Bacterial Library

USMS Bacterial Library

Bacteria are prokaryotic (no organized nucleus), single-celled (0.2-10 um) organisms.

Bacteria are divided into five basic groups based on morphology (shape): coccus, bacillus, spiral, coryneform, and filamentous. When bacteria are Gram-stained, they may be further classified as Gram-positive, Gram-negative, or Gram-variable depending on the ability of their cell walls to hold a specific type of stain. Gram-positive bacteria stain blue-purple and Gram-negative bacteria stain red.

Bacterial names are based on the binomial system: the first name is the genus, the second name is the species. When written, the genus name is capitalized and the species name is not. Both genus and species names are italicized (e.g., Escherichia coli).  A genus is a group of related species.  A species is a group of microorganisms that have similar genotypic and phenotypic characteristics.

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Acinetobacter species

Acinetobacter species are widely distributed in nature and the hospital environment and are the second most commonly isolated nonfermenters in patient specimens, with Psuedomonas aeruginosa being the first. Acinetobacter are able to survive on moist & dry surfaces, are found on fruits and vegetables, and on the healthy human skin.  These bacteria are generally nonpathogenic to healthy individuals but may cause infections in debilitated persons.  The species most commonly isolated from human specimens is A. baumannii with 19 biotypes being identified.


Acinetobacter baumannii

Acinetobacter baumannii is the species most often associated with healthcare-associated infections.  The ability of this organism to become multi-drug resistant and to survive on moist environmental surfaces has led to a heightened concern regarding healthcare-associated infections.  The gastrointestinal tract of ICU patients is an important epidemiologic reservoir for multi-resistant A. baumannii in hospital outbreaks.  American troops in Iraq and Afghanistan have suffered severe wound infections and osteomyelitis from multi-resistant A. baumannii.


Acinetobacter haemolyticus

Acinetobacter haemolyticus, Pseudomonas stutzeri, and other nonfermentative gram-negative rods are often isolated from soil and stagnant water sources such as improperly drained drip pans, humidifiers, cooling towers, sink traps, factories, and waste and sewage treatment plants.


Acinetobacter lwoffii

Acinetobacter lwoffi is a Gram-negative coccobacillus often isolated from stagnant water sources such as improperly drained drip pans, water fountains, faucets, humidifiers, cooling towers, sink traps, factories, and waste and sewage treatment plants.  It has been suggested that several Acinetobacter species including A. lwoffii are natural inhabitants of the human skin and may also be commensals in the oropharynx.  A. lwoffii rarely causes disease in humans.


Actinobacillus spp.

Actinobacillus spp. are slow growing Gram-negative bacilli.  They are considered normal flora of the human oral cavity and of animals such as cows, sheep, and pigs.



Actinomycetes are rod-shaped to branching Gram-positive bacteria that are widely distributed in terrestrial and aquatic habitats.  Most are saprophytes, but form parasitic associations with plants. Actinomycetes are common in compost piles and often occur in high concentrations in the air when compost is disturbed.  The frequent presence of actinomycetes can be regarded as a sign of moisture damage in concrete buildings.  Actinomycetes include Nocardia, Rhodococcus, Gordonia, Actinomadura, Streptomyces, and others.

Thermophilic actinomycetes which include Saccharopolyspora, Saccharomonspora, Thermoactinomyces spp. are common in composts that have been heated during fermentation. They are important causative agents of occupation-related respiratory allergies (hypersensitivity pneumonitis, commonly known as "farmers lung"), often occurring in high concentrations in air when compost is disturbed.


Aeromonas spp.

Members of the genus Aeromonas are Gram-negative facultative anaerobes that are straight rods or coccoid cells.  Aeromonads are inhabitants of aquatic ecosystems worldwide.  These include groundwater and drinking water at treatment plants, distribution systems reservoirs as well as clean or polluted lakes and rivers.  Aeromonas may also be found in marine environments but only in brackish water or water with a low saline content.

Aeromona hydrophila complex includes (A. hydrophila, A. bestiarum, and A. salmonicida). A. salmonicida is a psychrophilic strain that causes severe infections in fisheries resulting in considerable economic loss.


Alcaligenes faecalis

Alcaligenes faecalis is a nonfermentative Gram-negative rod often isolated from the environment in soil and water.



Arthrobacter species are Gram-positive rods that are environmental bacteria and are not part of normal human flora.

Bacillus spp.

Bacillus species are Gram-positive bacteria that are commonly recovered from a variety of environmental sites such as soil, air, dust, debris, and surfaces that come into contact with water (e.g., fountains, condensation pans). READ MORE.


Brevibacterium spp.

Brevibacterium spp. is a coryneform Gram-positive rod and is part of normal human flora.  It can be isolated from various foods.


Brevundimonas spp.

