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Bacteria, (singular: Bacterium) are the simplest microscopic prokaryotes that belong to the Kingdom Monera. They lack membrane-bound nucleus and internal organelles.

Bacteria live in a variety of habitats such as the soil, the ocean, and even the insides of the human gut.

They exist either as free-living organisms or as parasites. These are most successful living forms as they live in the diverse environment.

General Characteristics

A bacterial cell consists of cytoplasm, enclosed by cell membrane and cell wall. It contains DNA and a plasmid in the cytoplasm (Figure 1).

In the 1970s, Carl Woese and colleagues classified prokaryotes in two distinct groups of organisms– Bacteria (formerly known as eubacteria) and Archaea (formerly known as archaebacteria).

Figure 1. Structure of Bacterial Cell (Cutaway vector diagram of a typical bacterial cell illustrating structural components)
Figure 1. Structure of Bacterial Cell (Cutaway vector diagram of a typical bacterial cell illustrating structural components)

Bacterial cells are smaller and simpler than eukaryotic cells. They are an exceedingly diverse group of organisms that differ in size, shape, habitat, and even in metabolism.

This course covers classification of bacteria, gram staining, and bacterial reproduction.

Classification of Bacteria Based on the Morphology

Based on their body-type (morphology), bacteria can be classified into six distinct groups. Cocci and bacilli are the most common ones. These groups are described below.


These are oval or spherical shaped bacteria (Figure 2). They are arranged in diverse ways. Cocci can be classified on the basis of arrangement.

  1. Diplococcus: coccus in pairs. E.g, Neissseria gonorrhoae, Pneumococcus
  2. Streptococcus: coccus in chains or rows. Eg. Streptococcus salivarius
  3. Staphylococcus: coccus in irregular (grape-like) bunch. Eg. Streptococcus salivarius. Staphylococcus infections are commonly seen in food poisoning.
  4. Tetrad: Coccus in group of four. E.g. Micrococcus luteus, found in dust, soil, air and the skin of mammals.
  5. Sarcina: coccus in cubical arrangement of cell. E.g. Sporosarcina
Figure 2. Cocci types (Common bacteria infecting human)
Figure 2. Cocci types (Common bacteria infecting human)


These are rod-shaped bacteria. E.coli is the most commonly found bacilli present in human body. Based on arrangement, bacilli are further classified as shown below:

  1. Coccobacilli: E.g. Brucella
  2. Streptobacilli: chain of rod shape bacteria: E.g. Bacillus subtilis
  3. Comma shaped bacilli: E.g. Vibrio cholerae
Figure 3. Escherichia coli (E. coli) cells
Figure 3. Escherichia coli (E. coli) cells


They are bacteria that lack a cell wall. Mycoplasma is known as PPLO (Pleuropneumonia like organism).

It can cause sore throat, bronchitis, and pneumonia. These are smallest free-living organisms. E.g. Mycoplasma pneumoniae (Figure 4).

Figure 4. A scanning electron microscopy of filamentous M. pneumoniae
Figure 4. A scanning electron microscopy of filamentous M. pneumoniae


These are spiral-shaped bacteria. Spirochetes are a group comprised of six genera of bacteria. Examples of Spirochaetes are Spirochaeta, Treponema, Borrelia, and Leptospira.

They are causative agents of diseases like, syphilis and Lyme disease.

Figure 5. Scanning electron micrograph of Borrelia hermsii
Figure 5. Scanning electron micrograph of Borrelia hermsii

Rickettsiae and Chlamydiae

Rickettsiae and Chlamydiae (Figure 6) are gram negative bacteria and obligate intracellular parasite. They use host adenosine triphosphate (ATP), a source of energy, for their survival.

Both cannot be cultured on non-living artificial media; instead they are inoculated into living cells for culture. They are sensitive to antibiotics.

Figure 6. Chlamydia trachomatis, an obligate intracellular human pathogen
Figure 6. Chlamydia trachomatis, an obligate intracellular human pathogen


Actinomycetes are heterogeneous group of gram-positive, generally anaerobic bacteria (Figure 7).

