What is the Microbiome, and How does it Impact Health?

Take a tour of the amazing world of bacteria that lives inside each one of us.


Healthy co-existence

Gut microbes play a fundamental role in human health. They help us digest food, fight infection and illness, and regulate metabolism. They also play a key role in early life development. They may influence our mood and behavior and the long-term health of our brain. Recent research suggests that our microbes may even influence our personality and choice of partner.

In a healthy body, human and bacterial cells co-exist peacefully in the gut microbiome. Their relationship is a mutually beneficial one, known as symbiosis. Stress, antibiotics, an unhealthy diet, and parasites can disrupt the balance of the microbiome. This imbalance, called dysbiosis, fuels a range of illnesses.

These include physical illnesses (such as obesity, asthma, heart disease, certain cancers, allergies, autoimmune disease, skin disorders, digestive disorders, and diabetes) and mental illnesses, including anxiety, depression, ADHD, autism, bipolar, and schizophrenia.

Anatomy and the biome

Although the large intestine houses the highest density of microbes, other components of the digestive tract are important for normal gut function. The stomach is highly acidic and kills most of the microbes that enter it. Food then travels through the 7-meter-long small intestine, where it is digested by enzymes and absorbed into the bloodstream.

The juncture where the small and large intestine meet is the epicenter of microbial activity in the gut. Meet the cecum – a small pouch shaped like a tennis ball, at the start of the large intestine, where trillions of microbes tackle partially digested food from the small intestine.

The tough bits, like resistant starches from plant fibers, are digested in the large intestine. The large intestine provides food for its resident microbes, as well as a nutrient-rich layer of mucus, which microbes can feed off in times of famine. The cecum is attached to the appendix. Far from being an evolutionary relic, the appendix serves as a “safe-house” (in the words of Alanna Collen) for the microbes in the human body and is filled with specialized immune cells and molecules.


What if I told you that there’s a community of organisms living inside and on you, teeming with life, like a tropical rainforest? In a state of homeostasis, this forest is an ecosystem, with each organism dutifully playing its part to maintain the balance and keep the system running smoothly.

Like all ecosystems, the one inside us is made up of living organisms as well as the physical environment they live and interact in. If one part of the ecosystem collapses, the entire system is compromised. Likewise, the introduction of an invasive species not naturally found in the ecosystem can upset the balance.

Every human on Earth is home to such an ecosystem, known as the microbiome. The human microbiome is as diverse as the Amazon Rainforest, but like the Amazon, it is under threat. Unless we take immediate steps to preserve the diversity and balance of our fragile microbiome, some species may become extinct.

The study of microbiota

The study of human gut microbiota is an interdisciplinary field that has exploded in recent years. Studies of gut microbes are no longer limited to microbiologists. The microbiome has caught the attention of geneticists, evolutionary biologists, epidemiologists, gastroenterologists, hepatologists, and even neuroscientists.

Historically, microbiology was limited to visualization techniques, like microscopy, and culturing microbes (in other words, growing them in isolation in a laboratory). Thanks to recent advances, microbiologists can now use DNA in addition to microscopy and culturing. DNA studies give a much more accurate understanding of our microbiota because we can see everything – not just what is grown in a lab.

Human stool contains about 4,000 species of bacteria, so fecal samples are a common method of analysis. Samples are also taken during endoscopy and biopsy. Thanks to bioinformatics platforms, scientists can analyze data and visualize the composition of the gut microbiome.

Stanford University’s Center for Human Microbiome Studies focuses on connecting scientists from different disciplines and leveraging technology to harness the biomedical potential of our microbiota.

Mental illness

Neglecting our gut microbiota has profound consequences for human health. Alanna Collen estimates that by 2050, 50% of the world’s population will be obese. She notes wryly that for future generations, the 20th Century will be known not only for its two world wars and the invention of the internet, but for being the age of obesity.

Regarding the link between our microbes and mental illness, some studies suggest that every family in the United States will have a child on the autism spectrum by 2050. In Missing Microbes, Dr Martin Blaser describes modern epidemics (such as asthma, metabolic disease, obesity, and allergies) as “external signs of internal change”. He raises the alarm about rare, ancient microbes becoming extinct due to the overuse of antibiotics, and warns of an “antibiotic winter”, fueled by degraded immune defenses and globalization.

