Classification of bacteria – A comprehensive notes


The bacterial microorganisms, which are present in a wide range of diversity and play a significant role in the operation of diverse ecosystems. In order to gain an understanding of their traits and interconnections, researchers have developed a multitude of classification schemes. This article will explore nine unique methodologies for bacterial classification, which include morphological and growth features, biochemical characteristics, and antigenic properties. Every taxonomic approach provides unique perspectives on the complex world of microorganisms.

Morphological characteristics

The morphological diversity of bacteria enables their taxonomic classification on the basis of their structural and shape characteristics. There are three fundamental morphological classifications:

Also read: Bacterial Morphology

Cocci ( Spherical-shaped)

  • Cocci, spherical-shaped microorganisms, are a significant taxonomic group in the bacterial kingdom.
  • The microorganisms have a wide range of sizes, and their condensed morphology facilitates their colonization in diverse ecological habitats.
  • Example includes Streptococcus pneumoniae, the etiological agent of pneumonia, and Staphylococcus aureus, a Common cutaneous pathogen.

Bacilli (Rod-shaped)

  • The bacilli morphology is characterized by a cylindrical shape, which resembles to elongated rods.
  • The bacterial cells have an increased surface-to-volume ratio, which enhances their capacity for nutrient uptake and metabolic activities.
  • Common example of this taxonomic assemblage Consists of Escherichia coli, a commensal of the gastrointestinal tract, and Bacillus anthracis, the etiological agent of anthrax.

Spirilla (Spiral shape)

  • The spirilla are a unique group distinguished by their spiral or helical morphology.
  • The helical morphology facilitates improved mobility and motility in dense media.
  • Common examples consist of Vibrio cholerae, the etiologic pathogen of cholera, and Treponema pallidum, the causal pathogen of syphilis.

Growth characteristics

The growth patterns and rates of bacteria have significant criteria used for their classification. Which includes

Slow growing bacteria

  • Bacteria with a slow growth rate demonstrate a comparatively low rate of duplication and cellular division.
  • These microorganisms have complex metabolic pathways, which facilitate their ability to adapt in environments with limited nutrient availability.
  • Mycobacterium tuberculosis and Helicobacter pylori are classified as slow-growing bacteria. The former is responsible for the onset of tuberculosis, while the latter is linked to the development of gastric ulcers.

Rapidly growing microorganisms.

  • Bacteria with high growth rates have high rates of replication and cellular division.
  • These microorganisms have optimized metabolic pathways, enabling them to effectively uptake accessible nutrients.
  • For example, Escherichia coli, a widely studied model organism in the field of microbiology, and Pseudomonas aeruginosa, an opportunistic pathogen.

Antigens and Phage Susceptibility

The presence of surface antigens and bacteriophage susceptibility are crucial determinants in the classification of bacteria.

Presence or absence of specific surface antigens

  • Bacterial diversity and antigenic variation depend on surface antigens, including lipopolysaccharides and proteins.
  • Different antigenic profiles have changed by various species, which helps in their identification and differentiation.
  • Bacterial strains such as Neisseria meningitis, linked to meningitis, and Salmonella enterica, accountable for foodborne diseases, have distinctive surface antigens.

Susceptibility to bacteriophages

  • Bacteriophages, also known as bacterial viruses, are capable of displaying host-specificity by selectively infecting particular bacterial species.
  • The variability in bacterial susceptibility to bacteriophages can aid in the classification of bacteria into distinct phage susceptibility categories.
  • Bacterial strains, including Staphylococcus aureus and Escherichia coli, may display distinct phage susceptibility profiles, which can aid in their categorization.

Microbial biochemical characteristics.

The classification of bacteria based on their biochemical characteristics is primarily depend on their distinct metabolic capacities and biochemical responses.

Utilization of specific sugars

  • Microbial communities display a wide range of substrate preferences for catabolic processes, particularly the utilization of distinct saccharides as energy sources.
  • This characteristic has the potential to facilitate differentiation among diverse bacterial taxa.
  • Escherichia coli haves lactose fermentation capability, whereas Salmonella enterica lacks this trait.