These are one of the most diverse groups of filamentous bacteria. Examples of Actinomycetes are: Nocardia asteroids, Dermatophilus

Figure 7. Actinomycetes, gram-positive anaerobic bacteria
Figure 7. Actinomycetes, gram-positive anaerobic bacteria

Classification of Bacteria based on the Optimum pH for Growth

Based on the optimum acidity (pH) required for their growth, bacteria can be of three types:- acidophiles, alkaliphiles, and neutriphiles.

These types are described below.


  • Bacteria that have grow optimally between pH 0 and 5.5 are called acidophiles.
  • The cytoplasm of these bacteria is acidic in nature.
  • Some acidopiles are thermophilic in nature. Such bacteria are called thermoacidophiles.
  • Examples: Thiobacillus ferroxidans, Helicobacter pylori (Figure 8), Thermoplasma, Sulfolobus, Acidianus, Oligotropha corboxydovorans
Figure 8. Helicobacter pylori bacterium under the microscope
Figure 8. Helicobacter pylori bacterium under the microscope


  • Bacteria that grow best in an alkaline environment (pH 9-11) are called alkaliphiles.
  • Example: Vibrio cholerae, bacteria belonging to the genera Bacillus, Micrococcus, Pseudomonas, and Streptomyces
Figure 9. Vibrio cholerae, Gram-negative bacteria
Figure 9. Vibrio cholerae, Gram-negative bacteria


  • Bacteria that grow best in a neutral environment (pH 6.5-7.5) are called neutrophiles.
  • Most of the bacteria live in soil or water and grow at neutral pH.
  • Example: E. coli (Figure 10)
Figure 10. Escherichia coli (E.coli) gram-negative rod-shaped bacteria
Figure 10. Escherichia coli (E.coli) gram-negative rod-shaped bacteria

Classification of Bacteria based on the Structure

A few different criteria are used to classify bacteria. They can be distinguished by the nature of their cell walls, by their shape, or by differences in their genetic makeup.

The structure of a bacterium is very simple as compared to the eukaryotic cells (Figure 11). It consists of following components discussed below.

Figure 11. Bacterial cell structure
Figure 11. Bacterial cell structure

Cell Envelope

Cell envelope is the outermost layer covering the protoplasm of the bacterial cell. It consists of cell wall, cell membrane, and glycocalyx.

Cell wall

Cell wall is found outside of the cell membrane. Peptidogylcan and Techoic acid are major components of the cell wall. Peptidoglycan is a porous cross-linked polymer that provides strength to cell wall.

Teichoic acid is water soluble polymer of glycerol or ribitol. Phosphate is present in gram positive bacteria. It is the major surface antigen.

Bacterial cells are surrounded by a variety of surface structures that allow them to survive in extreme environments.

The major function of the cell wall is to provide rigidity, strength, structural support, protection against mechanical stress, and infection. It also aids in osmotic regulation and diffusion of gases in and out of the cell.

Gram Staining

In 1884, Dr. Christian Gram developed “Gram stain”. This stain helps to distinguish between Gram-positive and Gram-negative bacteria.

It is based on differential staining with a crystal violet-iodine complex and a safranin counterstain.

Theory Involved

Gram stain is the most important and widely used microbiological differential staining technique. It also allows determination of cell morphology, size, and arrangement.

When stained with gram stain and fixed by a mordant, some bacteria are able to retain the stain by resisting decolorization after washing with decolorizer (acetone and absolute alcohol), while others get decolorized.

The bacteria that retain the primary stain are called Gram positive and those that get decolorized and then counterstained are called Gram negative (Figure 12).

Figure 12. Difference between Gram-positive and Gram-negative bacteria
Figure 12. Difference between Gram-positive and Gram-negative bacteria

The table below differentiates the gram-positive and gram-negative bacteria.

