Microbiome diet and nutrition - the scientific background

What about pre- and probiotics?



Probiotics are live bacteria we can ingest with our food or as food supplements. The International Scientific Association on Probiotics and Prebiotics (ISAPP) just recently ratified the FAO/WHO definition of probiotics: "live micro-organisms that, when administered in adequate amounts, confer a health benefit on the host." The ISAPP definition includes that notion that the bacterial composition and bacterial count in the probiotic product must be clearly defined and safe to use. Dead microbes, microbial products or components and undefined microbial mixes do not fall under the probiotic classification, thus fermented foods with undefined microbiota are not probiotics.

Probiotics: live micro-organisms that, when administered in adequate amounts, confer a health benefit on the host

In Europe, however, the situation is a bit different: to this day, only one product has been (recently) accepted by the European Food Safety Authority (EFSA) as a probiotic: the bacterium Propionibacterium freudenreichii W200, fermented and produced by Winclove Probiotics. It contains adequate amounts of vitamin B12 to make EFSA-validated health claims. EFSA stated in 2011 that the use of the word "probiotic" on products refers to a health claim which must be scientifically validated. Surprisingly, although there is a huge "probiotic" market out there, none of the "probiotic" products in Europe (except the one mentioned above) is allowed to bear the name "probiotic", due to the lack of clinical evidence on the claim.

Bifidobacterium and Lactobacillus are the most abundant probiotics

The most abundant bacterial strains used in "probiotic" products belong to the genus Lactobacillus or Bifidobacterium. The genus Bifidobacterium contains species that produce short chain fatty acids (SCFAs), specifically lactate and acetate. During one study, the administering of probiotic Bifidobacteria showed an increase infecal SCFAs in different human and pigeon subjects. These SCFAs have positive effects on the human GI tract, either directly or by conversion to other SCFA such as butyrate by other members of the microbiota. SCFAs have a positive effect on motile and contractile functions of the gut (via SCFA receptors) and confer an anti-inflammatory effect by stimulation of the anti-inflammatory cytokine IL-10.

Lactobacilli and Bifidobacteria have “hair”, which makes them stick to the gut

The cell surface of gram-positive bacteria (such as Lactobacillus or Bifidobacterium) inhabits special properties which enable the direct interaction between the host and the bacterium. This is one property which is crucial for the colonization of the probiotic in the gut. One specific cell surface structure, called pili, is kind of a bacterial appendix which looks like hair and enables the bacterium to stick to the endothelium. This function impacts competitive exclusion of pathogens, immunomodulation and structural integrity of the intestinal mucosa. These pili are found in both Bifidobacterium and Lactobacillus. Experiments have shown that in particular the strain Lactobacillus rhamnosus GG outcompetes the pathogen Enterococcus faecium, including Vancomycin-resistant enterococci (VRE).

Lactobacillus rhamnosus GG outcompetes vancomycin-resistant enterococci (VRE)

A further feature of the cell surface of gram-positive bacteria is the immunomodulation by the cell wall structure as such (e.g. the peptidoglycan and lipoteichoic acids). These specific cell wall structures are well preserved among lactobacilli and bifidobacteria and have a positive impact on the intestinal barrier function, which is a major probiotic mechanism.

Lactobacillus rhamnosus GG is the best characterized probiotic strain

So what is behind this probiotic hype? Looking at the mechanisms of the most frequently used probiotics, a health benefit seems obvious. The world’s best documented probiotic strain L. rhamnosus GG (GG for Sherwood Gorbach and Barry Goldin, who discovered the strain in 1985 in human intestinal microbiota) has been investigated in over 300 clinical trials. A great deal of research has been conducted in pediatrics: it has been proven effective for the treatment of acute gastroenteritis and the prevention of antibiotic-associated diarrhea (AAD) in children. Furthermore, L. rhamnosus GG was proven to effectively prevent nosocomial diarrhea and respiratory tract infection. However, a significant result in adults could only be observed when associated with antibiotic treatment of the bacterium Helicobacter pylori.

Probiotics confer a health benefit mostly by outcompeting adverse bacteria

Taking into consideration all these scientific publications about probiotics, the bottom line is that probiotics may be a great form of therapy for patients with a dysfunctional gut microbiome and/or a weakened immune system. Studies have shown beneficial outcomes of probiotics for children, extreme sports athletes, and patients with certain conditions either following antibiotic therapy or suffering from irritable bowel disease (IBD) – they all share a common trait: the outcompeting of opportunistic bacterial infections. In healthy adult people, changes in the microbiome were observed after probiotic use, though no health benefit could be detected. Additionally, probiotics are recommended for prophylactic use before travelling – even for healthy people – with the aim of preventing the proliferation of adverse bacteria which may cause diarrhea.

When eating or taking probiotics, it is crucial to know about the specific strain and the amount of bacteria in the product. The probiotic strain needs to be able to survive the highly acidic stomach, and should be able to colonize in the gut. Further, the probiotic strain must be well-characterized, including possible side effects. Probiotics most likely won't be able to dramatically alter the composition of the whole gut’s microbiome, especially not in a healthy-colonized human gut, but probiotics may prevent colonization of adverse bacteria following an intervention such as the administering of antibiotics or in an unbalanced ecosystem which is vulnerable against pathogenic invasion.




