Gut Microbiota: The 1000 Species Of Bacteria That Live In Your Belly

Two kilograms of microorganisms, over a thousand different species, one hundred and fifty times more genes than you: this is what lives in your intestines, and especially what this little community produces for you at every meal.

The gut microbiota, an invisible world to discover.

From a distance, a tree looks like a spoon: a straight trunk topped with an oval mass. Except that there are as many roots underground as there are branches above. Our body works a bit the same way: we only see the outer shell, and we forget everything that is bustling beneath.

Now, under your skin, a lot is happening. And the most densely populated place in your entire organism is neither the mouth, nor the skin, nor the armpits: it’s the intestine. Of all the microorganisms that live in and on you, 99% are found there, in the last meters of the digestive tract.

The mapping of these bacterial populations is recent: it began in 2007, with swab samples taken from various places on volunteers (mouth, forehead, armpits, feces...). The result: places thought to be sterile, like the lungs, turned out to be inhabited. In short, we are just beginning to explore this little world.

100 trillion microorganisms housed in your belly

The numbers are dizzying. Your gut microbiome can weigh up to two kilograms and hosts about 100 trillion bacteria. To give you a more relatable idea: a single gram of feces contains more bacteria than there are humans on Earth.

They are not distributed randomly. In the upper segments of the digestive tract, they are very few in number. It is as you go down that the population explodes: the large intestine and rectum are the most populated areas. Some species prefer the small intestine, others live exclusively in the large intestine, and still others never leave the mucosa or the appendix.

This distribution is not trivial. Bacteria are concentrated where digestion is nearly complete, so they do not steal your meal: they take care of the leftovers. When this balance is disrupted and they massively colonize the small intestine, it is referred to as chronic bacterial overgrowth of the small intestine, which can cause bloating, stomach pain, joint pain, deficiencies, and anemia.

One last tasty detail: more than half of these bacteria are so accustomed to you that they cannot survive anywhere else. When placed in Petri dishes in the lab, they go on strike. Your intestine is their home: sheltered from oxygen, warm, moist, and with the food already pre-chewed.

The five major bacterial strains that make up your microbiome.

Despite this diversity, the vast majority of your gut bacteria descend from only five major strains. At the forefront are two heavyweights: Bacteroidetes and Firmicutes. They make up the bulk of the population.

Next are three less massive but still significant strains: Actinobacteria (actinomycetes), Proteobacteria (proteobacteria), and Verrucomicrobia. There you have it, the framework of your gut flora.

These names may seem abstract, but they are useful: lactobacilli, the bacteria whose name you have likely seen on a yogurt container, belong to the Firmicutes, for example. Each strain has its dietary habits, preferred companions, and metabolic specialties.

From strain to species: understanding bacterial classification

Inside each strain, we subdivide, reclassify, and refine until we arrive at a family of bacteria. And within a family, we resemble each other quite a bit: we eat the same things, we have roughly the same appearance, the same skills, and the same acquaintances.

Going down another level, we encounter species, with those well-known two-part names familiar to microbiologists: Bacteroides uniformis, Lactobacillus acidophilus, Helicobacter pylori. In total, the small intestine and large intestine host more than a thousand different species of bacteria, not to mention the minorities: viruses, yeasts, fungi, and various unicellular organisms.

Why does this level of detail matter? Because two bacteria from the same family can have radically opposite effects. E. coli, a perfectly ordinary tenant of our intestines, and its twin EHEC, responsible for severe hemorrhages and diarrhea, are very close on paper. In other words, reasoning solely in terms of large strains is not enough when trying to determine who causes damage.

Nota Bene: For a long time, it was believed that the flora was roughly the same in everyone, simply because E. coli was always found in culture media. We now know that E. coli represents less than 1% of all the organisms present in the intestine.

Microbiota, microbiome, gut flora: what are the differences?

Three words circulate, often used incorrectly. Let's clarify, it's simple.

The expression gut flora is a historical legacy: at a time when bacteria were poorly understood, they were classified within the plant kingdom. The term is therefore not accurate, but it remains very descriptive, as like plants, bacteria are categorized according to their habitat, their food, and their level of toxicity.

The correct term, from a scientific perspective, is microbiota (from Greek "small" and "life"): it refers to the population of microbes that inhabit you. The microbiome, on the other hand, refers both to the environment in which they live and the total sum of all their genes.

Keep this distinction in mind, it appears everywhere: the microbiota refers to the inhabitants, while the microbiome refers to the territory and genetic heritage of these inhabitants.

Enterotypes, or the bacterial profiles that bring us together.

Faced with this apparent chaos, researchers from Heidelberg expected to find a joyful mix without logic. Surprise: despite the diversity, an order emerges. In every intestine, it is always one of the same major bacterial families that dominates. These profiles, called enterotypes, were highlighted in 2011 among Asians, Americans, and Europeans, regardless of age or gender.

