Ultrastructure of a Bacterial Cell: Labeled Guide

By Dr. Zubair Khalid, DVM, MS, PhD · 2026-09-20

The ultrastructure of a bacterial cell is the arrangement of its parts at the level resolved by electron microscopy, from the outer capsule to the nucleoid, ribosomes, and storage granules inside the cytoplasm. A bacterium is a prokaryote, which means it has no membrane-bound organelles and no true nucleus, so its DNA sits free in the cytoplasm and every other function is handled by the plasma membrane, the ribosomes, or the cell wall.

This matters in veterinary practice because almost every antibacterial drug and every host defense mechanism acts on one of these structures. Penicillin attacks the peptidoglycan wall. Lysozyme, an enzyme in tears and saliva, cuts the same wall. Antibodies and phagocytes must first get past a capsule. Knowing which structure does what, and which structures differ between Gram-positive and Gram-negative bacteria, is the foundation for understanding pathogenesis, immunity, and why some bacteria stain pink and others purple.

This article is educational and is not a substitute for veterinary diagnosis or treatment.

The Prokaryote Rule: No Membrane-Bound Organelles, No True Nucleus

The single most testable fact about bacterial ultrastructure is what is absent. Bacteria lack mitochondria, endoplasmic reticulum, Golgi apparatus, lysosomes, and a membrane-bound nucleus. There is no nuclear envelope, so the genetic material is not separated from the cytoplasm by a membrane. There are no histone-wrapped chromosomes in the eukaryotic sense, although some bacteria do use histone-like proteins to compact DNA.

This absence has practical consequences. Energy production happens across the plasma membrane itself rather than inside a mitochondrion. Protein trafficking is direct, with no organelle-to-organelle shuttle. Cell division is not mitotic. When a student sees an electron micrograph of a bacterium, the correct mental model is a single compartment bounded by a membrane, wrapped in a wall, with a tangle of DNA and thousands of ribosomes floating in the same space.

The Labeled Structures, One by One

Capsule

The capsule is the outermost layer, a polysaccharide coat that sits outside the cell wall. It is not present in all bacteria, and it can be lost on laboratory subculture, which is why capsulated clinical isolates often look mucoid while laboratory-adapted strains look smooth or rough.

The capsule is a virulence factor because it resists phagocytosis. It blocks the physical engagement of phagocyte receptors with underlying surface molecules. In a study of the Stenotrophomonas maltophilia complex, capsulated clinical isolates resisted blood plasma-mediated killing, phagocytosis, and desiccation, while capsule-deficient mutants lost these protections [1]. The same study found a trade-off: capsule formation limited biofilm formation and adhesion to epithelial cells in some isolates [1].

Capsules are also targets. A cationic protein derived from platelet factor 4 binds the negatively charged capsule of Klebsiella pneumoniae and acts as an opsonin, creating recognition sites for the CR3 receptor on leukocytes and enhancing phagocytosis of both high-virulence K2 and low-virulence K3 strains, including carbapenem-resistant isolates [2]. Bacteriophage tailspike proteins degrade capsules to reach the bacterial surface, and mutations in these proteins shift host range, which is one reason capsule variation drives phage specificity [3].

Capsule production is regulated, not fixed. In Acinetobacter baumannii, knocking out the quorum sensing gene abaI reduced capsule production and virulence and lowered inflammation in infected mice [4]. In Streptococcus agalactiae, loss of the type VII secretion system component essC downregulated capsule biosynthesis genes cpsA, cpsB, and cpsD, reduced capsular polysaccharide, impaired capsule integrity, and attenuated virulence in vivo [5].

Cell Wall: Gram-Positive Versus Gram-Negative

The cell wall is the rigid layer that gives the bacterium its shape and protects it from osmotic lysis. Its core component is peptidoglycan (PG), a mesh-like polymer of glycan chains crosslinked by short peptide stems [6]. Peptidoglycan provides mechanical strength and maintains cell shape, and it is chemically heterogeneous, which is why defined fragments are valuable for studying the enzymes that build and break it [6].

