A glossary of words associated with Food Microbiology.

Acid dyes: Dyes that are anionic or have negatively charged groups such as carboxyls. Acid fast: Bacteria like the mycobacteria that cannot be easily decolorized with acid alcohol after being stained with dyes such as basic fuchsin. 

Acid-fast staining: Staining procedure that differentiates between bacteria based on their ability to retain a dye when washed with an acid alcohol solution.


Acidophile: Microorganism that has its growth optimum between about pH 0 and 5.5.


Actinobacteria: Group of gram-positive bacteria containing the actinomycetes and their high G 1 C relatives.

Actinomycete: Aerobic, gram-positive bacterium that forms branching filaments (hyphae) and asexual spores.

Aerobe: The descriptive name given to a microorganism that can grow in conditions where oxygen is present. Such organisms are capable of growing in normal air, equivalent to 20% oxygen, or in aerated liquids containing dissolved oxygen. Many aerobes are equally able to grow in the absence of oxygen. These are termed facultative anaerobes.

Allele: One of two or more alternative nucleotide sequences at a single gene locus which occurs on either of two homologous chromosomes in a diploid organism.

Anaerobe: A microorganism that is capable of growing in the complete absence of oxygen. Some of these organisms may also be able to grow in oxygenated conditions (facultative aerobes), whereas others cannot tolerate oxygen and are killed when exposed to air. Such organisms are termed obligate anaerobes.

Antibody: An inducible immunoglobulin protein produced by B lymphocytes of the immune system, in humans and other higher animals, which recognizes and binds to a specific antigen molecule of a foreign substance introduced into the organism. When antibodies bind to corresponding antigens they set in motion a process to eliminate the antigens.

Antigen: Any foreign substance, such as virus, bacterium, or protein, which after introduction into an organism (humans and higher animals), elicits an immune response by stimulating the production of specific antibodies; or any large molecule which binds specifically to an antibody.

Antimicrobial: A chemical agent that kills microorganisms or inhibits their growth.

Apoptosis: Programmed cell death, the body's normal method of ending the lifecycle of cells through the cellular self-destruction. When either heritable or somatic cell mutations cause malfunctions to occur in the apoptotic pathway, uncontrolled cell growth may proceed unchecked and cancer may result.

Bacterial growth: Can exhibit at least four different phases: lag phase, growth phase, stationary phase and death phase.

Bacterial strain: Population of bacterial cells all descended from a single pure isolate.

Base pair (bp): Two complementary nitrogenous bases in a DNA molecule, such as the nucleotide coupling of adenine with thymine (A:T) and guanine with cytosine (G:C); also, a unit of measurement for DNA sequences.

Biofilm: Adherent layer of bacteria and/or other microorganisms on a solid surface bound together in a bacterially-derived polysaccharide matrix that is protective for the organisms; generally occuring at a liquid/solid interface and often developing into a complex ecological community (e.g., dental plaque bound tother by dextrans).

Bleaching: The loss of fluorescence usually due to photochemical reactions.

cDNA (complementary or copy DNA): DNA copies synthesized from a messenger RNA template using the enzyme reverse transcriptase; the single-stranded copy is often used as a probe to identify complementary sequences in DNA fragments or genes of interest.

Chromosome: A single DNA molecule that is the self-replicating genetic structure within the cell which carries the linear nucleotide sequence of genes. In humans (or eukaryotes), the DNA is supercoiled, compacted, and complexed with accessory proteins, and organized into a number of such structures. Normal human cells contain 46 chromosomes (except the germ cells, egg and sperm): 22 homologous pairs of autosomes and the sex-determining X and Y chromosomes (XX for females and XY for males). Prokaryotes carry their entire genome on one circular chromosome of DNA.

Coccus: (singular): Spherical-shaped cell; cocci (plural).


Coliform bacteria (coliforms): Any fermentative (specifically lactose-fermenting) Gram-negative anaerobic enteric bacilli (E. coli-like).


