- The microbiome refers to the entire community of microorganisms—including bacteria, archaea, fungi, viruses, and protozoa—that live in association with a particular environment or host.
- In humans and other animals, the microbiome encompasses not only the microbes themselves but also their collective genetic material and metabolic products. These microbial communities inhabit nearly every surface and cavity of the body, such as the skin, oral cavity, respiratory tract, urogenital tract, and, most notably, the gastrointestinal system. Far from being mere passengers, these microorganisms form dynamic and symbiotic relationships with their host, influencing physiology, immunity, nutrition, and health.
- The human gut microbiome is the most extensively studied and is considered the densest and most diverse microbial ecosystem associated with the body. It consists of trillions of microorganisms, predominantly bacteria belonging to the phyla Firmicutes and Bacteroidetes, along with smaller populations of Actinobacteria, Proteobacteria, and others. The gut microbiome contributes to digestion by breaking down complex carbohydrates, fibers, and other nutrients that humans cannot digest unaided. In doing so, it produces metabolites such as short-chain fatty acids (SCFAs), which serve as energy sources for intestinal cells and have systemic effects on metabolism, immunity, and even brain function.
- Beyond digestion, the microbiome plays a central role in the immune system. It helps train immune cells to distinguish between harmful pathogens and benign or beneficial microbes, thereby reducing the risk of autoimmune reactions. It also provides colonization resistance, where the presence of beneficial microbes prevents pathogenic organisms from establishing themselves, either by competing for nutrients or producing antimicrobial compounds. This symbiosis demonstrates the intricate balance between host and microbiota in maintaining health.
- The microbiome is also increasingly recognized as a key player in the so-called gut–brain axis, a bidirectional communication network between the gastrointestinal system and the central nervous system. Microbial metabolites, such as SCFAs and neurotransmitter precursors, can influence mood, cognition, and behavior. Studies suggest links between microbiome composition and neurological or psychiatric conditions, including depression, anxiety, and autism spectrum disorders. Similarly, disruptions in the microbiome, a state known as dysbiosis, have been associated with a wide range of health issues, including obesity, inflammatory bowel disease, allergies, metabolic syndrome, and even certain cancers.
- Importantly, the microbiome is not static; it changes in response to diet, age, lifestyle, environment, and medical interventions such as antibiotics or probiotics. For example, high-fiber diets promote the growth of bacteria that produce beneficial SCFAs, while high-fat, low-fiber diets can reduce microbial diversity and favor pro-inflammatory species. Infancy and early childhood are critical periods for microbiome development, with factors such as mode of birth delivery, breastfeeding, and early antibiotic exposure shaping microbial colonization patterns that can have long-term health consequences.
- Beyond human health, microbiomes exist in virtually every environment on Earth—from soil and oceans to plants and animals—where they play critical ecological roles. In plants, the root-associated microbiome aids nutrient uptake and enhances resistance to pathogens, while in soil and aquatic ecosystems, microbial communities drive nutrient cycling and carbon sequestration. Thus, microbiomes represent fundamental engines of biogeochemical processes at both micro and global scales.
