Bacteria can be classified into aerobes and anaerobes. The main difference between aerobic and anaerobic bacteria is the fact that aerobic bacteria require oxygen to remain alive, while anaerobic bacteria do not rely on oxygen for metabolic processes and survival. While aerobes are able to thrive in habitats that have abundant oxygen, anaerobic bacteria may die in the presence of oxygen. Anaerobic bacteria have a growth advantage in areas of the body unexposed to oxygen, and may become virulent pathogens. The difference in the capacity to utilize oxygen among aerobes and anaerobes is important in the treatment of bodily infections.

The classification of bacteria may be based on how they utilize oxygen. Obligate aerobes are microorganisms that need oxygen to survive and die in the absence of oxygen. An example is the bacterium Bacillus anthracis. Obligate anaerobes are organisms that die when exposed to oxygen. Examples include Clostridium tetani and Clostridium botulinum, which cause tetanus and botulism, respectively.

Facultative anaerobes can live in the presence or absence of oxygen, but prefer to use oxygen. Examples include Escherichia coli (E. coli) and Staphylococcus, or simply staph. Subtypes of E. coli, such as the O157:H7, cause hemorrhagic diarrhea, while staph is known for causing skin infections such as boils, folliculitis, and impetigo. When a deep skin laceration becomes infected with staph, a more severe form of infection called cellulitis can occur.

The other two classifications are microaerophilic bacteria and aerotolerant bacteria. Microaerophiles can live in habitats that have lower levels of oxygen compared to the atmosphere. Examples of microaerophiles are Helicobacter pylori, which causes peptic ulcers, and Borrelia burgdorferi, which causes Lyme disease.

Aerotolerant anaerobic bacteria do not have any use for oxygen and are not adversely affected by its presence. An example is the genus Lactobacillus, which is normally found in the gut, skin, and vagina. When the populations of Lactobacillus in the vagina become depleted, anaerobic bacteria such as Gardnerella vaginalis and Bacteroides multiply, leading to bacterial vaginosis.

Bacteria are cultured in a microbiology laboratory to provide an important clue of their identity. In particular, when grown in a test tube, the following observations may be documented. Obligate aerobes gather on the surface of the culture medium to maximize oxygen absorption, while obligate anaerobes gather at the bottom to keep away from oxygen. Facultative bacteria gather near the top, while microaerophiles gather near the upper part, but not on the surface. Aerotolerant anaerobes are evenly spread along the depth of the medium.

Identifying whether a bacterium is an aerobe or an anaerobe is important in the treatment of bacterial infections. Treatment of infections caused by anaerobic bacteria is often more challenging because they are resistant to usual antibiotic therapies. For instance, treatment of Gram-negative anaerobic bacteria, such as Bacillus fragilis, usually includes combination antibiotics such as piperacillin/tazobactam, imipenem/cilastatin, amoxicillin/clavulanate, and metronidazole plus ciprofloxacin or gentamicin.