Three families share the role of leader. Bacteroides, the most well-known and massive, excels in carbohydrate assimilation: it has a battery of genetic plans allowing it to produce almost any enzyme, no matter what you consume. It is more commonly found in heavy consumers of meat and saturated fatty acids, and it produces a lot of biotin.

Prevotella is somewhat its opposite: more frequent in vegetarians but also present in meat eaters. Its work produces sulfur compounds (the characteristic smell of hard-boiled eggs), which are fortunately captured on the fly by its colleagues Desulfovibrionales, equipped with small flagella. Its emblematic vitamin is thiamine, vitamin B1.

Ruminococcus is a topic of debate: some teams have not found it, others swear it exists, while others still talk about a fourth or fifth group. Its supposed food source: the cell walls of plants. These bacteria produce heme, a substance that the body needs to produce blood. Ultimately, knowing one's enterotype may help predict concrete things: the ability to assimilate soy, nerve strength, risk of developing certain diseases.

The essential role of bacteria in digestion.

When feeding a child while reciting "one spoon for dad, one spoon for mom," we forget a good part of the guests. A small portion of each spoonful goes to the Bacteroides, another to the Prevotella, and a crumb to the other microbes seated in the belly.

And this sharing lasts a lifetime. Your bacteria break down for you the foods that you would be unable to digest on your own, particularly plant fibers, and they return the favor in the form of nutrients small enough to cross your intestinal cells. They also supply your intestines with energy, break down toxins and medications, and train your immune system.

The large intestine is their workshop. It no longer has the velvety villi of the small intestine, but it takes its time: about sixteen hours meticulously sorting through the leftovers. It is here that important minerals like calcium are finally absorbed, and where collaboration with the flora provides an extra dose of highly energetic fatty acids.

A little practical advice: if you mainly eat low-fiber products (pasta, white bread, pizza), do not suddenly increase your fiber intake. A bacterial community already in poor shape will then start to metabolize everything that passes through, leading to a big festival of gas. Increase gradually, without exaggerating the doses.

Vitamin factories nestled in our intestines.

Your bacteria do not just digest: they produce. The collaboration between the large intestine and the microbiota provides you with vitamin K, vitamin B12, thiamine (B1), and riboflavin (B2). A useful cocktail for coagulation, nerve balance, or migraine prevention.

Let’s take biotin, also known as vitamin B8 in France (B7 in Anglo-Saxon countries, formerly vitamin H). It is known that intestinal microbes produce it, simply because some people excrete more than they ingest, and no human cell is capable of producing it. Beyond the promises of strong nails and shiny hair, biotin is used to manufacture carbohydrates and lipids and to break down proteins.

Thiamine (B1), on the other hand, nourishes nerve cells and allows them to be wrapped in an insulating fat sheath. A deficiency can therefore cause muscle tremors, memory loss, irritability, headaches, and concentration problems. Beriberi, described as early as 500 AD in Asia, corresponds to a severe deficiency: damaged nerves, atrophied muscles, impossible walking.

A word of caution: when talking about vitamin deficiency, the list of symptoms is always so long that everyone feels concerned by one point or another. One can be tired or have a cold without lacking anything. The true at-risk populations are more targeted: prolonged antibiotic treatments, high alcohol consumption, removal of part of the small intestine, dialysis, certain medications, and pregnant women, whose fetus consumes a lot of biotin.

Bacterial genes, a remarkable reservoir of skills

Genes are primarily plans, possibilities. They are useless until they are read and utilized. However, collectively, your gut bacteria possess one hundred fifty times more genes than you do.

Acquiring bacterial skills is astonishingly easy: you just need to swallow them. They settle in, adapt to your living conditions, and get to work. And unlike a fixed genetic heritage, this stock evolves: the milk-digesting assistants, very active in infants, gradually disappear after weaning.

These genes tell us a lot of very concrete things. In an infant, there are more active genes dedicated to digesting breast milk than in an adult. The intestines of overweight individuals often harbor more bacterial genes dedicated to carbohydrate breakdown, while those of elderly people have fewer anti-stress genes. The intestines of Tokyo can break down seaweed, while those of Châtillon-sur-Seine can do so much less.

Two telling examples for everyday life. Paracetamol is more toxic for some people than for others because gut bacteria produce a substance that affects the liver's ability to eliminate the molecule. And the protective effect of soy, which is real, benefits over 50% of Asians compared to 25 to 30% of Westerners: the difference does not come from our own genes, but from a type of bacteria more commonly found in Asian intestines, which tickles tofu until it releases its best substances.

Thousands of genes per bacterium: a colossal genetic heritage.

Let's do the math. A bacterium generally has a few thousand genes. And there can be up to a hundred trillion bacteria per intestine. The total far exceeds what a three-column table can represent: the first diagrams of the microbiome resemble contemporary art more than a school diagram.

This gigantism poses a real methodological problem, very similar to that of the Google generation: you ask a question, six million sources respond at once. It's impossible to say "one at a time." Therefore, it is necessary to form relevant groups, radically sort, and look for recurring patterns. The discovery of enterotypes in 2011 was a first step in this direction.