Commensal: Organisms existing in or on an animal or human without causing disease.

Conjugation (or bio-conjugation): The chemical joining of a biomolecule to another.

Death phase: The death phase occurs when cells are being inactivated or killed because conditions no longer support growth or survival. Some environmental factors such as temperature can cause acute inactivation. Others may cause mild inactivation as with growth in the presence of organic acids.

DNA (deoxyribonucleic acid): The nucleic acid molecule consisting of deoxyribonucleotide building blocks that encode genetic information. The genome of most organisms is contained in a double-stranded, double-helical form held together with chemical bonds between each strand of complementary nucleotide base pairs.

DNA probe: A single-stranded piece of DNA that binds specifically to a complementary DNA sequence; the probe is labeled (e.g., with a fluorescent or radioactive tag) in order to detect its incorporation through hybridization with DNA in a sample.

Dot blot: A method for detecting proteins by the specific binding of an antibody or binding molecule to a sample spot on nitrocellulose paper. The bound sample is visualized using an enzymatic or fluorimetric reporter conjugated to the probe.

Doubling time: The time taken for a population to increase in number by a factor of two.

Enteric (entero-): Relating to the intestine.

Enterotoxin: Proteins produced by bacteria that are either ingested as pre-formed toxins or are produced by a pathogen that has colonised the gastro-intestinal tract. Usually the toxin has specific targets and either disrupts cell function or kills the cell.

Eukaryote: (meaning "true nucleus") An organism which possesses a nucleus with a double layer of membrane and other membrane-bound organelles; includes such unicellular or multicellular members as all members of the protist, fungi, plant, and animal kingdoms.

Exons: The segment of a gene present in mature mRNA transcripts that specify the amino acid sequence of a polypeptide during translation; exons of a gene are linked together by mRNA splicing.

Exotoxin: Potent toxic substance formed and released extracellularly by species of certain bacteria.

Exponential phase: The period in which the cells of a defined bacterial population are growing and dividing continuously.

Extracellular: Produced, then excreted outside the organism.

Facultative: Ability to adapt and live under various conditions.

Facultative anaerobe: Anaerobe that can survive with or without oxygen.


Family: Taxonomic level below order and above genus.


Fastidious: Complex nutritional or cultural requirements, making isolation and culture of a fastidious organism more difficult.


Fermentation: Enzymatic breakdown (catabolism) of carbohydrates generally in the absence of oxygen.


Fimbriae: Short, hair-like projections or appendages (organelles) on the outer surface of certain bacteria composed of protein subunits (pilin) extending outward from the surface that act as a virulence factor by promoting adherence; formerly known as pili; fimbria (singular). 

Flagellum: whip-like bacterial locomotory (provide motility) organelles anchored in the cell membranes that are composed of helically-coiled protein subunits (flagellin); flagella (plural).

FISH (Fluorescence In Situ Hybridization): A technique that employs fluorescent molecular tags to detect probes hybridized to chromosomes or chromatin; useful for genetic mapping and detecting chromosomal abnormalities.

Flow cytometer: Analytical instrument for flow cytometry.

Flow cytometry: Automated analysis of cells or subcellular components by detection of the fluorescence or light-scatter of sample fractions passing in narrow-stream droplets through a laser beam.

Fluorophores: Molecules that produce a fluorescent emission when irradiated with light at a suitable excitation wavelength.

Fomite: Inanimate object capable of transmitting infectious organisms to a host, e.g., soiled clothes,  tissues and handkerchiefs, food processing equipment, dishrags, etc.

Gene amplification: The presence of multiple copies of a gene or segment of DNA; a mechanism by which proto-oncogenes are activated in malignant cells. A tumor cell amplifies, or copies, DNA segments as a result of cell signals or the effects of environmental insults.

Gene expression: The process by which the encoded information of the genome is converted into cellular components. The DNA-coding sequences of expressed genes include those that are transcribed into mRNA and then translated into proteins, and RNA that is transcribed from DNA, yet not translated into protein (i.e., transfer and ribosomal RNAs).