Production of specific enzymes

  • Bacterial microorganisms are capable of producing a diverse range of enzymes that have catalytic activity toward specific biochemical reactions.
  • The enzymatic profile of bacterial strains is a key factor in their taxonomic classification.
  • Important examples are the synthesis of coagulase by Staphylococcus aureus and the urease enzyme by Helicobacter pylori.

Classification on the basis of Bacterial Cell Wall

The use of Gram staining is a crucial methodology in microbiological studies for the purpose of distinguishing bacteria on the basis of their distinctive cell wall properties.

Gram-positive bacterial cells.

Also read: Gram positive bacteria – Its Cell wall Composition, and Structure

  • Gram-positive bacteria have a characteristic of retaining the crystal violet stain upon undergoing the Gram staining procedure.
  • This is due to the presence of a peptidoglycan layer in their cellular wall
  • Notable gram-positive bacterial strains examples are Staphylococcus, Streptococcus, and Clostridium species.

Gram-negative bacterial

Also read: Gram Negative Cell Wall – Its Composition, Function, and Structure

  • Gram-negative bacteria have a lack of retention of the crystal violet stain and instead have an uptake of the counterstain, such as safranin.
  • The cellular structure consists of a delicate peptidoglycan layer encircled by an external membrane.
  • Prominent examples of gram-negative bacteria are Escherichia coli, Pseudomonas aeruginosa, and Salmonella species.

Bacterial Characteristics is based on the nutritional mode of bacteria.

The taxonomic categorization of bacteria, predicated on their nutritional mode, centers on their capacity to obtain carbon and energy substrates.


  • Bacteria having autotrophic characteristics possess the ability to perform the synthesis of organic compounds utilizing inorganic sources.
  • Examples of autotrophic microorganisms are cyanobacteria that execute oxygenic photosynthesis and nitrifying bacteria that obtain energy from ammonia oxidation.


  • Heterotrophic bacteria are dependent on organic compounds obtained from their surroundings as energy and carbon sources.
  • Microorganisms can be classified into two groups based on their energy sources: chemoorganotrophs, which derive energy from organic chemicals, and photoorganotrophs, which utilize light energy in conjunction with organic compounds.
  • Heterotrophic bacteria, such as Escherichia coli and Rhodobacter sphaeroides, are classified as chemoorganotrophs and photoorganotrophs, respectively.


  • Bacteria have phototrophic abilities from light energy to fuel their metabolic pathways.
  • They are capable of executing oxygenic photosynthesis similar to plants and algae
  • For example, Cyanobacteria, acknowledged for executing oxygenic photosynthesis, and Purple sulfur bacteria, which conduct anoxygenic photosynthesis.


  • Chemotrophic bacteria obtain energy through chemical reactions.
  • Microorganisms can be classified into two groups based on their energy source: chemolithotrophs, which derive energy from inorganic compounds, and chemoorganotrophs, which utilize organic compounds.
  • For example, Nitrosomonas europaea, a chemolithotrophic microbe implicated in ammonia oxidation, and Escherichia coli, a chemoorganotrophic bacterium.

Bacterial classification based on temperature

The classification of bacteria based on their temperature requirements is depend on their optimal growth temperatures.


  • Bacteria that are psychrophilic have optimal growth and metabolism in environments with temperatures below 20°C.
  • These microorganisms have specialized features that facilitate their survival in cold environments, including enzymes with enhanced pliability.
  • Psychrophilic microorganisms, such as Pseudomonas syringae and Psychrobacter species, have been identified as causative agents of frost damage in plants and are commonly found in cold environments.

Mesophiles (moderate temperatures)

  • Bacteria having mesophilic characteristics demonstrate optimal growth rates within a moderate temperature range, typically ranging from 20°C to 45°C.
  • Escherichia coli and Staphylococcus aureus are mesophilic microorganisms that are commonly found in the human gut and are known to cause pathogenic infections in humans, respectively.

Thermophiles .

  • Thermophilic bacteria have optimal growth and metabolic activity in environments with temperatures that exceed 45°C.
  • These microorganisms have unique enzymatic and structural modifications that enable them to survive in high-temperature environments.
  • Thermus aquaticus and Sulfolobus species are noteworthy thermophiles. Thermus aquaticus is a valuable source of thermostable DNA polymerase utilized in PCR, while Sulfolobus species are commonly found in hot springs.