And when we look at the whole rather than the detail, it is the similarities that prevail. Each microbiome contains numerous genes that allow for the breakdown of carbohydrates and proteins, and the production of vitamins. The small local specialties (processing an analgesic, valuing soy) take a back seat.

Beneficial, neutral, or pathogenic bacteria: who inhabits your gut?

Every day, you swallow billions of live bacteria. They are on raw foods, some survive cooking, others come from your mouth, your distractedly bitten pinky finger, or a slightly passionate kiss. A small portion withstands the acidity of the stomach and arrives alive in the large intestine.

The majority of these bacteria are unknown to us. They are likely harmless, perhaps even beneficial, though we don't yet know why. A few are pathogens, but they generally cannot cause harm because they arrive in too small numbers at once.

In the intestine, the good and the bad coexist, and that's perfectly fine. Most bacteria are quietly settled in the mucous membranes: they teach the immune system, take care of the villi, consume what you don't need, and produce vitamins. Others, closer to the intestinal cells, occasionally poke them or produce toxins. When this coexistence is balanced, the bad makes you stronger, and the good takes care of you.

Bacterial toxins concern everyone. They appear, for example, when the scant available fibers are exhausted too early, and the late-stage bacteria rush for the unabsorbed proteins. An excess of these toxins damages the large intestine, and it is precisely in this last section that colon cancer most often occurs.

Probiotics, these recognized bacterial allies.

Among the thousands of species that pass through our intestines, few are known from A to Z and have been officially declared beneficial. These are what we call probiotics. Among the most resistant to digestion are Lactobacillus rhamnosus, Lactobacillus acidophilus, and Lactobacillus casei Shirota.

Research has identified three main areas of action. First, care: some produce small fatty acids, such as butyric acid, which coat the intestinal villi. As a result, these become larger and more stable, making them more effective at absorbing food, minerals, and vitamins, while being less permeable to waste.

Second, safety: good bacteria physically occupy the favorite spots of pathogens, produce small doses of antibiotics and antibodies, and acidify the environment to make it inhospitable. Some even engage in systematic food theft until the unwanted guests leave. Third, advice: by communicating with the intestine and immune cells, they indicate how much protective mucus to produce, how many defensins to manufacture, and whether the immune system should get agitated or remain calm.

In practice, their most solidly demonstrated competence is in fighting diarrhea: in cases of intestinal flu or antibiotic-related diarrhea, they reduce symptoms and shorten the episode by about a day, almost without side effects, which is valuable for children and the elderly. Regular consumption also seems to make colds less frequent or less severe, especially in seniors and highly active athletes. If you test a strain for another issue, the procedure is simple: note what you take, follow the treatment for four weeks, and if nothing changes, try another one.

Each individual, a unique bacterial ecosystem.

Your collection of bacteria belongs only to you. One could almost derive a personal bacterial fingerprint from it. Take microbes from a dog, analyze their genes, and you will most likely find its owner. The same goes for a computer keyboard: the objects we touch regularly carry our microbial signature.

In 2011, American researchers studied, with no other intention than to have fun, the flora of volunteers' belly buttons. In one of them, they found bacteria previously known only from the Japanese coast. The participant had never set foot in Asia. Every day, trillions of microorganisms travel around the planet without paying a dime for a ticket.

What determines your gut population is not your DNA: identical twins have the same genetic heritage but not the same flora, and they do not resemble each other any more in this regard than any other siblings. Three factors are particularly important: a microorganism settles if it likes the architecture of your intestinal cells, if it can tolerate the local climate, and if it enjoys the cuisine served.

This uniqueness obviously complicates the work of researchers, who are looking for patterns, not individual cases. But it also explains why your neighbor can digest a piece of moldy bread without flinching, or gains weight faster than you at equal quantities.

The human being rethought as a true living ecosystem.

Seen up close, each of us is a small planet: the forehead is an open meadow, the elbows a desert, the eyes salt lakes, and the intestines a gigantic jungle populated by the most astonishing creatures. We inhabit the Earth, and we ourselves are inhabited territories.

Science now considers the human being as a complete ecosystem. Research on the microbiome is still very young, and many questions remain unanswered: changes in bacterial life in the intestines are observed in cases of overweight, malnutrition, depression, nervous diseases, or chronic intestinal disorders, without always knowing which way the cause goes.

What you can do, however, is simple and concrete. Feed these inhabitants with real fibers, those from vegetables and the flesh of fruits, rather than with factory-processed white flour, and gradually increase the doses. You might also test live bacteria during difficult times (after an antibiotic treatment, for example), giving yourself four weeks to assess. And don’t worry about a little gas here and there: it’s a sign that your microbial organ is working.

Two kilograms, one hundred trillion microorganisms, over a thousand species, one hundred fifty times more genes than you: this is the team that digests for you, produces your vitamins, trains your defenses, and protects you. It deserves a bit of attention, and it will repay you well.