Gene mapping: A linear map determining the relative position of genes along a chromosome or plasmid. Distances are established by linkage analysis and measured in linkage units.

Gene: A nucleotide sequence of DNA that codes for a protein, or functional or structural RNA molecule; a locus on a chromosome. The element that determines a trait in an organism.

Genetic mutation: An alteration in the nucleotide sequence of a DNA molecule; often from one allelic form of a gene to another allele alternative.

Genome: The total amount of genetic material in a cell; in eukaryotes the haploid set of chromosomes of an organism. The chromosome set is species-specific for the number genes and linkage groups carried in genomic DNA.

Genomics: The study of genes and their biochemical function in an organism.  

Genotype: The genetic constitution of an organism; or, a reference to an individual's particular allele pair at a specific gene locus in the genome.

Genotyping: Analysis of genotype.

Genus: Taxonomic level below Family and above Species.

Gram-negative or Gram-positive: The classification given to bacteria according to their staining properties as defined by the Gram stain procedure.

Growth curve: A graph displaying the behaviour of a bacterial population over time.

Growth phase: During the growth phase, cells grow exponentially and at a constant rate. The maximum slope of the curve is the specific growth rate of the organism. Cell growth is dependent upon the current environment (nutrients, temperature, pH, etc.), but is not dependent upon the previous physiological state. In the field of predictive microbiology, growth rate is commonly expressed as the change in cell number per time interval.

Growth rate: This is an expression of population increase in numbers expressed as log10 cfu/hour.

Haploid: A cell or individual with a genetic complement containing one copy of each nuclear chromosome. (Diploid refers to the condition when a eukaryotic cell possesses two sets of chromosomes.)

Humectant: A solute that binds free water in a food, reducing the amount of water available to the microorganisms.

Hybridize (or hybridization): The process where the hydrogen bonding of complementary DNA and/or RNA sequences forms a duplex molecule.

Immunoassays: A technique that detects and measures a specific antigen or biological substance by employing antibodies (e.g., dot blot, western blot, and ELISA).

in situ hybridization (ISH): Use of a nucleic acid probe to detect and identify specific complementary sequences of DNA in chromosomes or RNA in bacteria, eukaryotic cells, and tissue.

in vitro: ("in glass") Refers to the recreation of biological processes in an artificial environment such as a test tube.

in vivo: ("in living") Refers to biological processes within a living organism or cell.

Inoculum: A medium containing microorganisms to be introduced into fresh media or food source in an experiment.

Intron: A nucleotide sequence intervening between exons (coding regions) that is excised from a gene transcript during RNA processing.

Kinetics: The properties of chemical agents or enzymes in the efficiency and speed of their action upon a chemical reaction.

Klebsiella: Gram-negative rods occur in human feces and clinical specimens, soil, water, grain, fruits, and vegetables. Some species are opportunistic pathogens. Kluyvera: Gram-negative rods occur in food, soil, sewage, and human clinical specimens. They are infrequently opportunistic pathogens. Kurthia: Gram-positive rods are widely distributed in the environment, and are common in animal feces and meat products.

Lag phase: During the lag phase, cells increase in size but not in number because they are adapting to a new environment, and, synthesis and repair are taking place. The length of the lag phase depends on the current environment as well as the previous physiological state of the cells. Cells that are from a very different environment or are damaged from their previous physiological state may require more time to adjust. In some foods a lag phase does not exist which results in cells that are ready for immediate growth. 

Lag time: The initial period in a bacterial population life when cells are adjusting to a new environment before commencing growth.

Legionella: Fastidious gram-negative rod is isolated from surface water, mud, and thermally polluted lakes and streams. There is no known soil or animal source. It is pathogenic for humans, causing pneumonia (Legionnaires’ disease) or a mild, febrile disease (Pontiac fever).

