Prebiotics vs Probiotics vs Fermented Foods: What’s the difference, what are the benefits of each and which one should I take?

May 03, 2023 11 min read

Prebiotics vs Probiotics vs Fermented Foods: What’s the difference, what are the benefits of each and which one should I take?

Besides diet and other lifestyle factors, there are three ways to help boost the abundance of beneficial bacteria in your gut; prebiotics, probiotics and fermented foods. They’re all pretty big topics in the nutrition world and they all have a wide-range of benefits for your gut and beyond.

Here, we’ll delve into what pre- and probiotics and fermented foods are, their benefits and where you can find them.

What are prebiotics and probiotics?

Although they sound relatively similar, pro- and prebiotics are very different, but both are important for your health.

Prebioticsare the foods that nourish your gut bacteria. They are a group of nutrients which are broken down (fermented) by bacteria in your gut and are transformed into beneficial metabolites like short-chain fatty acids (SCFAs)[i]. Nutrients like fibre are unable to be broken down and digested by your body alone, so your gut bacteria do it for you.

Probiotics,on the other hand, are live bacteria present in some foods and supplements. The World Health Organisation defines probiotics as “live microorganisms which when administered in adequate amounts confer a health benefit on the host”[ii].

The microbial inhabitants of your gut are collectively called the gut microbiome. Together, they perform many important functions. Prebiotics and probiotics can help to support the composition and abundance of beneficial bacteria in your gut, ensuring it is working optimally.

What are fermented foods?

Fermented foods are made by adding microorganisms to food. Fermentation was originally used as a food preservation technique by ancient populations because the metabolites produced, like ethanol, bacteriocins, and organic acids, reduce the risk of contamination with pathogenic bacteria, avoiding spoilage. However, fermented foods have grown in popularity because of their known health benefits as well as their enhanced flavour.

There are many different examples of fermented foods available, which can contain probiotics microbes such as lactic acid bacteria. Foods can be fermented in two ways. They are:

  1. “Wild” or “spontaneous ferments”– naturally present microbes in raw food are responsible for fermentation (sauerkraut, kimchi, and some fermented soy products)
  2. “Culture-dependent ferments” –foods are fermented by adding starter cultures, like kefir, kombucha, and natto

Generally, fermented foods can promote a more diverse gut microbiome and benefit other aspects of your health such as your digestive function and preventing chronic disease.

Why is the gut microbiome beneficial?

The gut microbiome is a unique and special ecosystem within your digestive tract, especially the colon. Within the ecosystem resides a combination of good and potentially bad microorganisms. To be healthy, the microbiome needs to be dominated by good or health-promoting bacteria, if these become out of balance, potentially harmful bacteria may become dominant, resulting in dysbiosis.

Dysbiosis, or an imbalanced microbiome, is linked to numerous negative health outcomes, such as illness, inflammation, and an increased risk of chronic disease.

Yet, a healthy microbiota can keep dysbiosis at bay, and even have positive effects for your gut and wider body health.

Diet and the gut microbiome

Have you ever heard the saying, “You are what you eat”? If so, you probably imagined as a child eating a carrot and looking like one, right? Although the saying isn’t literally true and doesn’t describe the way you look, there is an element of truth when it comes to your gut microbiome.

That’s because this tiny ecosystem in your colon is heavily influenced by the types of food you eat. For example, those of us who follow a predominantly Western diet, often have a less diverse microbiome, thanks to the high levels of sugar and saturated fat present in the typically consumed foods, as well as the low intake of dietary fibre, which your colonic bacteria love[iii].

Whereas a Mediterranean style diet is associated with promoting beneficial bacteria species and building a more balanced microbiome. One of the key reasons for this is the diet is rich in fruit, vegetables, legumes, wholegrains, and cereals that help to increase the abundance and activity of good gut species[iv]. In turn, these bacteria help to strengthen the gut lining, reduce inflammation, and boost the immune system.

And that’s not all, research has shown that the Mediterranean diet can reshape the gut microbiome and even prevent chronic diseases, such as obesity, diabetes, neurodegenerative diseases, and even cancer[v]. When you eat healthy foods, especially fibre, your body is unable to break it down, digest it, and extract the important nutrients. So, it travels largely untouched to your colon, where the bacteria residing there ferment it and transform it into useful metabolites, such as short-chain fatty acids (SCFAs) and other nutrients. The ability your gut microbes have to do this is effectively their superpower.