Brevundimonas species are aerobic straight and slender Gram-negative bacilli and were formerly classified in the genus Pseudomonas.  It is an environmental organism and infrequently causes human infections.


Burkholderia cepacia

Burkholderia cepacia complex are environmental bacteria found in water, soil, rhizospheres, and on plants, including fruits and vegetables. They have a worldwide distribution and are widely recognized as phytopathogens.  Because of their ability to survive in aqueous environments, these organisms have become particularly problematic as opportunistic nosocomial pathogens in hospitals and healthcare settings.


Members of the genera Cellulomonas are coryneform Gram-positive rods that have their habitats in the inanimate environment (soil and sludge). READ MORE.



The natural habitat of Chryseobacterium spp. is soil, plants, foodstuffs, and water sources, including those in hospitals.  C. indologenes is the most frequent  human isolate, although it rarely has clinical significance.  Chryseobacterium spp. and Sphingomonas paucimobilis are Gram-negative environmental organisms able to survive in chlorinated tap water.



The cells of Comamonas species are pleomorphic and may appear as long, paired, curved rods or filaments and are non-lactose fermenting.  Their habitats include soil and water environments.


Citrobacter freundii

Citrobacter freundii, Serratia rubidaea, Pantoea agglomerans ,and Enterobacter cloacae are Gram-negative bacilli that are widely distributed on plants and in soil, water, and the intestines of humans and animals.



Curtobacterium is a irregularly shaped nonsporing Gram-positive rod that occurs on plants, in soil, and in oil brine.  There have been 6 species identified with Curtobacterium flaccumfaciens being a plant pathogen causing vascular wilt of bean, vascular wilt and leaf spot of red beets, vascular disease and leaf and bulb spot of tulips, and stem canker and leaf spot of poinsettia. Curtobacterium albidum is ivory in color while the other 5 species are pigmented with yellow, orange, or pink colonial morphology.

Elizabethkingia meningoseptica

E. meningoseptica is a nonfermentative Gram-negative rod that can be isolated from soil, plants, foodstuffs, and water sources, including those in hospitals.


Pantoea agglomerans (Enterobacter)

Pantoea agglomerans (Enterobacter)  is widely distributed on plants and in soil, water, and the intestines of humans and animals. This very complex group of bacteria belongs to the family Enterobacteriaceae and it has been proposed that they be called the Pantoea agglomerans complex.



The Enterobacteriaceae family includes common organisms such as Citrobacter spp., Escherichia coli, Enterobacter cloacae, Klebsiella pneumoniae, Proteus spp., Providencia spp., and other glucose-fermenting Gram-negative rods.  These microorganisms inhabit a wide variety of niches that include the human gastrointestinal tract, the gastrointestinal tract of other animals, and various environmental sites.  This group of bacteria also includes several human enteric pathogens such as Salmonella, Shigella, Yersinia, and Shiga toxin-producing strains of E. coli  (e.g. 0157:H7).


Enterococcus spp.

Enterococcus species are found in soil, food, water, and as normal flora of animals, birds, and man.  Several species are normal flora of the human gastrointestinal tract (principally Enterococcus faecalis) and the female genitourinary tract.


Escherichia coli

Escherichia coli is considered a normal bowel inhabitant of humans and other animals.  E. coli is the species usually isolated from human specimens, however, other species of Escherichia can be found in the environment as well as the gastro-intestinal tract of man and animals. E. hermannii and E. vulneris are most often detected in human wound infections but have also been isolated from other body sites.  E. fergusonii is most often isolated from human feces.  E. blattae,which is a commensal organism of cockroaches, is not recovered from human specimens. READ MORE.

Certain strains of E. coli may cause extraintestinal and intestinal infections in immuno-compromised as well as healthy persons.  Urinary tract infections, bacteremia, meningitis, and diarrheal disease are the most frequent clinical syndromes caused by E. coli.  There are at least four categories of recognized toxin-producing E. coli that cause diarrheal disease.  Shiga toxin-producing E. coli (STEC ), also referred to as enterohemorrhagic E. coli (EHEC), enterotoxigenic E. coli (ETEC), enteropathogenic E. coli (EPEC), and enteroinvasive E. coli (EIEC).

E. coli  0157:H7 strains are capable of causing hemorrhagic colitis and hemolytic uremic syndrome (HUS) and are the most frequently identified diarrheal E. coli serotypes in North America and Europe.  Each year an estimated 70,000 cases of illness and 60 deaths are caused by 0157 STEC in the United States.  Vehicles of transmission include beef (most common), raw milk, sausage, unchlorinated municipal water, leafy vegetables, and apple cider.

Gram-positive bacteria - (cocci and bacilli)

These bacteria are widespread in nature and are commonly found on the skin of humans and mammals.  Examples of Gram-positive cocci are Micrococcus and Staphylococcus species.  Examples of Gram-positive bacilli are Corynebacterium and Bacillus species.


