The Ecology of Humans – Human Microbiome


“The human body and its symbionts can be viewed as a community of interacting cells.” ~ American microbiologist and immunologist David Relman et al

The human body is a rich ecosystem: a vast collective of microbial life. People lug around 10 times as many microbes as they have cells – the little ones are hard to tally.

A developing fetus get its 1st microbiome from its mother. From the moment you were born, every exposed surface and organ of the body has attracted microbes.

At the cellular level, a human is a world unto itself. Our bodies are in symbiotic relationships with microbes to accomplish most everything a mind-body does.

“The human-microbial ecosystem plays a variety of important roles in human health and disease.” ~ American microbiologist and immunologist Elizabeth Costello

There is a continuous intimate dialogue between body and microbiome. Microbial missives direct bodily development and functioning, including influencing desires. Conversely, host cell communication impacts the activities and populations of microbial communities within the body.

“The mind can affect the microbiome and the microbiome can affect the mind.” ~ American microbiologist Laura Sanders

Much of the microbiome comprises viruses and bacteria, but there are also protists and multicellular species, such as fungi. Then there are the parasites and pathogens, both internal (e.g., flukes) and on the skin (e.g., lice).

Eyelash mites are ubiquitous on adults, and common on children. These mites are snugly tucked into the sebaceous glands connected to hair follicles. They are permanent residents and cannot be washed off.

Microbiota are instrumental in defining the quality of its host’s life. The microbiome is personalized, localized, and specialized.

Even before birth, one’s microbiome is a determinant of health, and remains so throughout life. Changing diet can alter the ecosystem of gut microbiota within a matter of days.

Commensal microbes offer genes that complement the human genome in many ways, including such basic functions as metabolism. Microbes are critical for enzyme production. Our bodies possess a pathetic complement of enzymes whereas microbes carry an arsenal.

Mitochondria monitor the health of their cells. When stressed by lack of nutrition or pathogenic attack they initiate corrective responses. Among them are enlisting the assistance of local microbes. That the mitochondrion genome is related to bacterial genomes is conducive to communicating and coordinating activities.

There is an intricate interdependence among the many thousands of microbial colonies within the body. The human body comprises a metagenome of all its constituent life. The 1,000 species or so microbial species in the human digestive tract present 100 times as many genes as the human genome has. This is one reason that the quality of microbiome bodes for the health of its host. If microbiotic diversity is low, the toolkit for fighting infections is meager.

A few microbes interested in humans make people sick but most are commensal and call our body their home. Even unwelcome ones can be helpful. An established herpes virome in a human makes the body less susceptible to certain bacterial infections. More generally, resident viruses are instrumental in modulating metabolism and health. When the bacterial gut flora ecosystem is disrupted, such as by antibiotics, resident viral communities step up to protect the host from infection.

Infant Exposure

Fetuses are first exposed to their mother’s microbiome through the placenta. These microbes provide nutrients, guide growth, and help keep the fetus healthy.

An infant’s body relies upon microbial signals to properly develop. Microbiota are in constant communication with human cells as well as other microbes.

Microbiota transfer from mother to child is important to future health prospects. Babies born naturally are coated with the microbes from their mother’s birth canal. But babies born by surgical Caesarean section are covered in microbes typically found on the adult skin. The difference can be telling. Babies delivered by C-section are more likely to have early health problems, particularly breathing and skin related. The risk is aggravated by early delivery.

Besides getting bathed in mom’s microbes during delivery, breast milk feeds commensal bacteria to infants. Bifidobacterium dominates the gut of healthy, breast-fed infants, and is important in a well-functioning immune system.

By contrast, the bacteria Staphylococcus aureus is more predominant in the digestive system of infants who become overweight children. Staph is famous for its resistance to antibiotics, and has been linked to chronic, low-grade inflammation, as well as being a factor in obesity.

“Microbial exposure is important to immune development.” ~ American pediatric immunologist Anthony Horner

The criticality of microbiotic transfer through breast milk is illustrated by the startling rise of autism in the United States from the late 20th century, as breastfeeding became less common. Recently, researchers have successfully ameliorated autism in young children through artificial microbiotic transfers.

Breast feeding is not just for baby. The microbiome must be fed.

“Breast milk contains large amounts of oligosaccharides that the baby cannot metabolize, but the microbiota can.” ~ English biologist Kevin Foster et al

Many animal moms deliberately transfer their microbiomes to their offspring. Infant elephants eat mom’s feces to acquire the microbes needed to digest food. Sand puppy pups plead for anal excretions from their parents, to get the healthy microbes they need. For many animals, motherly devotion involves slathering younglings with microbial cultures, giving new meaning to the tradition of passing culture down through the generations.


The personalized microbiome affects every facet of life, including psychology. Not only does the herpes virus help keep the engine running clean, it motivates sexual intercourse, based upon environmental cues it receives that the possibility of sex exists, such as increased oxytocin levels.

Eating the bacteria Lactobacillus rhamnosus, found in certain yogurts, cheeses, and breads, has a calming effect. Gut bacteria influence mood via the vagus nerve, which connects the digestive organs to the brain.

