The food human axis for driving the gut microbiome

The food-human axis for driving the gut microbiome

Digestive system

Digestive system's anatomy

Our digestive system comprises different tracts. The length of this system is 9 meters starting from the mouth to the anus, it is like a long channel.

Oral cavity

Digestion starts in the oral cavity which has 4 organs: tongue, teeth, palate, and palatine uvula. There are also salivary glands.

Oesophagus

Then we have the oesophagus, which is a channel connecting the oral cavity to the stomach.

Small intestine and large intestine

After the stomach, there’s the small intestine which includes 3 tracts: duodenum, jejunum, and ileum. From the small intestine, we pass to the large intestine through the colon which has three parts: ascending colon, transverse colon, and descending colon, then there’s the cecum and we reach the anus.

→ The digestive system includes organs from the oral cavity to the last tract of the large intestine.

• → Gut (gastrointestinal tract) refers to the stomach, large and small intestine.
• → Intestine refers to the small + large intestine.

Functionality of the digestive system

The functionality of the digestive system means what happens in the different tracts.

Oral cavity functionality

At the oral cavity level, there’s a mechanical process: moisturizing and mixing with a salivary secretion.

Oesophagus functionality

The oesophagus has the role to transport materials to the stomach.

Stomach functionality

The stomach has a pH lower than 2 so it’s an acidic environment: there’s the chemical breakdown of material via acid secretion and enzymes. We also have mechanical processes based on mechanical contraction (peristalsis).

Small intestine functionality

At the level of the small intestine, there is the enzymatic digestion and absorption of water, organic acid substrates, vitamins, and ions.

Large intestine functionality

At the level of the large intestine, there is the dehydration and compaction of indigestible material.

Functions of the digestive system

• The ingestion of food and the digestion starts at the oral cavity.
• The digestion of food and transformation into absorbable molecules occurs mainly at the stomach level.
• The absorption of nutrients takes place mainly at the level of the small intestine but also at the level of the large one.
• The elimination of waste occurs at the large intestine level.

Digestion of food

There are different enzymes present: amylase, → Salivary enzymes in the oral cavity secreted by salivary glands start the breakdown of carbohydrates (starch and other sugars).

Stomach enzymes

• Pepsin: breaks down proteins into smaller fragments (peptides and amino acids).
• Chymosin: responsible for the casein digestion.
• Gastric lipase: involved in lipid digestion.

Absorption of nutrients

It takes place mainly in the small intestine and also at the level of the large one. We absorb:

• Carbohydrates, just in the monosaccharide forms.
• Dietary proteins are degraded, absorbing amino acids, dipeptides, and tripeptides.
• Lipids in the form of triglycerides, phospholipids, cholesterol, steroids, and fat-soluble vitamins.
• Vitamins;
• Minerals or salts;
• Water;

Digestion of carbohydrates starts in the oral cavity with amylase, meanwhile, the protein and fat digestion starts at the stomach level.

Introduction to the human gut microbiome/microbiota

Microbiota vs. Microbiome

Microbiota refers to all the microbes that inhabit a given ecosystem. An ecosystem is food for example (cheese, bread, vegetable, fruit) but also our gastrointestinal tract. Microbiota refers to microbes.

Microbiome refers to all the genomes of microbes in a certain ecosystem. So genes of microbes form the microbiome. These refer to all communities, not just one particular species.

The first information about food science started 2 centuries ago. A lot of info has been accumulated. If we speak of the gut microbiota or the gut microbiome we speak of pioneer studies that date back 20-30 years ago. To change the opinion we need at least 10 years. We’re speaking about a very important science but it’s not that old, the info is changing every year because it’s a very recent science.

Human body and microbiomes

Organs that are densely populated by microbes include hands, hair, oral, lung, and skin. Trillions of microbes inhabit and create complex relationships with our bodies. Human ecosystems are specific and adaptive. Microbes that we can find in the lungs are different from the ones we can find in the gut. Each site of the human body contains microbes but microbes are different depending on the organ in which they are present.

The number of microbial cells is very elevated (10 times higher) compared to the number of human cells in our body:

• Human cells are 10¹³
• Microbial cells in our body are 10¹⁴ (bacteria especially, fungi, yeasts, and bacteriophages)

In our body, we have more microbes than human cells. The colonization starts the first day of our life, we already have a lot of microbial cells with respect to the human ones. The source of contamination is the mother (natural or cesarean birth). The main function of a virus is to keep the equilibrium: balance of the microbial population and our cells. [10¹²/g of fecal material]

Definition of gut microbiota

The gut microbiota is a mixture of bacteria, fungi, viruses, protozoa, and archaea. The number of microbes is ten times higher than the human cells. Microbes show 150 times as many genes as those contained in our human genome. We have more microbial genes in our body than our proper genes (human genes). The gut microbiota can be considered as another organ of our digestive system. The gut microbiota is like another organ that joins the human organ (it’s the fourth one).

