Bacterial Glossary
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  Bacterial Glossary

Bacterial Glossary

 
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 BACTERIAL GLOSSARY

Acidovorax

This is a gram-negative rod common in activated sludge and fresh water ditches. It is not considered clinically significant.

Acinetobacter

These gram-negative rods occur naturally in soil, water, and sewage.

Actinobacillus

These gram-negative rods are parasitic or commensal in humans, many mammals, and birds.

Actinomyces

These slender gram-positive rods occur mainly in the oral cavity and on mucous membranes of warm-blooded vertebrates. They commonly cause infections in association with other bacteria.

Aeromonas

These gram-negative rods occur in fresh water and sewage. Some species are pathogenic to frogs, fish, and humans (e.g. A. hydrophila for humans, which can cause gastrointestinal (GI) infections).

Alcaligenes

These gram-negative rods occur in water, soil and the intestinal tracts of vertebrates. They occasionally cause opportunistic infections in humans.

Aquaspirillium

This gram-negative rod usually occurs in stagnant freshwater environments.

Arthrobacter

These gram-positive rods are widely distributed in the environment, principally in soils.

Aureobacterium

These gram-positive rods are found in soil and dairy products, but are probably widely distributed in the environment.

Bacillus

Bacillus is a gram-positive rod that is found in a wide range of habitats. A few species are pathogenic to animals and humans (e.g. B. anthracis, and B.cereus, B. thuringiensis, which can cause GI infections.

Bergeyella

This is a zoonotic pathogen indigenous to dogs and cats.

Bifidobacterium

These gram-positive rods are found in the mouth and intestinal tract of warm-blooded vertebrates, in insects, and in sewage. They are usually considered nonpathogenic.

Brevibacterium

These gram-positive rods are widely distributed in dairy products and are found on human skin.

Brevundimonas (Originally named Pseudomonas)

These environmental organisms are found in water, soil, and on plants, including fruits and vegetables. They are rarely associated with human infection.

Campylobacter

 

This is a Gram negative rod that can be found in the reproductive organs, intestinal tract and oral cavity of humans and animals. Some species are pathogenic for humans.

Cardiobacterium

These gram-negative rods occur in the nasal flora of humans. They can be pathogenic to humans.

Cellulomonas

These gram-positive rods are widely distributed in soils and decaying vegetable matter.

Cellulosimicrobium

This gram-negative bacterium was first classified as Cellulomonas. It was originally isolatedfrom the hindgut contents of the Australian termite Mastotermesdarwiniensis (Froggatt). It has also been isolated from humus soils

Chromobacterium

These gram-negative rods are soil and water organisms. One species occasionally causes infections in mammals, including humans.

Chryseomonas

These gram-negative rods are not normally found in the environment but in warm-blooded animals, where they may be occasionally pathogenic.

Clavibacter

These gram-positive rods are obligate parasites of flowering plants, in which they are pathogenic.

Comamonas

This is a gram-negative rod commonly found in the environment. It constitutes a significant proportionof many terrestrial and aquatic environmental microbial communities

Corynebacterium

These gram-positive rods are primarily obligate parasites of mucous membranes or skin of mammals, but occasionally they are found in other sources. Some species are pathogenic for mammals (e.g. C. diphtheriae, which can cause diphtheria, and C. jeikeium, which can cause urinary tract infections)

Curtobacterium

These gram-positive rods occur on plants, in soil, and in oil brine. One species is a plant pathogen.

Deinobacter

This gram-positive coccus is probably widely distributed in the environment.

Escherichia coli (E. coli)

 

These are Gram negative rods that occur as normal flora in the lower part of the intestine of warm-blooded animals. E. coli strains that contain enterotoxins and/or other virulence factors including invasiveness and colonization factors cause diarrheal disease. E. coli is also a major cause of urinary tract infections and nosocomial infections including septicemia and meningitis.

Enterobacter

These gram-negative rods are widely distributed in nature, occurring in fresh water, soil, sewage, plants, vegetables, and animal and human feces. Several species are opportunistic pathogens.

 

Enterococcus

This gram-positive coccus occurs widely in the environment, particularly in the feces of vertebrates. Sometimes this organism can cause infections (e.g. E.faecalis and E. faecium, which can cause urinary tract infections and septicaemia).

Erwinia

Members of this genus (gram-negative rods) are a diverse group of organisms that primarily colonize plants, and have rarely been isolated from humans. Some of them are important pathogens of potato and other crops.

