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Bacteria (singular: bacterium) is a primary domain of single-celled prokaryotic microorganisms characterized by peptidoglycan cell walls, ester-linked phospholipid membranes, and circular DNA chromosomes lacking a membrane-bound nucleus. They typically measure a few micrometers in length, although the range is from about 0.2 μm to more than 700 μm in the largest known species (Thiomargarita magnifica). Bacteria live in nearly every habitat on Earth, including soil, fresh and salt water, the deep subsurface, hot springs, ice, the atmosphere, and the bodies of animals and plants. They are among the oldest forms of life, with fossil evidence of bacteria-like cells and stromatolites from at least 3.4 to 3.5 billion years ago, and they are the most abundant cellular organisms by number, with an estimated 10³⁰ cells on Earth. They are not the most abundant in biomass, which is dominated by plants, and bacteria account for roughly 15 percent of the biomass of the biosphere.

Bacteria are important in biogeochemical cycles, in agriculture, in industry, in the health of humans and other organisms, and as agents of disease. Most bacteria are harmless or beneficial, and only a small fraction of species cause disease. The study of bacteria is bacteriology, a branch of microbiology.

The Three-Domain System and 16S rRNA Phylogenetics

Bacteria are one of the three domains of life in the three-domain system, with Archaea and Eukaryota. Bacteria and archaea are both prokaryotes, but they are distinct lineages. Prokaryote is a description of cell organization and not a clade. Many recent phylogenomic analyses place eukaryotes within or as a sister group to the Archaea, which makes the archaea more closely related to eukaryotes than to bacteria in their information-processing machinery.

Whole-Genome Taxonomy and Uncultured Candidate Phyla

Bacterial taxonomy is based on genome sequences, in particular the sequences of the 16S ribosomal RNA gene and, more recently, whole-genome comparisons, such as average nucleotide identity (about 95 to 96 percent is the usual threshold for a species). Major phyla (names validly published under the International Code of Nomenclature of Prokaryotes, or used in the Genome Taxonomy Database) include Pseudomonadota (formerly Proteobacteria), Bacillota (Firmicutes), Actinomycetota (Actinobacteria), Bacteroidota, Cyanobacteriota, Spirochaetota, Chlamydiota, and many others. Most bacterial lineages have never been grown in culture. Sequencing of environmental DNA (metagenomics) has shown large uncultured groups, such as the candidate phyla radiation, which consists of small-celled bacteria with reduced genomes that probably depend on other organisms. Formal estimates of the number of species range from millions to a trillion, and fewer than 20,000 have been formally named in a valid manner.

Cell shape and size

Common shapes are spheres (cocci), rods (bacilli), curved rods (vibrios), and spirals (spirilla and spirochetes). Shape is determined mainly by the cell wall and by the cytoskeleton. The protein MreB, a homolog of actin, directs the synthesis of the cell wall in rod-shaped cells, and FtsZ, a homolog of tubulin, forms the ring that divides the cell. Small size gives a large surface-to-volume ratio, which favors rapid exchange of nutrients and fast growth. For a sphere of radius r, the ratio is:

so that a cell of radius 0.5 μm has a ratio of 6 μm⁻¹, which is ten times higher than that of a cell of radius 5 μm.

Cell envelope

• Cytoplasmic membrane. A phospholipid bilayer that contains proteins for transport, energy generation (the respiratory chain and ATP synthase), and sensing. Bacteria lack sterols in most cases, although hopanoids play a similar role in some.
• Cell wall. Most bacteria have a wall of peptidoglycan (murein), a mesh of glycan strands of alternating _N_-acetylglucosamine and _N_-acetylmuramic acid that are cross-linked by short peptides. It resists the turgor pressure of the cytoplasm and prevents osmotic lysis. It is the target of beta-lactam antibiotics, such as penicillin, and of the enzyme lysozyme. A few bacteria, such as Mycoplasma, lack a wall.
• Gram stain. The Gram stain, which was devised by Hans Christian Gram in 1884, divides most bacteria into two groups that correlate with the structure of the envelope. Gram-positive bacteria have a thick peptidoglycan layer (about 20 to 80 nm) that retains the crystal violet dye and appear purple. They contain teichoic acids. Gram-negative bacteria have a thin peptidoglycan layer in the periplasm, between the cytoplasmic membrane and an outer membrane, and they stain pink with the counterstain. The outer membrane has lipopolysaccharide (LPS) in its outer leaflet, which acts as an endotoxin and reduces the permeability to many antibiotics. Mycobacteria have an unusual envelope with mycolic acids and are acid-fast.
• Capsule and S-layer. Many bacteria have an outer capsule of polysaccharide that resists phagocytosis, or a surface layer (S-layer) of protein.