Prebiotic foods

Prebiotic foods are those that help to nourish your microbiota, and in turn, they break them down into the metabolites and nutrients your body needs to stay healthy. You’ve probably seen all kinds of prebiotic supplements available in your local health food shop, but there is an abundance of prebiotic foods readily available in the supermarket and maybe even in your back garden.

Prebiotics are abundant in many types of fibre found in plant-based foods and, even though you may not be able to digest them, your gut bacteria certainly can. There are four types of prebiotic fibre available to consume. They are:

  1. Inulin
  2. Human milk oligosaccharides (HMOs)
  3. Fructooligosaccharides (FOS)
  4. Galacto-oligosaccharides (GOS)

Some examples of prebiotic foods are:








Chicory root

Dandelion greens



Jerusalem artichokes





It’s important to remember that not all fibres are prebiotic. Although both prebiotics and fibres are non-digestible, they have slightly different roles within the body. For example, fibre is largely a natural bulking agent for your stools, preventing constipation by regulating bowel movements and producing larger stools.

Prebiotics, on the other hand, are sustenance for your friendly gut bacteria. Once these fibrous foods reach your large intestine, bacteria such as Bifidobacteriaand Lactobacilli, get to work breaking down or fermenting them. One of the great advantages of this is it helps to increase the growth and activity of the good bacteria in your gut[vi]. By doing this, not only does the prebiotic fibre serve as food for these micro-organisms, but they transform it into SCFAs, like butyrate.

Butyrate has many potent benefits in the human body, perhaps the most notable is it serves as the main energy source for the cells that line the gut, called colonocytes. But research has shown it is also important in the prevention of obesity, heart disease, diabetes, cancer, and lowers the incidence of inflammation[vii].

Are HMOs prebiotic?

Yes, human milk oligosaccharides are prebiotics[viii] because they nourish beneficial species, particularly Bifidobacteriain the infant and adult microbiome. HMOs are a type of sugar present in human breast milk.

They are non-digestible carbohydrates that make their way to the intestine where they unleash their power. HMOs are associated with benefits in the gut, immune system, and brain. Although they are naturally found in breast milk, through the process of fermentation and the use of enzymes, HMOs can be produced using cow’s milk, so that adults can reap the benefits too.

Check out our full PureHMO® range in our shop.


As well as prebiotics, you’ve probably heard of probiotics too, most likely in the form of supplements or through the advertisement of certain yoghurt-based drinks. But probiotics are also naturally present in some foods.

The most common probiotic bacteria are those that are classified as lactic-acid bacteria and Bifidobacteria.Examples include:

  • Lactobacillus acidophilus
  • casei
  • gasseri
  • paracasei
  • plantarum
  • reuteri
  • rhamnosus
  • Bifidobacteria adolescentis
  • animalis
  • bifidum
  • breve
  • infantis
  • lactis
  • longum[ix]

Probiotic supplements

Probiotic supplements are usually capsules, powders, or liquids that contain live bacteria or yeast known to have health benefits.

People take probiotic supplements for many reasons, but they are most notably known for restoring the balance in the gut. You may have been prescribed or advised to take probiotics if you have been given a course of antibiotics. That’s because antibiotics disrupt the microflora in the gut, causing it to become imbalanced, and can result in infections such as antibiotic-associated diarrhoea (AAD)[x].

The incidence rate of AAD is high, with 5% to 35% of people developing AAD while taking antibiotics, and symptoms can occur within just hours of starting the course. In the worst cases, approximately 17%, AAD can be fatal. A meta-analysis conducted in 2013 found that probiotics are effective at treating and preventing AAD in children and adults. It also found that there was a 66% decrease in C. difficile-associated diarrhoea in people taking probiotics and antibiotics[xi].

Health benefits of probiotics

As well as treating and preventing AAD, through their ability to modulate the gut microbiome, probiotics have also been associated with:

  • Better health outcomes for illnesses such as irritable bowel syndrome (IBS) and irritable bowel disease (IBD)
  • Better mood
  • Improved heart health
  • Reduced risk of allergies
  • Better digestive health

What are probiotic foods?

Probiotic supplements are not the only way you can increase your intake and boost the abundance and activity of the beneficial bacteria in your gut. There are plenty of foods available that naturally contain live cultures, such as yoghurt and fermented foods.

However, not all fermented foods contain probiotics, particularly those that are pasteurised. So, if you’re buying them from a shop, it’s always best to check the label.

