What microbiome analysis shows that conventional tests don't: from genetics to personal risks
The evolution of the view of the invisible "superorgan"
Modern 4P medicine (personalized, predictive, preventive, patient-centered) has fundamentally changed our understanding of human health. It has been proven that the human body is a giant symbiotic ecosystem. According to scientific estimates, the number of human cells in our body is about 30 trillion, while the number of bacterial cells reaches 38 trillion. In fact, in terms of the number of cells, we are less than half as human.
For a long time, medicine considered the gastrointestinal tract simply as a tube for digesting food. When problems arose, patients were prescribed a standard bacteriological culture of feces (analysis for dysbacteriosis). However, today scientists note that the concept of "dysbacteriosis" in its classical sense is somewhat outdated. Traditional intestinal diagnostics turned out to be "blind" to a huge layer of information. A real revolution occurred with the advent of molecular genetic methods that allowed for an accurate analysis of the microbiome . In this article, we will analyze in detail how genetic and metabolomic research differs from conventional analyzes, why commensal and conditionally pathogenic bacteria cannot be divided into absolute good and evil, how the correct ratio of microorganisms forms immunity, and how modern science determines your personal risks long before the appearance of symptoms of diseases.
1. Microflora vs Microbiome: Why conventional tests are "blind"
To understand the value of the latest methods, it is necessary to distinguish between two fundamental concepts: microbiota and microbiome.
Microbiota is the collection of living microorganisms in a particular environment that can be isolated and cultivated (grown in a Petri dish) using available microbiology methods.
The microbiome is a much broader concept. It encompasses the genes of all microorganisms (bacteria, viruses, microscopic fungi) that inhabit us, as well as the products of their vital activity and the environment in which they exist ("theater of activity").
Conventional stool analysis (bacteriological culture) can only show a small part of microorganisms that can survive and grow in laboratory conditions in the presence of oxygen or in special chambers. However, the vast majority of intestinal microflora are strict anaerobes (bacteria that die at the slightest contact with oxygen). In addition, there is a huge number of bacteria that, in principle, cannot be cultivated artificially. Conventional analysis simply does not see them.
Modern microbiome analysis (for example, next-generation sequencing - NGS or 16S rRNA sequencing) does not require growing bacteria at all. Instead, laboratory technicians isolate total DNA or RNA from a sample and read the genetic code. This method allows you to identify all intestinal bacteria to the level of family, genus and even species, regardless of whether they are cultivated at all. Thus, genetic analysis opens up to the doctor a complete, 100% map of your inner world, which classic bacterial culture cannot do a priori.
2. The illusion of "good" and "bad": Commensals and opportunistic bacteria
In classical medicine, it was customary to consider certain bacteria as beneficial (for example, bifidobacteria or lactobacteria), while others were exclusively harmful. Modern science about the microbiome destroys this dogma: there are practically no absolutely "bad" or absolutely "good" bacteria in our body (unless they are direct pathogens of acute infections).
Most of our flora is made up of commensals - bacteria that have evolved with us and perform a symbiotic function. They form the so-called "colonization resistance": by physically occupying space on the intestinal mucosa and producing specific substances, they prevent external pathogens from gaining a foothold and causing infection.
In turn, opportunistic bacteria (for example, certain strains of Escherichia coliCandida, fungi, or Enterococcus faecalis ) are also a normal part of our ecosystem. In small quantities, they train our immunity, keeping it in a state of constant readiness. Problems begin only when the ecological balance is disturbed. If commensal bacteria die en masse under the influence of stress, antibiotics, or an excess of sugars, opportunistic flora begins to multiply rapidly in an empty place, secreting toxins and provoking acute inflammation. That is, the disease is caused not by the presence of bacteria, but by the loss of environmental control over it.Candida , or Enterococcus faecalis ) is also a normal part of our ecosystem. In small quantities, they train our immunity, keeping it in a state of constant readiness. Problems begin only when the ecological balance is disturbed. If commensal bacteria die en masse under the influence of stress, antibiotics or excess sugars, opportunistic flora begins to multiply rapidly in an empty place, secreting toxins and provoking acute inflammation. That is, the disease is caused not by the presence of bacteria, but by the loss of ecological control over it.
Moreover, microbiologists note: even an excess of "beneficial" bacteria can be harmful. If, for example, the population of bifidobacteria or lactobacteria grows excessively, this is also an imbalance that can lead to metabolic disorders or hyperactivity of the immune system. That is why modern intestinal diagnostics does not look for a way to "kill" bacteria, it looks for ways to restore balance.
3. Diagnostic ratio and biodiversity indices
The main thing that genetic analysis of the microbiome shows is the individual diagnostic ratio between different groups of microorganisms. Conventional analysis only gives absolute numbers (e.g. 105 CFU/g), which say little without the context of the ecosystem.
What is analyzed in modern practice (in particular, using the algorithms of the biotech company Ediens):
Species balance and biodiversity: The Shannon index (an indicator of the species diversity of an ecosystem) and the Pillow index (the even distribution of these species) are determined. High biodiversity is the main marker of the organism's resistance to stress and infections.
Firmicutes/Bacteroidetes ratio: This is a global marker that is directly associated with metabolism. Disruption of this balance (a shift towards Firmicutes) is strongly associated with obesity, the ability of bacteria to extract more energy from food and store it as fat.