Internal structures

• Nucleoid. The chromosome is usually a single circular molecule of DNA of about 0.5 to 10 million base pairs (the exceptions include linear chromosomes in Borrelia and Streptomyces, and multiple chromosomes in Vibrio). It is compacted by nucleoid-associated proteins and supercoiling in an irregular region, the nucleoid. Bacteria do not have a nucleus, but they are not unorganized. Some have protein-bound compartments (for example carboxysomes), lipid-bound organelles (such as magnetosomes in magnetotactic bacteria), and in the Planctomycetota and some other groups, internal membranes. Genes are often arranged in operons, in which several genes are transcribed together.
• Plasmids. Small, usually circular DNA molecules that replicate independently and often carry genes for antibiotic resistance, toxins, or the metabolism of unusual compounds.
• Ribosomes. Bacteria have 70S ribosomes, composed of 30S and 50S subunits. They differ from the 80S ribosomes of the eukaryotic cytoplasm, and this difference is the basis for the action of antibiotics, such as tetracyclines, aminoglycosides, and macrolides, that inhibit bacterial protein synthesis.
• Inclusions and endospores. Granules store carbon (polyhydroxybutyrate and glycogen), phosphate (polyphosphate), or sulfur. Some members of the Bacillota, such as Bacillus and Clostridium, form endospores in response to stress. These are dormant, very resistant to heat and desiccation, and can survive for long periods.

Surface appendages and motility

Many bacteria swim by rotating flagella, which are driven by the flow of protons or sodium ions across the membrane through a motor of stator and rotor proteins. Cells respond to gradients of nutrients and toxins by chemotaxis, with a biased random walk of "runs" and "tumbles". Other forms of motility include twitching by type IV pili, gliding, and the rotation of periplasmic flagella in spirochetes. Pili (fimbriae) mediate attachment to surfaces and host cells, and conjugative pili transfer DNA between cells.

Binary Fission and Exponential Growth Kinetics

Bacteria reproduce mostly by binary fission, in which a cell elongates, replicates its chromosome, and divides in two at a septum formed by FtsZ. Some bacteria reproduce by budding or by multiple fission. Growth in a batch culture goes through a lag phase, an exponential phase, a stationary phase, and a death phase. In the exponential phase, the number of cells is:

where t_d is the doubling time and μ = ln 2 / t_d is the specific growth rate. For Escherichia coli with a doubling time of 20 minutes, a single cell would produce 2²⁴ ≈ 1.7 × 10⁷ cells in 8 hours of unrestricted growth. Doubling times range from about 10 minutes in the fastest species to days or longer in species in nutrient-poor environments, and many bacteria in nature grow slowly or remain dormant. Cells in a population are not identical, and a small fraction of persister cells are able to survive antibiotic treatment without being genetically resistant.

Biofilms and Quorum Sensing

Bacteria also grow in communities. A biofilm is a community of cells that are attached to a surface and embedded in a matrix of extracellular polysaccharides, proteins, and DNA. Biofilms are more tolerant to antibiotics and to the immune system and are responsible for many chronic infections. Cells coordinate behavior by quorum sensing, in which they produce and detect signaling molecules (autoinducers) whose concentration reflects the density of the population.

Mutation Rates, Horizontal Gene Transfer, and CRISPR Defense

Bacterial mutation rates are low per base but the population sizes are very large, and the combination of mutation, selection, and horizontal gene transfer allows rapid evolution. In E. coli, the mutation rate is about 2 × 10⁻¹⁰ per base pair per generation. Because bacteria are haploid, a mutation is exposed to selection immediately. Bacteria do not reproduce sexually, but they exchange genes in three main ways:

• Transformation is the uptake of free DNA from the environment by competent cells.
• Transduction is the transfer of DNA by a bacteriophage.
• Conjugation is the transfer of DNA, often on a plasmid, from a donor to a recipient through a pilus and a type IV secretion system.

These processes spread genes for antibiotic resistance, virulence, and metabolism among species. The genome of a species can be divided into a core genome, which is shared by all strains, and an accessory genome, and the whole set of genes of a species is its pan-genome. Bacteria defend against phages with restriction-modification systems, CRISPR-Cas adaptive immunity, and many other systems.

