Bacteria

A bacterium (. bacteria) is a single-celled organism lacking the more complex organelles such as mitochondria and chloroplasts, which are themselves thought to be symbiotic bacteria (see endosymbiosis). They reproduce by binary fission and share genes through transfer of plasmids, small ring-shaped chains of DNA.

Bacteria are sometimes thought to be the "oldest" domain (or kingdom) of living organisms, in the sense that they probably appeared first in the history of life on Earth, before Archaea (and long before eukaryotes). Whether this specific statement is true or not, microfossils going back hundreds of millions of years before the origin of eukaryotic life show that they are true evolutionary heavyweights, collectively robust against every major climatic change or other environmental disruption in their very long history. Their endurance and diversity, with more than a dozen phyla represented comprising millions of species, and a truly massive array of different biochemistries across a staggering variety of environments, arguably make them the most successful form of life that has ever existed.

Classification
As a taxonomic kingdom, bacteria are immensely varied, so a proper taxonomy involves subdividing them in a variety of ways. One of the most basic of these is the use of the Gram stain, a violet dye which is absorbed into the cell walls of some bacteria but not others, followed by a counterstain. Bacteria that take up the first stain are termed Gram-positive, and develop a deep violet color as a result of the procedure. Bacteria that reject the stain are given a red or pink color by the counterstain, and are termed Gram-negative. The results of this procedure, while not perfect (Gram-variable and Gram-indeterminate bacteria exist), provide taxonomically valuable information about the physical structure of the organism(s). While it is hardly a be-all and end-all, it remains critically important to bacteriology long after its discovery.

Today, with the advent of molecular biology, it is possible to classify bacteria much more specifically than traditional methods such as the Gram stain allowed for. Molecular studies have allowed the creation of detailed bacterial phylogenies.

Microbiomes
Bacteria interact with more specialized forms of life in a variety of ways. The human body is home to hundreds of distinct species of bacteria living in the mouth, gut, on the skin and elsewhere. Most of these are harmless passengers and some, such as E. coli are actually very important in keeping the body running properly. (The amount of E. coli present is often used to indicate how many pathogens there are in water, but they themselves are actually quite harmless.) Some of these bacteria can become pathogenic under certain circumstances, such as when a person's immune system is compromised. Other species of bacteria, such as Neisseria meningitidis (also known as meningococcus), Staphylococcus aureus, Yersinia pestis (the cause of the Black Death) and Mycobacterium tuberculosis (which causes tuberculosis) can cause illnesses ranging from trivial to severe. In plants, nitrogen-fixing bacteria such as those found on the root nodules of legumes (e.g. peas, beans, soy, lentils and peanuts) can be very important to maintaining healthy soil.

Bacteria also interact with viruses, for example by serving as "prey" for a group of viruses called bacteriophages. Because of their extreme selectivity in the cells they attack (sometimes restricted to specific species of bacteria, and generally ignoring eukaryotic cells), these viruses have been studied for use as medical treatments in a set of techniques called phage therapy.

Importance of microbiomes
It was once thought that the microbiome primarily or even exclusively existed in the mouth, gut, vagina and skin, but new research has found microbes in healthy people in the uterus, breast milk, urine, and blood. The gut microbiome also has an effect on brain functioning, and mice that have had their gut microbiomes removed by chronic antibiotics have impaired memory and reduced nerve cell growth in the hippocampus.

The estimates of how many microbial cells human carry around has varied rather wildly in recent years, ranging from 100 microbes to 1 human cell down to 1-to-1, the latter being the most recent estimate for bacteria-only to human cells as of 2016.

Germ-free mice (that is mice that are free of bacteria, fungi and parasites) have inherited viral diseases that regular mice do not. Germ-free mice are also subject to inflammation of the lungs and colon (comparable to asthma and colitis) that regular mice do not normally experience. And germ-free mice appear to have a compromised blood-brain barrier; a compromised blood-brain barrier is associated with several diseases. Germ-free mice also suffer from behavioral problems including abnormal movement, memory problems, risk-taking, and stress. An explanation for this is that several genera of bacteria have been shown to release neural-messaging chemicals: Bacillus (dopamine, norepinephrine), Bifido-bacterium (γ-aminobutyric acid or GABA), Enterococcus (serotonin), Escherichia (norepinephrine, serotonin), Lactobacillus (acetylcholine, GABA) and Streptococcus (serotonin).

Research
Due to their simplicity, small genome, ease of culture and not being a major focus of any animal-rights groups, bacteria are used in biological research, such as in studies of genetic engineering and of evolution. The most well-known example of the latter is the use of E. coli in Lenski's famous experiment.

Advertising
The common association of bacteria with disease leads many people to think of all bacteria as "bad." Of course there are non-pathogenic bacteria but so strong is the popular link that adverts for probiotic drinks steer clear of the B-word: