Normal Flora (Microbiota) of Mouth and Gastrointestinal Tract

Normal floras are the microorganisms that are constantly present in the skin and mucous membrane of every human without causing any infection in a healthy individual. Only bacteria and fungus are considered normal flora. They are present in relatively stable conditions, either for a short or specific period or throughout the life of an individual. Their composition may vary on different individuals.

Normal Flora (Microbiota) of Mouth and Gastrointestinal Tract
Normal Flora (Microbiota) of Mouth and Gastrointestinal Tract

The gastrointestinal tract (GI tract or alimentary canal) is a passage of the digestive system for food ingestion, mechanical and chemical digestion, and digestive waste excretion. It is a tract from mouth to anus including the oral (buccal) cavity, oropharynx, esophagus, stomach, small intestine, and large intestine. These various parts have various physicochemical properties, hence a wide diversity of microflora are found in the GI tract. From mouth to anus, every part of the GI tract is full of different species of the normal microbiota. Intestinal flora contains more than 400 species of bacteria.

List of Normal Flora of Mouth and Gastrointestinal Tract

Gram-Positive BacteriaGram-Negative BacteriaOthers
Streptococcus spp.
Lactobacillus spp.
Staphylococcus spp.
Clostridium spp.
Bacillus spp.
Corynebacterium spp.
Actinomyces spp. 
Propionibacterium spp.
Rothia spp.
Eubacterium spp.
Gemella spp.
Peptostreptococcus spp. 
E. coli
Klebsiella spp.
Enterobacter spp.
Enterococcus spp.
Citrobacter spp.
Vibrio spp.
Campylobacter spp.
Helicobacter pylori 
Proteus spp.
Fusobacterium spp.
Neisseria spp.
Moraxella spp.
Kingella spp.
Actinobacillus spp.
Bacteroides spp.
Porphyromonas spp.
Prevotella spp.
Selenomonas spp.
Cardiobacterium spp.
Eikenella spp.
Veillonella spp. 
Leminorella spp. 
Morganella spp. 
Providencia spp. 
Yersinia spp. 
Serratia spp.
Candida spp.

Normal Flora on Specific Location of Mouth and Gastrointestinal Tract

LocationNormal Microflora
Mouth and teethStreptococcus spp., Neisseria spp., Lactobacillus spp., Veillonella spp.,  Staphylococcus spp., Peptostreptococcus spp., Treponema spp.,  
OropharynxPeptostreptococcus 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.,
EsophagusStreptococcus spp., Candida spp., Bacteroides spp., 
Stomach   Lactobacillus spp., Streptococcus spp., Helicobacter pylori
Small Intestine Lactobacillus spp., Streptococcus spp., Peptostreptococcus spp., Porphyromonas spp., Prevotella spp.,
Large IntestineBifidobacterium spp., Bacteroides spp., Eubacterium spp., Enterococcus spp., E. coli, Citrobacter spp., Klebsiella spp., Enterobacter spp., Proteus spp., Streptococcus spp., Actinomyces spp., Peptostreptococcus spp., Gemella spp., Bacillus spp., Clostridium spp., Vibrio spp., Fusobacterium spp., Porphyromonas spp., Prevotella spp., Leminorella spp., Morganella spp., Providencia spp., Yersinia spp., Serratia spp., 

Gram +ve and Gram -ve Bacteria of Mouth and Gastrointestinal Tract

Staphylococcus spp.

  • Gram-positive
  • Catalase-positive 
  • Coagulase positive and coagulase-negative
  • Aerobic
  • Cocci bacteria 
  • Family Staphylococcaceae
  • Known for producing grape-like clusters under a microscope 

Staphylococci are the transient flora of the mouth and oropharynx.  

S. epidermidis and S. aureus are the most dominant species in the mouth and oropharynx. They are especially present in children. S. epidermidis enters in the nasal and oral cavity during birth from vaginal skin. During breastfeeding, S. epidermidis is transferred to the mouth from the mother’s breast skin. 

Streptococcus spp.

  • Gram-positive
  • Anaerobic and facultative anaerobic 
  • Catalase-negative 
  • Cocci bacteria 
  • Family – Streptococcaceae 
  • A characteristic arrangement of cells in the form of a chain of spheres under a microscope

They are present in every part of the GI tract. They are mostly considered transient flora. 

S. agalactiae (Group B Streptococci), S. mutans, S. mitis, S. oralis, S. parasanguis,  S. sanguis, S. salivarius, S. cristatus, S. constellatus, S. anginosus group (viridans Streptococci), etc. are commonly reported species in GI tract. 

