Respiratory Microbiota- Normal Flora of Respiratory Tract

Normal floras are the microorganisms present in the skin and mucous membrane of every human in a relatively stable manner without causing any disease/infection in a healthy individual. They are present either throughout the life of for short period of time.

The respiratory tract can be divided into the upper respiratory tract (URT) and the lower respiratory tract (LRT). URT is inhabited by a diverse group of commensal bacteria and fungi species. LRT is normally sterile and free of any normal microbiota.

Respiratory Microbiota- Normal Flora of Respiratory Tract
Respiratory Microbiota- Normal Flora of Respiratory Tract

List of Normal Flora of Respiratory Tract

Gram-Positive BacteriaGram-Negative BacteriaOthers Microbes
Streptococcus spp.
Staphylococcus spp.
Corynebacterium spp.
Haemophilus spp.
Fusobacterium spp.
Propionibacterium spp.
Rothia spp.
Actinobacillus spp.
Eubacterium spp.
Gemella spp.
Peptostreptococcus spp. 
E. coli
Proteus spp.
Neisseria spp.
Moraxella spp.
Kingella spp.
Bacteroides spp.
Porphyromonas spp.
Prevotella spp.
Selenomonas spp.
Cardiobacterium spp.
Eikenella spp.
Veillonella spp. 
Candida spp.
Mycoplasma spp.

Normal Flora on Specific Location of Respiratory Tract

Location of Respiratory TractNormal Microflora
Nares  Staphylococcus spp., Corynebacterium spp., Peptostreptococcus spp., Fusobacterium spp. 
NasopharynxStreptococcus spp., Corynebacterium spp., Neisseria spp., Moraxella spp., Kingella spp., Haemophilus spp.
Oropharynx  Peptostreptococcus spp., Veillonella spp., Actinomyces spp., Fusobacterium spp., Streptococcus spp., Corynebacterium spp.,  Lactobacillus spp., Neisseria spp., Staphylococcus spp., Gemella spp., Moraxella spp., Kingella spp., Cardiobacterium spp., Eikenella spp., Actinobacillus spp., Propionibacterium spp., Bacteroides spp., Porphyromonas spp., Rothia spp., Prevotella spp., Selenomonas spp., Eubacterium spp., Mycoplasma spp., Candida spp.
Lower Respiratory TractNONE

Gram +ve and Gram -ve Bacteria of Respiratory Microbiota

Staphylococcus spp.

  • Gram-positive
  • Catalase-positive 
  • Cocci bacteria 
  • Family- Staphylococcaceae 
  • Characteristic grape-like clusters under a microscope 

Staphylococci are the most abundant aerobic flora of nasal passages. They are found in the nasal passage of more than 90% of people. 

S. epidermidis is a normal flora of the skin and is present abundantly in the skin of the anterior portion of the nares. It is present in the anterior nares of about 90% of the individuals. 

S. aureus is present in the nasal passages of about 30% of individuals. Methicillin-Resistant S. aureus (MRSA) is also found as commensals in hospitals and healthcare workers.   

S. lugdunensis, S. capitis, S. haemolyticus, S. warneri, S. hominis, S. cohnii, and S. auricularis are other species found as commensal in anterior nares and nasal cavity of about <10% of people. 

Corynebacterium spp. 

  • Gram-positive 
  • Rod-shaped (club-shaped) 
  • Aerobic bacteria 
  • Family- Corynebacteriaceae

Corynebacteria are abundantly found as aerobic bacteria in the nares and nasopharynx region.  

C. accolens and C. propinquum are the dominant Corynebacteria present in the nares, nasopharynx, and oropharynx. They account for more than 40% of Corynebacteria in the nose. 

C. pseudodiphtheriticum, C. jeikeium, C. macginleyi are other common Corynebacteria of the nasal passage. 

Propionibacterium spp.

  • Gram-positive 
  • Rod-shaped 
  • Anaerobic bacteria 
  • Family –   Propionibacteriaceae 
  • Characteristic ability to synthesize propionic acid 

Propionibacterium spp. are the most abundant anaerobic species in adult nasal microbiota.  

P. acnes is the most abundant species in this genus covering about 50 – 70% of anaerobic bacteria in the nasal passage. 

P. acidifaciens and P. propionicus are other species of normal nasal flora in a low proportion of people. 

Peptostreptococcus spp.

  • Gram-positive 
  • Spherical (cocci) 
  • Non-motile 
  • Anaerobic bacteria 
  • Family –   Peptostreptococcaceae

P. anaerobius, P. asaccharolyticus, P. micros are common species in the oropharynx. 

Fusobacterium spp.

  • Gram-negative
  • Non-sporing 
  • Rod-shaped 
  • Anaerobic bacteria 
  • Family –  Fusobacteriaceae. 

They are widely present in anterior nares, nasopharynx, and oropharynx. 

F. nucleatum subspecies, F. necrophorum, F. peridonticum are the most prevalent species in the oropharynx and the nasopharynx. 

Streptococcus spp.

  • Gram-positive 
  • Anaerobic and facultative anaerobic 
  • Catalase-negative 
  • Cocci bacteria 
  • Family –  Streptococcaceae 
  • Characteristic arrangement in the form of a chain of spheres 

Streptococci are widely distributed bacterial genera in the nasopharynx and the oropharynx. 

S. salivarius, S. sanguis, S. mutans, S. vestibularis, S. pneumoniae, and S. parasanguis are normal microbiota of the pharynx region. 

Neisseria spp.

  • Gram-negative 
  • Aerobic or facultative anaerobic 
  • Cocci (and diplococci) 
  • Betaproteobacteria 
  • Family –  Neisseriaceae 

Neisseria is commensal to the nasopharynx and oropharynx. 12 species of Neisseria are recovered from the nasopharynx region. 