Everyone has heard of prebiotics and we all feel good about including them in our daily nutritional routines – right? Not so fast. Let´s be honest: do we really know what they are good for and what they do to our microbiota and to our body? The following chapter will dive deeper into the matter and will give you all the facts we have so far!

What are prebiotics?

Prebiotics: a substrate that is selectively utilized by host microorganisms and confers a health benefit.

The current definition of a prebiotic is the one proposed by the International Scientific Association for Probiotics and Prebiotics (ISAPP): a substrate that is selectively utilized by host microorganisms and confers a health benefit. Although the definition of prebiotics is not limited to carbohydrates, most studies performed on prebiotics have been performed on different kinds of oligosaccharides:

Human milk oligosaccharides (HMOs): over 200 HMOs have been identified and these stimulate the growth of specific bacterial groups such as Staphylococci and Bifidobacteria.

Dietary fiber and starch are broken down by bacteria into short chain fatty acids (SCFAs)

  • Dietary fiber and starch: The production of short chain fatty acids (SCFAs) by bacteria in the gut. The most abundant SCFAs are butyrate, acetate and propionate which are end products of anaerobic fermentation.
    • Resistant Starch: Starch that passes through the small intestine and reaches the large intestine to be fermented by bacteria. Fermentation of RS by the bacteria in the large intestine results in the formation of SCFAs (especially butyrate) and a higher bacterial diversity in the gut.
    • Fiber: Non-digestible compounds, mostly carbohydrates, in most cases derived from plants such as grains, legumes, fruits or vegetables. Satiation occurs due to long duration of chewing and slow digestion: Decreases the rate of glucose absorption in the small intestine.
      • Non-digestible oligosaccharides (NDOs): Intermediates between simple sugars and polysaccharides. They improve the gut microbial ecosystem, including diversity, biochemistry and physiology.
      • Out of NDOs, Fructo-oligosaccharides(FOS) such as inulin and oligofructose are the best-studied prebiotics.

Although there are many indications that show that prebiotics are good for us and our microbiome, the scientific studies behind these indications are rather thin.

Most studies focus on the research of fiber such as FOS:

Overall, the intake of resistant starch and prebiotics does alter levels of specific bacteria that specifically metabolize special prebiotics and carbohydrates: these include Bifidobacteria and Lactobacilli. In controlled human studies, the intake of fiber correlated with an increase in Bifidobacteria and short chain fatty acids, in particular butyrate, which lowers the intestinal pH.


Other food ingredients and what they do to us

Food ingredients

Emulsifiers aid texture and extend the shelf life of processed food.

Mary K. Holder and her research team established a mouse model. They used the two commonly-used emulsifiers, polysorbate 80 (P80) and carboxymethylcellulose (CMC), at doses that seek to mimic the broad consumption of processed food. In their mouse model, Holder and colleagues observed an increase in gut-microbiota with pro-inflammatory potential. The major inflammatory molecules found were lipopolysaccharide (LPS, deriving from the outer cell membrane of gram-negative bacteria) and flagellin (a protein which derives from the bacterial flagellum, kind of a bacterial motor bacteria use to move or "walk").

Mice developed chronic intestinal inflammation and metabolic syndrome

These two molecules are well known for the activation of the innate immune system. As a consequence, the mice developed chronic intestinal inflammation (promoting chronic colitis) and metabolic syndrome (a clustering of at least three of the five following medical conditions: abdominal obesity, high blood pressure, high blood sugar, high serum triglycerides and low high-density lipoprotein (HDL) levels), which is associated with the risk of developing cardiovascular disease and type 2 diabetes. The altered microbiome was additionally capable of infiltrating the rigid mucus layer that lines the intestine. In other studies, the development of colorectal cancer was even enhanced by emulsifiers.

Increased anxiety in mice who were fed with emulsifiers

Holder and colleagues also took a look at the mice’s behavior after administering the emulsifier, since it is now widely known that a disturbance to the microbiome also influences our nervous system via the gut-brain-axis. What the team observed was an increased anxiety in mice who were fed with emulsifiers. Additionally, this group found that emulsifiers influenced peptides and hormones which influence appetite (agouti-related peptide AgRP and alpha melanocyte stimulating hormone αMSH), and thus emulsifiers may possibly contribute to increased food intake.

Since the chapter Microbiome diet is so very diverse and can be discussed from many perspectives, it will be expanded within further topics such as processing of foods, fermented foods, polyphenols, food examples and recommended recipes… stay tuned!

© Copyright 2018 - 2024 | MyMicrobiome
– The independent certification and research institute for our microbiome –

DISCLAIMER: Nothing on this site or blog is intended to provide medical advice, diagnosis or treatment.


By clicking "Accept all", you agree to cookies being stored on your local device. This improves navigation on the site, video content can be displayed and we can anonymously analyse whether the pages are being used as intended. All approvals are made in accordance with the provisions of the GDPR.

You are using an outdated browser. The website may not be displayed correctly. Close