Human microbiota: The microorganisms that make us their home

What makes a human body? According to researchers, human cells tell but half the story. The other half involves the myriad of microorganisms that make up the microbiota — “alien” environments all over our bodies that, as long as there is a healthy balance, help us thrive.

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Researchers continue to investigate the role of gut bacteria in the health of the brain and other areas of the body.

The human body contains trillions of specialized cells — tiny building blocks that come together to support the development and functioning of the body.

But human cells are not the only “materials” that make up our bodies. In fact, we live in symbiosis with trillions of microorganisms, too.

Researchers have long debated the true ratio of human cells to microorganisms in the average body. Estimates have fluctuated, but the most recent study to consider the matter — which appeared in PLOS Biology in 2016 — suggests that we likely have about as many microorganisms in and on our bodies as we do human cells.

In addition to bacteria and viruses, these microorganisms include archaea, primitive organisms with no nucleus, and eukaryotic microorganisms, or eukarya, a type with a nucleus that protects its chromosomes. In the latter group are fungi and protists, tiny organisms at the “border” between a plant and a fungus.

All of these together make up various microbiota: communities of microorganisms present at different sites on or in the human body.

The various microbiota make up the human microbiome: the totality of microorganism communities spread around the human body.

Collections of microorganisms in different areas play a crucial role in helping maintain our health — though to do so, the numbers of various types of bacteria, fungi, and other microorganisms have to remain in perfect balance.

When that balance is tipped and, for instance, one bacterial species overpopulates, this can lead to infections and other health problems.

This feature describes the various organisms that make their homes in the gut, mouth, vagina and uterus, penis, skin, eyes, and lungs.

The most talked-about environment for colonizing microorganisms, especially bacteria, is the human gut.

Studies show that the human gastrointestinal tract houses a vast “collection of bacteria, archaea, and eukarya” that play important roles in gut homeostasis, helping maintain the health of the gastrointestinal system.

Research has also suggested that gut bacteria moderate the connection between the gut and the brain through an interaction with the enteric nervous system and other mechanisms, which may be hormonal or immunological.

The main bacterial phyla, or types, present in the gut are Firmicutes and Bacteroidetes, which make up 90% of the gut microbiota.

Others are Actinobacteria, Proteobacteria, Fusobacterua, and Verrucomicrobia. These include some familiar bacterial groups, or genera, from the Firmicutes phyla, such as Lactobacillus, which is known for its positive impact on health.

On the other hand, some Firmicutes species can rapidly cause illness if they overgrow — such as Staphylococcus aureus and Clostridium perfringens.

The Proteobacteria phylum includes some well-known pathogenic groups, such as Enterobacter, Helicobacter, Shigella, and Salmonella bacteria, as well as Escherichia coli.

Meanwhile, the Actinobacteria phylum includes the Bifidobacterium bifidum species, which is generally beneficial for healthy individuals.

This list, however, is by no means exhaustive. There are around 2,172 bacterial species in the human gastrointestinal tract, according to compiled data.

If some of these names sounded uncomfortably familiar, it is because many of these bacteria can cause infection if they over-colonize. And some strains can infect the gut through food that has gone bad or contact with unclean surfaces.

Some strains of E. coli can cause infections that lead to diarrhea and vomiting, some strains of S. aureus can become resistant to antibiotics and cause severe illness, and Salmonella infections can cause diarrheal illness.

But gut bacteria can typically be strong allies in health maintenance, and specialists continue to study the many ways in which these microorganisms help keep us in good form.

“This is a new frontier of medicine, and many are looking at the gut microbiota as an additional organ system,” said infectious disease specialist Dr. Elizabeth Hohmann in an interview with Harvard Medical School.

“[The gut microbiota is] most important to the health of our gastrointestinal system but may have even more far-reaching effects on our well-being,” she added.

Other microorganisms present in the gut are viruses, but not the ones that typically cause illness.ges” — literally, bacteria eaters — that help maintain microbial balance by taking over the inner workings of bacteria.

Bacteriophages “make up the vast majority of the viral component of the gut microbiome,” and researchers have argued that part of their role is to infect certain bacteria to preserve a healthy balance of microorganisms in the gut. Still, much about them remains poorly understood.

Like the gut, the mouth also contains numerous bacteria necessary for homeostasis.

“A wide range of microorganisms are present in the oral cavity. It is in constant contact with and has been shown to be vulnerable to the effects of the environment,” explain the authors of a review published in the Journal of Oral and Maxillofacial Pathology in 2019.

They continue, noting that “Different surfaces in the mouth are colonized preferentially by the oral bacteria,” depending on the type of surface that they are adhering to, that of the cheek, tongue, or teeth, for instance.

The oral microbiota contains 12 bacterial phyla — Firmicutes, Fusobacteria, Proteobacteria, Actinobacteria, Bacteroidetes, Chlamydiae, Chloroflexi, Spirochaetes, SR1, Synergistetes, Saccharibacteria, and Gracilibacteria — with multiple species, named or unnamed.

But the mouth also houses other microorganisms, namely protozoa, the most common of which are Entamoeba gingivalis and Trichomonas tenax, as well as fungi and viruses.

There are 85 genera of fungi in the oral environment, including Candida, Cladosporium, Aureobasidium, Saccharomycetales, Aspergillus, Fusarium, and Cryptococcus.

“[The oral microbiota] plays a crucial role in maintaining oral homeostasis, protecting the oral cavity, and preventing disease development,” write the authors of the 2019 review.

As with other microbiota, if the numbers of microorganisms that populate the mouth become imbalanced, it can lead to the development of illness, such as various bacterial infections.

Human genitals and urinary tracts also harbor a large number of microorganisms.

In the vagina, research suggests that “bacteria dominate” the landscape, though which bacteria and in what quantities are questions not easily answered.