N. meningitidis is a very common commensal in the nasopharynx region. It is also an invasive and potential pathogen that is associated with meningitis. 

N. lactamica, N. subflava, N. mucosa, N. sicca are common species in the URT.  

Haemophilus spp.

  • Gram-negative 
  • Coccobacilli (pleomorphic) 
  • Aerobic or facultative anaerobic 
  • Gammaproteobacteria 
  • Family –  Pasteurellaceae 

Haemophilus species are the normal flora of the upper respiratory tract, oral cavity, lower GI tract, and the vagina. 

Non-capsulated H. influenzae and Nontypable H. influenzae strains are common Haemophilus species in the nasopharynx. H. aphrophilus, H. hemolyticus,  H. parainfluenzae are also found as commensals in the lower group of people in the nasopharynx and oropharynx region. 

Moraxella spp.

  • Gram-negative 
  • Coccobacilli (bacilli or diplococci in some), 
  • Strictly aerobic 
  • Gammaproteobacteria 
  • Family –  Moraxellaceae

M. catarrhalis is a normal inhabitant of the upper respiratory tract in the pharynx. It is more commonly found in children (~50%) and people older than 60 years of age (~26%), than in adults (~6%). 

M. nonliquefaciens and M. lincolnii are also found in the nasopharynx of a few people as commensal.   

Kingella spp.

  • Gram-negative 
  • Facultatively anaerobic 
  • Non-motile 
  • Coccobacilli 
  • Fastidious 
  • Betaproteobacteria 
  • Family –  Neisseriaceae

K. kingae is common bacteria in the nasopharynx of children. K. indologenes and K. denitrificans are other commensal species in the oropharynx of a few healthy children and adults.   

Veillonella spp.

  • Gram-negative 
  • Lactate fermenting, 
  • Anaerobic 
  • Cocci bacteria 
  • Family – Veillonellaceae

 They are common anaerobic bacteria in the oropharynx.

Actinomyces spp.

  • Gram-positive, 
  • Facultatively anaerobic (some strict anaerobic), 
  • Rod-shaped, 
  • Spore-forming 
  • Actinobacteria 
  • Family – Actinomycetaceae 

A. meyeri, A. israelii, A.  turicensis are common species reported from the oropharynx region. 

Gemella spp.

  • Gram-positive, 
  • Facultatively anaerobic 
  • Diplococci bacteria 
  • Family – Staphylococcaceae 

G. morbillorum and G. sanguinis are commensal in oropharynx region. 

Cardiobacterium spp.

  • Gram-negative
  • Rod-shaped 
  • Gammaproteobacteria 
  • Family –  Cardiobacteriaceae 

It is normally present in the nasopharynx and oropharynx. C. hominis is normally reported in URT. 

Eikenella spp.

  • Gram-negative, 
  • Rod-shaped, 
  • Facultatively anaerobic 
  • Betaproteobacteria 
  • Family – Neisseriaceae 

E. corrodens is found in the oral and nasopharynx region. 

Actinobacillus spp.

  • Gram-negative 
  • Coccobacilli 
  • Gammaproteobacteria 
  • Family –  Pasteurellaceae 

A. ureae and A. hominis are the commensals of URT. 

Bacteroides spp.

  • Gram-negative 
  • Rod-shaped 
  • Non-sporing 
  • Obligately anaerobic 
  • Motile, or nonmotile bacteria 
  • Family –  Bacteroidaceae. 

They are predominantly found in the oropharynx. 

Porphyromonas spp.

  • Gram-negative, 
  • Rod-shaped 
  • Non-sporing, 
  • Anaerobic bacteria 
  • Family –  Prophyromonadaceae 

They are mostly present in the oral cavity, but are also transient normal flora of the upper respiratory tract, especially the oropharynx. P. gingivalis, P. endodontalis, P. catoniae, P. pasteri are common transient flora of URT.  

Rothia spp.

  • Gram-positive 
  • Rod-shaped 
  • Non-motile
  • Aerobic bacteria 
  • Family – Micrococcaceae 

They are normal flora of the mouth and respiratory tract.

R. dentocarisa, R. mucilaginosa, R. aeria are transient normal flora of the upper respiratory tract. 

Prevotella spp.

  • Gram-negative 
  • Coccobacilli 
  • Anaerobic bacteria 
  • Family –  Prevotellaceae 

They are transient flora of lower airways. P. melaninogenica, P. nanceiensis, and P. salivae are common species. 

Selenomonas spp.

  • Gram-negative 
  • Crescent-shaped
  • Anaerobic
  • Fastidious bacteria 
  • Family –  Selenomonadaceae

They are predominant anaerobes in the oropharynx.

Eubacterium spp.

  • Gram-positive 
  • Pleomorphic rod 
  • Aerobic or anaerobic 
  • Motile or non-motile bacteria 
  • Family –  Eubacteriaceae

They are normal aerobic microbiota of the oropharynx. 

Other Normal Flora of Respiratory Tract

Mycoplasma spp.

These are bacteria lacking cell-wall, hence can’t be classified based on Gram staining (but stains pink). They are spherical bacteria in the family MycoplasmataceaeMycoplasma is a normal inhabitant of the upper respiratory tract but is often involved in some RTIS. M. salivarium, M. orale, M. amphoriforme, and M. pneumoniae are transient flora of the oropharynx.  

Candida spp.

Candida is a genus of yeasts in the Saccharomycetes class. It is a normal flora of the upper respiratory tract, gastrointestinal tract, and female reproductive tract. C. albicans is present in the oropharynx of most individuals. 

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