The names of bacteria are based on the binomial system: the first name is that of the genus, the second name is that of the species. When written, the genus name is capitalized and the species name is not. Both genus and species name are italicized (e.g., Escherichia coli).

A species of microorganisms are a group of individuals that are all basically similar. A genus is a group of related species. In the laboratory, the identification of bacteria to species level is a multifaceted task and can be expensive, especially with environmental bacteria with no clinical significance.

Bacteria are divided into five basic morphologic groups: cocci, bacilli, spirals, comma-shaped and filamentous. Cocci are spherical, bacilli are rod-shaped, comma-shaped are curved rods, spirals are helical forms, and actinomycetes are branched 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 stain red by the Gram stain procedure.

Bacteria include aerobic, anaerobic, facultatively anaerobic, and microaerophilic species; some members are obligate intracellular parasites. Aerobic bacteria require oxygen to survive and reproduce. Anaerobes require oxygen poor and carbon dioxide enriched atmospheres to reproduce. Facultative anaerobe is an aerobe that does not require oxygen for its metabolism and is capable of growth in the absence of oxygen. Microaerophilic species do not grow at atmosphere tensions of oxygen, but require a small amount of it in metabolism.

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Major Groups of Bacteria
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Gram-positive Cocci: typically represent a large percentage of the bacteria recovered from sampling the indoor environment. Genera commonly recovered from this group are Micrococcus, Staphylococcus and Streptococcus. Micrococci are widespread in nature and are commonly found along with coagulase-negative Staphylococcus on the skin of humans and mammals. Micrococci are not considered to be pathogenic (or very low pathogenicity) to humans. Staphylococcus aureus and many species of Streptococcus are pathogenic and cause a variety of disease states in humans and animals.

Gram-negative Cocci: The genera include Neisseria and Branhamella (seldom isolated outside the human host) with their habitat being the mucous membranes of man and animals.

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Gram-positive Bacilli: The major aerobic genus in this group is Bacillus. The genus Bacillus includes a large variety of mostly saprophytic bacteria widely distributed in worldwide habitats. Bacillus species 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). Bacillus species can survive in a spore form in cases of environmental extremes (such as nutrient deprivation). The majority of Bacillus species have little pathogenic potential and are rarely associated with disease. However, Bacillus cereus can cause one type of food poisoning and Bacillus anthracis is the etiologic agent of anthrax. Corynebacterium species are non-spore forming gram-positive rods. They can be recovered from a variety of habitats such as soil, food, plants and the skin and mucous membranes of mammals.

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Gram-negative Bacilli: This is by far the largest classification of bacteria. There are two major groups of gram-negative bacilli. The first group comprises those species that commonly colonize the human gastrointestinal tract and are associated with human disease. The majority of Enterobacteriaceae ferment glucose, are oxidase-negative and inhabit a wide variety of environmental niches. The group includes such bacteria as Escherichia coli, Salmonella, Yersinia, Klebsiella and Enterobacter species. The second group consists of what are considered as environmental inhabitants. These are the non-glucose fermenting bacteria and they are often associated with moisture. Their natural habitats range from plants, soil, intestinal tract of mammals, stagnant water sources such as improperly drained drip pans, humidifiers, cooling towers, sink traps, factories, waste and sewage treatment plants, fresh flowing water and seawater. This group includes bacteria such as Alcaligenes, Acinetobacter Pseudomonas, Chryseomonas, Comamonas and Sphingomonas.

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Actinomycetes: The actinomycetes are a large group of filamentous bacteria, usually gram-positive, which form branching filaments and in most species, spores are also produced. The differences in shape and arrangement of aerial filaments and spore-bearing structures of various species are among the fundamental features used in separating the species within a particular group. The clinically significant and main genera include Nocardia and Streptomyces. These bacteria can be isolated from soil, barns, silos, grain mills and poorly maintained air conditioning ducts. Streptomyces are widely distributed in terrestrial and aquatic habitats. Most are strict saprophytes, but form parasitic associations with plants and animals. Thermophilic actinomyces such as Thermoactinomyces vulgaris and Micropolyspora rectivirgula (synonym – faeni) have been reported in association with hypersensitivity pneumonitis and other allergic reactions. Exposure to thermophilic actinomyces, whose optimal growth temperature is >40oC, may occur near compost sites or municipal landfills.

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