Microorganisms within the gastrointestinal system are predominantly strict anaerobes, the study of these bacteria was greatly limited until culture techniques capable of excluding oxygen were developed. Prior to the 1940s, theories of microbial fermentations of fiber contributing energy to the host abounded, but little direct evidence was found. Since that time, microbiologists have refined the culture techniques and conditions to support the growth of numerous gastrointestinal bacteria. Additional works with nutritionists and physiologists have identified more specific interactions between the host and microbes.
The gastrointestinal tract begins at the mouth and ends at the anus and is colonized with bacteria in nearly its entirety. The system contains over 400 species of microorganisms and the gastrointestinal microbial cells outnumber the animal cells nearly 10:1. This diverse, dynamic population of bacteria in the gastrointestinal system is referred to as the microflora or microbiota. The specific species (or strains of species) of microorganisms can vary with animal host, diet, and environment, but in general the predominant species are associated with a limited number of bacterial genera.
Parasitic or pathogenic microorganisms incur a cost on the host and have been studied more extensively. The mutualistic microorganisms generate a benefit to the host. If the interaction is not parasitic or mutualistic, it is then considered to be commensal. However, animal/microbe interactions are difficult to define and study; thus, most interactions are considered commensal. The Vin diagram (Fig. 1) best indicates the complexity of these animal/ microbe interactions.
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