Biome Bible

The GI dictionary for Non-Scientists
An overview of the GI Scientific World

This explanation of most used words should give you enough knowledge to understand quickly better dietary articles or your next doctor visit and to make better decision to improve your gut health.


The Gut 

Saliva & Bile 
Saliva and bile are produced to have fluids for digestion and to introduce starch enzyme (alpha-amylase) to the digestive system. 

Gastric acidity
This acid is produced in the gastric gland of the stomach. The pH can vary between 4 to 2 depending on the location and the moment of food intake.

Gastric juice is a combination of acid and enzymes (lipase, pepsin). Its main function is to inactivate swallowed non-acid resistant microorganisms, thereby inhibiting infectious agents from reaching the intestine and activating enzymatic digestion.     

Gastrointestinal track or digestive system is defined from the mouth via stomach, small intestine and large intestine.

The gut is the part of the digestive system after the stomach with small intestine and hind gut. 

These are basically 3 steps. First, in the mouth, which helps micronize and add saliva to the food.

Second, the stomach and the small intestine help with enzymatic digestion.  The enzymes (pepsins, lipase, amylase) break the food into small particles that can be absorbed by the epithelia cells in the small intestine.

Third, the hind gut where the fermentation of fiber and polyphenols happens.

Oral microbiota is an important part of the human microbiota. Oral microbes can be colonized into the intestine in various ways. Oral microbiota is associated with a variety of oral diseases. Recently, increasing evidence has shown that the oral microbiota is closely related to the physical conditions of humans, such as diabetes, obesity and cancer. In the future, oral microbiota will become a new target for improving the physical state of humans.

The esophageal microbiome is similar in composition to the oral microbiome, with a relatively high abundance of the phylum Firmicutes and the genus Streptococcus. Limited studies to date suggest that there are certain microbiome alterations associated with esophageal diseases.

The epidemiology of various esophageal conditions such as Barrett’s esophagus and eosinophilic esophagitis point to the microbiome as potentially relevant players, although our understanding of the role of bacteria in the pathogenesis of these diseases remains limited.

The stomach has been thought to host few commensal bacteria because of the existence of barriers, such as gastric acid. However, recent culture-independent, sequencing-based microbial analysis has shown that the stomach also harbors a wide diversity of microbiota. One of the most discussed bacteria is Heliobacter pylori.

H. pylori colonizes the gastric mucosa using virulence properties, and causes acute and chronic gastritis, eventually progressing to more severe disorders, including peptic ulcer disease and gastric cancer. H. pylori infection is often acquired in childhood and persists throughout life without eradication therapy. H. pylori infection rarely occurs in adulthood, and when it does, it causes acute gastritis and is then eradicated. According to the results of different studies with probiotics, life beneficial lactic acid bacteria could be useful in the reduction of H. pylori infection in the mouse model. Due to the harsh conditions of the stomach acid it is important to administrate a lot of live and active beneficial bacteria, which act in the moment of consumption. These live and active bacteria do not need to go through an activation process like freeze dry probiotic bacteria capsule. In addition, fermented products do contain lactic acid which is reported to be anti-inflammatory and can contribute to the wound healing.

Small intestine 
The microbiota plays an important part to metabolize the carbohydrates and modulates the lipid digestion. As well, micronutrients like vitamins are produced in the small intestine. A major concept that has been shown across studies is that the small intestinal microbiota is phylogenetically less diverse than the colon, but more dynamic. Carbohydrate fermentation is a core function of this gut microbiota. This contrasts with colon communities, which are more equipped to degrade complex carbohydrates. Small intestine bacteria are enriched with genes for energy generation and are suggested to make a considerable contribution to primary digestion of food components in the small bowel, with fermentation products that support the growth of secondary fermenters.

Large intestine
Unfolded, it has the size of a badminton field with a hair thin layer of cell gut wall separating food bacteria… from the blood. This gut wall is covered with mucus as a secondary protection.    

The large intestine is the main location for bacteria metabolic activity which means:  

  • digestion and breakdown of fiber (carbohydrates), 
  • production of energy, 
  • exopolysaccharides (mucus), 
  • micronutrient (vitamins), 
  • production of molecules which directly or indirectly influences the production of hormones and neurotransmitters.

