Unlocking the Secrets of Your Inner Universe: How the Human Microbiome Shapes Your Health and Well-Being.

“Discover the groundbreaking science of the human microbiome, our body’s hidden ecosystem of trillions of microorganisms. Learn how this intricate community influences everything from digestion and immune function to mental health and chronic conditions like diabetes. Uncover why researchers call it our ‘second brain’ and how you can optimize it for better health and well-being.”

A healthy microbiome can help to:

  • Reduce LDL (bad) cholesterol levels
  • Lower blood pressure
  • Improve blood clotting function
  • Manage blood sugar levels
  • Reduce the risk of heart disease and stroke

The human microbiome is a fascinating and complex ecosystem coexisting with us. It’s almost like there’s a hidden universe within our bodies, one we’re just starting to explore. While we have yet to understand the full scope of the microbiome, current research offers intriguing insights into its role in health, disease, and even behaviour.

The Basics

The term “microbiome” refers to all the microorganisms—bacteria, viruses, fungi, and protozoa- living on and inside our bodies. Most are located in the gut, particularly in the large intestine, but they’re also found on the skin, mouth, and other bodily niches. The number of microbial cells in the human body is thought to be about the same or even outnumber human cells.


Digestion: The gut microbiome helps break down food substances that are difficult for our digestive enzymes to handle, such as complex carbohydrates.

Immunity: The microbiome trains our immune system to recognize harmful pathogens. It also competes with harmful microbes for resources, effectively limiting their growth.

Mental Health: Recent studies suggest that gut health could be linked to mental health through the “gut-brain axis.” Changes in the microbiome have been linked to conditions like depression and anxiety.

Nutrient Synthesis: Some microbes synthesize essential nutrients, like vitamin K and certain B vitamins.

Metabolic Regulation: Emerging research hints at a connection between gut bacteria and regulating blood sugar, fat storage, and even hunger-signaling hormones.

Gut permeability: The microbiome can also affect gut permeability, which is the ability of our intestines to keep harmful substances out of the bloodstream. Increased gut permeability can lead to inflammation and insulin resistance.

Mysteries Unveiled and Yet to Be Unveiled

You’re correct that science has only identified a small fraction of these microbes. One reason is that many of them are anaerobic and die when exposed to oxygen, making them difficult to culture in a lab. With advances in DNA sequencing technologies, especially metagenomics, we’ve ” seen” more of these microbes by analyzing their genetic material directly.

Dark Matter of Microbiome: The 99% is often considered the “dark matter” of the microbiome. These are species that we know exist but know little to nothing about. Just as in astronomy, where “dark matter” makes up most of the universe, this microbial “dark matter” could hold the keys to understanding health and diseases in ways we can’t yet imagine.

Personalized Medicine: One exciting possibility is the development of personalized medical treatments based on an individual’s unique microbiome. Theoretically, you could receive medication or probiotics tailored to your microbial composition.

Longevity and Aging: There’s ongoing research to understand whether the microbiome changes as we age, and whether those changes are linked to ageing-related diseases.

Microbiome Transplants: Fecal microbiota transplantation (FMT), wherein faecal matter from a healthy donor is transferred to a recipient, has already shown promise in treating certain conditions like C. difficile infection.

The Microbiome and Diabetes

Insulin Sensitivity: Research has shown that gut bacteria can affect how your body reacts to insulin. Certain bacteria produce short-chain fatty acids like butyrate, which improve insulin sensitivity.

Inflammation: Chronic low-grade inflammation is often observed in type 2 diabetes. Some gut bacteria can stimulate inflammatory responses, while others are anti-inflammatory. A balanced microbiome can, therefore, potentially help regulate inflammation levels.

Weight Management: Obesity is a risk factor for type 2 diabetes. Gut microbes can influence weight by affecting how your body stores fat and how you metabolize sugar and complex carbohydrates.

Gut-Brain Axis: Some studies suggest that gut microbes can even influence appetite and satiety through the gut-brain axis, indirectly affecting blood sugar levels.

The Microbiome and Blood Health

Cholesterol: Some bacteria play a role in bile acid metabolism, which can influence cholesterol levels in the blood.

Blood Pressure: A balanced microbiome helps maintain the integrity of the gut lining, preventing a “leaky gut,” which has been implicated in elevated blood pressure.

Nutrient Absorption: Microbes in the gut aid in the breakdown and absorption of nutrients that can affect blood composition, like iron, which is essential for red blood cells.

Foods Good for the Microbiome

Fiber-Rich Foods: Whole grains, fruits, and vegetables are excellent for feeding beneficial bacteria. They ferment fibre into short-chain fatty acids like butyrate, which benefit gut health.

Fermented Foods: Foods like yoghurt, kefir, sauerkraut, kimchi, and kombucha contain probiotics or live beneficial bacteria.

Polyphenol-Rich Foods: These are found in green tea, olive oil, dark chocolate, and red wine. Gut bacteria metabolize polyphenols into compounds that are beneficial for health.

Avoid Sugars and Artificial Sweeteners: High sugar intake can feed harmful bacteria, causing an imbalance in the microbiome. Some studies also suggest that artificial sweeteners can negatively affect gut bacteria.

Lean Proteins: Reducing red meat can benefit the microbiome and blood health.

Powerful Vegan options for lean proteins:


  • Lentils: Packed with protein, lentils also provide a good amount of fibre.
  • Chickpeas (Garbanzo Beans): These can be used in various dishes, from salads to hummus.
  • Black Beans: Another good source of protein, these are versatile in recipes like soups and veggie burgers.

Whole Grains

  • Quinoa: This grain contains all nine essential amino acids, making it a complete protein.
  • Brown Rice: While not as protein-rich as other options, it’s still a good choice in combination with legumes.

Nuts and Seeds

  • Almonds are nutrient-dense and provide a good amount of protein, but they are also high in calories and fats, so moderation is key.
  • Chia Seeds: High in protein and omega-3 fatty acids, these can be added to smoothies or used as an egg substitute in recipes.
  • Pumpkin Seeds: These are a good source of protein and can be eaten on their own or added to salads.

Soy Products

  • Tofu: Made from soybean curds, it’s a versatile ingredient that can be cooked in various ways.
  • Tempeh: Fermented soybeans form this dense, cake-like product high in protein and probiotics.
  • Edamame: Young, green soybeans can be steamed and eaten as a snack or added to dishes.

Plant-Based Meat Alternatives

  • Seitan: Made from gluten, the protein in wheat, it resembles the texture of meat and is high in protein.
  • Textured Vegetable Protein (TVP): Often used as a meat substitute in various dishes, it’s made from soy flour and is quite protein-rich.

Other Options

  • Spirulina: This algae is a complete protein and can be added to smoothies or taken as a supplement.
  • Nutritional Yeast: Often used to create a cheese-like flavour in vegan dishes, it’s also a good source of protein.

These vegan options can easily be incorporated into your meals to ensure you’re getting a balanced intake of proteins.

The human microbiome is a complex ecosystem of trillions of microorganisms that reside in and on our bodies, playing a pivotal role in everything from digestion and nutrient absorption to immune function and even mental health. This largely unexplored “inner universe” is essential for our well-being, influencing metabolic processes affecting diabetes, cholesterol levels, and overall blood health. As we decode more about this intricate microbial community, we unlock the potential for groundbreaking treatments, personalized medicine, and a deeper understanding of human biology.

Michael Plumstead

16 thoughts on “Unlocking the Secrets of Your Inner Universe: How the Human Microbiome Shapes Your Health and Well-Being.”

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