Enterotype: Depending on the dominant microbial communities, a person’s microbiome can be assigned to a specific enterotype (which is formed in the first three years of life). Enterotype largely determines how your body reacts to proteins, fats, or carbohydrates. Conventional tests do not determine enterotype in principle.
4. Metabolomic profiling: What bacteria "do", not just "who they are"
The most important difference in today's research is that it uses elements of transcriptomics and metabolomics. It is not enough for us to know the names of bacteria; it is critical for us to know their functional capacity.
Gut bacteria constantly produce biologically active substances. In-depth analysis reveals metabolic pathways:
Short-chain fatty acids (SCFA): Butyrate, acetate, propionate. These substances are the main source of energy for the cells of the intestine itself, they support the integrity of the mucosal barrier and relieve systemic inflammation.
Neurotransmitters (Gut-Brain Axis): A healthy microbiome is directly involved in the synthesis of serotonin (the hormone of happiness) and GABA (responsible for relaxation and sleep). Metabolomic analysis may explain why you feel anxious or sleepless — perhaps your bacteria simply lack the necessary enzymes.
Mucin degradation: The analysis shows the presence of mucin-degrading bacteria (such as Akkermansia ). They are responsible for renewing the protective mucous layer of the intestine.
5. Personal Risks: From Allergies to Type II Diabetes
By identifying specific biomarkers, microbiome analysis is a powerful tool for predictive medicine. What conventional tests don’t tell you is whether you’re at risk for systemic disease in the coming years.
The study allows you to predict and establish the causes of the development of:
Metabolic syndrome, obesity, and type 2 diabetes: Flora imbalance and certain microbial markers (e.g., a drop in bifidobacteria levels against the background of an increase in gas-producing microbes) lead to systemic inflammation and insulin resistance.
Cardiovascular disease (atherosclerosis): Some bacteria are able to metabolize food components (choline, carnitine) into toxic substances that provoke the formation of atherosclerotic plaques in the vessels.
Increased permeability syndrome ("leaky gut"): If metabolomic analysis shows a lack of CLFA, there is a direct risk that toxins will enter the bloodstream, causing autoimmune reactions, allergies and atopic dermatitis.
Ediens Solution: Individual Body Instructions
Having obtained such deep (Omics) data, Ediens does not leave the patient alone with complex numbers. Genetic analysis of the intestinal microbiome allows for the implementation of individual therapeutic strategies:
Personalized nutrition plan : Using proprietary IT algorithms, the company compares your enterotype, microbiome profile, and biochemical blood tests. As a result, you get a clear diet that will become a therapeutic fertilizer exclusively foryour bacteria. Different people digest the same apple completely differently precisely because of the different bacterial composition.
Targeted correction with pharmabiotics : Instead of "blindly" prescribing pharmacy probiotics, the company selects or develops individual pharmabiotic preparations (for example, the "My Second Brain" line). They purposefully suppress specific pathogens found and restore the mucosal barrier.
Personal microbiota bank : Your personal strong, healthy commensal strains, discovered during in-depth research, can be isolated, multiplied, and preserved. This is the best biological insurance against serious illnesses or aggressive therapies in the future.
Conclusions
Classic microbiological analyses are a thing of the past, as they are unable to show the complete picture of our "superorgan". Modern genetic and metabolomic analysis of the microbiome allows us to look into the very essence of our ecosystem. It proves that commensals and opportunistic pathogens exist in a complex symbiosis, where the correct diagnostic ratio is critically important , and not just the presence of microbes. New generation intestinal diagnostics allows us not only to treat the consequences (bloating or diarrhea), but also to predict deep personal risks of developing obesity, diabetes, depression and cardiovascular pathologies. Knowing our genetic profile of the microbiome, we get a unique opportunity to manage our own health with the help of personalized nutrition and evidence-based biologics.
Short questions and answers (Q&A)
1. What is the main difference between a conventional stool culture and a modern microbiome analysis? Answer: Conventional stool culture detects only the small number of microorganisms that can grow in the laboratory (in a Petri dish). Modern genetic analysis of the microbiome (sequencing) reads the DNA/RNA of all microbes, including those bacteria that are not cultured. In addition, it performs a metabolomic analysis - that is, it shows not only which microbes are present, but also what they synthesize (their functionality).
2. Why do opportunistic bacteria not always need to be destroyed immediately? Answer: Opportunistic bacteria (for example, certain fungi or enterococci) are a natural part of our body. In small quantities, they train the immune system. They cause harm only when the overall balance of microflora is disturbed: beneficial commensals die, resistance to colonization is lost, and opportunistic flora multiply uncontrollably, causing inflammation.
3. What is a diagnostic ratio and why is an excess of "good" bacteria also bad? Answer: The health of an ecosystem is determined by its balance (for example, the ratio of Firmicutes to Bacteroidetes). Each bacterium has its own role. If even very beneficial microorganisms (such as lacto- or bifidobacteria) are in excess and dominate others, this leads to metabolic imbalance, acid overload, or an inadequate immune response. Harmony and uniformity of species are important.
4. What personal risks can genetic analysis of the gut microbiome help identify? Answer: The analysis can detect disorders even before symptoms appear. Specific microbial markers and a lack of beneficial metabolites indicate high personal risks of developing obesity, insulin resistance (type 2 diabetes), atherosclerosis, leaky gut syndrome, autoimmune diseases, and even chronic anxiety or depression (due to disruption of the gut-brain axis).
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