If undigested food like sugars reaches the large intestine, it will create blooding and flatulence.

80-90% of our adaptive immune system is located in the large intestine. 

Transit time
A stomach that functions properly will empty in 4 to 6 hours. Food generally takes 5 hours to move through the small intestine and 10 to 59 hours to move through the colon. A daily transit is essential for the gut health and metabolic well-being.

Epithelia Cells 
They are the cells which form the gut skin. They are forming our skin or inside the tubes of the digestive system or lungs. The skin epithelia is only a hair thin layer dividing food toxins bacterial virus from the blood stream. 

All the bacteria which are covering the body, inside and outside. 90-99% of our body gens are bacterial gens just about 2 kg living inside and outside of our body. In total these are thousands of different species. 

All bacteria which are in the mouth up to the gut. There are more bacteria cells in the gut than body cells. It is unique for each person but similar to the person and pets close to you. Mostly it is related to your mother. Cesarean vs natural birth, breast feed vs non breast feed influences significantly our microbiota. In case of Cesarean birth the microbiota is more related to the skin and people around your birth. In general, all kinds of different situations of birth and early life are influencing most of our bacteria selection in a positive or negative way. 

The Microbiota from the mouth to the small intestine is not as defined and constant as the hind gut bacteria. 50-60% of the stool weight is bacterial mass. Most of your microbiota lives in your hind gut. The microbiota plays a significant role for our day-to-day wellness.

It is important to have a high quantity and a high diversity of beneficial bacteria in our gut.

Low diversity of food, ageing, stress, medication, alcohol and nicotine is influencing this balance negatively. Good food with good bacteria like fermented food will support the growth of beneficial bacteria in the lumen and the mucus of your gut walls and they will work for you.  

This happens when the bacterial balance in the gut got lost. Too many bad bacteria (inflammatory) not enough good or beneficial bacteria (anti-inflammatory)

Homeostasis The state when good (beneficial bacteria) are dominating the gut flora (microbiota)

Beneficial gut bacteria
These bacteria are creating the best fermenting milieu as well as making the digestion most efficient to avoid undigested food gets into the large intestine creatin bloating or diarrhea. In the small intestine we need a sour milieu to activate the mainly enzymatic digestion. In the hind gut the pH is towards neutral.

In the large intestine these bacteria are producing byproducts = metabolites = molecules which are essential for our immune system and metabolic health.  

Good gut bacteria have as well an active defense system against bacteria, viruses and parasites.  The official probiotic bacteria are just a small part of all beneficial bacteria existing. Probiotics are not supposed to colonize the hind gut and need a continuous external source.

Bad gut bacteria
There is no 100% frontier of good and bad bacteria. Normally bad bacteria producing toxins that could kill good bacteria can eliminate the mucus, cause inflammation on the gut liner and can even create holes in your gut. There will be always some bad bacteria in the gut. Our gut is protected as long as the beneficial bacteria are in majority. After the administration of antibiotics, it is very important that we support the re-colonialization actively with good beneficial bacteria. 

Once the gut has too much bad bacteria, (dysbiosis) it is very difficult to get out of this vicious circle. Consistent diverse plant diet with fibers and polyphenols, reduced sugar and meet intake is key to build a sustainable microbiota which is working in favor for you. 

Microbial diversity and quantity
A healthy gut can contain more the 1000 bacterial species. 50-60% of our stool is bacterial mass. This diversity is influenced by the diversity of our daily plant-based food intake. In the circuit of aging quantity and diversity is changing significantly. As we are getting older, we naturally lose both, but depending on nutrition, it will be significantly different. Bacteria diversity and quantity is key for the functioning of the immune system, organs metabolism and cognitive function.

Tight Junction
The epithelia cells are “glued” together with a collagen which is flexible. It is maintained and repaired by the body adaptive immune system. Via butyrate, the immune system is producing immunoglobulin A to maintain and repair the tight junction. Butyrate is a SCFA that is produced by the bacteria of a healthy gut.