Gram-positive wall. A thick peptidoglycan layer, often many nanometers deep, sits outside the plasma membrane. There is no outer membrane. Teichoic acids are threaded through the peptidoglycan. The thick wall retains crystal violet during Gram staining, which is why these bacteria appear purple.

Gram-negative wall. A thin peptidoglycan layer sits in the periplasm, between the plasma membrane and an outer membrane. The outer membrane is a lipid bilayer containing lipopolysaccharide (LPS) in its outer leaflet. LPS is a potent inflammatory inducer, and it is the classic Gram-negative endotoxin [7]. The outer membrane also carries porins and other outer membrane proteins that serve as receptors for phages and bacteriocins. Work on Escherichia coli O157:H7 showed that the glycan layers of the envelope (O-antigen capsule, O-antigen, LPS core) determine whether phages can reach their outer membrane protein receptors at all, with the same receptor proteins recognized across laboratory and pathogenic strains but access controlled by the glycan state [8].

Peptidoglycan is the target of penicillin, which blocks the crosslinking transpeptidation step, and of lysozyme, which cleaves the glycan backbone. A recent method generated defined, denuded peptidoglycan oligosaccharides from Staphylococcus cell walls and used them as substrates for lysozyme-catalyzed transglycosylation, enabling continuous colorimetric monitoring of PG-cleaving enzymes [6]. This is the biochemical basis for why lysozyme is a natural antibacterial in tears, saliva, and phagolysosomes.

Peptidoglycan fragments are also immune signals. Host pattern recognition receptors detect muropeptides, and structural variation in PG across and within species shapes how those fragments are sensed and whether they act as danger signals [9].

Plasma Membrane

The plasma membrane is the phospholipid bilayer that encloses the cytoplasm. It is the bacterial equivalent of a combined cell membrane and mitochondrial inner membrane: it handles selective transport, energy generation via the proton motive force, and secretion. It is also the site of cell wall precursor synthesis. Undecaprenyl phosphate (UndP) is the universal lipid carrier for these precursors, and a self-inserting transmembrane protein in Bacillus subtilis was shown to localize to division septa by binding UndP and related molecules, linking membrane dynamics to sites of active wall synthesis [10].

The plasma membrane is not a drug target in the same clean way that the wall is, but it is where many antibiotics that disrupt membrane integrity act, and it is the barrier that must be crossed by any agent that needs to reach the cytoplasm.

70S Ribosomes

Bacterial ribosomes are 70S particles, made of a 50S and a 30S subunit. They are structurally distinct from eukaryotic 80S ribosomes, which is why many antibiotics can selectively inhibit bacterial protein synthesis without harming host cells. Ribosomes are abundant, often thousands per cell, because bacteria grow and divide quickly.

Ribosome function is tightly coupled to the cell cycle. In Mycobacterium tuberculosis, the transcription factors WhiA and WhiB2 regulate genes involved in DNA replication and repair, ribosome function, cell wall synthesis, and septation, and both are essential for cell division [11]. This shows that ribosome biogenesis is not a background process but a regulated part of the division program.

Nucleoid

The nucleoid is the region of the cytoplasm that contains the bacterial chromosome. It is not enclosed by a membrane. The chromosome is typically a single circular DNA molecule, supercoiled and associated with proteins to fit inside the cell. Because there is no nuclear envelope, transcription and translation can occur simultaneously on the same DNA template, which is a fundamental difference from eukaryotic cells.

Plasmids

Plasmids are small, extrachromosomal DNA molecules that replicate independently of the chromosome. They are not essential for basic survival but often carry genes for antibiotic resistance, virulence factors, or metabolic capabilities. A single bacterial cell can carry multiple plasmids, and plasmids can be transferred between bacteria by conjugation, which is one route by which resistance spreads. Plasmids are a major reason why antibiotic resistance can move quickly through a bacterial population.

Flagella

Flagella are long, helical surface appendages that rotate to propel the bacterium. They are built from flagellin subunits and anchored by a basal body that spans the cell envelope. Assembly of the flagellar rod requires penetration of the peptidoglycan layer. In Salmonella enterica, the acetylglucosaminidase activity of the rod cap protein FlgJ enhances but is not strictly required for flagellum assembly, and deletion of the anti-sigma factor flgM increased both the proportion of flagellated cells and the number of flagellar filaments per cell [12]. This illustrates that flagellar assembly is a regulated, multi-step process with redundancy built in.

