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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.

For more research-backed information about the microbiome and how it affects your health, please visit our dedicated hub.

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 ActinobacteriaProteobacteriaFusobacterua, 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, HelicobacterShigella, 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 aninterview 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 — FirmicutesFusobacteriaProteobacteria,ActinobacteriaBacteroidetesChlamydiaeChloroflexiSpirochaetesSR1Synergistetes,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.