Nutritional Classifications and Terminal Electron Acceptors

Bacteria are classified by the source of energy and of carbon. Phototrophs obtain energy from light and chemotrophs from chemical compounds. Lithotrophs use inorganic electron donors and organotrophs use organic ones. Autotrophs fix carbon dioxide and heterotrophs use organic carbon.

Electrons from the oxidation of the energy source are passed to a terminal acceptor. In aerobic respiration the acceptor is oxygen. In anaerobic respiration it can be nitrate, sulfate, iron(III), or carbon dioxide (in methanogenesis, which is done by archaea and not by bacteria). In fermentation, an organic compound serves as the acceptor. Some bacteria carry out nitrogen fixation, and others perform anammox or oxidize methane. Bacteria can be aerobes, anaerobes, or facultative anaerobes, and are classified by temperature (psychrophiles, mesophiles, thermophiles, and hyperthermophiles), by pH, and by salinity. The ability to use almost any organic and many inorganic compounds is the reason that nearly every natural compound is decomposed by some bacteria, although not every compound is, and some synthetic compounds are persistent.

Oxygenic photosynthesis evolved in cyanobacteria and, through the accumulation of oxygen in the Great Oxidation Event about 2.4 billion years ago, changed the atmosphere and the oceans. Chemolithotrophs support ecosystems at hydrothermal vents and in the deep subsurface, where energy comes from chemical compounds and not directly from sunlight, although many vent animals depend on oxygen that is made by photosynthesis.

Nitrogen, Carbon, Sulfur, and Soil Cycling

Bacteria are essential for the cycling of elements.

• Nitrogen cycle. Atmospheric nitrogen (N₂) is not usable by most organisms, because the triple bond is very stable. Only some bacteria and archaea can fix it, using the enzyme nitrogenase, which reduces N₂ to ammonia. Nitrogen fixers include free-living bacteria, cyanobacteria (Trichodesmium, and heterocystous forms), and symbionts such as Rhizobium in legume root nodules. Nitrification (ammonia to nitrite to nitrate) is done by bacteria and archaea. Denitrification returns N₂ to the atmosphere, and anammox does so under anoxic conditions. Humans now fix more nitrogen industrially, with the Haber-Bosch process, than occurs naturally on land.
• Carbon cycle. Photosynthetic bacteria, in particular Prochlorococcus and Synechococcus, account for a large part of primary production in the oceans. Heterotrophic bacteria decompose organic matter and release CO₂, and in the ocean they process a large part of the organic carbon in the microbial loop. Anaerobic bacteria and archaea produce methane in wetlands, sediments, and the guts of animals, and methanotrophic bacteria consume it.
• Sulfur and iron cycles. Sulfate-reducing bacteria and sulfur oxidizers control the cycling of sulfur, and iron-oxidizing and iron-reducing bacteria influence the mobility of iron and of trace metals.
• Soil. Bacteria help to form soil structure, decompose organic matter, and affect the availability of nutrients to plants. Plant growth-promoting bacteria, and mycorrhizal associations in which bacteria interact with fungi, are also important.

Symbiosis and the microbiome

Bacteria live in symbiosis with many organisms. In humans, the community of bacteria, archaea, fungi, and viruses is the human microbiome. The human body has about as many bacterial cells as human cells (a ratio of roughly 1 to 1 in recent estimates), mostly in the colon. Gut bacteria ferment dietary fiber to short-chain fatty acids, make some vitamins (such as vitamin K and some B vitamins), train the immune system, and protect against colonization by pathogens. Disturbance of the microbiota (dysbiosis), for example by antibiotics, is associated with diseases such as Clostridioides difficile infection. The statement that animals rely "entirely" on the microbiome is too strong. Many animals, including germ-free laboratory animals that can be raised under sterile conditions, can survive without it, although their physiology and immunity are abnormal. Insects and other animals have obligate bacterial symbionts that provide nutrients, such as Buchnera in aphids, and Wolbachia is a widespread reproductive parasite and mutualist of arthropods. Mitochondria and plastids evolved from bacterial endosymbionts.

Virulence Factors, Antibiotics, and Antimicrobial Resistance

A small fraction of bacterial species cause disease in humans, animals, and plants. Pathogens use virulence factors that include adhesins, toxins, capsules, secretion systems (such as the type III secretion system that injects proteins into host cells), and means of evading the immune system. Examples of diseases include tuberculosis (Mycobacterium tuberculosis), cholera (Vibrio cholerae), plague (Yersinia pestis), pneumonia (Streptococcus pneumoniae), and typhoid fever (Salmonella Typhi). The germ theory of disease was established by Louis Pasteur and Robert Koch in the nineteenth century, and Koch's postulates set criteria for linking a microbe to a disease. Infections are treated with antibiotics, which were introduced widely in the 1940s. Antibiotics act on bacterial targets such as the cell wall, ribosomes, DNA gyrase, and folate synthesis. Antimicrobial resistance is a major global health problem, and bacterial infections that were resistant to drugs were estimated to be directly responsible for about 1.1 million deaths worldwide in 2021. Prevention includes sanitation, vaccination, and the sensible use of antibiotics.

