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:
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:
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.
- https://pmc.ncbi.nlm.nih.gov/articles/PMC10061322/
- https://en.wikipedia.org/wiki/Human_microbiome
- https://pmc.ncbi.nlm.nih.gov/articles/PMC7043356/
- https://www.nature.com/articles/s41392-022-00974-4
- https://www.psu.edu/news/eberly-college-science/story/gut-bacteria-variation-among-human-social-groups-emerges-three-months
- https://en.wikipedia.org/wiki/Vaginal_flora
- https://pmc.ncbi.nlm.nih.gov/articles/PMC8058480/
- https://pmc.ncbi.nlm.nih.gov/articles/PMC10224287/
- https://www.sciencedirect.com/science/article/pii/S0944501322000507
- https://pmc.ncbi.nlm.nih.gov/articles/PMC10252372/
- https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2021.617002/full
- https://pmc.ncbi.nlm.nih.gov/articles/PMC8775962/
- https://pmc.ncbi.nlm.nih.gov/articles/PMC7599718/
- https://www.nature.com/articles/s42003-024-05822-5
- https://pmc.ncbi.nlm.nih.gov/articles/PMC7074508/
- https://pmc.ncbi.nlm.nih.gov/articles/PMC8786117/
- https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2020.609765/full
- https://academic.oup.com/ofid/article/11/9/ofae471/7735779
- https://www.medicalnewstoday.com/articles/human-microbiota-the-microorganisms-that-make-us-their-home
- https://www.health.harvard.edu/blog/an-emerging-link-between-the-urinary-microbiome-and-urinary-incontinence-2020081220712
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