Understanding the Microbiome: Your Gut's Best Friends
The term microbiote refers to "all the microorganisms that inhabit a particular environment, like the intestine." In the gut, you'll find various microorganisms such as archaea, bacteria, fungi, and viruses. Our focus here will be on the bacteria, especially those that have a beneficial impact on human health. These beneficial bacteria are known as symbiotic bacteria because they form a long-lasting, mutually beneficial relationship with their human host.
Now, let's talk about the microbiome. This term refers to all the genetic material (genomes) of the microorganisms that make up the microbiote.
In essence, the microbiote is the community of microorganisms, and the microbiome is the collection of their genetic blueprints. Together, they play a crucial role in maintaining our health and well-being.
The Incredible World of Your Gut Microbiome
Did you know that your body hosts ten times more microbial cells than human cells? That's about 100 trillion microbial cells! When it comes to the microbiome, it's all about the genetic material of these microorganisms.
Back in 2008, the National Institute for Agricultural Research (INRA) led a groundbreaking European project called Meta-HIT (Metagenomics of the Human Intestinal Tract). This project aimed to create a comprehensive catalog of the human gut's microbial genes. The findings were astonishing: the human microbiome contains at least 3.3 million genes from over 1,000 species, with 99% of these species being bacterial. To put this into perspective, if you lined up all the gut bacteria end-to-end, they could reach the moon!
The mass of the gut microbiota is estimated to be between 1 and 2 kilograms, which is about the same weight as your brain. This fascinating micro-world inside us plays a huge role in our overall health and well-being.
Where Do Gut Bacteria Live?
The bacteria in your gut microbiota are strategically located between the digestive tract's lumen and the inner mucus layer. Their distribution follows an increasing gradient from the stomach to the colon. Here's a closer look at how they're spread out:
- Stomach: 10^1 - 10^3 colony-forming units per gram (CFU/g)
- Colon: 10^9 - 10^12 CFU/g
The colon, with its low oxygen levels, ample nutrients, and slow transit speed, provides a perfect habitat for these bacteria. In contrast, the acidic environment of the stomach is less hospitable to microbial life. This arrangement allows for a thriving community of bacteria in the colon, essential for your digestive health and overall well-being.
How Your Gut Microbiota Develops
The journey of your gut microbiota begins right at birth. If you're born through vaginal delivery, your first exposure to microbes comes from your mother's vaginal microbiota. For those born via cesarean section, the initial microbial colonization comes from healthcare workers and the environment.
According to Yatsunenko and colleagues, this microbial community continues to evolve, significantly influenced by diet, until it reaches a stable, functional composition between the ages of 2 and 4 years. This early development is crucial as it sets the foundation for your digestive health and immune system for years to come.
Dysbiosis: The Impact of Industrialization on Gut Health
Industrialization has significantly altered our gut microbiota, leading to what’s known as dysbiosis—an imbalance of the microbial community that can be harmful to our health. Here's how it happens:
A traditional diet, rich in fiber, helps beneficial gut bacteria produce Short-Chain Fatty Acids (SCFAs) like butyrate, acetate, and propionate. These SCFAs are crucial for maintaining a microbiota that is well-suited to our genetic makeup, thus reducing the incidence of chronic diseases.
However, a modern industrialized diet, high in fats and low in fiber, combined with antibiotic use, disrupts this balance. This new microbiota is less compatible with our genome, leading to a higher incidence of chronic diseases.
The short-term solution? Return to a fiber-rich diet (and as we’ll explore later, also rich in probiotics) to restore a microbiota that is more in line with our ancestral one and compatible with the human genome. Waiting for our genome to adapt to a new microbiota shaped by an industrialized diet is not a viable solution .
Function of the Gut Microbiota
The gut microbiota plays several crucial roles in maintaining the host’s health. Let's delve into its metabolic functions, protective roles against pathogens, and its impact on the maturation of the intestinal immune system.
Metabolic Functions
The metabolic activities of the microbiota involve the fermentation of carbohydrates, proteins, and lipids. This process produces gases and helps break down compounds that our bodies cannot digest on their own, such as fibers. Here's how it works:
1. Carbohydrate Fermentation:
- Polysaccharide-hydrolyzing bacteria break down carbohydrate polymers into sugars.
- Glycolysis of these sugars leads to the formation of pyruvate, which is ultimately transformed into Short-Chain Fatty Acids (SCFAs) like acetate, propionate, and butyrate.
- Acetate: Mainly produced by Bacteroidetes, it generates ATP.
-Propionate: Also produced by Bacteroidetes, it regulates cholesterol synthesis in the liver.
- Butyrate: Produced by Firmicutes, it is the primary nutrient for colon cells, reducing intestinal permeability and inflammation.
2. Protein Fermentation: Proteins are broken down into amino acids, which provide energy and nitrogen. These amino acids are deaminated into SCFAs and ammonia.
3. Cholesterol Transformation: The microbiota converts cholesterol from bile, diet, and shed intestinal cells into coprostanol.
4. Gas Production: Hydrogen is fermented into methane, acetate, and sulfide.
Vitamin and Neurotransmitter Synthesis: The microbiota synthesizes essential vitamins (K, B8, B9) and neurotransmitters.
Protective Functions Against Pathogens
The gut microbiota defends against both external and internal pathogens. Here’s how:
- Competition for Resources: Commensal bacteria compete with pathogens for nutrients and adhesion sites on epithelial cells.
- Antimicrobial Peptides and IgA Production: The microbiota induces epithelial cells to produce antimicrobial peptides and secretory IgA, which bind to antigens and prevent pathogen adhesion.
- Reinforcement of Tight Junctions: The microbiota strengthens epithelial cell junctions, blocking pathogens from entering the bloodstream.
Immune System Maturation
The gut microbiota is key in maintaining intestinal homeostasis and developing the Mucosal Immune System (SIAM). There’s a delicate balance between immune tolerance and pathogen defense. Disruption of this balance can lead to chronic inflammatory conditions. The microbiota also helps mature adaptive immune responses, involving mucosal Th17 lymphocytes.
Gut-Brain Axis
Beyond metabolic and immune functions, the microbiota influences the gut-brain axis through several pathways:
- Neural Pathway: Involving the vagus nerve.
- Hormonal Pathway: Involving hormones from the digestive tract, accessory glands, adipose tissue, or the hypothalamic-pituitary-adrenal axis.
- Immune Pathway: Involving cytokines.
Microbial molecules involved in gut-brain communication include:
- Microbial Products: Fermentation products and neurotransmitters (shown in yellow in figure 6). For instance, Lactobacillus colonization can reduce inflammatory cytokines via lactic acid production, lowering pH.
- Microbial Components: Elements like lipopolysaccharides from bacterial cell walls (shown in green).
These molecules can directly affect the Central Nervous System (CNS) through the circulatory system.
