Gut Microbiome: Understand Its Importance for Maintaining Health

Gut Microbiome: Understand Its Importance for Maintaining Health

Published by Synlab on 29 May 2024
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In recent times, the number of people experiencing discomfort related to the digestive system is growing. Even without severe symptoms, this often affects the quality of life. The gut microbiome, with all its components and interactions, forms a complete ecological niche that interacts with our physiology.


Today’s lifestyle, with high stress levels, inadequate diet or certain treatments, can alter the gut microbiome, causing an imbalance in the various types of microorganisms inhabiting our gut, which can negatively impact our health. Therefore, achieving a balanced microbiome is essential for good health (1).


What is the Gut Microbiome?

The term microbiome refers to the collective genome of a microbial community; it is the complete set of genes of microorganisms forming the microbiota, which includes the genetic material of all gut bacteria, viruses, fungi, and other microorganisms.


Additionally, the term also refers to the metabolic activities and capabilities of the present microorganisms (2), such as the metabolites produced and consumed by these microorganisms.


The Gut Microbiota

The gut microbiota represents a complex ecosystem that develops alongside its hosts and depends on their physiological environment. The gut bacterial population stabilizes during the first years of life and remains stable throughout our lives, dominated by four main phyla: Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria.


The number of microbial species in the human intestine is estimated to be between 1,000 and 1,150, with the number of genes in the intestinal microbiome exceeding the number of genes in the human genome by 150 times (3).


The gut microbiota can perform many processes that the host cannot. These processes result in microbially produced or modulated metabolites that act as metabolic substrates and signaling molecules in the host, with significant implications for metabolism and health.


Dietary composition is fundamental for the metabolic production of the gut microbiota, as it processes dietary nutrients into metabolites. Thus, diet affects the composition of the gut microbiota, influencing its metabolic potential and impact on the host (4).


The microbiota acquired at birth develops in parallel with the host’s development, maintaining its temporal stability and diversity throughout adult life until death.


The literature suggests that although part of the microbiota is conserved, dynamic members vary throughout the gastrointestinal tract from infancy to old age under different health conditions.


Despite being dynamic, the gut microbiota performs several basic functions in the immunological, metabolic, structural, and neurological scenarios of the human body.


It significantly influences both the physical and mental health of individuals (5), regulating many metabolic processes in the host, including energy homeostasis, glucose metabolism, and lipid metabolismo (6).


The gut microbiota functions in four distinct contexts in the human body (7):


  1. Metabolic: through dietary fibers, proteins, amino acids, and lipids;
  2. Protection: via the mucus layer, production of antimicrobial peptides (AMPs) from innate and adaptive immunity, and short-chain fatty acid production;
  3. Structural: by maintaining the structural integrity os the gut mucosa.
  4. Neurological: through the gut-brain axis, where the activities of the gut microbiota can control the central nervous system.


Importance of the Human Gut Microbiome

The complex communities of microorganisms inhabiting the human gastrointestinal tract are emerging as key elements in regulating health and disease. Various vital functions performed by the gut microbiome in the human body highlight its importance.


These include transforming indigestible food parts into absorbable substances, producing essential vitamins, eliminating toxic substances, competing with pathogens, strengthening the intestinal barrier, and regulating the immune system.


Many of these functions are closely linked to human physiology. For example, short-chain fatty acids produced by microbial fermentation are crucial for intestinal cells and play essential roles in regulating the immune system (8-10).


In the early stages of life, microbiome development influences immune function. Microorganisms acquired vertically, horizontally, and from the environment, as well as their metabolic products, have the potential to shape developmental courses impacting health throughout life (11).


Thus, the microbiome plays a crucial role in developing metabolic, immunological, and nutritional functions, necessitating careful attention. Understanding how complex microbial communities can affect the pathogenesis of various diseases has significant implications for their prevention, diagnosis, and treatment (12).


