID 120) and contribution to normal macronutrient metabolism (ID 4661) pursuant to Article 13(1) of Regulation (EC) No 1924/2006. EFSA Journal 2010; 8(10):1728.

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[19] EFSA, Scientific opinion on the substantiation of health claims related to vitamin B12 and red blood cell formation (ID 92, 101), cell division (ID 93), energy-yielding metabolism (ID 99, 190) and function of the immune system (ID 107) pursuant to Article 13(1) of Regulation (EC) No 1924/2006 on request from the European Commission. EFSA Journal, 2009. 7(9), 1223.

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This information is intended to provide health professionals with scientific and educational content on gut health and nutrition.