9 bacterial groups: gut, oral, skin, ear, eye, vaginal, urinary, nasal and respiratory

Bacterial Groups in the Human Body

Perplexity AI June 2025

The human body hosts a diverse array of bacterial communities, collectively known as the microbiome, which vary significantly across different anatomical sites. These microbial ecosystems play crucial roles in maintaining health, supporting immune function, and preventing pathogen colonization 1 2. Below is a comprehensive overview of the major bacterial groups found in various body sites.

Gut Microbiota

The gut harbors the largest and most diverse microbial community in the human body, with bacteria primarily belonging to four major phyla:

Bacteroidetes (Bacteroidota) 1 2 3
Firmicutes (Bacillota) 1 4 3
Actinobacteria (Actinomycetota) 1 3
Proteobacteria (Pseudomonadota) 1 4 3
Verrucomicrobia (Verrucomicrobiota) 1
Fusobacteria (in smaller amounts) 1

Common genera in the gut include:

Bacteroides
Clostridium
Faecalibacterium
Eubacterium
Ruminococcus
Bifidobacterium
Peptococcus
Peptostreptococcus 1 3 5

Oral Microbiota

The oral cavity contains the second most diverse microbiome in the body, with dominant phyla including:

Firmicutes
Proteobacteria
Bacteroidetes
Actinobacteria
Fusobacteria
Chlamydiae (less common) 1 4

Key genera found in the oral microbiome include:

Streptococcus (including mitis, sanguinis, anginosus, salivarius, downei, mutans groups)
Prevotella
Fusobacterium
Actinomyces
Veillonella
Neisseria 1 4 2

Skin Microbiota

The skin microbiome varies by body site, with different bacterial communities inhabiting sebaceous, moist, and dry areas:

Actinobacteria (Actinomycetota) - dominant in sebaceous areas
Firmicutes (Bacillota)
Proteobacteria (Pseudomonadota) - dominant in dry skin areas
Bacteroidetes (Bacteroidota) 1 2

Common genera on the skin include:

Staphylococcus (e.g., S. epidermidis, S. aureus)
Streptococcus (e.g., S. pyogenes, S. mitis)
Cutibacterium (formerly Propionibacterium, e.g., C. acnes)
Corynebacterium
Acinetobacter
Pseudomonas 1 2

The composition varies by site, with flat skin surfaces differing from infolded areas like armpits or gluteal clefts, which are dominated by Staphylococcus or Corynebacterium species 1.

Vaginal Microbiota

The vaginal microbiome is unique in being less diverse than other body sites and typically dominated by:

Lactobacillus species (90-95% in healthy individuals) 6 7
- L. crispatus
- L. iners
- L. jensenii
- L. gasseri

In bacterial vaginosis (a dysbiotic state), there's a shift toward:

Gardnerella vaginalis
Atopobium vaginae
Prevotella species
Peptostreptococcus species 6 7

The vaginal microbiome undergoes fluctuations during the menstrual cycle and throughout a woman's life 7.

Urinary Tract Microbiota

Contrary to previous beliefs about sterility, the urinary tract has its own microbiome:

Lactobacillus (dominant in females)
Corynebacterium (dominant in males)
Prevotella
Gardnerella
Streptococcus
Staphylococcus 8 9 10

The urinary microbiome can be classified into several "urotypes" based on the dominant genus 8 11 12.

Respiratory Tract Microbiota

The respiratory system hosts distinct microbial communities from the nasal cavity to the lungs:

Nasal/Nasopharyngeal Microbiota

Actinobacteria (Corynebacterium, Propionibacterium)
Firmicutes (Staphylococcus, particularly S. aureus and S. epidermidis)
Proteobacteria
Moraxella
Dolosigranulum 13 14 15

In children, the nasal microbiome often includes Streptococcaceae, Moraxellaceae, and Neisseriaceae families 13 15.

Lower Respiratory Tract

The lung microbiome includes:

Bacteroidetes
Firmicutes
Proteobacteria
Fusobacteria
Actinobacteria 13

Common genera include:

Prevotella
Veillonella
Streptococcus
Pseudomonas
Fusobacterium
Sphingomonas
Acinetobacter 13

Ear Microbiota

The ear canal has its own microbial ecosystem:

Firmicutes and Actinobacteria (dominant in healthy ears)
Proteobacteria and Bacteroides (more common in otitis) 16

Specific species include:

Cutibacterium acnes (most abundant in healthy ears)
Staphylococcus auricularis
Staphylococcus capitis/caprae
Corynebacterium otitidis 16

In ear infections, Pseudomonas aeruginosa, Staphylococcus aureus, and Corynebacterium jeikeium become more prevalent 16.

Ocular Microbiota

The eye surface, despite constant washing by tears, maintains a distinct microbiome:

Gram-positive genera predominate:
- Coagulase-negative Staphylococci (most common, present in 20-80% of conjunctival swabs)
- Streptococcus
- Propionibacterium
- Corynebacterium
- Micrococcus 17
Other genera found include:
- Acinetobacter
- Pseudomonas
- Sphingomonas
- Rothia
- Bacillus 17

The density of microbes is typically lowest in tears and highest on eyelids 17.

Conclusion

The human microbiome represents a complex ecosystem with hundreds to thousands of bacterial species distributed across various body sites 1 2 3. While certain phyla are common across multiple sites (particularly Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria), the specific genera and species vary significantly by location 1 2. These bacterial communities play essential roles in health maintenance, including digestion, immune modulation, and protection against pathogens 1 2 3. The composition of these microbial communities is influenced by numerous factors including body location, environment, diet, hygiene, and individual genetics 1 5.

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