A film of viscous liquid (exopolysaccharides) which protects the epithelia like a physical barrier. The mucus is one of the most important part of the first line of defense of the immune system. Among the factors influencing the mucus barrier, the microbiota and the dietary habits play a major role. Mucus is as well called mucins which do have different qualities depending on their function. In the mucus there are living good beneficial bacteria which additionally help antimicrobial activity. For example, bad bacteria like salmonella can eliminate and partially destroy the mucosa, with all its negative consequences. 

Goblet Cells
The intestinal wall is covered with a thick layer of mucus that is secreted by goblet cells and functions primarily as a first barrier from damage by toxic substances. The goblet cells are integrated in between the gut cell walls or villus. Recent studies showed that goblet cells and mucins are involved in complex immune function. 

Dendric cells  
In between our classic digestive gut cells, we have dendric cells which are part of gut immune cells. Dendritic cells (DCs) are antigen-presenting cells that play an essential role in linking the innate and adaptive immune systems. They function as the messenger in our immune system.

Mucosal dendritic cells constantly survey the luminal microenvironment which contains commensal microbiota and potentially harmful organisms regulating pathogen recognition and adaptive as well as innate defense activation. Distinct mechanisms are beginning to emerge by which intestinal antigen sampling and handling is achieved, ensuring specificity and contributing to redundancy in pathogen detection. 

The three lines of defense
The human microbial defense system can be simplistically viewed as consisting of three levels or three lines of defense: 

  • First: anatomic and physiologic barriers. An example is skin stomach acidity mucus. 
  • Second: innate immunity. This protection is performed by cells of both hematopoietic and nonhematopoietic origin. Macrophages are effector cells of the innate immune system that phagocytose bacteria and secrete both pro-inflammatory and antimicrobial mediators.
  • Third: the adaptive immunity, also referred to as acquired immunity or specific immunity

 picture emerges of a child born with an immature, adaptive immune system, which matures and acquires memory as he or she grows. Together with the dendric cells the microbiota is an intermediator of our immune system. The microbiota is training, informing and feeding this immune system.

Knowing that your gut skin makes 90% of its surface compared to your outside skin, it makes sense that most of the attention of our immune system is given to the gut.

Therefore 90% of your immune system is placed in your gut. Let’s think it now reverse: if your gut is not treated right, your immune system is in big jeopardy.  

Bacteria are fermenting (eating and converting) other bacteria or fibers (fiber and polyphenols) and producing thousands of molecules which are important for our metabolic functioning. Important examples for metabolites are SCFA (shortchange fatty acid) and exopolysaccharides. These and other metabolites are indirectly activating the production of hormones and neurotransmitters. With this process, 80-90% of hormones are produced in the gut. A not well functioning gut will produce significant less of these metabolites and thus miss out on this essential metabolic contribution.

Shortchange Fatty Acids (SCFA)
Butyrate, for instance, is a SCFA that is produced as a result of plant material fermented by a healthy gut microbiota in the hind gut. It’s a high sophisticated enzymatic breakdown. These enzymes are mainly microbiota based. SCFA provide 5 to 15% of our daily energy. Butyrate has a key role in our immune system. SCFA trigger the adaptive immune system via activation of immunoglobulin A and is very important for the epithelia health as well as the Blood Brain Barrier (BBB). Another very important SCFA are propionate. Butyrate and propionate need to be in a certain balanced level. It was observed that too high levels of propionate cause behavior issues.

Bad gut bacteria produce toxins like LPS (lipopolysaccharides) which can kill good gut bacteria. These toxins are as well able to destroy the mucus and even the tight junction which holds the gut cells together and lead to leaky gut. A not well functioning gut (dysbiosis) is producing significantly more toxins.

These are the toxins that are released by the bad bacteria or are placed on the bacterial wall like LPS. LPS can destroy beneficial gut bacteria, its mucus and cell wall.