Bacteria can be classified based on their oxygen requirement.

The taxonomic categorization of bacteria, which is determined by their oxygen requirements, highlights their dependence on atmospheric oxygen for both their development and metabolic processes.

Obligate aerobes

  • They are microorganisms that are dependent on oxygen for their metabolic processes and viability.
  • The bacterial cells have diverse enzymatic pathways that help in the metabolic conversion of oxygen into energy.
  • Mycobacterium tuberculosis and Nocardia species are classified as obligate aerobes, due to their dependence on oxygen for growth and survival. These microorganisms are known to cause tuberculosis and pulmonary infections, respectively.

Obligate anaerobes

  • They are microorganisms that require an oxygen-free environment to survive and grow.
  • Obligate anaerobic microorganisms are incapable of tolerating the existence of molecular oxygen and are exclusively capable of surviving in an oxygen-deprived environment.
  • The bacterial population has a deficiency or restricted presence of enzymatic pathways to mitigate the harmful impact of molecular oxygen.
  • Prominent obligate anaerobic microorganisms are Clostridium tetani, which is responsible for the onset of tetanus, and Bacteroides fragilis, an opportunistic pathogen.

Facultative anaerobes

  • They are microorganisms that are capable of surviving in both aerobic and anaerobic environments.
  • Facultative anaerobic microorganisms are capable of surviving in both oxygen-rich and oxygen-depleted environments.
  • These microorganisms have metabolic versatility, enabling them to alternate between aerobic and anaerobic respiration modes.
  • Escherichia coli and Staphylococcus aureus are noteworthy examples of facultative anaerobic microorganisms. The former is a versatile resident of the gastrointestinal tract, while the latter is an opportunistic pathogen.

Bacterial classification based on growth pH.

  • Microorganisms that survive in acidic environments, known as acidophiles.
  • Acidophilic microorganisms may survive in low pH environments and prefer acidic surroundings.
  • They have methods for preserving intracellular pH and safeguarding their cellular components from harm brought on by acids.
  • Acidophilic microorganisms such as Acidithiobacillus ferrooxidans, known to be involved in acid mine drainage, and Helicobacter pylori, commonly associated with gastric ulcers, are among the examples.


  • The microorganisms that survive in alkaline environments.
  • Bacteria with an alkaliphilic nature have optimal growth in alkaline environments and possess the ability to withstand high pH conditions.
  • These microorganisms have distinct adaptations to regulate intracellular pH and stabilize their cellular components in alkaline environments.
  • Natronomonas species and Bacillus halodurans are notable examples of alkaliphilic microorganisms, surviving in highly alkaline soda lakes, and alkaline environments, respectively.


  • Microorganisms live in environments with a neutral pH.
  • Bacteria having neutrophilic characteristics have optimal growth rates under pH conditions that are neutral, ranging from pH 6 to pH 8.
  • These microorganisms have a remarkable ability to adapt to a broad spectrum of pH levels and frequently inhabit a variety of ecological habitats.
  • Escherichia coli and Staphylococcus epidermidis are prominent neutrophilic microorganisms. The former is a versatile inhabitant of the gastrointestinal tract, while the latter is a prevalent commensal of the skin.

Bacterial classification based on osmotic pressure demand.

The taxonomic categorization of bacteria based on their osmotic pressure preferences centers on their ability to withstand varying levels of salt concentrations.


  • Microorganisms that have adapted to grow in high-salt environments.
  • Halophilic microorganisms have optimal growth in environments with high salinity levels and require increased salt concentrations for their proliferation.
  • These organisms have specialized features that enable them to regulate osmotic equilibrium and prevent cellular desiccation in saline environments.
  • Halophiles, such as species of Halobacterium inhabiting salt pans, and Vibrio parahaemolyticus, which is linked to seafood contamination, are among the known examples.


  • Bacteria having halotolerant are capable of surviving in environments with elevated salt concentrations, yet they do not require such conditions for their proliferation.
  • These microorganisms have remarkable adaptability to varying salinity levels, enabling them to survive in both saline and non-saline habitats.
  • For example, Staphylococcus species, which have tolerance towards varying salt concentrations, and Acinetobacter species which are ubiquitous in their distribution.