Ligand: The molecule which binds to a protein molecule (e.g., receptor). As a ligand binds through the interaction of many weak, noncovalent bonds formed to the binding site of a protein, the tight binding of a ligand depends upon a precise fit to the surface-exposed amino acid residues on the protein.

Listeria: Gram-positive rod widely distributed in the environment. Some species are pathogenic for humans and animals (e.g. L. monocytogenes).

Locus: (plural, loci) The specific site of a gene on a genetic map or chromosome.

Marker (genetic marker): Any genetically derived phenotypic difference used in the analysis of inheritance patterns or to differentiate between types of cells. An observable site on a chromosome that is heritable and can be either a genetically-expressed region or noncoding segment of DNA (intron).

Maximum population density: Point at which the maximum number of bacterial cells can exist in an environment.

Meiosis: Process that allows one diploid celll to divide in a special way to generate haploid cells in eukaryotes.

Mesophile: Microorganism able to grow well between 20°C and 45°C, having an optima of 30°C to 40°C. Many can sustain growth at below 10°C albeit very slow growth.

Metaphase: Stage in mitosis or meiosis during which the chromosomes are aligned along the equatorial plane of the cell.

Methylobacterium: Mostly isolated from water and leaf surface microflora, and are facultative methylotrophs, that is capable of growing on one-carbon compounds such as formate, formaldehyde, and methanol as the sole source of carbon and energy, as well as on a wide range of multicarbon substrates.

Microaerophilllic environment: Environment with reduced oxygen concentrations, often below 5%. Carbon dioxide levels may approach 10%.

Microbacterium: Gram-positive rod is found in dairy products, sewage, and insects.

Microbial load: Total number of living microorganisms in a given volume or mass of microbiological media or food.

Micrococcus: Gram-positive cocci occur primarily on mammalian skin and in soil, but are commonly isolated from food products and the air.

Microorganism: A living organism too small to be seen with the naked eye.

Mitosis: Process by which a cell separates its duplicated genome into two identical halves. It is generally followed immediately by cytokinesis which divides the cytoplasm and cell membrane. This results in two identical daughter cells with a roughly equal distribution of organelles and other cellular components.

Moraxella: Gram-negative rod is parasitic on the mucous membranes of humans and other warm-blooded animals.

MRNA (messenger RNA): The RNA molecule, transcribed from the DNA of a gene, which serves as a template and encodes the amino acid sequence of a protein.

Multiplexing: Method by which many parameters are tested and processed simultaneously.

Native microflora: Microorganisms that are normally found within a food source (often referred to as spoilage organisms). 

Northern blot: Technique used to separate and transfer mRNA from a gel to a filter in order to identify and locate mRNA sequences that are complementary to and hybridize with a labeled DNA probe.

Novosphingobium: Gram-negative rods were originally included with Sphingomonas (see Sphingomonas).

Nucleic acid: Molecule composed of nucleotide subunits. See DNA and RNA.

Nucleotide: Basic building block of nucleic acids that is a monomeric molecule of DNA or RNA composed of: a pentose sugar (with 5-carbons such as deoxyribose in DNA, ribose in RNA), an organic nitrogenous base, and a phosophate group. DNA consists of the four bases: adenine (A), guanine (G), cytosine (C), and thymine (T); likewise for RNA, except for the substitution of uracil (U) for T.

Oligonucleotide: ("oligo" means few) A short length of DNA nucleotides, often used as primers for DNA synthesis or probes for arrays and ISH/FISH; usually referred to as "oligo(s)."

Opportunistic: Microorganism that will only cause disease in a patient with a poor or somehow weakened immune system. 

Organelle: Microscopic bodies in the cytoplasm of cells that have distinctive functions (e.g., nucleus, mitochondria, endoplasmic reticulum, etc.).

Pasteurisation: Mild heat treatment process given to foods. The process is designed to eradicate potential vegetative pathogens (not bacterial spores) and reduce other microorganism numbers in an effort to decrease the rate of spoilage.