Gram-negative diplococci

Gram-negative diplococci are often from the genera Neisseria or Moraxella.  These bacteria can be normal human flora of the upper respiratory tract.


Hyphomicrobium is from a group of diverse bacteria noted for their unusual cell shapes, appendages, and life cycles.  Their habitat is soil and fresh water, and carbon dioxide is required for growth.

Klebsiella oxytoca

Klebsiella oxytoca is widely distributed on plants, in the soil, water, and is normal flora within the intestines of humans and animals.


Kocuria rosea

Kocuria rosea and Micrococcus spp. are Gram-positive bacteria widespread in nature and commonly found along with coagulase-negative Staphylococcus spp. on the skin of humans and mammals. READ MORE.

Leclercia adecarboxylata

Leclercia adecarboxylata has been recovered from a variety of foods, water, and animals (snails and slugs) and are most likely ubiquitous in the environment.


Leifsonia aquatica

Leifsonia aquatica (formerly Corynebacterium aquaticum) can be recovered from fresh water.


Methylobacterium species are pink-pigmented bacteria that occur mostly on vegetation but may also be found in the hospital environment. Methylobacterium species have been reported to cause infections, especially in immunocompromised patients.  Tap water has been implicated as a possible agent of transmission in hospital environments. Methylobacterium mesophilicum is not part of normal human flora and does not generally pose a threat to human health.



Microbacterium species are environmental Gram-positive rods.


Micrococcus spp.

Micrococcus spp. are Gram-positive cocci widespread in nature and are commonly found along with Corynebacterium spp. on the skin of humans and mammals.


Miscellaneous Gram-Negative Bacteria

Burkholderia, Stenotrophomonas, Ralstonia, Cupriavidus, Pandoraea, Brevundimonas, Comamonas, Delftia, and Acidovorax spp. are environmental microorganisms found in water, soil, rhizospheres, and in and on plants, including fruits and vegetables.  They have worldwide distribution.  Members of these genera are widely recognized as phytopathogens.  Because of their ability to survive in aqueous environments, these organisms have become particularly problematic as opportunistic nosocomial pathogens in hospitals and healthcare settings.



Moraxella species are Gram-negative coccobacilli which are normal human flora of mucous membranes (nose, throat, respiratory tract) and skin.

Neisseria weaveri

Neisseria weaveri are either Gram-negative coccobacilli or short to medium-sized rods which are common in the oral flora of dogs.


Nonfermentative gram-negative rods

This large and diverse group of microorganisms includes Acinetobacter, Achromobacter, Alcaligenes, Chryseobacterium, Methylobacterium, Moraxella, Sphingobacterium, and other glucose nonfermenting Gram-negative rods.  These bacteria are widely distributed in nature and in the hospital environment.  Most species are generally nonpathogenic to healthy individuals but may cause infections in the debilited patient.  Some genera (e.g. Pseudomonas and Acinetobacter) are able to survive on moist and dry surfaces, and may be present in foodstuffs, and on the healthy human skin.

Non-fermenting Gram-negative rods are often isolated from stagnant water sources such as improperly drained drip pans, humidifiers, cooling towers, sink traps, factories, and waste and sewage treatment plants.

Ochrobactrum anthropi

Ochrobactrum anthropi is a nonfermentative Gram-negative rod that has been isolated from various environmental and human sources, predominantly from patients with catheter-related bacteremias and rarely with other infections.


Pantoea spp. (formerly Enterobacter) belongs to the Enterobacteriaceae group of fermentative Gram-negative rods and is widely distributed on plants and in soil.


Pseudomonas spp.

Pseudomonas makes up a large and complex group of aerobic, non-spore-forming Gram-negative rods and includes species with both clinical and environmental implications.  Most Pseudomonasspecies are able to reside in a wide variety of environmental niches, provided that moisture is available. The organisms can grow between 4 - 36° C and utilize a variety of nutrients.  Several species can be found in soil, water, plants, and hospital sources such as sinks and floors.  Pseudomonas species other than P. aeruginosa infrequently cause infection.  Because of their low virulence, infections due to these species are often iatrogenic and are associated with the administration of contaminated solutions, medicines, and blood products, or the presence of indwelling catheters.


Pseudomonas aeruginosa

Pseudomonas aeruginosa is a hydrophilic nonfermentative Gram-negative rod and can be readily isolated from moist environments, such as sink drains, fresh vegetables, river water, and even antiseptic solutions.  It also survives well in domestic environments (e.g., swimming pools, water slides, hot tubs, whirlpools, contact lens solution, sponges), and hospital environments (e.g., sinks, showers, respiratory equipment). P . aeruginosa rarely colonizes healthy humans, but immuno-compromised patients are at risk of gastrointestinal colonization after receiving frequent courses of antibiotic therapy.  It is from this reservoir of colonization that the patient is at risk for P. aeruginosa sepsis.