Exiguobacterium

This is a gram-positive rod found in the environment, which is not considered clinically significant.

Flavimonas

This gram-negative rod is found in the general environment, and in warm-blooded animals, where it may be occasionally pathogenic.

Flavobacterium

These gram-negative rods are widely distributed in soil and water. They are also found in raw meat, milk and other food, in the hospital environment, and in human clinical material.

Gordona

These gram-positive or gram-variable rods are isolated from soil and some sputa.

Hydrogenophaga

This is a gram-negative rod found in the environment, specifically in activated sludge and lake snow.

Janthinobacterium

This is a gram-negative rod, occurring in soil and water, common in temperate climates. It occasionally causes food spoilage.

Klebsiella

These gram-negative rods occur in human feces and clinical specimens, soil, water, grain, fruits, and vegetables. Some species are opportunistic pathogens.

Kluyvera

These gram-negative rods occur in food, soil, sewage, and human clinical specimens. They are infrequently opportunistic pathogens.

Kurthia

These gram-positive rods are widely distributed in the environment, and are common in animal feces and meat products.

Lactobacillus

 

These long Gram positive rods are widely distributed in the environment, especially in animal and vegetable food products. They normally inhabit the gastrointestinal tract of birds and mammals and the mammalian vagina. They are rarely pathogenic but are considered to be spoilage organisms in the food industry.

Legionella

This 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).

Listeria

This gram-positive rod is widely distributed in the environment. Some species are pathogenic for humans and animals (e.g. L. monocytogenes).

Methylobacterium

These are 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.

 

Microbacterium

This gram-positive rod is found in dairy products, sewage, and insects.

Micrococcus

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

Moraxella

This gram-negative rod is parasitic on the mucous membranes of humans and other warm-blooded animals.

Mycobacterium

 

This rod is not readily stained by Gram’s method, usually weakly Gram positive, grows very slowly. Widely distributed in soil and water, some species are obligate parasites and pathogens of vertebrates.

Novosphingobium

These gram negative rods were originally included with Sphingomonas (see Sphingomonas).

Pantoea

These 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.

Providencia

These gram-negative rods are isolated from human clinical specimens and from penguins.

Pseudomonas

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

Psychrobacter

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

Rahnella

These 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.

Rhodococcus

These organisms are 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

This is the common name given to a 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.

Salmonella

 

These Gram negative rods occur in humans, warm and cold blooded animals, foods and the environment. They are pathogenic for humans and many animal species. They are the causative agents of typhoid fever, enteric fevers, gastroenteritis and septicemia.

Serratia

These 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.

Shigella

 

These Gram negative rods are intestinal pathogens of humans and other primates, causing bacillary dysentery.

Sphingobacterium

This is a gram-negative rod found in soil, on plants, foodstuffs, and in water sources.

Sphingobium

These gram negative rods were originally included with Sphingomonas (see Sphingomonas).

Sphingomonas

This is a 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.

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.

Stenotrophomonas

See Pseudomonas

Streptococcus

 

The Gram positive cocci are parasites of vertebrates, mainly inhabiting the mouth and upper respiratory tract. Some species are pathogenic for humans and animals.

Tsukamurella

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

 

Weeksella

This 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.

Yersinia

These 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 of these gram-negative rods are plant pathogens, or occur in association with plants. X.maltophilia is the only exception, being an opportunistic pathogen of humans.

 

 

REFERENCES

Bergey’s Manual of Determinative Bacteriology, Ninth Edition

Bernhard Schweitzer, Ingrid Huber, Rudolf Amann, Wolfgang Ludwig, and Meinhard Simon-ß Proteobacteria Control the Consumption and Release of Amino Acids on Lake Snow Aggregates.Appl. Envir. Microbiol. 2001 67: 632-645.
Olaf Kniemeyer, Christina Probian, Ramon Rosselló-Mora, and Jens Harder Anaerobic Mineralization of Quaternary Carbon Atoms: Isolation of Denitrifying Bacteria on Dimethylmalonate. Appl. Envir. Microbiol. 1999 65: 3319-3324.
Manual of Clinical Microbiology, Sixth and Seventh Editions (ASM Press)
Mark E. Fuller, Sheryl H. Streger, Randi K. Rothmel, Brian J. Mailloux, James A. Hall, Tullis C. Onstott, James K. Fredrickson, David L. Balkwill, and Mary F. DeFlaun Development of a Vital Fluorescent Staining Method for Monitoring Bacterial Transport in Subsurface Environments. Appl. Envir. Microbiol. 2000 66: 4486-4496
G Funke, A von Graevenitz, JE Clarridge, 3rd, and KA Bernard. Clinical Microbiology of Coryneform Bacteria Clin. Microbiol. Rev. 1997 10: 125-159.
Anna O. Avrova, Lizbeth J. Hyman, Rachel L. Toth, and Ian K. Toth . Application of Amplified Fragment Length Polymorphism Fingerprinting for Taxonomy and Identification of the Soft Rot Bacteria Erwinia carotovora and Erwinia chrysanthemi. Appl. Envir. Microbiol. 2002 68: 1499-1508.