Pantoea: Gram-negative rods are isolated from plant surfaces, seeds, soil, and water, as well as from animals and human clinical specimens. They are opportunistic human pathogens.

Pathogen: Microorganism associated with disease in man.

pH: Measure of the acidity or alkalinity of a solution, defined as the - log10 of the hydrogen ion concentration.

Phenotype: Observable manifestation of a genetic trait, resulting from a specific genotype and its interaction with the environment.

Physical map: Map indicating physical locations on a DNA molecule such as restriction enzyme recognition sites, RFLPs, and genes; measured in base pairs (bp).

Predictive microbiology: Area of food microbiology that uses mathematical models to define growth kinetics of microorganisms in food.

Primary model: Model that describes changes in microbial numbers in response to time.

Primer: Short segment of DNA or RNA that anneals to a single strand of DNA in order to initiate template-directed synthesis and extend a new DNA strand by the enzymatic action of DNA polymerase to produce a duplex-stranded molecule.

Probe: Single-stranded DNA or RNA molecule of specific base sequence, either radioactively or fluorescently labeled, that is used to identify the complementary nucleotide sequence by hybridization to the DNA fragment or gene of interest.

Protein translocation: Spatial movement of protein within a cell (e.g., from the cytoplasm to nucleus, or into organelles).

Protein: High-molecular weight biological molecule composed of a polymer of amino acids linked via peptide bonds; may consist of more than one polypeptide molecule that is folded into complex shapes such as helices or sheet-like structures. Proteins are encoded by the specific sequence of DNA nucleotides in a gene and give rise to the structure, function, and regulation of cells, tissues, and organs within the body. Protein classes include enzymes, antibodies, receptors, hormones, and growth factors.

Proteome: Entire protein make-up of a particular organism.

Proteomics: Study of proteins and their biochemical function in an organism.

Providencia: Gram-negative rods are isolated from human clinical specimens and from penguins. 

Pseudomonas: Gram-negative rod is widely distributed in nature. Some species are pathogenic for humans, animals, or plants (e.g. P. aeruginosa). 

Psychrobacter: Gram-negative rod is associated with fish, processed meat and poultry products. Some strains have been isolated from pathological specimens from humans and animals.

Psychrotroph: Microorganism able to grow well between 0°C and 7°C, having an optima of 20°C to 30°C.

Rahnella: Gram-negative rods occur in freshwater. They are occasionally isolated from human clinical specimens, but are not considered clinically significant.  

Ralstonia: see Pseudomonas. 

Raoultella: see Klebsiella.

Rathayibacter: Some of these species are phytopathogens of terrestial plants. Their main habitats are their respective plant hosts.

Receptor: Surface-exposed membrane protein on a cell which binds to a specific ligand molecule with high affinity, in order to transmit an extracellular signal and trigger intracellular biochemical events within the target cell.

Reporter: Gene which codes for an easily measured protein product and is fused downstream of the gene of interest in order to assess the activity in the region upstream of the reporter gene. Colorimetric and fluorimetric reporters also can be conjugated to probes to monitor biological events.

Rhodococcus: Aerobic, Gram-positive actinomycetes. These widely-occurring organisms are of considerable environmental and biotechnological importance due to their broad metabolic diversity and array of unique enzymatic capabilities, plus their capacity to degrade hydro-carbons. They are able to survive for a long time in soil. They are the most efficient in oil degradation and, relatively speaking, the most abundant in soils and marine environments.

Rhizobium: Group of small, rod-shaped, gram-negative bacteria, which are able to produce nodules on the roots, or on some cases the stems, of leguminous plants.

RNA (ribonucleic acid): DNA-like organic molecule that consists of nucleotide subunits--such as adenine, guanine, cytosine, and uracil--which contain ribose sugars linked through phosphodiester bonds. Different types of RNA function in the process of gene expression.

Saprophyte: Microorganism that normally grows on dead material.