  • Bacteria that are non-halophilic are unable to survive in environments with high salt concentrations.
  • These microorganisms are commonly observed in habitats with isotonic saline concentrations, such as terrestrial or limnic ecosystems.
  • For example.  Escherichia coli, a prevalent gastrointestinal commensal, and Pseudomonas aeruginosa, an harmful pathogen.

Bacterial classification based on the flagellar count.

Also read: Bacterial flagella – Its structure and mechanism of movement

The taxonomic categorization of bacteria, which is determined by the quantity and configuration of their flagella, yields valuable information regarding their ability to move.

  • The observed morphology is characterized by the presence of a single flagellum, which is referred to as monotrichous.
  • Bacteria having monotrichous morphology are characterized by the presence of a solitary flagellum, which is usually situated at a singular pole of the cellular structure.
  • The flagellum is a crucial organelle that allows for unidirectional movement and promotes bacterial motility.
  • For example Vibrio cholerae, which displays a solitary polar flagellum, and Pseudomonas aeruginosa, which harbors a singular flagellum for motility.
  • peritrichous are those bacteria that have multiple flagella are dispersed over the surface of the cell.
  • The peritrichous bacterial morphology is characterized by the presence of numerous flagella that are distributed uniformly across the entire cellular surface.
  • The coordinated action of flagella facilitates bacterial motility in multiple orientations.
  • For example, Escherichia coli, having peritrichous flagella, and Proteus mirabilis, are recognized for their swarming motility.
  • The cellular morphology in question is characterized by the presence of multiple flagella at one or both ends of the cell, which is commonly referred to as lophotrichous.
  • Bacteria having lophotrichous morphology are characterized by the presence of poly flagellated structures localized at either one or both of the cell poles.
  • Spirillum volutans, a prominent lophotrichous bacterium, haves peritrichous flagellation on both poles, while Helicobacter pylori showcase monotrichous flagellation on one pole.
  • The cell haves amphitrichous flagella, if flagella present at both poles.
  • Bacteria having amphitrichous morphology possess flagella located at both poles of the cell, thereby giving the ability to move.
  • The synchronized motility of the flagellar apparatus located at both poles of the cell enables efficient locomotion.
  • For example Alcaligenes faecalis, which displays peritrichous flagella, and Magnetospirillum magneticum, recognized for its magnetotactic response.

Bacterial classification based on spore formation

Also read: Endospore Stain – Its Principle, Methods, and Procedure

  • Certain Gram-positive bacteria are capable of forming endospores, which are a type of spore produced by these microorganisms.
  • Certain bacterial species have an exceptional ability to produce spores as a means of survival in adverse environments.
  • Endospores, which have remarkable resistance to high temperatures, chemicals, and dehydration.
  • Bacillus subtilis is a noteworthy bacterium that is capable of forming endospores. Similarly, Clostridium difficile is a spore-forming pathogen that is accountable for causing antibiotic-associated diarrhea.


  • Tortora, G. J., Funke, B. R., & Case, C. L. (2021). Microbiology: An introduction. Pearson Education Limited.
  • Willey, J. M., Sandman, K. M., Wood, D. H., & Prescott, L. M. (2019). Prescott’s microbiology (11th ed.). McGraw Hill.
  • Procop, G. W., Church, D. L., & Koneman, E. W. (2020). Koneman’s Color Atlas and Textbook of Diagnostic Microbiology. Jones & Bartlett Learning.
  • Atlas, R. M. (2010). Handbook of Microbiological Media. CRC Press.
Mubashir Iqbal
Mubashir Iqbal

Mubashir Iqbal is a highly dedicated and motivated Microbiologist with an MPhil in Microbiology from the University of Veterinary and Animal Sciences. Currently, he is researching the efficacy of commercially available SARS Cov-2 vaccines to neutralize the omicron variant in Pakistan. He holds a Bachelor's degree in Microbiology and has experience in chemical and microbiological analysis of water samples, managing SOPs and documents according to standard ISO 17025. Additionally, he has worked as an internee in BSL 3, Institute of Microbiology, UVAS, where he gained experience in RNA extraction, sample processing, and microscopy.

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