Hint: For “atmosphere” you can listen to the music of this clip while reading…
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Let’s see now, briefly, how much the researchers struggled to “scratch” the subject of the microbiome. But in reality, know it is a long, very long way to this true beginning…
The story begins from ancient times, the first “intuitive” records being those of China, with the “yellow soup” I mentioned earlier…
Then there would be the “writings” of Aristotle and his student, Theophrastus (4th century BC).
They are the first “scientists” to mention and describe what they termed to be “little water animals”, also called “worms”, that live in water, soil, food, meat, and plants.
And, in those days, even though they found that they were invisible to the naked eye, they “managed” to observe them with a magnifying glass, their observations being essentially correct.
It would follow, also in Antiquity, from the 1st century, in the writings of Marcus Terentius Varro, who called them “animalcules” or in the Jain essays of 6th century India, which attributed to them the name “nigodas”…
There followed Avicenna’s intuitive remarks suggesting that tuberculosis was contagious, Akshamsaddin’s (a Turkish researcher) writings called “Maddat ul-Hayat” (The Matter of Life) from the 1400s, Girolamo Fracastoro’s remarks describing a mechanism of disease transmission, and others, but all were intuitive…
The next steps would be related to the discovery of microorganisms, starting in 1679 when Antoni Van Leeuwenhoek built the first microscope and opened the way to their real perception…
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But, the real discovery of microorganisms began “explosively” in the 1850s, with the discoveries of Louis Pasteur, then in 1876 with the “postulates” of Robert Koch, with the discoveries of John Hogg (1860), Ernst Haeckel (1866) and all thus, the discoveries “multiplied” considerably, with a cadence that led to the totality of today’s discoveries…
From my point of view, the story of the microbiome begins in 1845, with the birth of Ilya Metchnikov, who was to receive the Nobel Prize in 1908, for the discovery of phagocytosis, a process that underlies the role of the immune system.
And, this Ilya discovered the first “things” in 1892 when, in a study on cholera, he decided to drink cholera “soup” to get infected and “have study material”.
And, it didn’t make the disease. But, after several attempts, he managed to sicken a colleague participating in the experiment (who narrowly escaped with his life).
Thus he was able to study cholera under a microscope, and Metchnikov discovered that inside the human intestines, there are many species of bacteria, some attacking and destroying cholera, others supporting and stimulating cholera.
From here he quickly deduced that the human microbiome, even specifying the one in the digestive tract, is essential for the health of the individual, a correct balance of microbe populations being able to prevent infections, although the scientific world of those moments declared the final part of the digestive tube, the colon, as being a true reservoir of toxins.
In those days surgeons removed entire portions of the human intestine from patients with intestinal discomfort and Ilya failed to convince the scientific and medical world of the beneficial importance of bacteria in the human body.
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A decade later antibiotics were discovered (Alexander Fleming, 1928) and their use immediately increased.
The same thing happened “in time” (after the 50s), quite “correlated” with the practice of “increasing” (be it through the effect of demographic growth together with what would be the “increase in the quality of medical services)” of cesarean births, reaching in our times that one child out of three is born this way…
Then the diet was also becoming more and more processed, the risk of obesity already exceeding 25% (especially in the “Western” areas), all competing for a real war against the human microbiome with its results reflected in asthma, immune deficiencies, allergies, inflammatory diseases (of course, also in connection with “natural environmental problems”).
But this microbiome was devastated but not defeated… It cannot even be said that there is any control over it after almost 100 years of “successful” or “unsuccessful” “struggles” at the level of humanity…
Fortunately, in our times, the microbiome can no longer be neglected, even if only if we analyze its actual weight…
The term microbiome was first used in 1980 by the American microbiologist Thomas Cavalier-Smith. He used this term to describe the collection of microorganisms living in a particular habitat.
Then, it wasn’t until the 1990s that new DNA sequencing techniques were developed that allowed researchers to study the human microbiome in detail, following the “Human Microbiome Project” I mentioned earlier.
However, research into the human microbiome is ongoing. Scientists are trying to better understand the role of the microbiome in human health and disease.
For example, the bacteria in the gut alone can exceed a weight of 1.3 kg, the same weight as the brain.
So, we can already discuss a real, distinct organ… That it’s a different kind of brain, that it’s a gland, that it’s almost everything else.
And this without taking into account the reality that “tells” us that the microbiome represents 90% of our body (sorry for the continuous repetition of this information, but this is the reality)…
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Humans have already learned that the microbiome is an organ that helps digest our food, produces essential vitamins, and hormones (aka “sort of…”), responds to drugs, controls blood glucose and cholesterol levels, and other unknown functions, reacting essentially in what would be the “levers” of our health, from obesity and diabetes, going all the way to osteoporosis, getting involved in almost every process of the human body, functioning almost like a second brain…
But this role, of the second brain, is still underestimated…
For example, mice “colonized” with the microbe Toxoplasma Gondii lost their fear of cats, becoming attracted to cats… Favoring the development of cats that had easier access to food…
So, a microbial environment that takes control of an individual’s brain (behavior), even to their detriment, by “nullifying” the perceptions that make the individual survive?!?
Remember the Ophiocordyceps fungus that invades the body of ants (of several species) ends up taking control of the ant’s brain, isolating it (by abandoning the nest) and then killing it so that it can develop until the next spore reproduction? !?
