How Many Types of Microbiota Are There?
Microbiota are the communities of microorganisms that live on and inside the human body. They are an important part of human biology, with different microbial communities occupying distinct body sites and serving different functions. In this guide, we explain how many types of microbiota there are, how microbiota differs from microbiome, and why gut microbiota is the most studied example.
Types of microbiota
There is no single universal number of microbiota types, because the answer depends on whether you classify them by body site, microbial composition, or function. A practical way to think about microbiota is by localized regions of the body:
- Gut microbiota: Lives mainly in the gastrointestinal tract, especially the colon, and helps support digestion, nutrient metabolism, and immune signaling.
- Oral microbiota: Lives in the mouth, including the teeth, tongue, and gums, where it interacts with saliva and food particles.
- Skin microbiota: Lives on the surface of the skin and in follicles, varying by oily, dry, and moist areas.
- Respiratory microbiota: Found in parts of the nose and airways, where it may help shape local microbial balance.
- Vaginal microbiota: Lives in the vaginal tract and is often discussed separately because of its distinct ecology and pH environment.
These are the most commonly discussed types, but researchers may also describe urinary, nasal, and other site-specific microbial communities.
Discover the Microbiome Test
ISO-certified EU lab • Sample stays stable during shipping • GDPR-secure data
Microbiota vs microbiome
The words microbiota and microbiome are often used together, but they are not identical. Microbiota usually refers to the microorganisms themselves. Microbiome is often used to describe the community plus its genetic material and environment. In practice, many readers use the terms interchangeably, especially when talking about gut health and testing.
What makes up microbiota?
Human microbiota can include multiple groups of microorganisms:
- Bacteria
- Archaea
- Fungi
- Viruses and bacteriophages
- Eukaryotes, such as certain protozoa in some contexts
Not every body site contains the same mix, and the relative abundance of these groups can vary widely from person to person.
View example recommendations from the InnerBuddies platform
Preview the nutrition, supplement, food diary and food recipe platform recommendations that InnerBuddies can generate based on your gut microbiome test
Types of microbiota by body site
| Microbiota type | Where it lives | Main microbial groups | What it may influence |
|---|---|---|---|
| Gut microbiota | Gastrointestinal tract | Bacteria, archaea, fungi, viruses | Digestion, fiber fermentation, vitamin production, immune signaling |
| Oral microbiota | Mouth and oral surfaces | Bacteria, fungi, viruses | Oral ecology, plaque formation, local balance |
| Skin microbiota | Skin surface and follicles | Bacteria, fungi, viruses | Barrier function, niche protection, local immune interactions |
| Respiratory microbiota | Nose and upper airways | Bacteria, viruses | Localized microbial balance in the airways |
| Vaginal microbiota | Vaginal tract | Bacteria, fungi, viruses | Local ecology, pH-related balance, microbial dominance patterns |
How many types of gut microbiota are there?
If you are asking specifically about the gut, the answer depends on how you define “types.” Some people mean broad microbial groups, while others mean functional patterns or bacterial phyla. There is not one fixed number, but these are common ways to frame the topic:
- Five gut types: Sometimes used informally to describe broad gut microbial groupings by function or location, not a universal scientific standard.
- Four types of gut bacteria: Often refers to the major bacterial phyla commonly discussed in gut studies: Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria.
- Five types of microbes: A broad shorthand that may refer to bacteria, archaea, fungi, viruses, and protozoa/eukaryotes depending on the source.
- Seven classes of microbes: Another flexible category used in education to group microorganisms by broad biological class rather than one strict gut taxonomy.
So, when someone asks how many types of microbiota are there, the most accurate answer is that the number depends on the classification system being used.
Common gut microbial groups
In gut microbiome research, several bacterial phyla are discussed often:
- Firmicutes: A large group that includes many fiber-fermenting organisms.
- Bacteroidetes: Common gut bacteria involved in breaking down complex nutrients.
- Actinobacteria: Includes Bifidobacterium, which is often discussed in relation to gut ecology.
- Proteobacteria: A broad group that includes many species found in the gut; relative abundance can vary.
