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


What if I told you that there’s a community of organisms living inside and on you, teeming with life, like a tropical rainforest? The forest flourishes as each organism dutifully plays its part to maintain the balance and keep the system running smoothly. This state of balance is known as homeostasis (“the ability or tendency of the body or a cell to seek and maintain a condition of equilibrium – a stable internal environment — as it deals with external changes”1). 

Like the forest ecosystem, the one inside us consists of living organisms as well as the physical environment in which they live and interact. If one part of the ecosystem collapses, the entire system is compromised. Likewise, the introduction of an invasive species into the environment can upset the balance. 

Every human on Earth is home to such an ecosystem, known as the microbiome. The human microbiome is a population of microscopic organisms as diverse as the Amazon Rainforest; and 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.2

Modern threats to gut health

Our modern lifestyles may be fueling chronic disease.3 These diseases have reached such epidemic proportions that Martin Blaser, Head of the Human Microbiome Program at New York University, describes them as “modern plagues”.  Blaser notes, “Unlike most lethal plagues of the past that struck relatively fast and hard, these are chronic conditions that diminish and degrade their victims’ quality of life for decades”.4

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 Alanna Collen, evolutionary biologist and science writer, these innovations include vaccination, hygienic medical practice, water sanitation, and the discovery and development of penicillin. 

Perhaps the most pernicious of these innovations was the discovery and development of penicillin.5 Effective in their mission to destroy bacteria – and once considered a panacea to cure all ills – antibiotics have been over-prescribed for decades. We realized too late that antibiotics do not discriminate; they destroy the good bacteria in our guts along with the bad.  We also discovered that overuse  promotes antibiotic resistance. We’ll take a closer look at the havoc wreaked on human gut health by urbanization, industrialization, and the overuse of antibiotics in the tile “Antibiotics and immunity”.

Composition of the gut microbiota

There are over 100 trillion bacterial cells in the human body; outnumbering human cells at a ratio of 10:1. We are therefore, as Alanna 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.6

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. 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.

Gut microbes and digestion

Although the large intestine houses the highest density of microbes, other components of the digestive tract are important for normal gut function. Under optimal conditions, the stomach is highly acidic and kills most of the harmful microbes that enter it. Stripped of some of its accompanying microbes, food from the stomach 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, forming the first part of the large intestine. In the cecum, 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 mucosal layer (literally, a layer of mucus), which microbes can feed off in times of famine.

Vagus nerve and gut-brain axis

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, as our gut communicates directly with our brain. 

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 the tile “The microbiota-gut-brain axis”.

Microbial diversity

Just like a healthy rainforest contains a wide array of species, a healthy gut contains a wide array of microbes. This diversity makes our microbiota more capable and resilient, because if one microbe cannot fulfill its function, another one can step in to lend a hand.

When we talk about microbial diversity, we’re referring to the number and distribution of different species of microbes in our gut.  The microbiota living inside each of us are as unique as our fingerprints. We call this unique pattern of microbes a “microbial signature”.  

Nowhere was this better illustrated than when the results of the much-anticipated Human Genome Project were 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.

Functions of gut microbes

Gut microbes play a fundamental role in human health.7 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, as well as 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, can lead to a range of illnesses.8 A disrupted gut microbiome has been associated with 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. We’ll explore the link between gut microbes and physical and mental health in the tiles “Antibiotics and immunity”, “Gut microbes and metabolic health” and “The microbiota-gut-brain axis”.

Who studies gut microbes, and why?

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 (a thin tube attached to a camera, inserted into the esophagus, to examine the digestive organs) and biopsy (taking a sample of tissue to check for the presence of cancerous or pre-cancerous cells). 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. This is where bacteria with the potential to heal the gut are genetically engineered and research is conducted to understand the health impact of changes to the microbiota that have occurred with industrialization.

The risks of neglecting our gut microbes

Neglecting our gut microbiota has profound consequences for human health.9 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. 

Neglect of gut health also poses a risk to mental wellbeing. 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 2050.10 In Missing Microbes, Martin Blaser describes modern epidemics (such as asthma, metabolic disease, obesity and allergies) as “external signs of internal change”.11 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 the tile “Antibiotics and immunity”. The “Gut microbes and metabolic health” tile examines the link between antibiotic overuse and obesity.

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. 

Advancements in technology are fueling the gut health revolution. The innovative 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. With a promise to improve gut health and reduce inflammation, ZOE offers personalized nutrition guidance based on test kit results.  The tile, “The future of gut health”, also explores future trends in more detail.

[1] Biology Online, https://www.biologyonline.com/dictionary/homeostasis#Homeostasis_Definition

[2] Food for thought: How your belly controls your brain | Ruairi Robertson | TEDx Fulbright Santa Monica. Available at: https://www.youtube.com/watch?v=awtmTJW9ic8

[3] Collen, Alanna. 10% Human: How Your Body’s Microbes Hold the Key to Health and Happiness (p. 64). HarperCollins Publishers. Kindle Edition. (2014); Blaser, M. The theory of disappearing microbiota and the epidemics of chronic diseases. Nat Rev Immunol 17, 461–463 (2017). Retrieved from: https://doi.org/10.1038/nri.2017.77)

[4] Blaser, Michael. Missing Microbes: How Killing Bacteria Creates Modern Plagues (2014), p. 9, eBook Edition.

[5] Blaser, M. Antibiotic use and its consequences for the normal microbiome. Science. 2016 April 29; 352(6285): 544–545. doi:10.1126/science.aad9358. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4939477/pdf/nihms795663.pdf

[6] Sonnenburg, Justin. Professor of Microbiology & Immunology at Stanford University, Gut Reaction.

[7] Collen, Alanna. 10% Human: How Your Body’s Microbes Hold the Key to Health and Happiness (2014, pp. 307, 309, 317, 320, 323, 413). HarperCollins Publishers. Kindle Edition.

[8] Collen, Alanna. 10% Human: How Your Body’s Microbes Hold the Key to Health and Happiness (2014). HarperCollins Publishers. Kindle Edition; Blaser, Michael. Missing Microbes: How Killing Bacteria Creates Modern Plagues (2014) eBook Edition.

[9] Blaser, Michael. Missing Microbes: How Killing Bacteria Creates Modern Plagues (2014), p. 12, eBook Edition.

[10] Collen, Alanna. 10% Human: How Your Body’s Microbes Hold the Key to Health and Happiness (p. 105). HarperCollins Publishers. Kindle Edition.

[11] Blaser, Michael. Missing Microbes: How Killing Bacteria Creates Modern Plagues (2014), p. 151, eBook Edition.

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