Secondary model: Model that predicts changes in primary model parameters based on environmental conditions.


Serratia: Gram-negative rods occur in human clinical specimens, soil, water, plant surfaces, and other environmental sites, digestive tracts of rodents, and insects. Some species are opportunistic pathogens.

SNP (Single Nucleotide Polymorphism): Variations in the sequence of DNA among individuals that are present in humans with a frequency of about once in every 1000 bases, and useful in assessing the patterns of inheritance in genetic linkage studies.

Somatic cell mutation: Mutation in a cell that is acquired during the lifetime of an organism and which cannot be genetically inherited by offspring.

Somatic cell: Any cell in the body except the germ-line cells (sperm or egg cells).

Southern blot: Procedure which transfers elecrophoretically separated DNA fragments on an agarose gel to nitrocellulose filters for detection by hybridization with a labeled probe complementary to the sequence of interest; the position on the filter of the probe, when exposed to x-ray film, appears as a band on an autoradiogram.

Sphingobacterium: Gram-negative rod found in soil, on plants, foodstuffs, and in water sources. Sphingobium: Gram negative rods were originally included with Sphingomonas (see Sphingomonas).

Sphingomonas: Relatively new genus derived from Pseudomonas paucimobilis. These organisms are widely distributed, including having been found in water. Only Sphingomonas paucimobilis is considered clinically significant, and has been isolated from a variety of clinical specimens

Spoilage organisms: Microorganisms naturally found within a food source that cause food spoilage.

Staphylococcus: This gram-positive coccus is mainly associated with the skin and mucous membranes of warm-blooded vertebrates, but they are often isolated from food products, dust and water. Some species are opportunistic pathogens of humans and animals, or produce extracellular toxins.

Stationary phase: The stationary phase occurs at the maximum population density, the point at which the maximum number of bacterial cells can exist in an environment. This typically represents the carrying capacity of the environment. However, environmental factors such as pH, preservatives, antimicrobials, native microflora and atmospheric composition as well as depletion of growth-limiting nutrients can affect the maximum population density.

Stenotrophomonas: see Pseudomonas.

Sub-lethal injury: This is cellular damage which results in disruption of metabolic processes which, under ideal conditions, is repairable. Such damage must be repaired before normal growth can recommence.

Tertiary model: Computer software routines that turn the primary and secondary models into "user-friendly" programs.

Tsukamurella: Gram-positive rods are isolated from soil, human sputum, and parts of bed bugs. Some strains can be pathogenic.

Toxins: Compounds produced by a microorganism that are poisonous to other organisms.

Vegetative cell: The vegetative cell state is the form in which an organism is able to grow and divide continuously, given favourable conditions. Unlike endospores, vegetative cells are relatively poor at surviving environmental stresses such as high temperature and drying.

Water activity (aW): Water activity is a measure of the amount of free unassociated water molecules in a system. It runs on a scale of 0 to 1.0, where pure water equals 1.0. This parameter can also be expressed as a percentage referred to as the relative humidity. It is influenced by dissolved solutes and insoluble food components which act to bind water, thus reducing the available free water and hence aW value.

Weeksella: Gram-negative rod is not known in the general environment. It is apparently a parasite, saprophyte, or commensal of the internal surfaces of humans or other warm-blooded animals.

Western blot: A technique which transfers proteins electrophoretically separated in a polyacrylamide gel to a nitrocellulose membrane and uses specific antibodies to bind, locate, and visualize the protein of interest.

Yersinia: Gram-negative rods occur in a broad spectrum of habitats, including humans, animals, soil, water, dairy products, and other foods. Some species are pathogenic for humans and animals; others are opportunistic pathogens, yet others are nonpathogenic. 

Xanthomonas: Most Gram-negative rods are plant pathogens, or occur in association with plants. X.maltophilia is the only exception, being an opportunistic pathogen of humans.

Zoonotic: Microorganism normally found in or on animals.

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