Fermented food examples

  • Kefir
  • Kimchi
  • Kombucha
  • Miso
  • Natto
  • Probiotic yoghurt
  • Sauerkraut
  • Tempeh

Why are fermented foods good for you?

Lactic acid bacteria are probably the most studied microorganisms, and they’re often present in many fermented foods. During the fermentation process, the bacteria are responsible for making (synthesising) various vitamins and minerals as well as biologically active peptides, famous for their health benefits[xii].

These bioactive health compounds that are isolated directly from fermented foods have functions relating to:

  • Anti-hypertension
  • Antioxidant
  • Antibacterial[xiii]

A review published in 2022 found that fermented foods that contain either live cultures or inactive postbiotics, could improve cardiometabolic health due to the inclusion of fermentation-enhancing metabolites[xiv]. Furthermore, a study by Adiloğlu et al., (2013), discovered that consuming 200 mL of kefir every day for six weeks was associated with a reduction in certain pro-inflammatory cytokines. The researchers also concluded that an increase in interleukin-5 could stimulate the secretion of IgA in the gut lining, resulting in a better immune response[xv].

Interestingly a Japanese study by Ikeda et al. (2006), found that natto, or fermented soy beans, could help to prevent bone loss in postmenopausal women, particularly in the hip and arm[xvi]. The reason for this is natto contains high levels of menaquinone-7 (MK-7), a type of vitamin K. MK-7 is known to increase bone mineral density and improve bone quality and strength[xvii].

If that wasn’t enough, a study with 21 prediabetic participants demonstrated that consumption of both fresh and fermented kimchi was associated with weight loss, lower body mass index(BMI), and a reduced waistline. Plus, the fermented kimchi also reduced insulin resistance and increased insulin sensitivity, positive outcomes for people who are on the verge of developing diabetes. It also significantly lowered blood pressure, showing that fermented kimchi has some potent benefits[xviii]

How often should I eat fermented foods?

After reading about the benefits of prebiotics, probiotics, and fermented foods it can be tempting to completely change your diet and incorporate them into every meal and snack. Although they have some great outcomes for health, consuming too much at once can actually cause some troublesome side effects, such as gas and bloating; no one wants that.

The Fermented Food Lab suggests starting out by eating 1 tablespoon of sauerkraut or 1 pickle per day, if you’re new to this cuisine, or ¼ of a cup of fermented drink (kefir or kombucha). You should then slowly work up to incorporating them into every meal.

How can I support my gut microbiota: Which one to use?

The best way to support your gut microbiota is to ensure you eat a healthy, balanced diet that is low in saturated fat and sugar, but rich in plant-based foods. Incorporating prebiotics through food and supplements, especially HMOs, alongside probiotics, will boost the abundance and activity of your healthy gut bacteria.

By combining prebiotics with probiotics, they will synergistically work together in the gut, ensuring that the bacteria do not die off before they benefit you. At Layer Origin Nutrition, we’ve done the hard work for you and produced our PureHMO® Synbiotic, a unique combination of 1000 mg of 2’-FL and 10 strains of probiotic bacteria strains to maximise synergy.

But be adventurous. Don’t be afraid to try a wide range of fruits, vegetables, nuts, seeds, and wholegrains in a variety of colours to help keep your gut ecosystem happy and thriving. And start off by gently experimenting with different fermented foods to see if you like the taste and monitor how your body reacts to them.


When it comes to pre- and probiotics, one is not more important than the other, they are both required to support a healthy gut microbiome. A balanced gut is essential for many aspects of your health.

Ensuring your daily diet incorporates a wide variety of foods and a combination of prebiotics and probiotics/or fermented foods is a great way to look after your microbiome.

Written by: Leanne Edermaniger, M.Sc. Leanne is a professional science writer who specializes in human health and enjoys writing about all things related to the gut microbiome. 


[i] Davani-Davari D, Negahdaripour M, Karimzadeh I, Seifan M, Mohkam M, Masoumi SJ, Berenjian A, Ghasemi Y. Prebiotics: Definition, Types, Sources, Mechanisms, and Clinical Applications. Foods. 2019 Mar 9;8(3):92. doi: 10.3390/foods8030092. PMID: 30857316; PMCID: PMC6463098.

[ii] Mack DR. Probiotics-mixed messages. Can Fam Physician. 2005 Nov;51(11):1455-7, 1462-4. PMID: 16353824; PMCID: PMC1479485.