Scientists have only begun to explore human-microbial codependence and interrelationship. The most rudimentary knowledge of human-microbe interdependence was just discovered at the turn of the millennium. Researchers have yet to discover the energetic interactivity that most essentially characterizes the ongoing dialogue between microbiome and host. Yet the microbiome was known by the mid-1600s, when Dutch lens-grinder Antonie van Leeuwenhoek scraped some scum off his teeth, put it under a microscope, and discovered a swarm of little swimmers. Each tooth, even each side of each tooth, has various combinations of different bacteria.

The skin is the physical ecological interface between a body and its environment. Microbes there play an essential protective role. They also define your presence. The microbiome can smooth your skin and make your hair shiny. They can collectively put a spring your step.

Everyone has their own biogeographical colonies of microbes. The hair, the forehead, the ear, around the eyes and the nose all have different bacterial colonies; as do the elbow and the forearm, and each finger. Bacteria from a person’s tongue can make a decent living on a dry forearm, but the oily forehead is tough going.

Human skin is a smorgasbord of microbial ecosystems: home to roughly 1,000 bacteria species, almost as many as working the intestinal tract. Colonies vary by individual and by health.

“The skin needs microbial signals for proper immune cell function.” ~ Indian immunologist Shruti Naik

Each type of microbe on the skin triggers a specific immune response. Microbial skin commensals and the host immune system form an effective team to protect the home turf.

The most bacterially diverse region of the skin is on the forearm: home to nearly 4 dozen species on average, double the number found in the most barren patch, behind the ears.

While many skin bacteria pose a potential infection risk if able to penetrate the skin’s multiple defenses, Staphylococcus epidermidis helps tune the immune system. S. epidermidis blocks aggressive inflammatory agents with a molecular signal. Unchecked, the agents would be hyperactive, igniting a rash reaction around even a slight scrape.

Belly-button bacteria are a stable group, lasting months with little change. There are other quiet portions of the body, while other parts, such as the mouth and skin, are transit centers and quite active microbiotically.

Commensal vaginal bacteria secrete compounds that keep pathogens in check, rendering the environment slightly acidic, which most microbes find unappealing.

Indigenous microbes in the mouth and lungs not only adhere to local cells, they comingle with them as well. Conditions are much different there than on the skin. The purpose and effects are not understood. It may well be an intimate form of communication and sharing.

Whereas the lower respiratory tract lacks a microbial community, the upper respiratory tract is densely populated with microbes, with a high species diversity for healthy humans which varies from site to site.

We are colonized by microbes every day of life: from surfaces touched, food consumed, and air breathed. Some microbes mitigate invasion. Bacteria in our nose manufacture antibiotics to kill dangerous pathogens that are sniffed.

Sex and the Microbiome

Sex provides the genetic diversity necessary to raise the odds against an onslaught of pathogenic marauders. It is may be that sex evolved for that purpose (among others).

However exciting courtship may be to its participants, it is also a communal ritual of microbiomes. Kissing is ubiquitous in human cultures; although in some it is more like sniffing. While swapping saliva risks contagion, that may be the point.

Humans carry various chronic viral colonies. Acquiring new viruses during pregnancy can harm a fetus. So, kissing well before the event allows infections from a father to settle in and lessen the odds of mishap. In this case, kissing is a form of self-vaccination.

Human sweat does not smell. The odor of armpits comes from microbe excretions after feeding on sweat. Armpits are fermentation crocks indicative of health by way of resident bacteria.

Women prefer men whose body odor suggests a complimentary immune system to their own. The scent of a man is not of the man, but of his microbiome.

Prolonged proximity among animal conspecifics is a communal rite for the microbes involved. Its more than just sharing parasites and ne’er-do-well prokaryotes.

Insect colonies share symbiotic microbes that ward off parasites. Some salamanders nest in groups to share bacteria that keep nefarious fungi at bay.

Primates that groom one another end up with similar microbiomes; so do people who live together.


A diet rich in meat, refined foods, sugars, and fats damages the internal habitat, reducing the diversity of gut bacteria. Start eating more plants and diversity blossoms.

While people constantly pick up and share microbes, one person’s biome varies from another depending upon genotype, age, sex, diet, hygiene practices, health, clothing, occupation, and climate. But variance is by degrees. Family members tend to have similar gut microbes, which is likely attributable to a shared diet. Not much research has been devoted yet to characterizing microbiomes among different cultures or baseline genetic makeup.

The distinct advantage of human-microbial interdependence comes from evolution. Microbes may live short lives, but that is to our advantage. Microbes selectively pick up genetic bits they consider valuable. Those same bits commonly prove helpful to their human hosts.

Regardless of scale, different organisms in ecosystems pass information and metabolic capabilities to each other. For a human and its microbiome that’s sharing the wealth. Considering that microbes live life in the fast line, they are the ones doing almost all the giving.

Our existence is an intertwined dance among trillions of cells, only a tiny fraction of which are human in the classical sense. That dance is to an ever-changing tune of environmental conditions, with diet a most important choice.