By convention, most of the gastrointestinal microorganisms are viewed as commensal. These microbes establish niches and benefit from the host environment, but appear to contribute little to the host. However, this view may be in error. As our understanding of biology and its complexities changes, so does our understanding of biological interactions and the assessment of commensal bacteria. Establishment of the commensal population is affected by host factors and the population typically recovers after a perturbation (i.e., antibiotic treatment).

Numerous studies with simple-stomach animals such as swine and rats reared in germ-free environments (without the gastrointestinal microflora) suggest that microorganisms are not essential for the animal's survival, but they are beneficial. In laboratory rats as a model, animals raised germ-free need to consume significantly more calories than conventionally raised animals to maintain their body weight.[6] Mutualistic bacteria can contribute some energy, amino acids, and/or vitamins (discussed earlier), but the commensal bacteria appear to stimulate development of the gastrointestinal capillary system and intestinal villi.[7]

A healthy commensal population colonizes the gastrointestinal tract and, as a result, competitively excludes transient pathogens. The presence of commensal bacteria helps fortify the gastrointestinal barrier, regulate postnatal maturation, affect nutrient uptake and metabolism, and aid in the processing of xenobiotics.[8] More important, commensal bacteria appear to communicate with specialized cells (Paneth cells) in the intestine to elicit the production by the host of antimicrobial factors called angiogenins, which that can help shape the microflora

composition. ]

Not all examples of commensal bacterial interactions are advantageous to the host. Some Clostridium species can transform secreted bile acids to form secondary products that may impact nutrient digestion and absorption. Metabolism of feedstuff components can generate toxic products that affect animal performance and health.

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