How the body and microbiomes interact
The human body does not function in isolation. It interacts continuously with microbes living on and within it, shaping digestion, immune function, communication between organs, and overall health.
Understanding these interactions provides new insight into human biology and health.
Humans evolved alongside microbes
Microbes existed billions of years before humans. As humans evolved, they developed alongside microorganisms that remain an essential part of human biology today. Microbial communities known as microbiomes live throughout the body — including the gut, skin, mouth, nose, eyes, lungs, and urogenital tract - where they interact continuously with human physiology.
The gut microbiome is the body’s largest and most densely populated microbiome. During the first years of life, it changes rapidly and by around 2–3 years of age begins to resemble a more stable, adult-like pattern. Even then, it continues to adapt over time in response to factors such as diet, stress, illness, medication, lifestyle, and environment.
Human physiology in the gut system
Gut barrier
The gut barrier forms an active interface between the contents of the intestine and the rest of the body. Although only one cell layer thick, it helps absorb nutrients while also acting as a barrier that supports the body’s natural protection system.
Immune system
A large part of the immune system is associated with the gut. Immune cells positioned close to the gut barrier continuously monitor microbial and dietary signals, helping maintain balance between tolerance and defense.
Nervous system
The gut has its own nervous system, known as the enteric nervous system. It helps regulate gut movement, secretion, and sensation, while also communicating with the brain.
Endocrine system
The gut is also an endocrine organ. Specialized cells release hormones involved in appetite, digestion, metabolism, and communication between the gut and other organs.
The gut as an
interconnected system
The gut microbiome is part of a larger gut system where multiple components work continuously together. Gut health is shaped by interactions between human physiology, the gut microbiome, digestive chemistry, and nutritional inputs. Each plays a distinct role, but together they influence digestion, barrier function, microbial activity, and communication within the body.
Digestive chemistry in the gut system
Stomach acid
Stomach acid supports digestion and helps limit the survival of potentially harmful ingested microbes.
Digestive enzymes
Digestive enzymes accelerate the breakdown of carbohydrates, proteins, and fats into smaller components that can be absorbed.
Bile acids
Bile acids help digest fats while also influencing microbial activity and human metabolism.
Nutritional inputs in the gut system
Microbiome substrates
Some fibers and resistant starches cannot be fully processed by the body’s own digestive enzymes and will instead be utilized by gut microbes.
Host substrates
Nutrients such as proteins, fats, vitamins, and minerals nourish the human body directly while also shaping the gut environment.
Bioactive compounds
Bioactive compounds – such as polyphenols found in plant foods – can interact with both human cells and microbes, contributing to signaling and regulation within the gut system.
The gut microbiome
The gut microbiome is the collection of microbes including bacteria, viruses and fungi that live in the gastrointestinal tract. These microbes interact with each other forming a dynamic ecosystem that interacts closely with the human body.
The gut microbiome is shaped across life by many factors, including early-life microbial exposure, feeding, diet, lifestyle, environment, illness, and medication use. Although it becomes more stable after the first years of life, it remains responsive to internal and external influences. This means the gut microbiome is both relatively stable and continuously adaptable.
A healthy gut microbiome is not defined by the presence of individual “beneficial” organisms, but by the overall composition, functional activity, and resilience of the microbial ecosystem. Higher microbial diversity is generally linked to a wider range of functions and greater resilience, although what is considered optimal can differ between individuals and contexts.
Probiotics can offer health benefits
Probiotics are defined as live microorganisms that confer a health benefit on the host when given in adequate amounts.
Discover more about their role in supporting human health.