Compromised GI 

First line of defense
The human microbial defense system can be simplistically viewed in three lines of defense. The first line are the anatomic and physiologic barriers. Examples of this are skin (outside & inside), stomach acidity and mucus. This line is essential and its malfunctioning is the beginning of most of our metabolic diseases. One example is the stomach acidity. It can be reduced by pharmaceutical molecules like Proton pump inhibitor (PPI). Unfortunately, the side effect of having less acidity in the stomach will permit more non beneficial bacteria to penetrate this important line of defense and ultimately alternate the microbiota in a way which would produce less butyrate. Butyrate is a key metabolite for gut skin wellness. As a result, gut cell inflammation cannot be repaired which might evolve to ulcers or leaky gut. As a consequence, this leads to further and deeper inflammation in the organs or even sepsis. The door to metabolic diseases has opened.

Dysbiosis is a condition caused by an imbalance in the bacterial community (microbiome) of the human gut. Dysbiosis disrupts the ecosystem of the gut, resulting in symptoms such as diarrhea, constipation, bloating and indigestion, among others. Dysbiosis is a result of environment and lifestyle. Dysbiosis favoring factors are: stress (physical and mental), antibiotics, pain killer (NSAIDS), pesticides, infections (bacterial and viral), nicotine, cesarian, not diverse diet, missing fermented food intake.  Long-term dysbiosis can result in following GI diseases.

Compromised Mucus Layer
Stress (physical and mental), pain killer (NSAIDS), bacterial infection (salmonella), dysbiosis, pour diet are compromising the mucus layer. Once the mucus of the epithelia is not complete, food and toxins are touching the gut and causing inflammation (immune reaction) to increase blood circulation on the gut liner. If this is chronic, we can get ulcers and later leaky gut. A lot of diseases are linked to the degradation of the mucus layer.

Leaky gut
The healthy gut liner is a non-interrupted epithelia cell wall, which is a hair thin layer. 

In a healthy gut the epithelium is covered with a mucus layer to protect this sensitive skin with its well-maintained tight junctions in between. External factors and dysbiosis can disrupt this skin cell conglomeration (tight junction) and holes are appearing. 

Leaky gut is one of the main contributors for food allergies. Undigested food gets unfiltered straight in the blood causing immunoreactions with different inflammation as a result.   

If our tight junction of the blood brain barrier (BBB) is not maintained, we can create similar situation and these toxins might migrate through the BBB.

Strong inflammation points due to the loss of mucosa. Chronic ulcers are mostly benign, but they can sometimes develop into a malignant ulcer, termed stomach cancer, which is why an upper endoscopy with biopsy is essential to the diagnosis. Chronic ulcers sometimes don't cause any symptoms. When they do, the most common symptom is dyspepsia.

Gut Inflammation
Stress, pain killer, dysbiosis, bad bacteria, viruses and toxins can be the origin of gut cell inflammation. In the moment inflammation is very strong leaky gut can appear. Once we have a leaky gut, bacteria, viruses, toxins and food can migrate into the blood stream and cause inflammation in blood vessels or organs leading to general metabolic diseases like diabetes, non alcoholic fatty liver disease (NAFLD) and liver inflammation.

Gut bleeding:
Strong inflammation in the gut can be manifested with visual blood in the stool. If it’s dark, it is more likely from the small intestine. When it’s fresh, it is from the hind gut.

Sepsis derived by the gut 
When bacteria or their toxins migrate from the gut into the blood stream and all our organs. An example is salmonella poisoning. Leaky gut is the origin of such a sepsis.

Irritable Bowel Disease  (IBD)
IBD is a term for two conditions (Crohn's disease and ulcerative colitis) that are characterized by chronic inflammation of the gastrointestinal (GI) tract. Prolonged inflammation results in damage to the GI tract. 

Gastroesophageal Reflux Disease (GERD)
Gastroesophageal reflux disease (GERD) occurs when stomach acid repeatedly flows back into the tube connecting your mouth and stomach (esophagus). This backwash (acid reflux) can irritate the lining of your esophagus. It is widely recognized that GERD is related to dysbiosis. Improvement of your microbiota can reduce or eliminate the symptoms.


Gut health natural influencer and supplements

Probiotic in general
These are bacteria which have a clinical proven health benefit in the digestive system. These bacteria are normally not meant to colonize the gut. During the way through the gut, they have beneficial functions like antimicrobial, anti-inflammatory and pro-activating the growth of the mucus. These specific beneficial bacteria were isolated from healthy animals, humans, soil or plants.