In recent decades, human microbiome research has evolved beyond merely cataloging microbial diversity to understanding how these microorganisms constitute an auxiliary and dynamic functional system that develops synergistically alongside physiological development and decline (13-15).


It is increasingly evident that a wide range of conditions, including chronic inflammatory diseases (16), metabolic diseases (17), neurological disorders and câncer (18, 19), are now linked to functional changes in the microbiome.


These changes can occur both at the disease manifestation site and in distant mucosal areas or organ systems, triggering metabolic and immunological changes in the host (20).


Various factors such as diet, antimicrobial agents, and immunity influence human microbiomes, particularly the gut microbiome, which houses the largest quantity and variety of microorganisms. In response, bioactive products from the microbiome shape human cell function (2, 21).


What Affects the Gut Microbiome?

After reaching the age of two to three, the gut microbiome becomes more stable and, at this stage, closely resembles an adult microbiome (20). However, the adult gut microbiome can still be influenced by many factors, with diet being the most influential, followed by medications.


Stress also plays a significant role as the brain can influence the gut microbiome by sending stress hormones to the gut through the vagus nerve. Exercise habits, age, genetics, geographic location, and ethnicity are other elements that impact the gut microbiome (16).


Gut Microbiome: Understand Its Importance for Maintaining Health



What is the Relationship Between the Gut Microbiome and Diseases?

Imbalances in the gut microbiome can be qualitative or quantitative, affecting both its distribution and activity, which has a proven effect on intestinal and overall health.


Diseases related to gut microbiome imbalance include conditions such as:

  • Digestive diseases: inflammatory bowel disease, irritable bowel syndrome, diarrhea, constipation;
  • Metabolic: obesity, type 2 diabetes;
  • Cardiovascular: atherosclerosis, hypertension;
  • Neurodegenerative: Parkinson’s, Alzheimer’s, multiple sclerosis;
  • Neurological: depression, anxiety;
  • Immunological diseases.


The mechanism of this relationship stems from the fact that microorganisms can produce different biologically active metabolites, which can play a role in disease states.


The causality between the gut and each disease is still being established, and it is unknown whether the disease causes changes in the gut microbiome or a change in the gut microbiome causes the disease.


Several intestinal diseases linked to inflammation have been correlated with changes in the gut microbiome. These include diseases such as colon cancer, ulcerative colitis, Crohn’s disease, and irritable bowel syndrome (3, 22, 23).


Relationship Between the Gut Microbiome and Crohn’s Disease

Crohn’s disease (CD) is an inflammatory bowel disease (IBD) that can affect any part of the gastrointestinal tract. CD has been related to functional abnormalities favoring a marked pro-inflammatory phenotype and structural imbalances in the intestinal ecosystem, resulting in a decrease in the growth rates of beneficial microorganisms and an increase in the growth rates of certain pathogenic or opportunistic bacteria.


Intestinal microorganisms have recently gained much attention as potential drivers of CD. This idea is supported by the fact that the close interaction between the gut microbiota and the intestinal mucosa continually influences the intestinal immune system, and any imbalance of the normal microbiome state can likely trigger immune dysfunction through pro-inflammatory signals (24).


The microbiome and Colorectal Cancer

With the advancement of metagenomic technology, growing evidence suggests that intestinal dysbiosis, or the imbalance in normal gut microbiota, can promote chronic inflammatory conditions and the production of carcinogenic metabolites leading to neoplasia (25).


Although genes contribute to colorectal cancer, the gut microbiota plays a significant role. Scientific evidence suggests that chronic infection and subsequent inflammation contribute to tumor initiation and progression.


Various bacterial species and tumor-promoting virulence mechanisms have been investigated. Significant advances have been made in understanding the composition and functional capabilities of the gut microbiome and its role in cancer (3).


