Bacterial commensalism and microbial communities

Bacteria are classically studied as pure cultures in the laboratory. These cultures are regarded as clonal and genetically stable. However, the situation in the environment is somewhat different: Bacteria and Archaea rarely grow as pure cultures more often forming associations with organisms around them. These associations can range from the symbiotic in Table 1 to the pathogenic. The diversity of life in a particular niche often makes functional ecology challenging. Many ecosystems have evolved to include many Bacteria and Archaea exchanging and competing for metabolic intermediates to a state where no single chemical compound is completely metabolized by a single organism.