[iii] Statovci D, Aguilera M, MacSharry J, Melgar S. The impact of western diet and nutrients on the microbiota and immune response at mucosal interfaces. Frontiers in Immunology. 2017;8.

[iv] De Filippis F, Pellegrini N, Vannini L, Jeffery IB, La Storia A, Laghi L, et al. High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome. Gut. 2015;65(11):1812–21.

[v] Nagpal R, Shively CA, Register TC, Craft S, Yadav H. Gut microbiome-Mediterranean diet interactions in improving host health. F1000Res. 2019 May 21;8:699. doi: 10.12688/f1000research.18992.1. PMID: 32704349; PMCID: PMC7359750.

[vi] Slavin J. Fiber and prebiotics: mechanisms and health benefits. Nutrients. 2013 Apr 22;5(4):1417-35. doi: 10.3390/nu5041417. PMID: 23609775; PMCID: PMC3705355.

[vii] Amiri P, Hosseini SA, Ghaffari S, Tutunchi H, Ghaffari S, Mosharkesh E, et al. Role of butyrate, a gut microbiota derived metabolite, in cardiovascular diseases: A comprehensive narrative review. Frontiers in Pharmacology. 2022;12.

[viii] Nolan LS, Rimer JM, Good M. The Role of Human Milk Oligosaccharides and Probiotics on the Neonatal Microbiome and Risk of Necrotizing Enterocolitis: A Narrative Review. Nutrients. 2020 Oct 6;12(10):3052. doi: 10.3390/nu12103052. PMID: 33036184; PMCID: PMC7600747.

[ix] Kechagia M, Basoulis D, Konstantopoulou S, Dimitriadi D, Gyftopoulou K, Skarmoutsou N, Fakiri EM. Health benefits of probiotics: a review. ISRN Nutr. 2013 Jan 2;2013:481651. doi: 10.5402/2013/481651. PMID: 24959545; PMCID: PMC4045285.

[x] Ma H, Zhang L, Zhang Y, Liu Y, He Y, Guo L. Combined administration of antibiotics increases the incidence of antibiotic-associated diarrhea in critically ill patients. Infect Drug Resist. 2019 May 1;12:1047-1054. doi: 10.2147/IDR.S194715. PMID: 31118710; PMCID: PMC6503325.

[xi] Rodgers B, Kirley K, Mounsey A. PURLs: prescribing an antibiotic? Pair it with probiotics. J Fam Pract. 2013 Mar;62(3):148-50. PMID: 23520586; PMCID: PMC3601687.

[xii] Şanlier N, Gökcen BB, Sezgin AC. Health benefits of fermented foods. Critical Reviews in Food Science and Nutrition. 2017;59(3):506–27.

[xiii] Guo Q, Chen P, Chen X. Bioactive peptides derived from fermented foods: Preparation and biological activities. Journal of Functional Foods. 2023;101:105422.

[xiv] Li KJ, Burton-Pimentel KJ, Vergères G, Feskens EJ, Brouwer-Brolsma EM. Fermented foods and cardiometabolic health: Definitions, current evidence, and future perspectives. Frontiers in Nutrition. 2022;9.

[xv] Adiloğlu, A. K., Gönülateş, N., Işler, M., & Senol, A. (2013). Kefir tüketiminin insan bağışıklık sistemi üzerine etkileri: Bir sitokin çalışması [The effect of kefir consumption on human immune system: a cytokine study]. Mikrobiyoloji bulteni47(2), 273–281.

[xvi] Ikeda Y, Iki M, Morita A, Kajita E, Kagamimori S, Kagawa Y, et al. Intake of fermented soybeans, natto, is associated with reduced bone loss in postmenopausal women: Japanese population-based osteoporosis (jpos) study. The Journal of Nutrition. 2006;136(5):1323–8.

[xvii] Sato T, Inaba N, Yamashita T. MK-7 and Its Effects on Bone Quality and Strength. Nutrients. 2020 Mar 31;12(4):965. doi: 10.3390/nu12040965. PMID: 32244313; PMCID: PMC7230802.

[xviii] An SY, Lee MS, Jeon JY, Ha ES, Kim TH, Yoon JY, Ok CO, Lee HK, Hwang WS, Choe SJ, Han SJ, Kim HJ, Kim DJ, Lee KW. Beneficial effects of fresh and fermented kimchi in prediabetic individuals. Ann Nutr Metab. 2013;63(1-2):111-9. doi: 10.1159/000353583. Epub 2013 Aug 17. PMID: 23969321.


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