Researchers also describe core microbiota and variable microbiota. Core microbiota refers to microbes commonly shared across many people, while variable microbiota changes more easily based on diet, age, medication, environment, and other factors.
Why gut microbiota gets so much attention
Gut microbiota is the most studied type of microbiota because it is dense, diverse, and relatively accessible for analysis through stool samples. It is associated with several normal body functions, including:
- Breaking down dietary fiber
- Producing short-chain fatty acids such as butyrate
- Supporting nutrient metabolism
- Helping shape immune responses
- Contributing to the gut-brain axis
These relationships are complex and vary from person to person. Microbiota should be understood as part of a broader ecosystem, not as isolated single organisms acting alone.
2-minute self-check Is a gut microbiome test useful for you? Answer a few quick questions and find out if a microbiome test is actually useful for you. ✔ Takes 2 minutes ✔ Based on your symptoms & lifestyle ✔ Clear yes/no recommendation Check if a test is right for me →How gut microbiome testing works
Gut microbiome testing analyzes stool samples to identify which microbes are present and how abundant they appear to be. Depending on the method used, the report may show relative abundance, microbial diversity, and patterns that suggest a balanced or less balanced ecosystem.
Common testing methods include:
- 16S rRNA sequencing: Used to profile bacterial communities
- Shotgun metagenomic sequencing: Can provide broader information about genes and microbial potential
InnerBuddies' gut microbiome test is designed to help users explore their gut microbial populations in a consumer-friendly format.
Microbiome diversity and localized regions
Microbiome diversity is often described using terms like richness and evenness. Richness refers to how many different microbes are present, while evenness describes how evenly they are distributed. Diversity can vary across localized regions of the body, which is one reason the skin, mouth, and gut each have distinct microbial communities.
Health-related interpretations should be made carefully. A diverse microbiome is often associated with resilience, but there is no single ideal profile that applies to everyone.
Become a member of the InnerBuddies community
Perform a gut microbiome test every couple of months and view your progress while following-up on our recommendations
Types of microbes you may see in microbiome discussions
When reading about gut microbial populations, you may also see functional terms such as:
- Commensals: Microbes that generally coexist without obvious harm or benefit in a given context
- Probiotics: Live microorganisms that, when used appropriately, may support health
- Pathobionts: Microbes that are usually tolerated but may become problematic in certain conditions
- Opportunistic microbes: Organisms that may take advantage of imbalances or weakened defenses
These terms describe roles in an ecosystem, not fixed labels of “good” or “bad” for all situations.
FAQ
What are microbiota?
Microbiota are communities of microorganisms living in a specific body site, such as the gut, skin, mouth, or vaginal tract.
How many types of microbiota are there?
There is no single number. The answer depends on whether you classify microbiota by body site, microbial group, or function.
What are the five types of microbiota?
A common simplified list includes gut, oral, skin, respiratory, and vaginal microbiota.
What are the four types of gut bacteria?
The four major bacterial groups often discussed in the gut are Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria.
2-minute self-check Is a gut microbiome test useful for you? Answer a few quick questions and find out if a microbiome test is actually useful for you. ✔ Takes 2 minutes ✔ Based on your symptoms & lifestyle ✔ Clear yes/no recommendation Check if a test is right for me →What are the five types of microbes?
Some educational sources group microbes into bacteria, archaea, fungi, viruses, and protozoa or other eukaryotes.
What are the seven classes of microbes?
This can vary by source, but the phrase usually refers to broad teaching categories rather than one fixed scientific system.
What is the difference between microbiota and microbiome?
Microbiota refers to the microorganisms themselves, while microbiome often refers to the organisms plus their genetic material and environment.
Conclusion
There are many ways to classify microbiota, and the most useful answer depends on the context. By body site, the main types include gut, oral, skin, respiratory, and vaginal microbiota. By composition, microbiota can include bacteria, archaea, fungi, viruses, and other microbes. For most readers, gut microbiota remains the best-known example because it is closely studied and widely discussed in gut health and microbiome testing.
If you want a better understanding of your own gut microbial populations, tools like InnerBuddies' microbiome test may help you explore your gut ecosystem in more detail.