The Basics


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Bacteria are the microscopic cells that are everywhere we go. Billions of them are inside of us, on our skin, in our food, in the air we breathe and the water we drink. Bacteria are important for human life for many reasons. They greatly benefit us, for example, by helping us digest our food, by producing vitamins, and by breaking down toxic chemicals in water and soil. We also fear them because some cause disease, but we should remember that the majority of bacteria are harmless and are in fact essential for our survival.

One particular phenomenon that is of great concern is the rapidly increasing resistance of pathogens to multiple antibiotics. Below we describe this in more detail.

What is Antibiotic Resistance? It is the ability of disease-causing bacteria to resist the antibiotics (drugs that kill bacteria) we use to treat particular infections. This is becoming a big problem, as evidenced by the recent outbreaks of MRSA (methicillin-resistant Staphylococcus aureus), the drug resistant skin infection. This “staph” infection was mostly found in hospitals, but is now being found in the general population.

But how do bacteria become drug resistant? This can happen when the bacterium has a change in its DNA, or genetic makeup either through mutation or horizonal gene transfer. To understand this, we need to start with the structure of the bacterial cell and the code carriers.

There are several characteristic traits of bacteria that we need to know before moving on. First, bacteria are prokaryotes, which means they are single-cell organisms that do not have a nucleus or organelles. A common misconception is that bacteria are simple due to their size. While bacteria are very small, they are complex in structure and function; the complexity of bacteria is apparent in the molecules (proteins) that perform the hundreds of tasks and provide the structure of the cell.

The Interactive Cell

There is almost no place on the face of the earth where bacteria don’t make a living. Bacteria are able to live at the bottom of the ocean, at the mouth of boiling vents, in the depths of both the arctic and the desert, as well as the wastes of our nuclear reactors. Bacteria are also capable of all manner of metabolic processes: they are able to eat everything you can think of, from wood and sugar to pesticides and oil. Everything that they are capable of doing is because of the information encoded in their genetic material.

Different bacteria cells are programmed through their genetic makeup to perform different functions. It's in their genes. They also come in different shapes, from round or oval (coccus), and rod (bacillus), to helical or corkscrew (spiral); their very structure is also determined by their genetic code.


Understanding the details of bacterial physiology takes years of devoted study, but we can share some key ideas that will help to understand the microbial world. One of the primary molecules in the cell is DNA, which contains the genetic code. This is the same kind of molecule that is present in every living cell. Although the term is used frequently in popular media today, we will describe some of the basic features and behaviors of DNA.

DNA is composed of 2 basic parts. The bases (ATCG)w which make up the code and the sugar backbone which holds the whole molecule together, which is simply a description of the physical structure of DNA.


As an information source, DNA is composed of coding and non-coding sections. The non-coding segments are often referred to as ‘junk DNA’ although little is known about the potential function of these segments. The coding segments are dispersed throughout the molecule and, by and large, are made up of genes. Genes can be seen as the tools that a cell has at its disposal. The diversity of genes available for bacteria to use is astonishingly vast.

In a bacteria cell DNA is tightly wound (super-coiled) into structures called chromosomes and plasmids. We start here by describing the chromosome and how it is replicated when a cell divides and becomes two cells. The chromosome of a bacterial species contains almost all of the information for it to eat, grow and divide.

View the image   DNA: Chromosome


A bacterial cell contains all the necessary genetic information to reproduce – without a partner. This is done through cell division – the cell splits in half after duplication of its genetic material/chromosomes.

cell division poster

Cell Division without Plasmids
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Plasmids are circular (or linear) extra-chromosomal DNA molecules that replicate separately from the chromosome. They are important because they move around genes between different bacteria (and even yeast, fungi and plants) and thus spread phenotypic traits very rapidly. These genes can code for functions that are useful to us, like the degradation of unwanted chemicals in our environment, but also for functions that threaten our health, such as resistance to the antibiotics we use in the fight against infectious diseases.

cell division poster

Cell Division with Plasmids
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Many plasmids can transfer between bacterial cells from the same or even distantly related species through a process called conjugation. This process can change the genetic makeup of a cell much more rapidly than the usual mutation process. Conjugation is one of the mechanisms of horizontal gene transfer (HGT).

cell conjugation poster

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The transfer of plasmids from one cell to another by conjugation is now well recognized as a major mechanism by which bacteria can easily and rapidly acquire a variety of phenotypic traits and thus rapidly adapt to changing environments; plasmids can be spread among bacterial cells, such that a phenotypic trait on a plasmid can be distributed among a wide range of bacterial species.

The most well known example of bacterial adaptation by HGT is the rapid spread of bacterial resistance to all kinds of antibiotics, which makes it harder and harder for us to treat infections that used to be easily cured with drugs in a few days. In this case the genetic information in a plasmid makes its host cell resistant to antibiotics, providing the cell with an evolutionary advantage in the presence of antibiotics.

While the transfer of these genes through plasmids can be threatening to our health, there are other genes certain plasmids carry that are useful for humans. One such example is a gene that makes bacteria be able to degrade some of the harmful pollutants that we use and that seep into our environment, like herbicides and pesticides or compounds in petroleum products (1).

The genes on a bacterial plasmid can be categorized in two major groups, backbone genes and accessory genes.

Backbone genes are those that contribute to the replication and maintenance of the plasmid or help it transfer between host cells; these genes are often conserved among members of the same family of plasmids and are used to categorize plasmids into groups.

Accessory genes encode functions that are frequently beneficial to the host cell. These functions benefit the host cell in many different ways, e.g. degrading environmental pollutants and using them as a carbon or nitrogen source or providing resistance to an antibiotic or a heavy metal. These accessory genes, as the name suggests, are not necessary for the stable replication or transfer of the plasmid, but may in some cases give the host cell an evolutionary advantage. If this is the case, then the host cell will thrive and replicate, producing more host cells with copies of the plasmid inside. An example of this would be genes that encode for resistance to antibiotics, which are essential for survival of a host cell in the presence of antibiotics.

Accessory genes are thought to frequently arrive in the plasmid from the genome of a previous host. Mixing and matching of genetic information is often what leads to the genetic innovation that pays of as a huge boost in fitness of a plasmid that gets the combination right.

cur and paste Plasmid poster

Cut and Paste
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Copy Paste poster

Copy Paste
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We should no longer think of bacteria as having static genomes that only change slowly over time due to mutations. It is now clear that horizontal (or lateral) gene transfer (HGT) between closely and even distantly related bacteria plays a very important role in their evolution, and in rapid adaptation to changing environments.


  1. Thomas, C. M. 2000. The horizontal gene pool. Bacterial plasmids and gene spread. Harwood Academic Publishers, Amsterdam.

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The Virtual Genome Project is funded by the National Science Foundation Microbial Genome Sequencing Program, Grant number: EF-0627988.
For more information contact: Dr. Eva Top, Professor of Biology, Department of Biological Sciences, University of Idaho, Moscow, I.D. 83844-3051 U.S.A.
email: etop [at]