Bacteria and Antibiotics
Antimicrobial Resistance (AMR)
Causes and Spread of AMR

Bacteria and Antibiotics


Bacteria are microscopic single celled organisms that are present almost everywhere on Earth. They play key roles in various ecosystems, including functioning of the human body. The main types of bacteria and their role in human infections are discussed here. This article also introduces antibiotics and provides an overview of how they can help us overcome infections.

Types of Bacteria

Bacterial cells may be shaped like rods, commas, spirals, or spheres. Yet, based on the structural composition of their cell walls, all bacteria can be divided into two distinct types - Gram-positive and Gram-negative (Figure 1), depending on the ability to be stained by a specific stain. Both these types of bacteria have peptidoglycans - a layer made of sugars and short peptide chains cross-linked to each. While the peptidoglycan layer in Gram-positive bacteria cell walls can be 30-100 nm thick (Silhavy et al., 2010), that layer in Gram-negative bacteria are only a few nanometers thick.

Some of the key differences between these types of bacteria are listed below:

Gram-positive bacterial cell walls have a single membrane:

  • The peptidoglycan layer features a more extensive cross-linking network. An additional pentapeptide serves as an inter-peptide bridge between the stem peptides. The branched stem peptides are believed to have evolved to protect bacteria from beta lactam antibiotics. The beta lactams target transpeptidase, enzymes needed for the biosynthesis of peptidoglycans. Certain Gram-positive bacteria use transpeptidases that specifically recognize branched stem peptides, so they are unaffected by the beta lactam antibiotics.
  • Teichoic acid, a polymer consisting of glycerol phosphate and carbohydrates linked by phosphodiester bonds is present. The polymers exist in two distinct classes of teichoic acid within the cell wall: wall teichoic acids and lipoteichoic acids. Wall teichoic acids are directly attached to peptidoglycans via covalent interactions while lipoteichoic acids are attached to lipids anchored in the cell membrane at a lipid head. These anionic polymers are thought to contribute to the durability of the cell wall and are integral to maintenance of a proton motive force for cellular pathways.

Gram-negative bacterial cell walls are complex since they have two membranes:

  • The thin Gram-negative bacterial peptidoglycan is covered by an external or outer membrane. This outer membrane is structurally very similar to the cell membrane. Both are composed of a lipid bi-layer containing hydrophilic heads, hydrophobic tails, and integral membrane proteins.
  • The key difference between the outer membrane and cellular membrane is the presence of lipopolysaccharides (LPS) in the outer membrane (Langley and Beveridge, 1999). Unlike the phospholipid bilayer cell membrane, the outer membrane consists of an inner layer of phospholipids and an outer layer of glycolipids, mostly containing LPS. LPS is made of three main components: lipid A, a core polysaccharide, and an O-antigen or O-polysaccharide. Like teichoic acid in Gram-positive bacteria, LPS provides the net negative charge for the cell wall in Gram-negative bacteria. The presence of LPS is of clinical importance because lipid A acts as an endotoxin which explains the pathogenicity of many Gram-negative bacteria.
Figure 1. Direct comparison between the cell walls of Gram-positive and Gram-negative bacteria reveals differences in peptidoglycan content.
Figure 1. Direct comparison between the cell walls of Gram-positive and Gram-negative bacteria reveals differences in peptidoglycan content.

Gram Staining to Distinguishing Bacteria

Gram-positive and Gram-negative bacteria derive their names from a diagnostic technique called Gram staining, which differentiates bacteria into the two distinct groups on the basis of cell wall type using a differential stain in process. In 1884, Hans Christian Gram developed the method that would bear his name, without knowing the structure of the bacterial cell wall. He observed that certain bacteria retained an applied crystal violet stain that could be visualized with an optical light microscope (Gram-positive bacteria). Other bacteria did not retain the crystal violet stain (Gram-negative bacteria).

Gram staining involves three steps: staining, washing, and counterstaining. A water-soluble, crystal violet dye is initially applied to all bacterial cells after which an iodine solution is added. The crystal violet and iodine will form a water-insoluble complex that crucially is larger in molecular weight than either moiety alone. After the complex forms, a decolorizer such as ethanol is used to wash the bacterial cells, causing the peptidoglycan layer in the cell walls to shrink as a result of dehydration. Gram-positive bacteria exhibit a tightening of the thick peptidoglycan layer and the crystal violet-iodine complex is unable to be released during the wash. In the case of Gram-negative bacteria, the alcohol wash degrades the outer membrane and the crystal violet-iodine complex is able to leave the thin peptidoglycan layer, resulting in bleaching of the bacterial cells. In the final stage of Gram staining, a counter dye such as the pink-colored safranin is used to dye Gram-negative bacteria a different color from the purple Gram-positive bacteria. Light microscopic inspection of the different staining of bacterial cells at the final stage allows for determination of bacterial cell wall type.

Figure 2. A flow chart detailing the process of Gram staining.
Figure 2. A flow chart detailing the process of Gram staining.

