No. 03 Microbes Among Us

Right now, you have trillions of microbes living inside you.

They depend on you for their survival.
These little microbes are not just- take take take, they work behind the scenes helping you digest food, boost your immune system, regulate your mood, and even support glowing skin. Your gut microbiome is like an internal ecosystem, like a bustling city, or a thriving rain forest. Or a bustling city in a thriving rain forest! But like one that lives in harmony with nature and has a symbiotic relationship with the earth lol. Diversity is key to its health.

The exciting part? You have the ability to shape and strengthen it. With the right foods, lifestyle habits, and a little understanding, you can create a gut environment that fuels your energy, supports your metabolism, and keeps you feeling your best. So, let’s explore what’s really going on there, how did this rainforest city get inside you and why? How can you make sure you are a good host or hostess and how can you make sure it's working for you in return.

Let's do this timeline style. We’ll start with why/how did these microbe civilizations make residence inside us. To look at this we will take things way way….way way back. To a time when the earth was only inhabited by microbes. Trillions of microorganisms just boppin around -little explorers. These were the first true pioneers. Truly ancient settlers. As I would imagine with any community, over time these microbes began to learn how to communicate with each other in intricate ways. And as life does it continued to evolve and become more complex.

Eventually the first multicellular organisms started showing up to town. This was the first time microbes found solace, stability, and nutrition inside the digestive system of another organism. Like a landlord and a renter. This landlord's name was Hydra. The microbe renters were very appreciative and made sure to help make the landlord Hydra’s life easier. It was a symbiotic relationship -mutually beneficial. And really the microbes weren’t helping Hydra to be kind…. I don't think they have feelings… This symbiosis just worked. The things the microbes needed, the hydra provided and that need aided the hydra, aw beautiful balance. The microbes had food and safety, and the Hydra received valuable aid with digestion.

This relationship persevered, up through the emergence of humans. Here’s the tea, humans were the perfect environment for countless species of microbes. Lol I really can't get away from this apartment analogy. Imagine a human is a big tall new shiny apartment building, and the real estate is hot hot hot. Microbes were moving in ASAP. Microbes could live really anywhere throughout the human digestive system but the hottest real estate was in the colon. That's where the who’s who of microbes live. Translation: microbes do live all throughout your digestive system but the vast majority live in your colon. This residence of microbes inside the human gut is what we have lovingly come to know as the HUMAN GUT MICROBIOME. Catchy.

Like with the hydra this relationship between human and microbe is symbiotic -mutually beneficial. They get a safe gorgeous temple of a home, with foodservice and all the amenities. In turn humans receive aid that is essential to our health in a lot of ways, which we will get into.

Back to the story! As humans spread across the planet building complex societies, they adapted to different environments and diets with the help of their microbial partners. Whether living in the Amazon, Sahara, or Arctic humans relied on microbes to process diverse food sources, and ensure survival.

Pause the story! Let's talk really quickly about the microbiome and what it is. I think often when people think of the gut, they picture the stomach, however the gut includes the esophagus, stomach, small intestine, and colon (here is an article detailing the anatomy of the gut click here to give it a read). We have trillions (with a t) of microbes and hundreds of species living in our gi tract. All of them coexisting, interacting with one another and forming complex ecosystems. It's giving, natural, safe, New York City (I truly can’t stop) This is a microbiome.

For a long time when we have thought of bacteria we’ve considered it harmful. Especially the thought of bacteria entering our bodies. It is now understood that these trillions of microbes living in our gut are not harmful, not just benign, but often health promoting.

The term microbiome refers to the collection of bacteria and their gene pool. This is kind of crazy to think about, it turns out that our human genome is a small percentage of the total genome we carry around. Humans are a composite organism of human cells and microbial cells. The human cells of our body only encompass about 1% of the total genetic material we carry around. Our microbiome is over 99% of our associated genetic material. The microbial genes are hundreds of millions of genes compared to our 20,000. (mind
blown emoji)

While our human genome is fixed at conception, our microbial genome is not. We have control in a sense over our microbial genome development. Babies are born basically microbe free. Microbes begin to colonize upon birth. Babies pick up microbes from their mother’s vagina, or skin if born by c-section. Microbes are introduced through the hospital room, or swimming pool, or wherever little baby is birthed. The hands that help baby make his/her entrance introduce microbes. When baby goes home, microbes from that environment move in. If pets are in the home, other siblings, caretakers, breastfed or formula fed, all of this is unique to each baby’s experience and it all adds to the development and colonization of their gut microbiome. (mind blown emoji!)

