“The microbiome” isn't just one thing. It's lots of things.
And each habitat has its own microbiome.
To say the human microbiome is complicated is an understatement.
It's generally agreed that a microbiome is the community of organisms (bacteria, fungi, viruses, archaea) that live and interact in a particular habitat inclusive of the environmental, physical and chemical properties of that habitat.
This means that we're surrounded by microbiomes and if we're talking about them from the human perspective, there are at least 6 that we need to discuss:
Respiratory tract - The upper airway, your nose and the cavity behind it are colonized by specific microbes that thrive in the mucosa that helps to warm, humidify and filter the air that we breathe. Similarly, the lower respiratory tract and lungs host their own crew of microbes. The microbiomes in these regions change significantly during respiratory infections or after the development of respiratory diseases like asthma.
Eye - Anyone who has ever suffered from conjunctivitis (infection of the eye) understands the importance of having a healthy eye microbiome. But the eye has three distinct habitats which include the outer eye, the conjunctiva (the membrane that covers the eye), and the meibum (the fatty, slippery, liquid that lubricates our eyes!). Each of these are inhabited by specific microbes that thrive in these ocular environments!
Oral - Our mouth is one of the microbiomes we’re most conscious of. Dental hygiene is extremely important for human health, and a dysfunctional oral microbiome is typified by unpleasant odors as a result of infections of our gums and teeth.
Skin - This is one of the more complicated microbiomes to classify since “skin” is present on every outer surface of our body. The skin microbiome can differ significantly depending on whether we’re talking about our armpit, scalp, or face! But be aware, this surface that you scrub clean every day is host to trillions of microbes!
Urogenital - This primarily refers to the vaginal microbiome which changes throughout a woman’s cycle and during pregnancy. The microbial community here is sensitive to changes in pH (and can cause changes in pH!). Dysfunction can lead to infertility or even miscarriages.
Digestive - The “gut” microbiome is probably the one that we’ve heard the most about. But the digestive tract is made up of the stomach, small intestine, large intestine, and colon. Each of these has a distinct physical and chemical environment, and you guessed it, each supports its own unique microbial community!
While we contain multitudes of microbes that form communities on and in various parts of our body, we’re still at the earliest stages of trying to tease out the cause and effect relationships here that impact human health.