Cell density of microbes

The cell density of microbes depends on the organ: we have a high cell density in the oral tract but in the stomach, there aren’t many microbes because of the low pH. From the stomach level on, there’s an increase in microbes. The small intestine has an increase in microbes but it increases towards the large intestine (more distance from the stomach and more microbes present).

Taxonomy of gut microbes

Taxonomy is important to speak the same language. Species, genus, family, order, class. Phylum is the highest level of taxonomy. At the gut level, there are 4-5 different phyla that are very important: actinobacteria, firmicutes, bacteroidetes, and proteobacteria.

Firmicutes

This is the dominant phylum in the gut level, bacteria of this phylum are Gram+ and the main representatives of this phylum are Clostridium, Eubacterium, Lactobacillus, Faecalibacterium, and Ruminococcus. Not good nor bad microbes: commensal species. Clostridium can be both commensal and pathogenic depending on the species.

Bacteroidetes

They’re Gram-, mostly present in the large intestine (colon), then in the small one. They’re opportunistic pathogens: microbes that under normal conditions are not pathogens but when there are some other diseases, immunodepression, or antibiotic treatment, can become pathogens (under specific conditions). Some genera are:

• Bacteroides
• Prevotella

Proteobacteria

They’re Gram-, it includes a wide range of pathogens. They may have a role in protein digestion, but they’re mainly pathogens. When there’s a gut disease the number of this phylum increases: they can be the cause or they can be the consequence of this disease. Genera include Escherichia, Helicobacter, Pseudomonas, and Salmonella.

Actinobacteria

They’re Gram+, in most cases, they’ve a mycelium growth. Some genera are known as probiotic bacteria (pro our well-being). The genus of probiotic is Bifidobacterium. The other genera are Actinomyces and Streptomyces.

Homeostasis (eubiosis) vs. Dysbiosis

We speak about homeostasis when everything is balanced, in normal conditions. When something happens (inflammation, diseases, antibiotics) there’s a certain condition in which the equilibrium is not present anymore. In this case, we speak about dysbiosis (increase of pathogens). We go from eubiosis to dysbiosis when the equilibrium is not present anymore (unbalanced condition).

Model systems for studying the gut microbiota

We need a model system (it means a piece representative of the system we want to study) in order to study the gut microbiota. All the info is taken from fecal material and saliva. Biopsies are another method but they are made just when a patient has a disease (e.g. celiac disease) and goes to hospital to get a diagnosis. They make the diagnosis but they keep the biopsies for other studies, scientific purposes. In some cases, also urine can be used to analyze the metabolites of microbes.

So the model systems for studying the gut microbiota are:

• → Saliva representative for the microbes present in our oral cavity;
• → Feces representative for the microbes present at the intestine level;
• → Urine useful because it may give further info about human and microbial metabolites;
• → Blood microbes increase and decrease the inflammatory, antioxidant status. Analyzing blood for markers, related to some inflammatory status, for instance, can give us further information.

The oral microbiota has a different microbial composition with respect to the gut microbiota. Most of the sites of the human body which are colonized by microbes have a different microbial composition. So we can expect that each model system (saliva, feces) the microbiota will have a different composition although the genera and species are almost the same. At least the number and some types of microbes are different.

Factors that drive the normal variation of the gut microbiota

The potential factors that may have an influence on the composition and functionality of the gut microbiota in normal conditions are:

• Genetics → it’s very important; based on the different genetics of people the microbes at the intestine level may differ. For instance, peptides coming from gluten may have an inflammatory activity towards individuals that are genetically predisposed. Genetics may predispose to some diseases or to something beneficial.
• Mode of birth → (natural or cesarean) humans are contaminated by microbes since the first day of life; the microbes may vary depending on the mode of birth: with the natural birth there’s a first contamination coming from the mother meanwhile with caesarean birth the first source of contamination comes from the environment (hands of the doctor, hospital etc…).
• Antibiotics → usage in most cases while using antibiotics, the use of probiotics is recommended. This happens because antibiotics have a large spectrum of activity, they do not kill just the microbes responsible for a disease but they may also kill the other microbes that are commensal or beneficial for our body so we need to restore the group of beneficial microbes that may be killed by the ingestion of antibiotics.
• Geographical factors → the lifestyle could be very different from one country to another one and the lifestyle, social-economic conditions have a marked influence on the composition of the gut microbiota.
• Age → in the first year of human life the composition is different from the one present in adulthood.
• Dietary habits → is one of the main factors having an impact on the composition of the gut microbiota. Nutrients and food are not just nourishment for humans but they are also useful for the microbes that inhabit our intestine.
• Infant feeding patterns → (e.g., breast-fed vs. formula-fed babies, type, and time for weaning) in the human milk may be present prebiotics substances that can’t be found in the formula-fed. The type and time for weaning have an influence especially regarding the type of the diet.
• Environmental factors → (e.g., sanitary living conditions and socioeconomic status) the hygiene situation may vary from one country to another so it will have an influence on the gut microbiota and also the socioeconomic status have an influence on the diet adopted.
• Diseases → the main concern is regarding the fact that the variation/alteration of the gut microbiota may be a consequence of a disease or it may be responsible for it (cause). The conclusion is that speaking about most of the diseases that can affect humans, we always find a variation with respect to the normal composition of the normal microbiota. The main current issue is to establish if the variation/alteration of the microbiota composition is a consequence or a cause of a disease.