Some bacteria have been consistently increased (Fusobacteria, Alistipes, Porphyromonadaceae, Coriobacteridae, Staphylococcaceae, Akkermansia spp., Methanobacteriales) while others have been consistently decreased in colorectal cancer (Bifidobacterium, Lactobacillus, Ruminococcus, Faecalibacterium spp., Roseburia, Treponema). It has also been shown that bacterial amino acid metabolites are increased, and butyrate is decreased during carcinogenesis (26).


The Small Intestine Microbiome in Celiac Disease

Celiac disease is a digestive disorder affecting approximately 1% of the population, although a much higher percentage carries genes related to genetic susceptibility.


A study demonstrated that the microbiome could be a cofactor in the development of the disease in genetically predisposed people. The study conducted on mice showed that the duodenal microbiome could protect or provoke celiac disease in genetically susceptible mice, depending on the microbial composition and the balance between pathobionts and commensals.


In other words, microorganisms that have the potential to cause diseases if conditions are favorable, and commensals, which are microorganisms that live in symbiosis with the host, benefiting from the relationship without causing harm (27).


The Gut Microbiome and Its Role in Depressive Disorders

Depression is one of the most common mental disorders. However, its causes are still partially unknown, and its diagnosis is complex. A group of Dutch researchers detected variations in the gut microbiome characteristic of individuals with depression, verifying that such variations are independent of the ethnic group.


The study indicates that some of the involved bacteria are producers of metabolites such as glutamate, butyrate, serotonin, and gamma-aminobutyric acid (GABA), which are substances with potent neurological action. These substances would exert their effect through the vagus nerve, which connects the gut and the brain, influencing mood and depression (28).


Science Advances in Favor of the Gut Microbiome

With technological advancements, knowledge about the gut microbiome has expanded considerably in recent years. The influence of the gut microbiome on health and disease is currently one of the most explored areas of Science.


Deepening our understanding of how disruptions to the early-life gut microbiome, combined with other life stresses, impact health, can provide new insights into the treatment of many complex disorders and diseases (such as fibromyalgia, inflammatory bowel disease, autism).


Future research should focus on the gut microbiome as a biomarker for dietary intake and disease development, the effect of probiotic supplementation on clinical outcomes, and bacterial therapy for intestinal health, immunity, and therapeutic treatments (29).


Gut Microbiome: Understand Its Importance for Maintaining Health



What gut microbiome test does SYNLAB offer?

SYNLAB offers the MyBiome test, a unique diagnostic test of the gut microbiome, as it performs a complete reading of the gut microbial genome through shotgun metagenomics sequencing, allowing for a thorough, objective and actionable study of all microorganisms that make up the intestinal ecosystem, providing analysis:


  • High sensitivity and coverage, as it detects all microorganisms present in the sample, such as bacteria, archaea, yeasts, fungi, and parasites.
  • High resolution, allowing for the taxonomic level of species (differentiating between species belonging to the same genus that may have very distinct and even opposite impacts on health (for example: Streptococcus thermophilus: probiotic and Streptococcus salivarius: high concentrations of this species in the gut are associated with hypertension, Crohn’s disease, and arteriosclerosis).
  • High resolution also enables reaching the strain taxonomic level (the species Fecalibacterium prausnitzii has different strains, and only strains C and K are responsible for the anti-inflammatory effect described mediated by a high production of butyrate, for example).
  • The shotgun technique allows for the identification of the potential functionality of the microbiome through the real quantification of genes encoding for 25 metabolites relevant to health.
  • Microbiome reading enables the detection of non-usual microorganisms; extraintestinal microorganisms that, when found in large quantities in the gut, may be related to harmful effects on health (for example, oral, vaginal, pet-derived, foodborne pathogens).
  • The differentiated MyBiome report is accompanied by the most relevant scientific literature with the aim of helping to understand how each parameter is related to patient health based on what is described by science. This makes it a clinically applicable test.
  • Personalized recommendations aimed at restoring functions and promoting the growth of beneficial species.