Acid tolerant species of Streptococcus like acid tolerant strains of S. anginosus are also found in the stomach. 

Clostridium spp.

  • Gram-positive 
  • Rod-shaped 
  • Strictly anaerobic
  • Spore-forming bacteria 
  • Family – Clostridiaceae 

Clostridium clusters XIVa and IV are the predominant commensal bacteria in the gut, covering about 10 – 40% of total gut bacteria. C. aerotolerans, C. aminophilus, C. aminovalericum, C. clostridiiforme, C. coccoides, C. nexile, C. oroticum, C. polysaccharolyticum, C. symbiosum, C. leptum, C. difficile strain 630, C. sordelli, C. absonum, C. butyricum, C. paraputrificum, C. xylanolyticum, etc. are common species in human intestine.   

Clostridium perfringens are also the normal flora of the small intestine and the large intestine.

Bacillus spp.

  • Gram-positive
  • Rod-shaped
  • Motile
  • Obligate aerobic and some facultative anaerobic
  • Spore forming
  • Family – Bacillaceae

B. clausii, B. licheniformis, B. coagulans are some commonly isolated intestinal flora. 

Corynebacterium spp.

  • Gram-positive 
  • Rod-shaped (club-shaped), 
  • Aerobic bacteria 
  • Family –  Corynebacteriaceae
  • The characteristic features of high mesodiaminopimelic acid and highly repeated arabinogalactan

C. matruchotii is a normal inhabitant of oral cavity. Corynebacterium species are also found in the large intestine.    

Actinomyces spp.

  • Gram-positive
  • Rod-shaped (branched)
  • Obligate anaerobic and facultatively anaerobic
  • Endospore forming
  • Family – Actinomycetaceae

A. viscous, A. naeslundii, A. israelii, etc. are commonly found in the mouth. Some species are also found in the small and the large intestine as transient flora. 

Helicobacter pylori 

  • Gram-negative 
  • Helical 
  • Microaerophilic 
  • Epsilonproteobacteria 
  • Family – Helicobaceteriaceae 

They are adapted to tolerate the acidity of a human stomach. They are normal flora of the stomach and the duodenum.  

Fusobacterium spp.

  • Gram-negative
  • Anaerobic
  • Non-sporing
  • Rod-shaped with pointed ends
  • Family – Fusobacteriaceae

Fusobacterium spp. is normal flora of the mouth and intestine. They are found in relatively small number.  F. nucleatum is found in the mouth. 

Propionibacterium spp.

  • Gram-positive
  • Rod-shaped
  • Anaerobic
  • Family – Propionibacteriaceae
  • Unique ability to produce propionic acid using transcarboxylase enzymes

Propionibacterium spp. are normal flora in the large intestine. P. acidifaciens and P. propionicus are present in the oral cavity of relatively very few people.

Campylobacter spp.

  • Gram-negative
  • S-shaped (comma shaped)
  • Microaerophilic
  • Motile
  • Non-sporing
  • Family – Campylobacteriaceae

Campylobacter spp. are found in the large intestine and mouth. C. sputorum, C. coli. C. upsaliensis, etc. are some species of commensal Campylobacter

Rothia spp.

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

They are normal flora of the mouth and respiratory tract. R. mucilaginosa, R. dentocariosa are normal flora of mouth. Rothia spp. are also isolated from distal ileum and even in the stomach. 

Actinobacillus spp.

  • Gram-negative
  • Rod-shaped or oval (coccobacilli)
  • Non-motile
  • Non-sporing
  • Facutative anaerobic or aerobic

A. actinomycetemcomitans is human oral microflora. 

Eubacterium spp.

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

Eubacterium are normal microflora of the mouth and the GI tract. They are among the dominant anaerobic species in the intestine; the second most abundant bacterial genera in the large intestine. E. aerofaciens, E. cylindroides, E. lentum, and E. rectale are the most common species in the large intestine. 

Gemella spp.

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

Gemella are a common species in the oral cavity and human intestine. 

Peptostreptococcus spp. 

  • Gram-positive
  • Spherical (in pair or chain)
  • Anaerobic
  • Non-sporing
  • Motile
  • Family – Peptostreptococcaceae

Peptostreptococcus are among the most abundant anaerobic bacteria in the human GI tract. P. intermedius is the dominant species in the human intestine. 

Lactobacillus spp.