Features Gram-negative Bacteria

Gram-positive Bacteria

Reaction to Gram Stain Stain red or pink, they don’t retain the Gram stain when washed with absolute alcohol and acetone Stain dark violet or purple, they retain the color even after washing
Peptidoglycan layer Single layered and thin

Multilayered and thick

Outer membrane Present


Teichoic acid Absent


Lipopolysaccharides High


Lipid and lipoprotein content High (due to presence of outer membrane) Low
Flagellar structure Four rings in basal body Two rings in basal body
Toxin production Produces endotoxins

Produces exdotoxins

Cell wall composition Cell wall is 70-120A0 thick and two layered. Lipid content is 20-30%, Murein content is 10-20% Cell wall is 100-120 A0 thick and single layered. Lipid content of the cell wall is low, whereas Murein content is 70-80%
Antibiotic resistance Resistant to antibiotics

Susceptible to antibiotics

S layer S layer is attached to outer membrane S layer is attached to the peptidogycan
Resistance to sodium azide solution High Low
Magnetosomes Present

Usually absent

Pathogenecity Most of them are pathogenic to humans and other animals Very few forms are pathogenic to humans and other animals
Examples Escherichia coli, Rhizobium, Vibrio, Acetobacter Streptococcus, Clostridium, Lactobacillus, Bacillus subtilis

Along with their differences, gram-positive and gram-negative bacteria have several similarities, as enumerated below:

  1. They both are prokaryotic, bacterial cells and lack membrane-bound organelles.
  2. They contain plasmid DNA along with circular DNA.
  3. Their cell wall is made of peptidoglycan and cytoplasm is surrounded by lipid bilayer with several proteins spanning it.
  4. They have both flagellated and non-flagellated forms.
  5. They undergo transformation, conjugation, and transduction

Cell membrane

Bacterial cell membrane is also referred as cytoplasmic or inner membrane. It lies internal to the cell wall and encloses cytoplasm of the bacterium. This membrane is a functional equivalent of eukaryotic plasma membrane.

This membrane is a fluid phospholipid bilayer embedded with proteins. The phospholipid bilayer is arranged so that the polar ends of the molecules form the outermost and the innermost surfaces of the membrane.

The non-polar ends form the center of the membrane. Functions of cell membrane are listed below:

  1. Selective permeability
  2. Energy production
  3. Motility
  4. Removal of waste
  5. Endospore formation


It is a network of carbohydrates covering the membrane of the cell. Structural and chemical compositions of glycocalyces differ depending on the species of bacteria.

Glycocalyx helps in adhesion, protection from desiccation, and attack by a host’s immune system.


Capsule is present in capsulated bacteria (Baciilus subtilis, Haemplhilus influenza, Streptococcus pneumoniae, Klebsiella pneumoniae etc).

Most prokaryotes contain a polysaccharide layer outside of the cell wall. This layer is called capsule.

This capsule is 0.2µm thick layer firmly attached to the cell wall of the capsulated bacteria.

It is composed of 98% water and 2% polysaccharide or glycoprotein/ polypeptide, hemicellulose (homopolysaccharide).

In leuconostoc, it is composed of cellulose, consisting of glucose or fructose. In Klebsiella pneumoniae, capsule is made up of glucose, galactose, rhamnose.

In Bacillus anthracis, it is made up of polypeptide (a polymer of D-glutamic acid) and in Streptococci, it is made of L-aminoacids.

Functions of capsule are as follows:

  • Virulence factor: capsule enhances the ability of bacteria to cause disease by preventing their phagocytosis.
  • Capsule prevents the cell from desiccation as it is hygroscopic and drying.
  • Attachment: capsule helps in attachment on diverse surface (of host) even on bacteriophage.
  • Capsule protects bacteria from mechanical injury, temperature, drying.
  • Capsule resists phagocytosis by WBCs hence it is anti-phagocytic.
  • Capsule is a source of nutrition whenever nutrient supply gets very low in the cell.
  • mutants use their capsules as a source of energy.


Flagella is a filamentous (hair-like) extension through the membrane or the wall of a cell. They vary from 15-20nm in diameter and help in motility of the bacteria (Figure 13).