Flagella are important for motility, chemotaxis, and in many pathogens for adhesion and invasion. They are also highly immunogenic, which is why flagellar antigens are used in serotyping schemes such as the H antigen system.

Pili (Fimbriae)

Pili are shorter, thinner surface appendages than flagella. They mediate adhesion to host tissues, and some specialized pili mediate DNA transfer during conjugation. In Gram-positive bacteria, pili are often covalently attached to the cell wall by sortase enzymes. In Clostridium perfringens, the pilus is built from shaft pilin CppA and tip pilin CppB, with CppB at the tip for adhesion to host cells, and the covalent bonds are catalyzed by class C sortase CpSrtC [13]. Structural analysis showed an elongated arrangement of beta-sandwich domains with a specific amide bond between Thr688 of CppB and Lys174 of CppA [13].

Pili are critical for the initial adhesion step of colonization, which is why they are often called colonization factors. Blocking pili is a strategy for preventing infection at the mucosal surface.

Inclusion Bodies

Inclusion bodies are intracellular storage granules. They are not membrane-bound organelles in the eukaryotic sense, although some are surrounded by a thin protein or lipid shell. Common examples include glycogen granules, polyhydroxybutyrate (PHB) granules, polyphosphate granules, and sulfur granules. They store carbon, energy, or nutrients for use when external supplies are low. In diagnostic microbiology, inclusion bodies can sometimes be seen on stained smears and can help identify certain species, but they are not a primary identification criterion for most bacteria.

Summary Table: Structure, Function, and Gram Status

How These Structures Are Observed in Practice

Gram staining is the first-line method. The thick peptidoglycan of Gram-positive bacteria retains crystal violet and appears purple. The thin peptidoglycan and outer membrane of Gram-negative bacteria lose crystal violet during decolorization and take up the safranin counterstain, appearing pink. This is a direct readout of cell wall ultrastructure.

Capsule staining uses negative stains such as India ink or nigrosin, which darken the background and leave the capsule as a clear halo around the cell. This is useful for confirming capsule production in clinical isolates that look mucoid.

Electron microscopy resolves the individual layers. Transmission electron microscopy shows the plasma membrane, peptidoglycan, and outer membrane as distinct bands. Scanning electron microscopy shows surface appendages such as flagella and pili. Cryo-electron microscopy and X-ray crystallography are used to determine the atomic structure of individual components such as pilin complexes [13].

Molecular methods detect the genes behind these structures. PCR and sequencing can identify capsule biosynthesis genes, pilin genes, flagellar genes, and plasmid-borne resistance genes. In E. coli isolated from prostate secretions of men with chronic bacterial prostatitis, virulence genes encoding adhesins, toxins, capsule antigens, siderophores, invasins, and anti-immunity factors were detected, with adhesin and siderophore genes predominating [14]. This kind of genotyping links ultrastructure to clinical behavior.

Biochemical methods study the wall directly. Defined peptidoglycan oligosaccharides generated from Staphylococcus cell walls serve as substrates for PG-active enzymes that cleave or modify the glycan backbone, and lysozyme-catalyzed transglycosylation of these oligosaccharides produces derivatives that allow continuous colorimetric monitoring of enzyme activity [6]. This is how researchers dissect the enzymes that build and break the wall.

Clinical Relevance, Limitations and Common Mistakes

The capsule is the most common reason a bacterium can survive in the bloodstream long enough to cause systemic disease. Encapsulated strains of Klebsiella pneumoniae, Streptococcus agalactiae, and Acinetobacter baumannii are more virulent than their capsule-deficient counterparts [2][4][5]. In S. maltophilia, capsule formation protected against plasma killing and phagocytosis but reduced biofilm formation and epithelial adhesion in some isolates, which means the capsule is not uniformly advantageous in every niche [1].