Probiotic frieze dry frozen pills
These pills normally contain a variety of different beneficial bacteria (Probiotics).

They are not active but in a dormant status. They do not contain any fermentates or postbiotics like lactic acid, exopolysaccharides (EPS) and beta glucans. In the passage of the digestive track the bacteria need to wake up and get adapted to the environmental conditions in order to support the gut with fermentation and its metabolites. These are not always in favor for survival and even less for fermentation. Profound Fermented coconut water is a perfect source for a beneficial bacteria blend. These bacteria are alive and support your body naturally in the moment they reach your mouth and throughout your whole GI system.

Prebiotic and fiber
Prebiotics are meant not to be digested in the small intestine and are specific food sources for all your different bacteria in the hind gut. Fiber is a long chain sugar molecule (larger than 3) like 

  • FOS Fructo-Oligosaccharides, 
  • Inulin
  • GOS Galacto-Oligosaccharides,  
  • Beta glucans 
  • Exopolysaccharides
  • and many more...
For example, GOS do have dozens and more of different variants. There are fare more than 100 different fibers which have all different functions to feed different bacteria and produce different metabolites which directly or indirectly activate the immune system or the metabolic functions in our body. If we do not administrate our gut multiple fibers, certain beneficial bacteria will not grow and certain metabolites will not be produced. The intake of a singular fiber source like inulin is good for some bacteria and frequent stool but does not sufficiently contribute for a diverse microbiota and its diverse and essential metabolites. 

If you want to improve your digestive gut health, it is very important to combine beneficial fermented food with prebiotics. 

Prebiotic polyphenols
Polyphenols are not meant to be digested in the small intestine and are food for our bacteria.

Polyphenols are hundreds of different plant molecules which have all different functions to feed different bacteria and produce different metabolites which directly or indirectly activate the immune system or the metabolic functions in our body. Most common food with good sources of polyphenols are present in coffee, tea, ginger, turmeric, pomegranate, cranberry and blueberry . In resent research polyphenols are often related with anti-inflammatory beneficial effects. It is recommended to have 500 to 1000 mg of daily polyphenols intake.  

Polyphenols can boost, but also could individually limit the growth of specific bacteria. It is important not to overdose and feel the reaction of your body.

Postbiotics are functional bioactive compounds, generated in a matrix during fermentation, which maybe promote health benefits. The term postbiotics can be regarded as an umbrella term for all synonyms and related terms of these microbial fermentation components and / or fermentates. Therefore, postbiotics can include many different constituents including metabolites, short-chain fatty acids (SCFAs), microbial cell fractions, functional proteins, extracellular polysaccharides (EPS), cell lysates, teichoic acid, peptidoglycan-derived muropeptides and pili-type structures.

Studies provided evidence that even non-living probiotic bacteria can prevent the development of severe forms of intestinal inflammation by strengthening the integrity of intestinal barrier and modulation of gut microenvironment. Profound fermented coconut water is a perfect natural source of postbiotics.

Lactoferrin is a multifunctional protein that is found in milk. It is involved in fighting against infection and inflammation in the gut and it acts as an antioxidant. Lactoferrin is a multifunctional protein of the transferrin family. Lactoferrin is one of the components of the immune system of the body; it has antimicrobial activity (bacteriocide, fungicide) and is part of the innate defense, mainly at the mucosa. In particular, lactoferrin provides antibacterial activity in the gut of human infants.

Omega 3
The unsaturated fatty acid Omega 3 is present in fish oil which has proven anti-inflammatory properties to maintain or heal inflamed gut wall. Big part in the immune system is to keep the gut wall / epithelium intact and healthy. Once it is inflamed, it has the risk to break and create holes (leaky gut), which then leads to more inflammation throughout the body. A vicious circle which is difficult to break. Omega 3 is another natural and sustainable way to support to heal the inflammations.

