Bacterial Species Are Made in Intestines

Gut Bacteria (Flora) Constantly Exchange Genetic Material

Mar 25, 2009

The species concept of stable genetic composition does not apply to the complex, promiscuous community of the digestive tract. The gut environment defines gut flora.

Powerful molecular mechanisms usually prohibit the exchange of genes between species, but this is not always true for bacteria. Only pollen from appropriate flowers, for example, can fertilize other flowers of the same species. In animals, courtship behaviors make certain that only sperm and egg of the same species will fuse. These species-perpetuating mechanisms are, however, only marginally effective in the human gut, where gene exchange across species barriers is rampant among bacteria.

Defining Bacterial Species

How are species of bacteria defined? The answer is, not very well. It is now technically possible to determine the nucleotide base sequence of a typical gut bacterium, such as Escherichia coli K12 (E. coli, 8,312 proteins, 4,686,137 base pairs). Unfortunately the E. coli obtained from Boise, Idaho does not have the same sequence as the E. coli from Stockholm or Singapore. The E. coli found in the guts of identical twins living in the same house also have very different DNA sequences.

Why are all of these different bacteria called E. coli? The definition of bacteria is based on their niche, i.e. what they eat and do for a living. If two bacteria have the same metabolism, e.g. can live on the same nutrients and produce the same byproducts, then they are given the same species name. Other convenient characteristics, such as appearance of colonies of bacteria growing on defined nutrient agars, and staining with particular dyes for microscopic observation, can also be used to define bacterial species.

How Do Bacteria Change?

Bacteria must replicate their genetic material each time that they divide, and each time they replicate their DNA mistakes are made and the DNA sequence is subtly changed. These changes are called mutations and as a result of mutation, each bacterium, although superficially identical to its siblings, is unique.

In addition to replication errors, bacteria also exchange genes with other bacteria. Some bacteria have genes that permit them to transfer copies of their DNA directly into other bacteria in a process called conjugation. Other bacteria have mechanisms (transformation) to salvage DNA that has been released from other damaged bacteria. Viruses can also infect bacteria and transfer pieces of bacterial DNA during the infection (transduction) of new bacteria.

Through conjugation, transformation and transduction, foreign DNA can enter a bacterium and natural repair systems will integrate the foreign DNA into the resident genetic material. The result will be another new type of bacteria. If the bacterium retains the same metabolic characteristics as the original bacterium, then it will be defined as the same species. If, however, the metabolic characteristics are changed, then the new bacterium will be defined as a different species.

Constantly Changing Genes Undermine the Species Concept in Gut Flora

The metabolic characteristics that are the signature of E. coli species, do not reflect all of the genes present in a particular bacterium. Thus, bacteria designated as E. coli isolated from people in different parts of the world may have more dissimilar genes than mice and cows. At the same time, the normal, necessary E. coli in the human gut have the same name as the E. coli (O157:H7) that have picked up an extra piece of DNA that permits the bacteria to stick to intestinal cells, secrete a toxin (Shiga) and produce food poisoning.

Gut Biofilms Enhance Production of New Bacterial Species

The bacteria present in the human gut change with each meal, and yet there are consistent environments within the intestines and colon, and it is these persistent environments that select for bacteria with particular metabolic activities. The unique environment of biofilms that line the intestines, stimulates DNA exchange. Presented with a broad spectrum of different bacteria with different genes coding for different enzymes and associated metabolic capabilities, the gut selects for the bacteria best able to grow and replicate. Thus, in a sense, the gut by its selection, makes persistent bacterial species, despite the promiscuous exchange of genetic information.

The copyright of the article Bacterial Species Are Made in Intestines in Biology is owned by Art Ayers. Permission to republish Bacterial Species Are Made in Intestines in print or online must be granted by the author in writing.