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Overview of Bacteria


Brian J. Werth

, PharmD, University of Washington School of Pharmacy

Last full review/revision May 2020| Content last modified May 2020
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Bacteria are microorganisms that have circular double-stranded DNA and (except for mycoplasmas) cell walls. Most bacteria live extracellularly. Some bacteria (eg, Salmonella typhi; Neisseria gonorrhoeae; Legionella, Mycobacteria, Rickettsia, Chlamydia, and Chlamydophila species) preferentially reside and replicate intracellularly. Some bacteria such as chlamydiae, Chlamydophila species, and rickettsiae are obligate intracellular pathogens (ie, able to grow, reproduce, and cause disease only within the cells of the host). Others (eg, Salmonella typhi, Brucella species, Francisella tularensis, N. gonorrhoeae, Neisseria meningitidis, Legionella and Listeria species, Mycobacterium tuberculosis) are facultative intracellular pathogens.

Many bacteria are present in humans as normal flora, often in large numbers and in many areas (eg, in the gastrointestinal tract). Only a few bacterial species are human pathogens.

Bacteria are classified by the following criteria (see also table Classification of Common Pathogenic Bacteria):

  • Morphology

  • Staining

  • Encapsulation

  • Oxygen requirements


Bacteria may be

  • Cylindric (bacilli)

  • Spherical (cocci)

  • Spiral (spirochetes)

A few coccal, many bacillary, and most spirochetal species are motile.


Gram stain is the most common stain for general bacterial identification. Gram-positive bacteria retain crystal violet dye (appearing dark blue) after iodine fixation, alcohol decolorization, and counterstaining with safranin; gram-negative bacteria, which do not retain crystal violet, appear red. Gram-negative bacteria have an additional outer membrane containing lipopolysaccharide (endotoxin), increasing the virulence of these bacteria. (For other factors that enhance bacterial pathogenicity, see Factors Facilitating Microbial Invasion.)

Ziehl-Neelsen and Kinyoun stains are acid-fast stains used to identify mainly mycobacteria, particularly M. tuberculosis. They also can identify the gram-positive bacilli Nocardia and the protozoans Cryptosporidia, Cyclospora, and Cystoisospora. Carbolfuchsin is applied, followed by decolorization with hydrochloric acid and ethanol and then counterstaining with methylene blue.

Fluorochrome stains (eg, auramine-rhodamine) also identify acid-fast organisms, but a special fluorescent microscope is required.


Some bacteria are enclosed in capsules; for some encapsulated bacteria (eg, Streptococcus pneumoniae, Haemophilus influenzae), the capsule helps protect them from ingestion by phagocytes. Encapsulation increases bacterial virulence.

Oxygen requirements

Aerobic bacteria (obligate aerobes) require oxygen to produce energy and to grow in culture. They produce energy using aerobic cellular respiration.

Anaerobic bacteria (obligate anaerobes) do not require oxygen and do not grow in culture if air is present. They produce energy using fermentation or anaerobic respiration. Anaerobic bacteria are common in the gastrointestinal tract, vagina, dental crevices, and chronic wounds when blood supply is impaired.

Facultative bacteria can grow with or without oxygen. They produce energy by fermentation or anaerobic respiration when oxygen is absent and by aerobic cellular respiration when oxygen is present. Microaerophilic bacteria prefer a reduced oxygen tension (eg, 2 to 10%).

Chlamydiae are obligate intracellular parasites that acquire energy from the host cell and do not produce it themselves.


Classification of Common Pathogenic Bacteria



Obligate aerobic

Gram-negative cocci

Gram-positive bacilli

Corynebacterium jeikeium

Acid-fast bacilli

Mycobacterium avium complex, M. kansasii, M. leprae, M. tuberculosis, Nocardia species

Nonfermentative, non-Enterobacteriaceae

Acinetobacter calcoaceticus, Elizabethkingia meningoseptica (previously Flavobacterium meningosepticum), Pseudomonas aeruginosa, P. alcaligenes, other Pseudomonas species, Stenotrophomonas maltophilia

Fastidious gram-negative coccobacilli and bacilli

Brucella, Bordetella, Francisella, and Legionella species

Leptospiraceae (spiral bacteria)

Leptospira species

Obligate anaerobic

Bacteroides fragilis, other Bacteroides species, Fusobacterium species, Prevotella species

Gram-negative cocci

Veillonella species

Gram-positive cocci

Peptococcus niger, Peptostreptococcus species

Non–spore-forming gram-positive bacilli

Actinomyces, Bifidobacterium, Eubacterium, and Cutibacterium (previously Propionibacterium) species

Endospore-forming gram-positive bacilli

Clostridium botulinum, C. perfringens, C. tetani, other Clostridium species

Facultative anaerobic

Gram-positive cocci, catalase-positive

Staphylococcus aureus (coagulase-positive), S. epidermidis (coagulase-negative), other coagulase-negative staphylococci

Gram-positive cocci, catalase-negative

Enterococcus faecalis, E. faecium, Streptococcus agalactiae (group B streptococcus), S. bovis, S. pneumoniae, S. pyogenes (group A streptococcus), viridans group streptococci (S. mutans, S. mitis, S. salivarius, S. sanguis), S. anginosus group (S. anginosus, S. milleri, S. constellatus), Gemella morbillorum

Gram-positive bacilli

Bacillus anthracis, Erysipelothrix rhusiopathiae, Gardnerella vaginalis (gram-variable)

Enterobacteriaceae (Citrobacter species, Enterobacter species, Escherichia coli, Klebsiella species, Morganella morganii, Proteus species, Plesiomonas shigelloides, Providencia rettgeri, Salmonella typhi, other Salmonella species, Serratia marcescens, Shigella species, Yersinia enterocolitica, Y. pestis)

Fermentative, non-Enterobacteriaceae

Aeromonas hydrophila, Chromobacterium violaceum, Pasteurella multocida

Fastidious gram-negative coccobacilli and bacilli

Actinobacillus actinomycetemcomitans, Bartonella bacilliformis, B. henselae, B. quintana, Eikenella corrodens, Haemophilus influenzae, other Haemophilus species


Curved bacilli

Campylobacter jejuni, Helicobacter pylori, Vibrio cholerae, V. vulnificus

Spirochaetaceae (spiral bacteria)

Obligate intracellular parasitic


Chlamydia trachomatis, Chlamydophila pneumoniae, C. psittaci


Rickettsia prowazekii, R. rickettsii, R. typhi, Orientia tsutsugamushi, Ehrlichia chaffeensis, Anaplasma phagocytophilum

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