Our bodies are home to countless microscopic organisms, forming intricate communities known as microbiomes. These diverse microbial residents, including bacteria, fungi, and viruses, live on and within us, creating a complex ecosystem. They are active participants, performing various functions within their unique habitats.
Microbiome Versus Microbiota
The terms “microbiome” and “microbiota” are often used interchangeably, but they have distinct scientific meanings. Microbiota refers specifically to the collection of microorganisms themselves, such as bacteria, viruses, fungi, and archaea living in a particular environment.
The microbiome, on the other hand, encompasses the entire habitat, including all these microorganisms, their collective genetic material (genomes), and the surrounding environmental conditions. Scientists study the microbiome to understand the functional potential of these microbes, deciphering what they are capable of doing based on the genes they possess.
Composition of a Microbiome
A microbiome is a diverse collection of various microorganism types, each contributing to the community. While their exact proportions vary by location, several major groups are consistently present.
Bacteria
Bacteria are the most numerous and well-studied members of any microbiome, especially in the human gut. They come in countless species and strains, playing varied roles depending on their specific location and environment. These single-celled organisms are a primary focus of microbiome research due to their abundance and diverse metabolic activities.
Archaea
Archaea are single-celled microorganisms, distinct from bacteria, often found alongside them in microbiomes. While less abundant, certain archaea, such as Methanobrevibacter smithii, are common in the human gut and oral cavity. They are known for unique metabolic processes, like producing methane gas.
Fungi
Fungi, including yeasts and molds, also form a part of the microbiome. A common example is Candida species, found on various body surfaces. Fungi constitute a smaller proportion of the microbial community compared to bacteria but contribute to the overall diversity.
Viruses
Viruses are ubiquitous members of microbiomes, with bacteriophages (viruses that infect bacteria) being particularly prevalent. These viruses play a significant role in shaping bacterial populations by infecting and lysing specific bacterial cells. Their presence adds another layer of dynamic interaction within these complex microbial ecosystems.
Locations of Microbiomes
The human body hosts distinct microbial communities across various anatomical sites, each with unique environmental conditions that shape its specific microbiome. These localized communities are adapted to their particular surroundings, influencing how they interact with the host. The diversity of microbial makeup for a given site often varies from person to person.
The Gut Microbiome
The gut microbiome, residing primarily in the large intestine, is the most densely populated and extensively studied. It contains trillions of microorganisms, mainly dominated by two bacterial phyla: Bacteroidetes and Firmicutes. Many of its organisms are rarely found living independently outside a host.
The Skin Microbiome
The skin microbiome differs significantly depending on the specific skin region. Areas like the oily forehead harbor different communities than drier forearms or moist armpits. For example, sebaceous sites are dominated by Propionibacterium species, while moist areas have more Staphylococcus and Corynebacterium species.
The Oral Microbiome
The oral microbiome encompasses the diverse community of microbes found throughout the mouth, including on the teeth, gums, and tongue. This environment contains several distinct niches, each supporting specific microbial groups. An estimated 500-700 bacterial species are common to most oral microbiomes, forming biofilms like dental plaque.
Other Microbiome Locations
Beyond these major sites, microbiomes also inhabit other parts of the body, such as the nasal passages, lungs, and the vaginal tract. For instance, the healthy lung contains bacterial phyla like Firmicutes and Proteobacteria. Microbiomes are not limited to humans but also exist in various external environments like soil and oceans, forming complex ecosystems globally.
Formation and Development of the Microbiome
A human’s microbiome begins to establish itself early in life, with initial colonization occurring around the time of birth. The most significant initial seeding happens during delivery.
Newborns delivered vaginally are exposed to the mother’s vaginal and fecal microbiota, leading to a microbiome dominated by bacteria like Prevotella and Lactobacillus. Infants born via Cesarean section, however, do not encounter these maternal microbes directly and have microbiomes resembling the mother’s skin or the hospital environment, featuring bacteria such as Corynebacterium and Staphylococcus. These initial differences in microbial composition normalize after about three to five years.
Early diet plays a significant role in shaping the developing microbiome. Breast milk, for instance, contains human milk oligosaccharides that act as prebiotics, selectively feeding beneficial bacteria like Bifidobacterium. In contrast, formula feeding results in a different microbial profile. The microbiome continues to diversify and stabilize throughout the first few years of life, establishing a relatively stable adult-like community structure by around three years of age.
Factors That Influence Microbiome Composition
Once established, the composition of a person’s microbiome can continue to change throughout life due to various influencing factors. These shifts are dynamic and reflect ongoing interactions with the environment and lifestyle choices. The resilience of microbiomes allows them to recover from many disruptions, but sustained exposure to certain factors can lead to lasting alterations.
Diet
Diet is a primary driver of microbiome changes, as the food consumed directly feeds the resident microbes. Diets rich in fiber, for example, promote the growth of beneficial bacteria that ferment these compounds, producing beneficial metabolites. Conversely, diets high in fats and proteins favor different bacterial profiles.
Antibiotics
Antibiotics are well-known for their broad-spectrum effects, killing both harmful and beneficial bacteria indiscriminately. This leads to a reduction in overall microbial diversity and a temporary imbalance in the microbiome. The overuse of antibiotics has been linked to various disorders associated with gut microbial disruption.
Lifestyle and Environmental Factors
Lifestyle and environmental factors also contribute to microbiome variability. Geographical location, living with pets, and cohabitation with other people introduce diverse microbes, influencing an individual’s microbial makeup. Physical and psychological stress, alcohol consumption, and exposure to environmental toxins are additional elements that alter microbiome composition over time.