  • Gram-positive
  • Rod-shaped
  • Non-motile
  • Non-sporing
  • Anaerobic or Microaerophilic
  • Lactic acid fermenting bacteria (LAB)
  • Family – Lactobacillaceae

They are normal flora of the mouth, GI tract, and the female reproductive tract. More than 50 species of Lactobacillus are found in the intestine of a healthy humans. L. casei, L. delbruckeii, L. murinus, L. plantarum, L. rhamnosus, and L. ruminus are the most abundant species.  

E. coli

  • Gram-negative 
  • Rod-shaped 
  • Motile
  • Lactose fermenting 
  • Facultatively anaerobic 
  • Mesophillic coliform bacteria 
  • Family – Enterobacteriaceae
  • Genus – Escherichia  

Non-pathogenic strains of E. coli are one of the most common aerobic microflora species of the human intestines. 

Klebsiella spp.

  • Gram-negative 
  • Rod-shaped 
  • Non-motile
  • Encapsulated
  • Lactose fermenting 
  • Facultatively anaerobic 
  • Mesophillic coliform bacteria 
  • Family – Enterobacteriaceae

Being a member of Enterobacteriaceae, it is common in the intestine of vertebrates including humans. K. oxytoca, K. pneumoniae are found in the intestine. 

Enterobacter spp.

  • Gram-negative
  • Rod-shaped 
  • Motile
  • Lactose fermenting 
  • Facultatively anaerobic 
  • Mesophillic coliform bacteria 
  • Family – Enterobacteriaceae

Enterobacter is normal microflora of the small and the large intestine. E. cloacae, E. ludwigii, E. hormaechei, E. cancerogenus, E. massiliensis are commensals in intestine. 

Citrobacter spp.

  • Gram-negative
  • Rod-shaped
  • Lactose fermenting
  • Mostly motile, few non-motile
  • Coliform
  • Gammaproteobacteria
  • Family – Enterobacteriaceae
  • Special ability to use citrate as the sole carbon source

Citrobacter are normal flora of the human GI tract. C. freundii, C. europaeus, C. koseri, C. sedlaki, C. werkmanii, C. gillenii, C. braakii, C. murliniae  are commensals of human intestine.  

Vibrio spp. 

  • Gram-negative 
  • Rod-shaped (comma-shaped) 
  • Motile 
  • Non-sporing 
  • Facultative anaerobic 
  • Gammaproteobacteria 
  • Family – Vibrionaceae 
  • Characteristic 2 chromosomes

V. parahaemolyticus are found in a low number of a few people. V. sputorum is present in the mouth of some people as normal microflora. 

Proteus spp.

  • Gram-negative 
  • Rod-shaped 
  • Aerobic and facultative anaerobic 
  • Motile bacteria 
  • Family – Enterobacteriaceae 
  • Capacity to produce swarming colonies

P. vulgarisP. mirabilis, and P. penneri are present in the human GI tract, but in a very low numbers comprising only about 0.05% of total gut microflora. 

Enterococcus spp.

  • Gram-positive 
  • Facultatively anaerobic 
  • Lactose fermenting 
  • Cocci (diplococci) bacteria 
  • Family –  Enterococcaceae 
  • Capacity to tolerate bile salt concentrations up to 40%

Enterococci are commensals of the GI tract. E. faecalis and E. faecium are the most common species of Enterococcus in the human intestine.    

Leminorella spp. 

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

Leminorella is a new genus in the Enterobacteriaceae family. L. richardii and L. grimontii colonize the human GI tract. 

Providencia spp. 

  • Gram-negative
  • Rod-shaped
  • Motile
  • Gammaproteobacteria 
  • Family – Morganellaceae

Providencia is present as a normal intestinal flora in relatively low numbers in some people. P. rettgeri, P. alaclifaciens, P. rustigianii are some common species.

Yersinia spp. 

  • Gram-negative 
  • Coccobacilli 
  • Facultative anaerobic 
  • Gammaproteobacteria 
  • Family – Yersiniaceae

Yersinia is found in the small and large intestine of humans. Y. aleksiciae, Y. bercovieri, Y. enterocolitica, Y. frederiksenii, Y. rohdei, Y. kristensenii are common Yersinia species that colonize in the human gastrointestinal tract. 

Bacteroides spp.

  • Gram-negative
  • Rod-shaped
  • Bile resistant
  • Non-sporing
  • Motile or non-motile
  • Obligate anaerobic 
  • Family –  Bacteroidaceae 

Bacteroides are part of the human gastrointestinal microflora. B. gingivalis, B. intermedius, B. fragilis, B. pneumosintes, B. melaninogenicus, and B. thetaiotaomicron are some common species in the mouth and large intestine.  

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