Recombinant DNA, Genome Editing, and Biomanufacturing

Because bacteria grow rapidly, are easy to manipulate genetically, and have diverse metabolism, they are used extensively.

• Recombinant DNA technology. Plasmids are used as vectors to clone genes. Bacteria, particularly E. coli, produce therapeutic proteins such as human insulin (the first recombinant drug, approved in 1982) and growth hormone, and industrial enzymes. Many proteins are produced in other hosts when they need post-translational modification that bacteria cannot do.
• Genome editing and tools. The adaptive immune system CRISPR-Cas of bacteria and archaea was developed into the CRISPR-Cas9 genome editing tool, and restriction enzymes and thermostable DNA polymerases (such as Taq, from Thermus aquaticus) are bacterial products that are essential in molecular biology.
• Food and fermentation. Lactic acid bacteria are used for yogurt, cheese, and fermented vegetables, acetic acid bacteria for vinegar, and other bacteria in the production of foods and in probiotics.
• Agriculture. Biofertilizers (such as rhizobia), and Bacillus thuringiensis (Bt), whose toxins are used as bioinsecticides and in transgenic crops.
• Bioremediation and industry. Bacteria degrade oil, solvents, and other pollutants and can transform or immobilize metals, and they are used in the treatment of wastewater and in the production of chemicals, biofuels, and antibiotics (many antibiotics come from Streptomyces).
• Synthetic biology. Bacteria are engineered to produce chemicals, to act as sensors, or to carry out new functions.

From Microscopy and Koch's Postulates to Molecular Phylogenetics

Antonie van Leeuwenhoek first saw bacteria with a microscope in the 1670s. Ferdinand Cohn classified them in the 1870s. Pasteur disproved spontaneous generation and showed the role of microbes in fermentation, and Koch developed pure culture methods, including the use of solid media, and identified the causes of anthrax, tuberculosis, and cholera. Martinus Beijerinck and Sergei Winogradsky studied the roles of bacteria in the environment, including nitrogen fixation and chemolithotrophy. Carl Woese and George Fox used 16S rRNA sequences in 1977 to show that the archaea are a separate lineage, which led to the three-domain system.

Why do Gram-negative bacteria exhibit higher intrinsic resistance to antibiotics than Gram-positive bacteria?

Gram-negative bacteria possess a bipartite cell envelope featuring an asymmetric outer membrane composed of phospholipids in the inner leaflet and lipopolysaccharide (LPS) in the outer leaflet, surrounding a thin periplasmic peptidoglycan layer. This outer membrane acts as a selective permeability barrier that physically excludes large hydrophilic antibiotics (such as vancomycin) and hydrophobic macrolides, while hydrophilic molecules must traverse narrow beta-barrel porin channels alongside active RND-family multidrug efflux pumps.

How does the bacterial flagellar motor generate rotational torque?

The bacterial flagellum is a rotary nanomachine powered by an electrochemical ion gradient (proton motive force or sodium motive force) across the cytoplasmic membrane rather than direct ATP hydrolysis. As protons (H⁺) flow down their electrochemical gradient through membrane-embedded MotA/MotB stator complexes, electrostatic interactions between the stator subunits and the FliG proteins of the rotor C-ring induce conformational shifts that drive rotation at speeds up to 300–1,000 Hz.

How do bacterial persister cells survive bactericidal antibiotic treatments without genetic resistance?

Bacterial persister cells are a small, phenotypically dormant subpopulation (typically 10⁻⁶ to 10⁻⁴ of a clonal population) that transiently arrest growth and downregulate core metabolic processes via toxin-antitoxin modules and alarmone (ppGpp) signaling. Because bactericidal antibiotics (such as beta-lactams, fluoroquinolones, and aminoglycosides) require active peptidoglycan synthesis, DNA replication, or translation to corrupt cellular targets, metabolically dormant persisters tolerate lethal concentrations and resume growth once antibiotic pressure subsides.

• Archaea
• Microbiology
• Prokaryote
• Human microbiome
• Antibiotic resistance
• Bacteriophage
• Horizontal gene transfer