We’ll look at antibiotic resistance and immunity in tile 5. Tile 6 examines the link between antibiotic overuse and obesity.

Gut feelings

Have you ever wondered why we have so many expressions relating to the gut and emotions? We speak about having a “gut feeling” to describe our intuition, or instinct. When we’re nervous, we say we have “butterflies in our stomach”. These expressions are rooted in biology.

The average human gut weighs about 3 pounds and has its own nervous system, called the enteric nervous system. It is frequently referred to as the “second brain”, and with good reason. The vagus nerve provides a physical link between the gut and the brain and allows them to talk to each other. Even when the physical link is severed, these two organs can continue to communicate.

While we used to think that most signals were sent from the brain to the gut, we now know that the majority are sent from the gut to the brain. We’ll take a deep dive into this superhighway, known as the gut-brain axis, in tile 7.

Current studies on gut health give us insight into future trends. The American Gut Project, based at the laboratory of Professor Rob Knight at the University of Colorado, is the world’s largest citizen science microbiome project. The Project analyzes human stool samples to learn more about the species in our guts and their health impacts. This service is available to anyone around the world in exchange for a donation.

Advances in tech are fueling the gut health revolution. The ZOE Project, co-founded by Professor Tim Spector, has developed a home test kit that tracks and analyzes gut, blood fat and blood sugar responses, to give personalized nutrition guidance to improve gut health and reduce inflammation. We are likely to continue to see highly personalized nutrition regimes based on massive datasets. Research into psychobiotics is likely to continue. Tile 10 explores the future of gut health in more detail.

A trillion cells

There are over 100 trillion bacterial cells in the human body; outnumbering human cells at a ratio of 10:1. We are, as Allana Collen puts it in her book by the same title, just “10% human”. To put these numbers into perspective, consider that if you were to line up your bacterial cells end-to-end, they would reach the moon.

The gut is the center of microbial activity in the human body. The community of microbes (bacteria, viruses, fungi, and archaea – but mostly, bacteria) living inside our intestines is called the microbiota. Their genes are called the microbiome. Some microbiota live in the stomach and small intestine, but the vast majority reside in the large intestine.

The bacteria in the large intestine live in such close quarters that each teaspoon of intestinal contents contains 500 billion cells. This is the highest microbial density recorded in any habitat on Earth.

Microbial diversity

Microbial diversity refers to the number and distribution of different species of microbes. Every one of us contains a unique network of microbiota. The microbiota living inside each of us are as unique as our fingerprints.

Nowhere was this illustrated better than when the results of the much-anticipated Human Genome Project were published and compared to those of the Human Microbiome Project (which mapped the DNA of microbes taken from healthy young adults). These studies concluded that while all humans share 99.9% of the same genetic material, we share only roughly 90% of our microbiomes. In other words, if we want to unlock the key to human health, we would be better off studying our microbes than our genetic material.

A healthy gut contains a wide array of microbes. This diversity makes our microbiome more capable and resilient because if one microbe cannot fulfill its function, another one can step in.

Modern Lifestyles

Our modern lifestyles are fueling chronic disease. These diseases have reached such epidemic proportions that Martin Blaser, Professor of Medicine and Microbiology at Rutgers University, describes them as “modern plagues”.

The same innovations that revolutionized public health in the late 19th and early 20th Centuries by eradicating most infectious diseases have also led to harmful changes in our gut microbiome. According to science writer and evolutionary biologist Alanna Collen, these innovations include vaccination, hygienic medical practice, water sanitation, and the discovery of penicillin.

Perhaps the most pernicious of these innovations was the discovery and development of penicillin. Once seen as a panacea to cure all ills, antibiotics have been over-prescribed for decades. We realized too late that antibiotics do not discriminate, and they destroy the good bacteria in our guts along with the bad. We’ll take a closer look at the havoc wreaked on human gut health by urbanization, industrialization, and the over-use of antibiotics in tile 4.

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