Decades after the development of Gram staining, the advent of electron microscopy provided insights into the structural basis for crystal violet retention or loss. The Gram staining method is still a universally used technique to distinguish amongst the two main bacterial cell wall types. However, certain bacteria species are not readily classifiable as either Gram-positive or Gram-negative. The bacterial cell walls of certain species contain additional structural modifications and peptidoglycan thicknesses can vary amongst cells in a single species depending on the stage in cell growth. Moreover, some bacteria species may not incorporate peptidoglycan within their cell walls and some species do not even possess a cell wall. Hence, Gram staining sometimes reveals Gram-variable and Gram-indeterminant species.

Bacteria and Infections

Microorganisms regularly found in the human body are known as normal flora, which consists primarily of bacteria plus a few eukaryotic fungi and protists. Humans carry large numbers of bacteria on their skin and within the gastrointestinal (GI) and genitourinary (GU) tracts. It is estimated that there are ten viable bacterial cells found in the GI tract for every one human cell in the body (Berg 1996). These indigenous bacteria may cause disease if they are introduced into the bloodstream or any internal tissues. In most cases, however, they are harmless and actually benefit the human host. For example, these microorganisms are thought to stimulate the human immune system so that it can respond more quickly to potential pathogens. The most important benefit of GI microflora is the protective barrier that these bacteria present to incoming pathogenic bacteria, making it more difficult for them to colonize the GI tract and cause an infection (Berg 1996). When pathogenic bacteria are able to cause infections, treatment with broad or narrow spectrum antibiotics will typically kill the invader, at the expense of normal flora. In some cases, this disruption of normal flora will allow Clostridium difficile to overgrow in the GI tract, causing diarrhea and requiring further antibiotic treatment.

Figure 3. The illustration shows how indigenous microorganisms are distributed throughout the human body and the relative number of human cells to bacterial cells in the body. Portions of the figure were adapted from Servier Medical Art. Source: adapted from (Berg, 1996).
Figure 3. The illustration shows how indigenous microorganisms are distributed throughout the human body and the relative number of human cells to bacterial cells in the body. Portions of the figure were adapted from Servier Medical Art. Source: adapted from (Berg, 1996).


What are Antibiotics?

Antibiotics include a wide range of drugs used to treat bacterial infections. In 1947, Selman A. Waksman first used the term “antibiotic” to define a chemical substance that is produced by one microorganism to selectively restrict the growth of or to kill another microorganism (Bennett, 2015). These microorganisms include bacteria, viruses, and fungi. His definition, however, excluded the substances produced by plants and animals as well as synthetic and semisynthetic agents that could also target microbes.

The term “antimicrobial” refers to all substances, natural and synthetic, that act against all types of microorganisms, including bacteria, viruses, and fungi. One specific class of antimicrobial substances would be antibacterial agents, which as the name suggests, specifically target bacterial growth.

Currently, Waksman’s definition of the term “antibiotic” is still acknowledged and used; however, contemporary usage has expanded and altered the meaning of the term so that it can also be used synonymously with “antibacterial” and/or “antimicrobial”, as it will be throughout the PDB-101 Global Health pages.

How do Antibiotics Work?

Antibiotics or antibacterial agents either inhibit bacterial growth or cause bacterial death. If the drug only inhibits bacterial cells from proliferating, it is known as a bacteriostatic agent. However, if the drug causes the death of bacterial cells, it is referred to as a bactericidal agent.

Antibacterial drugs exploit genetic, biochemical, and metabolic differences between bacterial cells and human cells, which explains why these agents do not usually cause harm to human cells. Bacteria and humans come from different branches of the tree of life. Bacteria are prokaryotes. Humans are eukaryotic - containing a nucleus. Beyond the presence of the nucleus, there are many differences between prokaryotic and eukaryotic cells. The molecular machines used for DNA replication, RNA synthesis or transcription, protein synthesis, and synthesis of key metabolites (e.g., Folate synthesis) differ significantly between humans and bacteria. Molecular differences at the surfaces of these two types of cells are also profound. As single-cellular organisms, bacterial survival depends on a protective cell wall structure unlike anything seen in human cells. They have a whole set of enzymes involved in the biosynthesis of cell walls. It is, therefore, not surprising that many of the antimicrobial agents used to treat bacterial infections target molecular machines necessary for these processes.


Berg R. D. (1996). The indigenous gastrointestinal microflora. Trends in microbiology, 4(11), 430–435. doi:10.1016/0966-842x(96)10057-3

Langley, S., & Beveridge, T. J. (1999). Effect of O-side-chain-lipopolysaccharide chemistry on metal binding. Applied and environmental microbiology, 65(2), 489–498. doi: 10.1128/AEM.65.2.489-498.1999

Silhavy, T. J., Kahne, D., & Walker, S. (2010). The bacterial cell envelope. Cold Spring Harbor perspectives in biology, 2(5), a000414. doi: 10.1101/cshperspect.a000414

May 2024, Gauri Patel; Reviewed by Dr. Tanaya Bhowmick
doi: ####