“A combination of a lot of raw fresh fruits and veggies go into a healthy gut friendly diet. Diversity and richness is the hallmark of a healthy microbiome.” - Dr. Justin Sonnenburg (Stanford University School of Medicine)

Okay let's keep moving, humans begin the cooking of food! This was the first step in the development of processed foods. Now all of a sudden our microbe friends didn’t need to break down raw veggies, leaves, nuts, or berries. Cooking made foods softer and easier to digest.

Another dramatic change was the agricultural revolution where all of a sudden humans were growing certain foods at mass. They suddenly had farm animals. This meant access to food was easier, but the diversity suffered. The human gut microbiome definitely went through a change at this point in human history.

It's worth noting that while all of this is happening the ancient practice of fermented foods was being used throughout history. These are naturally fermented foods which have microbes in them.

Sidebar for fermentation because this is quite interesting! Fermentation has been integral in human history. Early civilizations were not so worried about understanding the science of fermentation. So while early civilizations may not have understood the science, they knew that fermenting foods preserved the food and improved digestion. The microbes responsible for fermentation—bacteria and yeasts—are the same microbes that live within our gut. Coincidence, I think not. There is a strong link between the foods we’ve historically sought to eat and preserve using microbial life and their impact on our well being.

Science has revealed that the guts resume lists much more than just digesting food. The gut microbiome plays a huge role in maintaining homeostasis (balance) within the body, regulating hormones, neurotransmitters, and immune function. For example certain gut bacteria influence our appetite, hormonal cells in the gut release a hormone that
finds its way to the brain which then creates the feeling of fullness after a meal. We never think about the gut in this way, some of our bacteria telling the cells in our gut to send a signal to the brain to stop eating. Others produce neurotransmitters like dopamine and
serotonin, directly impacting our mood and behavior.

Back to my thriving city metaphor! Different microbes act like specialized workers—some break down food like chefs, others protect against invaders like security guards, and many more contribute to the overall infrastructure of your health. Just like a city needs balance
and proper resources to function smoothly, your microbiome relies on diet and lifestyle to maintain harmony. Which as science is finding out leaves room for error.

We live in a world that has changed dramatically in the last 75 years. Unintentionally through processed foods, industrialized agriculture, and ultra-sanitized environments have stripped away microbial diversity. As our modern lifestyles spread, so do non-infectious chronic diseases — autoimmune diseases, anxiety, depression, obesity, diabetes, heart
disease, cancer, and even neurodegenerative disorders like Alzheimer’s and Parkinson’s. Alarmingly, these diseases are appearing at younger and younger ages.

Surprisingly, science is revealing that all of these issues have at least one thing in common: gut health. Our ancestors lived in symbiosis with microbes, eating diverse, fiber-rich diets that nourished a flourishing gut ecosystem. But today? Our microbiomes are depleted, and our health is suffering as a result.

A lab at Stanford University School of Medicine led by Doctors Justin and Erica Sonnenburg have been analyzing stool samples from different populations, and have discovered that the microbiomes of industrialized societies look vastly different from those of hunter-gatherers. Indigenous groups in Tanzania and Peru, who follow traditional diets, have microbiomes with over 750 different species of bacteria, while the average Californian has
only around 250. The loss of microbial diversity in the modern world is staggering, and with it comes a rise in the previously mentioned chronic diseases.

If a diverse microbiome functions like a thriving rainforest—rich, resilient, and self sustaining. The typical Western microbiome, in contrast, resembles a clear-cut forest, stripped of its biodiversity and struggling to support health.

The good news? You can do something about it. You are capable of rebuilding your gut microbiome by implementing a few really pretty simple practices:

• Eating a diverse, whole-food diet rich in fiber (fruits, vegetables, nuts, and legumes)

• Incorporating fermented foods (sauerkraut, kimchi, kefir, kombucha) for beneficial probiotics

• Avoiding ultra-processed foods and excessive antibiotics

• Spending time in nature and interacting with the environment

I hope this has helped you have a more clear picture of what your gut microbiome is, how those little guys got inside you and why. And what is at stake for both you and your microbes if the microbiome isn’t taken care of.

Follow along as we dive deeper into gut health, microbiome restoration, and practical ways to support your body and oh so much more. ha. Subscribe to the newsletter and follow Coleture on social to stay informed, inspired, and empowered on your gut health journey!