M Takeuchi, K Hamana and A Hiraishi

. Proposal of the Genus Sphingomonas sensu stricto and Three New Genera, Sphingobium, Novosphingobium and Sphingopyxis, on the Basis of Phylogenetic and Chemotaxonomic Analyses. International Journal of Systematic and Evolutionary Microbiology, Vol 51, 1405-1417, Copyright © 2001 by Society for General Microbiologyhttp://www.rhizobium.umn.edu/FAQ/whatrhizobia.htm"What are Rhizobia?"

Sorkhoh NA, Ghannoum MA, Ibrahim AS, Stretton RJ, Radwan SS. Crude oil and Hydrocarbon-Degrading Strains of Rhodococcus rhodochrous Isolated from Soil and Marine Environments in Kuwait. Environ Pollut. 1990;65(1):1-17.

Hahn MW, Lunsdorf H, Wu Q, Schauer M, Hofle MG, Boenigk J, Stadler P. Isolation of Novel Ultramicrobacteria Classified as Actinobacteria from Five Freshwater Habitats in Europe and Asia. Appl Environ Microbiol. 2003 Mar;69(3):1442-51.

Lubov V Dorofeeva, Lyudmila I Evtushenko et al. Rathayibacter caricis sp. nov and R.festucae sp. nov, Isolated from the Phyllosphere of Carex Species and the leaf gall induced by the nematode Anguina graminis on Festuca rubra L., respectively

. International journal of systematic and evolutionary microbiology (2002), 52, 1917-1923.

Sanjay, K Shukla, et al. Isolation of a Fastidious Bergeyella Species Associated with Cellulitis after a Cat Bite and a Phylogenetic Comparison with Bergeyella zoolhelcum Strains. Journal of Clinical Microbiology, Jan 2004, p 290-293.

GLOSSARY OF TERMS

Commensal – organisms existing in or on an animal or human without causing disease.

Extracellular – produced, then excreted outside the organism.

Gram-positive – bacteria that stain purple (positive) with the gram stain.

Gram-negative – bacteria that do not stain purple (pink – negative) with the gram stain.

Habitat – where an organism is found.

Indigenous – where normally found

Opportunistic – an organism that will only cause disease in a patient with a poor or somehow weakened immune system.

Pathogens – organisms that cause disease.

Saprophyte – an organism that normally grows on dead material.

Toxins – compounds produced by an organism that are poisonous to other organisms

Zoonotic – organism normally found in or on animals.

BACTERIAL GUIDELINES

Bacteria are naturally present in the environment and on and in humans and animals. They have many good uses:

  • They line the gut, where they aid digestion.
  • They remove debris on the skin.
  • They are important in many foodstuffs, such as cheeses and yogurts.
  • They aid in the maturation of meat.
  • They remove trash in the environment.

A "normal" environmental system will have an assortment of different bacterial types, none of which will be particularly predominant. In areas where there are high numbers of humans, there may be higher levels of gram-positive cocci, such as Staphylococcus and Micrococcus, in the environment. Unlike molds, higher numbers of bacteria in the air inside can be normal.

High levels of one type of bacteria, especially gram-negative rods, notably those in the Enterobacteriaceae, are considered significant:

  • Enterobacteriaceae are indicative of sewage contamination, and therefore of pathogenic organisms. Pathogenic bacteria themselves are rarely recovered, as they are rapidly outgrown by environmental bacteria, hence the development of the sewage screen to detect potential gastrointestinal pathogens.
  • When one organism has removed the natural competition, it implies more than just simple co-existence of several different types, but suggests a more aggressive role by the dominant organism.























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