The Gram-negative outer membrane and its LPS are the reason Gram-negative sepsis can be so severe. LPS is a potent inflammatory inducer, and it drives cytokine release and tissue injury [7]. This is why Gram-negative bacteremia is a medical emergency.

Peptidoglycan is the reason penicillin and lysozyme work. Penicillin blocks the crosslinking step, and lysozyme cleaves the glycan backbone. Both weaken the wall until the bacterium lyses under osmotic pressure. This is also why bacteria that lack a wall entirely, such as Mycoplasma species, are intrinsically resistant to penicillin.

Common mistakes students make:

1. Calling the nucleoid a nucleus. It is not membrane-bound, and it is not a true nucleus.
2. Assuming all bacteria have capsules. Many do not, and capsule expression can be lost on subculture.
3. Confusing pili with flagella. Pili are for adhesion and conjugation. Flagella are for motility.
4. Thinking the Gram-negative outer membrane is the same as the plasma membrane. It is a separate bilayer with different composition and function.
5. Forgetting that peptidoglycan is present in both Gram types, just in different thicknesses. The Gram-negative wall still has peptidoglycan, it is just thin and located in the periplasm.
6. Assuming inclusion bodies are organelles. They are storage granules, not membrane-bound functional compartments in the eukaryotic sense.

Individual cases require veterinary assessment, and the clinical significance of any specific isolate depends on the host species, the site of infection, and the host immune status.

Quick Review: Seven Points Worth Memorizing

1. Bacteria have no membrane-bound organelles and no true nucleus.
2. The capsule resists phagocytosis and is a virulence factor.
3. Gram-positive walls have thick peptidoglycan. Gram-negative walls have thin peptidoglycan plus an outer membrane with LPS.
4. Peptidoglycan is the target of penicillin and lysozyme.
5. The plasma membrane handles transport, energy, and wall precursor synthesis.
6. Ribosomes are 70S, which is why many antibiotics selectively inhibit bacterial protein synthesis.
7. The nucleoid holds chromosomal DNA, and plasmids carry extra genes such as antibiotic resistance.

Frequently Asked Questions

What is the ultrastructure of a bacterial cell?

The ultrastructure of a bacterial cell is the arrangement of its components at electron microscope resolution, including the capsule, cell wall, plasma membrane, ribosomes, nucleoid, plasmids, flagella, pili, and inclusion bodies. Bacteria lack membrane-bound organelles and a true nucleus.

Do all bacteria have a capsule?

No. The capsule is present in some species and some strains, and it can be lost on laboratory subculture. When present, it resists phagocytosis and acts as a virulence factor.

What is the difference between Gram-positive and Gram-negative cell walls?

Gram-positive walls have a thick peptidoglycan layer and no outer membrane. Gram-negative walls have a thin peptidoglycan layer plus an outer membrane containing lipopolysaccharide.

Why does penicillin kill bacteria but not host cells?

Penicillin targets peptidoglycan crosslinking, a structure that host cells do not have. This selective target is why penicillin is effective against susceptible bacteria with relatively little direct toxicity to mammalian cells.

What is the difference between pili and flagella?

Pili are short appendages used for adhesion and conjugation. Flagella are long appendages used for motility. Both are surface structures, but they serve different functions.

Do bacteria have a nucleus?

No. Bacteria have a nucleoid, which is a region of the cytoplasm containing chromosomal DNA, but it is not enclosed by a membrane and is not a true nucleus.

Related Articles

• Bacterial Cell Components
• Bacterial Cell Anatomy
• Protein Synthesis Diagram Labeled
• How to Calculate the Copy Number of a Plasmid in Bacterial Cells
• Ribosome Diagram: Structure, Function, and Labeled Parts
• Replication Fork Labeled: A Visual Guide to DNA Synthesis
• Sec System: Bacterial Protein Secretion Explained

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4. Quorum sensing gene abaI enhancing capsule production and pathogenicity of Acinetobacter baumannii.
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7. Empagliflozin mitigates lipopolysaccharide-induced tracheal injury in rats via downregulation of IL-6/JAK/STAT3 signaling pathway and stem cell preservation: histological and molecular study.
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