The gastrointestinal tract (GI tract) serves as one of the biggest interfaces between the body and the external environment (3). This GI tract is a highly specialized organ system that allows us to consume food in discrete meals as well as a very diverse array of foodstuffs to meet our nutrient needs. The organs of the GI tract include the oral cavity, esophagus, stomach, small and large intestine; in addition, the pancreas and liver secrete into the small intestine. The system is connected to the vascular, lymphatic, and nervous systems to facilitate regulation of the digestive response, delivery of absorbed compounds to organs of the body, and regulation of the food intake.
One of the characteristic aspects of the GI tract is the presence of numerous endogenous microbes colonizing the surface of the GI tract throughout the life of the host. It consists of a complex community inside the host, known as the intestinal microbiota. In healthy adults, the intestinal microbial cells have been estimated to outnumber the host's somatic and germ cells by a ratio of 10:1 (4). The development of this microbiota is initiated during the birth process. The fetus exists in a sterile environment until birth. After being born, the infant is progressively colonized by bacteria from the mother's vagina and feces and from the environment. As long as nutrients and space are not limited, the commensals with high division rates predominate, e.g., enterobacteria (Escherichia coli) and Enterococcus appear. The succession of microbes in an infant's intestinal tract also depends on the feeding mode. The fecal microbiota of breast-fed babies has been found to be relatively simple, usually exclusively dominated by Bifidobacterium (5). However, recent comparative studies showed that bifidobacteria were the predominate fecal bacteria in both group of infants (6,7). In bottle-fed infants, the count and frequencies of occurrence of Bacteroides, Enterobacteriaceae and streptococci were significantly higher than those in the breast-fed infants (6,7). After weaning, when solid food is consumed, the stools of infants begin to shift to an adult-like microbiota: bifidobacteria decrease remarkably and constitute only 5% to 15% of total microbes. The number of Bacteroidacecea, eubacteria, Peptococcaceae and usually clostridia outnumber bifidobacteria, while aerobic bacteria such as E. coli and streptococci, which have been regarded as the predominant species are always detected, but account for less than 1% of the total bacterial count. Lactobacilli, Megasphaerae and Veillonellae are often found in adult feces, but the counts are usually less than 107 per gram of feces. By the end of the secondary year of life, the microbiota becomes more stable and resembles that of an adult (see also the chapter by McCartney and Gibson). As the microbial population increases nutrients become scarce and the intestinal niches become occupied with more specialized species with an advanced symbiotic relationship between the host and microbiota. Once the climax microbiota has become established, the major bacterial groups in the intestine of an adult usually remain relatively constant over time.
The habitats of the intestinal microbiota vary in different parts of the human GI tract (8). In healthy persons, acid stomach contents usually contain few microbes. Immediately after a meal, counts of around 105 bacteria per milliliter of gastric juice can be recorded: bacteria including streptococci, enterobacteriaceae, Bacteroides and bifidobacteria derived from the oral cavity and the meal. The microbiota of the small intestine is relatively simple and no large numbers of organisms are found. Total counts are generally 104 or less per milliliter, except for the distal ileum, where the total counts are usually about 106/ml. In the duodenum and jejunum, streptococci, lactobacilli and Veillonellae are mainly found. Towards the ileum, E. coli and anaerobic bacteria increase in number. In the caecum, the composition suddenly changes and is similar to that found in feces, and the concentration may reach 1011 per gram of content.
As more than 400 species have been estimated to reside in the colon of healthy adults, which may attain population levels nearly as high as 1012 /g in the colon and may make up almost half the content by weight (8,9). This bacterial community is dominated by strict anaerobes, and contains less facultative anaerobes with a rate of anaerobes and aerobes as 1000:1. In accordance with the metabolic activity, the major bacteria present in the intestinal microbiota of the healthy adult can be divided roughly into three groups (10).
Group one is lactic acid-producing bacteria including Bifidobacterium, Lactobacillus and Streptococcus (including Enterococcus), which may possess a symbiotic relationship with the host. Group two includes putrefactive bacteria such as Clostridium prefringens, Clostridium spp. Bacteroides, Peptococcaceae, Veillonella, E. coli, Staphylococcus and Pseudomonas aeruginosa. Others are like Eubacterium, Ruminococcus, Megasphaera, Mitsuokello, C. butyricum and Candida, group three. Normally, near-stability exists in these habitats and each person has an individually fixed microbiota as far as qualitative composition is concerned.
The intestinal microbiota play an important role in normal bowel function and maintenance of host health, through the formation of short chain fatty acids, modulation of immune responses, and development of colonization resistance (8,10). These functions of the intestinal microbiota are the consequence of the activities of the numerous intestinal bacteria as a whole community with a well-organized structure built on the balance among the various bacterial members. Therefore, the functions of the intestinal microbiota are very sensitive to factors that can alter the structure of the intestinal microbiota qualitatively and quantitatively such as aging, physiological state, disease, medication, diet, and stresses.
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