Introduction to Bacterial genomes
(BES, June 2021)
This page is designed as a basic introduction to understanding the bacterial species found in a sample based on the chromosomal DNA extracted from a sample.
Basic Information
1) Bacteria can be separated into two different types: Gram-positive and, 2) Gram-negative. This distinction between Gram-positive/negative is based on a lab staining procedure (by Gram) using crystal violet. Since Gram-negative bacteria have a more complex cell wall, the crystal violet does not "stain" the cell wall. The specific details of the cell walls can be found by clicking the links above. The type of bacteria is important to note since, as will be discussed below, we must break open the bacteria to collect DNA to identify the bacteria. Note: archaea are very similar to bacteria; they differ only in minor details.
2) Bacteria contain two different types of DNA: chromosomal/genomic DNA, and plasmid DNA. In a most basic sense, chromosomal DNA is the hardwired set of instructions defining all aspects of the certain bacteria. Different bacteria, with different functions, have different chromosomal DNA. Wikipedia has a list of sequenced bacterial "genomes", aka chromosomal DNA. Plasmids are considered an "extra" collection of genetic material that in NOT a part of the hardwired instructions, but can add some functionality to the bacteria. Plasmid DNA is not a unique identifier of a bacterial species; to identify a bacterial species the chromosomal DNA must be sequenced.
3) DNA is DeoxyriboNucleic Acid. DNA carries genetic instructions for the development, function, growth, and reproduction (ie. everything) of all known organisms and many viruses. DNA is very, very, very similar in similar organisms, but the information contained within DNA is expressed differently in different individuals leading to different physical traits. Regardless of how DNA is expressed, the DNA sequence is a representation of a particular organism/species.
4) DNA is a chemical substance composed of two polynucleotide chains that coil around each other to form a double helix. Each chain or polymer is made up of nucleotides which in turn are composed of three parts: a five-carbon sugar called deoxyribose, a nucleobase, either adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U), and a phosphate group. The nucleobase in one polynucleotide chain matched to the nucleobase in the other polynucleotide chain based on the pairing, A-T, C-G.