Age vs. gut microbiota composition

There are 7 stages, 5 of them are related to the first 2 years of life.

• During pregnancy the gastrointestinal tract is almost sterile;
• At birth depending on the mode of birth (caesarean or vaginal delivery) we may have a different composition of microbes.
• In the first month there’s an increase in Enterobacteria;
• During the first 6 months of life there’s an increase in Bifidobacteria and Bacteroides.
• After the first 24 months there’s still an increase in Bacteroidetes and also Firmicutes.
• From 2 years of life, there’s a jump to adulthood. In general, adults have an increase in Firmicutes and a decrease in Bacteroidetes. Higher content of Firmicutes with respect to Bacteroidetes.
• During elderly, there’s a decrease in Firmicutes and an increase in Bacteroidetes. The ratio is the opposite with respect to adulthood.

Most of the changes take place during the first 2 years of our life. The microbiota formed during the first years of life will follow us for the rest of our life with just a few changes.

Gut microbiota diversity throughout the lifespan

The Firmicutes/Bacteroidetes ratio is:

• Very low in babies;
• Very high in adults;
• It becomes low again in elders.

The ratio changes in the last part of our life. The age and all the factors related to it (lifestyle, dietary habits, etc.) have an influence on the microbial composition.

Diseases vs. gut microbiota composition

There is a correlation between the microbial composition of the gut and diseases. Depending on the disease, there might be a different composition of the gut microbiota (increase/decrease of some microbial groups). Also, depending on the type of antibiotic used, the effect on the gut microbiota is different. The main effect is the death of the microbes, including beneficial and commensal species.

The enterotype theory

Phylogenetic differences between enterotypes

In 2011, there was a revolutionary study on the gut microbiota. The conclusion of these works was the following: besides the age and other factors that we've already mentioned (genetics, diet…) there were essentially 3 enterotypes in the world. People had 1 of these 3 enterotypes. 3 enterotypes mean 3 different types of gut microbiota, and they’re as follows:

• The Bacteroides enterotype;
• The Prevotella enterotype;
• The Ruminococcus enterotype.

All these 3 enterotypes are connected, forming a network, with the microbes. The study showed that the gut microbiota is relatively stable and people can jump from one enterotype to another but the differences are not that big within the population.

A lot of publications showing pros and cons of the enterotypes hypothesis were released some years later. Many studies showed contradictory results for this hypothesis (e.g. larger fluctuations occurring within long intervals/periods of our lives; larger fluctuations occurring within short periods). They proved that the hypothesis is a simplification: not all the people have just 3 enterotypes, the situation is much more complicated. The main limit of the theory was related to the number of people who were subjected to the analysis. The theory was not valid anymore; in fact, increasing the number of people coming from different geographical parts of the world showed that the distribution was larger and not limited to these 3 enterotypes.

Functions of the gut microbiota

A number of studies showed that the gut microbiota has relevant functions for human health. The functions are:

• Protection against enteropathogens → Enteropathogens are pathogens which can be found at the intestinal level. So having a very good and balanced microbiota at the level of the intestine may ensure protection against pathogens. If the gut microbes are present at an elevated number there’s a competition for the space, colonization of the epithelium, nutrients and they may also synthesize antimicrobial compounds against enteropathogens. The microbiota may prevent the colonization of the intestine by pathogens.
• Immune-system maturation → Most of our immune-system develops/starts at the intestine level, most of the immune reactions take place at the intestinal level. If the intestine has 10¹⁴ microbial cells (1.5 kg) they inevitably have a role in our immune system activation and maturation. Our immune reactions are mediated by the microbes that are colonizing our intestine.
• Modulation of nutrient acquisition → Especially the small intestine but also the large one, are very important for nutrient intake/absorption/acquisition. If microbes are present at the level of the intestine, it means that they have a role in the modulation of nutrient acquisition. They may help us hydrolyzing complex carbohydrates, liberating SCFA, glucose, and so on. The activity of the gut microbiota can increase the bioavailability of some important nutrients (minerals, polyphenols, vitamins).
• Host energy metabolism → If nutrients are important for humans, also for the energetic metabolism, the host energy metabolism is somehow related to the gut microbiota composition.
• Cause-effect of several diseases? → There are ongoing studies about the role of the gut microbiota in numerous diseases.