These are unbranched, long, and mostly composed of the protein flagellin (known as H antigen). Motility plays important roles in survival and virulence of the bacteria.

Each flagellum consists of three main parts: filament, hook and basal body


Filament is a thin hair like structure that arises from hook and extends from the cell surface.


It is a wider region at the base of filament, embedded in the cell envelope, and acts as a flexible coupling between the filament and the basal body of the flagella.

Basal body

It consists of central rod inserted into several rings attached to cell membrane and cell wall.

Based on arrangement of flagella they are divided into five types shown below:

  1. Monotrichous: single flagella attached on one end of the cell. Examples; Vibrio cholera, Pseudomonas
  2. Lophotrichous: bundle of flagella present in one end of the cell. Example: Pseudomanas
  3. Amphitrichous: single or cluster of flagella present at both the end of cell. Example; Aquaspirillium.
  4. Peritrichous: flagella present all over the surface of the cell. Example; E. coli, Salmonella, Klebsiella.
  5.  Atrichous: flagella absent. Example, Shigella
Figure 13. Structure of bacterial flagellum
Figure 13. Structure of bacterial flagellum


Bacterial cytoplasm is composed of water, enzymes, nutrients, gases. It contains cell structures, such as ribosomes, chromosome, polypeptide (chaperones), cytoplasmic inclusions (volutin, polysaccharides, lipids etc.), and plasmids.

The components of cytoplasm are responsible for cell growth, respiration, metabolism, elimination of waste, cytoplasmic dynamics and replication of the cell.

Some bacteria also produce spores and cysts.

Chromosome is a single continuous strand of DNA, while plasmids are small, extrachromosomal genetic structures carried by many strains of bacteria.

Plasmids replicate independently of chromosome and appear to give bacteria a selective advantage to the bacteria.


Nucleoid or genophore, is a region inside the cell of prokaryotes that contains the genetic material (a single circular chromosome).

Nucleoid mainly consists of DNA but in addition to DNA, it also contains RNA and proteins. Unlike a eukaryotic nucleus, Nucleoid is not surrounded by nuclear membrane.


Ribosomes are the organelles that are major sites for protein synthesis. The main function of ribosomes is protein synthesis.

Many ribosomes are found free in the cytosol, while others are attached to rough endoplasmic reticulum (RER).

Ribosomes (70S) in bacteria are composed of two subunits:- one large (50S) and one small (30S) that only bind together during protein synthesis.


Pili or Fimbriae are hair-like filaments (tiny hollow projections) that protrude from the cell membrane of the bacteria into the external environment.

They are usually present in gram-negative bacteria. A pilus is composed of subunits of the protein pilin. They play a significant role in adhesion and conjugation.

Some pili are useful in biofilm formation, phage transduction, DNA uptake, and bacterial motility.

Bacterial Reproduction

Although bacteria are single-celled microscopic organisms, they reproduce in suitable conditions. Bacteria reproduce by vegetative, asexual, and sexual methods.

Vegetative reproduction includes binary fission, fragmentation, and budding. Sporulation (spore formation) is asexual form of reproduction in bacteria.

Sexual reproduction is by genetic recombination by three main processes: Conjugation, transduction, and transformation.

Binary Fission

Binary fission is the commonest form of propagation for bacteria, where parent cell divides into two similar daughter cells.

During this process, an organism duplicates its genetic material (DNA) and then undergo a process of cytokinesis (division of cytoplasm) forming two daughter cells. Each daughter cell receives one copy of DNA.

Process Involved

Once a bacterium reach a desired size, each cell produces a replica of its DNA thus forming two DNA molecules. These DNA molecules are attached to the cell membrane.

The cell membrane starts growing inwards and by cytokinesis two daughter clone cells are formed — each containing separate DNA molecules.

In suitable conditions, bacteria can double in number through binary fission in 10-20 minutes.


Fragmentation is commonly known as splitting, where parent organism divide into several pieces and each piece develops into a complete new individual.