There is increasing evidence that the following vitamins have modulating effect on the gut and gut bacteria (microbiota)

Following vitamins can be used, 

  • To increase the amount of gut bacteria (Vitamins A, B2, D, E)
  • To increase the diversity of gut bacteria (Vitamins A, B2, B3, C, K)
  • To Increase shortchange fat acid producer SCFA (Vitamins B2 E)
  • To maintain / improve gut barrier function (Vitamins A D) 


Fermented Food

Profound is fermented coconut water with a touch of malt. For the fermentation we use a specific variety of the world most studied lactic acid probiotic bacteria. We keep the acidity (pH) high to keep the beneficial bacteria alive. After the fermentation all the different initial sugars are almost completely converted into living bacteria and postbiotics, lactic acid, vinegar acids, EPS, beta glucan which do have beneficial anti-inflammatory effects. Profound was not developed to produce a specific pleasant taste but to apply the paramount techniques of precise fermentation in order to create the most important beneficial components of fermented food.

Profound does not contain yeast, lactose, alcohol or undefined wild cultures. Every batch of fermentation is producing the same bacteria and metabolites.

Kombucha is an Asian way to ferment tea with sugar via yeast-vinegar bacteria also called Scoby. Kombucha does contain mostly vinegar acid (acetate) and very little live bacteria due to the low pH of 3.2 or lower. Beneficial bacteria cannot survive this acidity. There are no clinical studies about kombucha tea or its bacteria available. Some are made with wild cultures, some use specific cultures. 

Kimchi is a Korean dish of spicy pickled fermented cabbage.

There are hundreds of different types of kimchi made with different vegetables as the main ingredients. Kimchi normally does contain a large unspecific variety of different cultures like Lactobacillus and yeast. Normally it only contains wild cultures.

Traditional yogurt is made from cow milk and two bacteria strains: lactobacillus thermophilus and streptococcus bulgaricus. Fermented yogurt contains live and active bacterial and lactic acid which is always beneficial for your gut, if you are looking for a natural way to support it.


Kefir is a fermented milk drink that is made from kefir grains, which house a wide blend of mesophilic symbiotic cultures bacteria. Apart from lactobacillus kefiranofacience, the grain contains multiple different lactobacillus and yeast cultures. The kefir grain contains yeast with significant CO2 production and has only a short shelf life. The grains can be purchased in the specialized stores. Most of the kefir you find in the shelves of the supermarket do not contain these mentioned strains. Overall, there are no clinical studies about the health benefits of Kefir, nevertheless there is a belief that the original kefir made out of the kefir grain might have beneficial benefits.

Traditionally all the cheese had been made in combination for rennet and bacterial fermentation. Because of industrial simplicity and cost saving, most of the cheeses do not contain any bacteria. If you want to increase bacterial diversity via natural classic food, you need to check if your cheese is fermented and contains lactic acid bacteria in the ingredient statement. 


Gut OTC Medication

Proton Pump
PPI Proton pump inhibitors, gastric acid and microbiota.

Proton pump inhibitors (PPIs) are common medications within the practice of gastroenterology. These drugs, which act through the irreversible inhibition of the hydrogen/potassium pump (H+/K+-ATPase pump) in the gastric parietal cells, are used in the treatment of several acid-related disorders. PPIs are generally well tolerated but, through the long-term reduction of gastric acid secretion, can increase the risk of an imbalance in gut microbiota composition (i.e., dysbiosis). The gastric acid has a protecting task to keep bad bacteria mainly not acid resistant out of the gut. The gut microbiota is a complex ecosystem in which microbes coexist and interact with the human host. Indeed, the resident gut bacteria are needed for multiple vital functions, such as nutrient and drug metabolism, the production of energy, defense against pathogens, the modulation of the immune system and support of the integrity of the gut mucosal barrier. 

After a long-term administration of PPI, it could be observed that the microbiota is shifting towards a less producing butyrate flora. Butyrate is a shortchange fatty acid, activating the immune system via immunoglobulin A, & Bile to maintain the tight junction of our gut epithelia. 

Even so PPI are GRAS, a long-term use of these OTC should be very closely discussed with you physician in the surge for more natural ways. 

It is widely recognized to combine the administration of PPI with beneficial bacteria such as probiotics postbiotics and fermented food.  


We're discovering more and more every day about how to optimize the gut biome.   Check back for more information soon!