My Microbiome at different body sites

If you look at the Earth from outer space you aren't able to see any animals,
plants, insects and everything 
else that lives on it… the same happens
when you look at a person.

Each of us is like our own planet and is host to trillions of “inhabitants.”

If you saw the human body through a microscope, you could explore deserts,
river valleys, dangerous swamps, acid lakes, humid jungles — just look at the nose:
with every sneeze, a 300 km/h hurricane occurs, with peptides killing invading strangers.

The ecosystems on this planet, the human body, are vastly diverse — and so are its inhabitants.

Among them, bacteria are the uncontested champions in adapting to a variety of ecosystems.


More than six billion microorganisms live in your mouth. They form different ecosystems on your oral mucosa, teeth and tongue.


Your stomach is an acid lake, only giving a few very specialized bacteria the chance to survive. These bacteria regulate your stomach's acidity and regulate your appetite!

Intestines and colon

The further down you go, the more bacteria are living in your gut. With a million times more bacteria than on your skin or in your mouth, your intestinal wall is covered with a carpet of bacteria.


Vaginal Microbiome

A very unique and specialized ecosystem, allowing only some Lactobacilli and friends to live there. These inhabitants are doing a great job at fighting invading adverse organisms.


The skin comprises widely differentiated landscapes, each with a unique ecosystem. You find deserts like the forearms, humid jungles like the axillary fault or greasy areas like the forehead. Through the intense hygiene in the western civilisation we already lost a great part of our microbial diversity on the skin.

The vaginal microbiome is extremely specialized
The vaginal microbiome is extremely specialized, allowing only a few bacterial species to live there.

If we look at the urogenital tract, we are looking at a very fussy area when it comes to its habitants. The vaginal microbiome is extremely specialized, allowing only a few bacterial species to live there. Despite its low microbial diversity, it is a unique ecosystem in humans set with the task of keeping the pH at the right level and keeping enemies out. The bacterium that loves to live here belongs to the species Lactobacillus. Most women harbor one of five different microbial communities, each dominated by one species of Lactobacillus (L. crispatus, L. iners, L. jensenii, or L. gasseri). By releasing lactic acid and chemical weapons (H2O2 and bacteriocins), it fights the colonisation of adverse organisms such as yeasts or pathogenic bacteria.


The skin, at 1.8 m2, is even more complicated because it comprises widely differentiated landscapes, each with a unique ecosystem. The so-called desert areas of the skin (dry skin such as the buttocks, forearms, and various parts of the hand) harbor the greatest microbial diversity including 19 different bacterial divisions with four main divisions (Actinobacteria (52%), Firmicutes (24%), Proteobacteria (17%) and Bacteroidetes (7%)). Even gram-negative species, which were once thought to be contaminations from the gastrointestinal tract, are present here. Interestingly, the dry skin sites harbor a greater phylogenetic diversity than the gut or the oral cavity of the same individual.

The greasy areas (sebaceous areas such as the forehead, behind the ear, the back, and the sides of the nostril) are mostly inhabited by Propionibacterium species. This bacterium usually is harmless, only fulfilling its duty to combat adverse colonizers. But with the arrival of puberty the chemical composition of the skin, primarily on the face, changes due to the shift in hormones. This change sets off a struggle between the immune system and the Propionibacteria, leading to infected sebaceous glands and thus acne.


The skin is even more complicated
The skin is even more complicated

The humid jungles (moist sites such as the navel, the axillary vault, groin, folds of the buttocks, soles of the feet, behind the knee and inner elbows) are home to the Corynebacterium and Staphylococci species. Although the microbial diversity in these areas is low compared to the dry skin sites, the amount of bacteria is the highest with about 15 million bacteria found within an area the size of a stamp.

One very important warrior of the skin is Staphlyococcus epidermidis, which actively cooperates with the skin’s immune system to keep the pathogenic bacteria (e.g. Staphylococcus aureus) out. As for all ecosystems on our body, a disturbance of this symbiosis can cause diseases. The skin diseases Atopic Dermatitis, Psoriasis, Acne vulgaris and chronic wounds are well-known examples for such dysbiosis.

Our mouth is dominated by Streptococcus.
Our mouth is dominated by one bacterial species: Streptococcus

Looking at the digestive system we begin with the mouth and its some six billion microorganisms belonging to four main microbial divisions (Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria and Fusobacteria). These are bacteria that settle in our oral mucosa, teeth and tongue, each again a different ecosystem of its own with distinctive diversity. Overall, our mouth is dominated by one bacterial species: Streptococcus.

Due to its acidity, the stomach harbors only a low diversity of microbiome, though no less important than the others. It is composed mostly of Actinobacteria and Helicobacter (e.g., H. pylori). Besides regulating the acidity in the stomach, H. pylori causes a decrease in the hormone ghrelin, which is involved in appetite regulation. Unfortunately, H. pylori has had a bad reputation throughout the last decades as a causative agent for peptic ulcers in susceptible people; consequently, it has almost been eradicated from our stomachs by antibiotics, which may be one explanation for the increase in child obesity, particularly in the United States.

The gastrointestinal tract harbors the biggest part of microbiota
The gastrointestinal tract harbors the biggest part of microbiota

If we go further down the gut to our small intestines and on through the colon, the amount of bacteria increases drastically the further we go. In our gut, there are a million times more bacteria than on the skin or in the mouth. In fact, you cannot see the intestinal wall of the colon because it is covered with a carpet of bacteria.

The gut microbiome is dominated by bacteria of two microbial divisions – Bacteroidetes and Firmicutes – their ratio is highly variable between individuals and plays an important role in obesity. A higher percentage of Firmicutes compared to Bacteroidetes in the gut was shown to cause obesity.

Besides the ability to either deposit more or less energy from food, the gut microbiome has further very important tasks. These, on one hand, include metabolic functions such as the synthesis of vitamins, the decomposition of chemicals and nutrients, the support of fat metabolism and, on the other hand, the interplay with the immune system such as the outcompeting of pathogens, and the stimulation and maturation of the immune system.

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