From birth to death, the gut is colonized by a diverse, complex, and dynamic bacterial ecosystem that constitutes the intestinal microbiota. In newborns, it develops sequentially according to the maturation of intestinal mucosa and dietary diversification. In healthy conditions, the human baby's intestine is sterile at birth but, within 48 hours, 108 to 109 bacteria can be found in 1 g of feces (9-11). The bacteria colonizing the baby's intestine come from the environment, where maternal vaginal and fecal microbes represent the most important source of bacterial contamination. However, the infant conducts an initial selection, since, out of all the bacteria present, only the facultative anaerobic bacteria such as Escherichia coli and Streptococcus will be able to colonize the intestinal tract, whatever the diet. Conditions under which this initial selection is operated have yet to be fully elucidated. They are related to endogenous factors, such as maturation of intestinal mucosa, mucus, growth promoters or inhibitors present in the meconium, or exogenous factors such as delivery conditions (natural childbirth, caesarean section), mother's status (antibiotic intake), and quality of the bacterial environment. Subsequently, obligate anaerobes such as Bacteroides, Clostridium, and Bifidobacterium colonize over the first week of life, following a second selection in which the diet factor plays a fundamental role. It has long been known that Bifidobacteria are predominant in exclusively breast-fed babies, while in bottle-fed babies it is not always present, or present at fluctuating levels and, in contrast to breast-fed babies, often associated with other anaerobic bacteria such as Bacteroides and Clostridia. Breast milk contains oligosaccharides enabling development of Bifidobacterium and may also function as receptor analogues of the mucus influencing the strains able to colonize the intestinal tract (12). A bacterial balance is obtained towards the end of the second week of life in which Bifidobacterium and E. coli predominate in exclusively breast-fed infants, while a more diverse microbiota, rich in E. coli, Bacteroides and, possibly Clostridium, Bifidobacterium, Staphylococcus, and other Enterobacteriaceae, is found in formula-fed infants. Thus the bacterial balance of the infantile microbiota mainly depends on two important factors: bacterial environment at birth and diet. During the last decade, some modifications of the microbiota balance in babies whatever the feeding have been observed, namely, dominance of Staphylococcus, low levels of E. coli, delayed colonization with anaerobic bacteria and absence or low levels of bifidobacteria (MJ Butel, personal communication). Excessive aseptic conditions present at birth, maternal antibiotic intake immediately before parturition or during childbirth could be, among other factors, responsible for such differences (13). Because of the fragility of the baby's digestive microbiota, which is poorly diversified, with about 10 bacterial species of micro-organism versus over 400 in adults, the consequences of its modification have to be considered in terms of health. For example, recent studies suggest that some infancy pathologies, such as food allergy, could be due to the modifications of the intestinal microbiota of newborns. The latter will be discussed in chapter 10.
Thereafter, according to dietary diversification, the digestive microbiota, enriched by the development of other strictly anaerobic bacteria, becomes more and more complex. It is considered to have assumed adult characteristics toward the age of 2 years (9-11).
In adults, a complex and diverse digestive microbiota is present, mainly in the distal parts of the gut. In the duodenum, the number of bacteria is approximately 104 bacteria/g of intestinal content while in the ileum, the number reaches 107-108. The large intestine is the most densely colonized region (1010-10n bacteria/g of content), essentially because of digestive stasis. Bacterial species established at levels over 107-108 bacteria/g characterize the predominant microbiota, whereas those below such a threshold compose the subdominant microbiota. In fact, it is proposed that only predominant bacteria are able to exert a measurable function. The dominant microbiota of human feces is mainly composed of strict anaerobic and extremely oxygen-sensitive bacteria. According to several authors, 30% to 70% of the microbiota is not identified because it is uncultivable with current techniques. The predominant species commonly isolated from the human feces belong to the genera Bacteroides, Eubacterium, Bifidobacterium, Ruminococcus, and Clostridium, and subdominant species include enterobacteria, particularly Escherichia coli and streptococci (14). Lactobacilli are frequently subdominant in humans or cannot even be detected. Some studies suggest that they may be abundant in the ileum.
Very little data exists on the evolution of intestinal microbiota in the elderly. Nonetheless, bifidobacteria have been reported to decrease at old age, which may be related to a reduced adhesion to the intestinal mucus (15).
Currently available molecular biology techniques should bring additional and complementary approaches to those offered by the usual culture techniques. Recent molecular methods have shown that every individual has his/her own gut microbial balance, which has been described to be stable (studies over a period of 6-9 months) (16).
In conclusion, depending on the intestinal sites (duodenum, ileum, and colon) and the various periods of life, childhood, adulthood, aging, the human's intestinal microbiota also varies. This is discussed further in more detail in chapter 3 by McCartney and Gibson.
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