Recent studies indicate that the components of bacterial populations in the vagina may not only fluctuate at different stages of the menstrual cycle, but may also vary among individuals of different races and ethnicities.

Some types of bacteria identified in the vaginal canal include Lactobacilli, Prevotella, Dialister, Gardnerella, Megasphaera, Eggerthella, and Aerococcus.

“The human vaginal microbiota seem to play a key role in preventing a number of urogenital diseases, such as bacterial vaginosis, yeast infections, sexually transmitted infections, urinary tract infections, and HIV infection,” says a PNAS review.

This is why specialists advise extreme care when it comes to intimate hygiene: Many products can destroy the delicate bacterial balance in the area.

However, the PNAS review also notes that “The means by which [bacteria protect against infection] are poorly understood.”

Furthermore, little is known about the microbiota of the uterus. Scientists have only started to study it recently and, so far, only in small cohorts. One study found that Lactobacillus and Flavobacterium appeared to be the most common bacteria in the uterus, regardless of whether a woman is pregnant. More in-depth research is ongoing.

Little is also known about the microbiota of the female bladder and urethra. A study published in Current Opinion in Urology in 2017 notes that “The vast majority of urinary health research has been conducted without knowledge or consideration of the female urinary microbiota.”

Following recent investigations, it appears that the most common types of bacteria in the female urethra are Lactobacillus, followed by Gardnerella, Corynebacterium, Streptococcus, and Staphylococcus.

And while some researchers suggest that the microbiota of the bladder and female urinary tract are largely the same, others beg to differ. One study published this year in the Journal of Urology has found significant differences.

Its authors also hypothesize that the bacterial populations of the female lower urinary tract may vary with age, level of sexual activity, and whether or not the person has entered menopause.

If researchers still know little about the microbiota of the female urogenital areas, they appear to know even less about those present in the male urogenital regions.

A PLOS One study from 2010 found differences in microbial communities on circumcised, compared with uncircumcised, penises, in a culture-independent investigation.

More specifically, bacteria of the Clostridiales and Prevotellaceae families appeared to be more abundant on uncircumcised penises.

Such differences, the paper’s authors note, may play a role in inflammation and exposure to infections.

“Men who are uncircumcised have significantly more bacteria on their penis, and the types of bacteria are also very different,” noted study co-author Dr. Cindy Liu in an interview.

Other than this, very little is understood about the penile microbiota. In the same interview, Prof. Deborah Anderson, who teaches obstetrics, gynecology, and microbiology at the Boston University School of Medicine, commented that:

“The penis is understudied. There could be a very interesting story there, but we haven’t really done the proper research.”

Much like the gut, the human skin houses a multitude of bacteria and many types of fungi.

A review — published in Nature Reviews Microbiology in 2018 — explains that the bacterial populations vary widely by skin region and also depend on a range of factors, such as the moisture of the skin and the amount of natural oil, or sebum.

According to the review, “Sebaceous sites were dominated by […] Propionibacterium species, whereas bacteria that thrive in humid environments, such as Staphylococcus and Corynebacterium species, were preferentially abundant in moist areas, including the bends of the elbows and the feet.”

Communities of fungi, however, appear to be fairly consistent in composition, regardless of the type of skin populated.

All over the body and on the skin of the arms, fungi of the genus Malassezia are the most common, according to the researchers. By contrast, a combination of Malassezia, Aspergillus, Cryptococcus, Rhodotorula, and Epicoccum, among others, are most abundant on the skin of the feet.

The most abundant microorganisms on human skin are bacteria, while the least common appear to be fungi.

Bacteria on the skin can serve to prevent the invasion of pathogens and promote disease, depending on which colonies prevail. As the study authors write:

“Interactions between members of the microbiota both shape the resident microbial community and prevent colonization by pathogenic bacteria in a process termed ‘colonization resistance’.”

“In certain contexts,” they continue, “bacteria that are ordinarily beneficial to their hosts can become pathogenic. Many common skin diseases are associated with changes in the microbiota, termed dysbiosis.”

Bacteria prevail on many stretches of epithelial tissue, including the conjunctiva, the tissue lining the inside of the eyelids.

According to a study from 2011, at least five bacterial phyla and 59 genera are present on the healthy human conjunctiva.

The predominant bacterial genera are: Pseudomonas, Propionibacterium, Bradyrhizobium, Corynebacterium, Acinetobacter, Brevundimonas, Staphylococci, Aquabacterium, Sphingomonas, Streptococcus, Streptophyta, and Methylobacterium.

Some fungi are also present, and these include species of Candida, Aspergillus, and Penicillium.

For now, the role of the conjunctiva microbiome remains unclear.

We often think of bacteria in the lungs only in the context of respiratory diseases. However, bacteria are present in healthy lungs, too.

Some of the most common bacterial phyla in healthy lungs are Firmicutes, Bacteriodetes, Proteobacteria, Fusobacteria, and Actinobacteria, according to a review from 2017. Some of the most common genera are Prevotella, Veillonella, and Streptococcus.

When the delicate balance of bacterial populations in the lungs is upset, it could lead to the development of diseases such as asthma and chronic obstructive pulmonary disease.

In asthma, for instance, Haemophilus and Neisseria bacteria increase in numbers, while numbers of Prevotella and Veillonella decrease. This supports the hypothesis that dysbiosis of the lung microbiome may be an underlying cause of asthma.

The team behind the 2017 review highlight a need for further investigations into the microbiota-related mechanisms that may be affecting lung health, noting that “The likely complex interactions between bacteria, viruses, and fungi should be considered in future research.”

The human microbiome is an intricate system, and researchers are continuing to discover more about its important role in human health and disease. Going forward, scientists strive to dive deeper into the mysteries of this microcosm.

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