Thus, MyBiome provides detailed information about the microorganisms inhabiting the gut and their functionality, the impact on health, which key functions for health are being performed by the detected microorganisms, and how to achieve balance through personalized nutritional recommendations.


What methodology is used in the MyBiome test?

The MyBiome test is performed using shotgun sequencing, a metagenomic technique that involves the random fragmentation of DNA fragments, followed by the individual sequencing of these fragments.


This approach is highly effective for sequencing whole genomes, especially of organisms whose genome is too large to be sequenced conventionally. Thus, shotgun sequencing enables a comprehensive analysis of the genome of all bacteria and microorganisms present in the intestinal microbiota. Through metagenomic sequencing, comprehensive information about the genome of an organism can be obtained, allowing for the analysis of genes, metabolic pathways, and regulatory regions, as the entire genome is sequenced, which includes millions to billions of base pairs.


In contrast, 16S gene sequencing is employed only to identify and classify bacteria present in a sample, as only a specific region of the 16S rRNA gene, relatively short (about 1,500 bases), is sequenced (30).


What are the advantages of MyBiome’s metagenomic study?

The use of metagenomic shotgun sequencing for gut microbiota analysis presents several advantages compared to studies based on 16S gene sequencing or PCR-RT.


Conventional analysis of bacterial populations by amplification of the 16S ribosomal RNA gene (16S rRNA) relies on amplification of hypervariable regions of this gene through primers (base-initiating sequences that complement and specifically bind to regions of interest in DNA), which amplify small regions of the 16S in most bacteria present in a sample.


However, this technique does not allow for the detection of microorganisms that have undergone modifications in the primer binding site (31). Therefore, these bacteria are technically “invisible” and escape analysis (32).


Furthermore, the 16S rRNA gene represents only a small part of a bacterium’s entire genome, making any analysis beyond phylogenetic classification difficult.


Compared to conventional microbiota studies based on 16S rRNA analysis, MyBiome allows for the detection of all genes present in sample microorganisms thanks to the use of metagenomic sequencing technique, avoiding amplification bias and facilitating a comprehensive sampling of all genes present in organisms (33).


The metagenomic approach provides a deeper analysis, providing information not only on all bacteria present down to the species and strain taxonomic level, but also on other microorganisms present in the sample such as fungi, archaea, and protists.


In addition to identification, metagenomic sequencing allows for the characterization and quantification of functional genes, providing information about the functions of microorganisms present in the sample.


The technology used in MyBiome also stands out for its high resolution compared to conventional 16S rRNA gene amplification analysis. While 16S gene sequencing does not allow discrimination between bacterial species with similar or identical 16S regions (34), metagenomic sequencing enables more precise identification of microorganisms and their functional genes.


This limitation implies significant loss of information, as different species within the same genus can have very distinct functions (35). Whole genome shotgun sequencing used in MyBiome is currently the highest resolution technique for identifying microorganisms and detecting their functional genes.


These characteristics, combined with personalized recommendations, make MyBiome a unique analysis in the market, providing detailed insights into intestinal microbiota and its functionality.


What are the indications for the MyBiome test?

MyBiome  is especially indicated for:


  • Patients with digestive disorders, metabolic diseases and/or cardiovascular diseases;
  • Patients with inflammatory and/or immune diseases;
  • Patients with neurodegenerative diseases and/or mood disorders;
  • Individuals with chronic fatigue;
  • Individuals who wish to proactively manage their health and prevent the development of pathologies associated with intestinal dysbiosis.


Get to know the SYNLAB group, a reference in the provision of medical diagnostics services!

Performing accurate and up-to-date tests, such as MyBiome, is essential for more accurate diagnoses and better treatment guidance. And SYNLAB is here to help you.


We offer diagnostic solutions with rigorous quality control to the companies, patients, and physicians we serve. We have been in Brazil for over 10 years, operating in 36 countries and three continents, and we are leaders in service provision in Europe.


Contact the SYNLAB team and learn about the available tests.



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