Coming back to humans, I think a simple underlining of the fact that the digestive tract is connected to the brain through numerous physical and biochemical “bridges” would be enough…
First of all, the digestive tract is physically connected to the brain via the vagus nerve, one of the most important nerves, which sends signals in both directions, even though without this connection the digestive tract works without a problem, independently, literally.
Second, our brain consists of hundreds of billions of cells (neurons, glial cells, etc.) that constantly send “instructions” to our body so that it can function. Interestingly, our digestive tract has about 100 million neurons… A significant figure, no doubt…
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There would also be the fact that it has already been proven that the microbiome is the center of our immune system, even in the case of local “reactions” that will spread throughout the body, obviously affecting the brain as well.
And, to complete this brief argument about “inter-relationship”, many of the “neurotransmitter” answers have their starting point in the digestive tract, especially about serotonin, our natural anti-depressant.
Da, ați citit bine, 90% din serotonina produsă de organismul uman provine de la nivelul tractului digestiv sau datorită lui, mai puțin de 10% având ca sursă creierul.
From all this, it follows that the microbiome influences and/or controls the general state of the organism, including how the brain of that organism thinks, reacts, etc. Should I mention “I feel something here in my stomach” or “butterflies in my stomach”?!?
Studies have revealed that certain species of bacteria activate and support memory processes, stress response (by directly controlling stress hormone levels), and more…
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Following them there have already been lists of foods that can act as prebiotics, stimulating the growth and health of the bacteria inside our digestive tract… Among them are “counted” whole wheat, apples, leeks, onions, garlic, bananas, asparagus, honey bees, artichokes, nuts, roots, various seeds, beans, lentils, chickpeas, green tea, red wine and others, but all vegetables…
As a parenthesis, there are human “groups” who also consume animal products, such as fermented milk, which contribute to the positive balance of health… But that’s all?!?
A quick conclusion, especially for “carnivores” is that our overall well-being does not necessarily depend on our nutrition but on the nutrition of our microbiome. So, the treatment of imbalances, of human ailments, where mental problems are also included, must always take into account the nutrition of our microbes.
Do you think this is all vegan or vegetarian bullshit?!? I can argue the massive “tools” used for scientists to assert such a thing…
To begin with, it would be the practice that “works” based on DNA “sampling”, applying it to microbial environments that have not “grown” and isolated them, starting from a form of sampling…
So a sample is taken and the “marker” DNA sample is taken, not forgetting that that DNA comes from any type of cell in that microbial environment (where there can be many types of microbes). The sample that will be obtained will be noted to be specific, such as the one called the 16th ribosomal RNA gene.
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This is a gene that can only be found in bacteria, not being found in any other form of more advanced life (apart from the symbiotic or parasitic case). It is thus a very good biomarker for identifying bacterial origin because it has certain regions in the structure of this gene that are truly conserved throughout all known bacteria.
So we’re going to use this biomarker as an anchor, a clearly defined area as a sort of starting point. And, copies are made of this region and those between these markers, determining areas called “hypervariable” that have various sequence variations. Which variations depend on the bacteria where the respective genes come from and help to identify them, becoming real “fingerprints”.
Of course, this process will lead to the deduction of some kind of relative density of that bacterium in the studied sample, but it becomes a possibility of comparison, of delimitation, which helps us to know which bacteria are in a sample and what contribution they have, of example in health.
Similar tools were also “built” in the study of fungi, with the same abundance of species in a sample taken, a technique that was called the “interspace region”, thus being able to analyze mushroom communities (microscopic, obviously).
From here, microbiome study tools have evolved rapidly in recent years and now, instead of identifying genetic biomarkers, the entire extracted DNA content is taken and sequenced in its entirety, thus reconstructing the entire genome of all the microbes in that sample ( especially due to the recent increase in digital information processing capacity), a technique called “shotgun metagenomics”.
So, while the biomarker technique tells us “who is” in the sample, metagenomics tells us quite a bit about the organisms’ genes and what they are capable of doing.
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But, it went further than this step. RNA was also extracted from the samples, which transcribes the genes. Thus it is analyzed exactly what the transcription element of their genome is for that community of microbes, and how it reacts to the current conditions.
The analysis of this accumulation of RNA extract, also through sequencing (an operation called meta-transcriptomics), will result in a kind of gene status that will be expressed at the time of sample collection by the organisms in the microbiome.
One can go even deeper with the next generation of sequencing tools using mass spectrometry. Which can identify small molecules and thus analyze the accumulations of proteins produced by the microbiome to understand the proteins it produces and “manipulates”, not forgetting the enzymes and catalysts/catalytic functions of the microbiome.
Associated with this technique is metabolomics (metabolomics) which analyzes the small molecules through which microbes communicate with each other, in reality with which cells communicate with each other. A technique that led to the discovery of a kind of lexicon that governs interactions between microbial hosts and human hosts. There would also be photo-spectrometry and others…
Well, it has since been realized that the use of these tools, especially the DNA-based ones, have revealed a whole new world of bacteria on the planet (not necessarily “from human”)…
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And what would be the “string” of these “findings” could continue, could be more and more particularized.
In any case, I think you already have a clear picture of what the human microbiome is, possibly with the possibility of expanding your perceptions to the entire manifestation of life.
But that’s not my goal, at least now! The basic idea is to give you details of what the human “symbiote” would be.
There will be another such “informative episode” and, later, we will move on to some kind of conclusions that will “attract” the “release” of materials about the human organism, individualized or as a whole, with its path from the famous “monkey” to “ the primate” that he is now.