P. aeruginosa is the predominant respiratory tract pathogen in patients with cystic fibrosis.  Superficial infections of the ear canal by P. aeruginosa may occur in those that participate in aquatic sports.  This condition is aptly called "swimmer's ear".  Hot tub users are at risk of P. aeruginosa folliculitis, a self-limiting condition for normal immune hosts that resolves rapidly.  Users of contact lenses are at risk of conjunctivitis with minor trauma to the cornea, especially if hygiene is poor or lenses are worn for extended periods of time.


Pseudomonas alcaligenes

Pseudomonas alcaligenes and Burkholderia cepacia are gram-negative bacteria that are inhabitants of the environment.  They are commonly found in plants, soil, and water.  They are not part of normal human flora.


Pseudomonas fluorescens

Pseudomonas fluorescens is a gram-negative bacterium with worldwide distribution with a predilection for moist environments.  The bacteria can be found in water, soil and on plants, including fruits and vegetables.


Pseudomonas luteola

Pseudomonas luteola is a gram-negative bacillus that is found in moist environments.  It is not part of normal human flora.


Pseudomonas oryzihabitans

Pseudomonas oryzihabitans is an environmental gram-negative bacillus that is often recovered in moist hospital environments (e.g., respiratory therapy equipment).  It is not part of normal human flora.


Pseudomonas putida

Pseudomonas putida is commonly found in soil, water, plants, and hospital sources as sinks and floors.


Pseudomonas stutzeri

Pseudomonas stutzeri is considered an environmental microorganism and is not part of normal human flora.



Psychrobacter species are non-lactose fermenting gram-negative bacilli whose habitats vary from the soil and water environment to the upper respiratory tract of various animals.  The natural habitat of Psychrobacterspecies remains unknown.

Ralstonia pickettii

Ralstonia pickettii is an environmental bacterium found in water, soil, and rhizospheres and on plants including fruits and vegetables. They have a worldwide distribution and are widely recognized as phytopathogens.  Because of its ability to survive in aqueous environments, this organism has become particularly problematic as opportunistic nosocomial pathogens in hospitals and health care settings.


Rhizobium radiobacter

Rhizobium radiobacter is a non-lactose fermenting gram-negative bacillus and is an environmental organism that can be recovered from soil and plants.  It is not part of the normal human flora.



Rhodococcus species are gram-positive, branching filamentous bacteria that can fragment into rods and cocci and are considered aerobic actinomycetes.  They can be isolated from several environmental sources, especially soil and farm animals, as well as fresh and salt waters.

Sphaerotilus natans

Sphaerotilus natans are iron bacteria that are observed microscopically from samples collected in lakes, rivers, streams, and slime growths in cooling-tower water.  Sphaerotilus natans is a filamentous bacterium that is a typical inhabitant of activated sludge.


Sphingobacterium multivorum

The gram-negative rod bacterium may be found in various environmental niches, most noted for its ability to survive in moist hospital environments.


Sphingomonas paucimobilis

Sphingomonas paucimobilis is a gram-negative rod that exists in environmental niches such as water, including hospital water systems.  It is not part of normal human flora.


Staphylococcus aureus

Staphylococcus aureus is a gram-positive coccus that can be isolated as normal flora of the human anterior nares and throat.  S. aureus is the most pathogenic species of Staphylococcus and is responsible for a variety of disease syndromes such as skin wound, and deep tissue infections as well as food poisoning. READ MORE.

Methicillin-resistant Staphylococcus aureus (MRSA) is a multiple drug resistant bacteria that causes over 90,000 infections including both Community-Associate (CA) MRSA and Healthcare-Associated (HCA) MRSA.  Over 75% of all MRSA infections are skin and soft tissues infections while 33% of the U.S. population is nasal carriers of MRSA.


Stenotrophomonas maltophilia

Stenotrophomonas maltophilia is a gram-negative non-fermenting bacillus that is widely distributed in nature including moist environments, water, and on fruits and vegetables.  This bacterium has a high prevalence in hospitals and frequently colonizes the skin and respiratory tract of hospitalized patients.



The viridans Streptococci are gram-positive cocci that are transient colonizers of skin and resident colonizers of mucous membranes.  They are part of the normal flora of the alimentary, respiratory, and genital tracts.  They are well characterized as residents of the oral cavity and some strains form part of the normal dental plaque flora.



Streptomyces spp. (gram-positive bacteria) are widely distributed in terrestrial and aquatic habitats.  Most are strict saprophytes, but form parasitic associations with plants and animals.  Streptomyces are capable of occasionally causing disease with the most common type of disease being mycetoma.

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