Budding is a form of vegetative reproduction that results from the outgrowth of a part of a cell leading to a separation of the original organism into two individuals.

The parent cell forms a bud at one end and forms a nucleus for the bud by the process of mitosis. Later, the bud separates from the parent cell and forms a different organism.


During unfavorable conditions, metabolically-dormant structure called spores are formed by the process of sporulation (Figure 14).

This process is divided into several stages. In Bacillus subtilis, the entire process of sporulation takes 8 hours to complete.

Spores can be produced within (endospores) or outside (exospores) the bacterial cells.

Bacteria producing endospore are Bacillus, Clostridium, Paenibacillus, Sporosarcina and bacteria producing exospore are Methylosinus.

Figure 14. Process of sporulation in Bacillus subtilis
Figure 14. Process of sporulation in Bacillus subtilis


Bacterial conjugation is a process by which a bacterial cell transfers genetic material to another bacterial cell (Figure 15). The bacterial DNA that is transferred by this process is called F-Plasmid (F is for plasmid).

A cell that has a copy of the F-plasmid is called F-positive, F-plus or F+ cell, and is a donor cell, while a cell that does not contain F-plasmid is called F-negative, F-minus or F cell, and is considered a recipient cell.

Process of bacterial conjugation
Figure 15. Process of bacterial conjugation


Transformation is the process by which foreign DNA is introduced into a cell (Figure 16). Bacterial transformation plays a very important role in genetic engineering and molecular cloning.

After transformation, the host cells may express the acquired genetic information, which may serve as a source of genetic diversity and potentially provide benefits to them (e.g., antibiotic resistance).

Process Involved

The natural process of transformation was first reported by Frederick Griffith in 1928. The first protocol for artificial transformation of E. coli was published by Mandel and Higa in 1970.

The procedure indicated enhanced permeability of the bacterial cells to DNA after treatment with calcium (Ca2+) and brief exposure to an elevated temperature, known as heat shock.

This method became the basis for chemical transformation. Later it was discovered that an electrical field application to the cells also enhances the uptake of DNA, called an electroporation.

Figure 16. Transformation of plasmid in bacterial cells
Figure 16. Transformation of plasmid in bacterial cells


Bacterial transduction is a type of gene transfer where a bacterium transfers its DNA (or a part of the DNA) to another bacterium with the help of a virus called transducer or vector.

Bacteriophage is most commonly used virus for bacterial transduction (Figure 17). Random or generalized and specialized are the two kinds of transduction.

The table below shows the major points of difference between the two.


Generalized Transduction

Specialized Transduction
Discovery Generalized transduction was discovered in 1952 by Norton Zinder and Joshua Lederberg Morse discovered specialized transduction in 1956
Phages Mediated by lytic phages Mediated by lysogenic phages
Process involved Phage accidently packages a random piece of bacterial DNA just before the bacterial lysis Phage DNA gets integrated in the bacterial DNA. During the unfavorable conditions, the viral DNA excise and sometimes carries a part of bacterial DNA too
DNA transferred Phages can carry any part of the bacterial chromosome Phages carry only restricted part of the bacterial chromosome
A process of bacterial transduction
Figure 17. A process of bacterial transduction

Bacteria are not always “bad”. A human body encounters both good and bad bacteria every day.

Bacteria is called “good” as they help us digest our food and protects us from infections, whereas bad or pathogenic bacteria make us sick or even lead to mortality.

Examples of Various Bacteria

A few examples of good/harmless bacteria are Escherichia Coli, Lactobacillus Johnsonii, Bacteroides Thetaiotamicron, Staphylococcus epidermidis, Bifidobacterium Longum, Viridans Streptococci etc.

Neisseria gonorrhoeae, Mycobacteria, Staphylococcus aureus, Streptococcus pneumoniae, Streptococcus pyogenes, Clostridium tetani, Clostridium botulimum, Bacillus anthracis, Bordetella pertussis, Borrelia burgdorferi are a few examples of harmful/bad bacteria.

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