The microbiome refers to the specific community of microscopic organisms living within a particular environment of a larger host organism, such as in humans (1). In humans, there are around 10 to 100 trillion microorganisms present, primarily located in the gut, generally known as the “gut microflora” (2).Although generally initially thought of as harmful, the microbiome is in fact incredibly important for various processes in the body.
From producing important vitamins, to regulating the immune system and helping in the digestion of food, to protecting against other, harmful, bacteria, they are essential in maintaining human health (3,4). In fact, its’ complex nature, the fact that it can be inherited from a parent, and the functioning of the microbiome in a manner similar to organs have led to the theory that the microbiome itself is another human organ (5).
In general, increased diversity in the microbe species in the human gut has been linked to protective function (6) and lower diversity a has been linked to various disorders including obesity, psoriatic arthritis, type 1 and 2 diabetes and coeliac disease. (7,8,9,10,11)
The Infant Microbiome Begins to Develop as Early as in the Womb
The microbiome in an infant develops from the womb itself, with it’s first exposure to microbes in the amniotic fluid of the mother (12). The microbiome of an infant is less diverse at birth, and develops the most during the first three years of its’ life.
This diversity can be determined by various factors, including maternal stress, feeding patterns, exposure to antibiotics and even mode of delivery. The effect of the latter can be seen in the difference between infants born vaginally, and those born by C-section.
Infants born vaginally have a gut microbiome similar to that of the mother (13) with bacteria known as Lactobacillus and Prevotella dominant after birth, and larger distribution of bacteria like Bifidobacterium and Bacteroides developing after a few months. But the infants born by C-section have a different microbiota, with species such as Clostridium and Staphylococcus which can lead to important health differences. This is due to the fact that Bifidobacterium and Lactobacillus, found more in the vaginal babies, are considered to be more protective microbes (14), while certain species of Clostridium and Staphylococcus could evolve to become pathogenic (15).
It has also been shown that even short-term exposure to antibiotics, usually given during C-sections or to the mother during pregnancy, have also been shown to cause changes in the gut microflora (16,17.)
The First Year of Infancy
Most of the changes in the gut microflora occur during the first year of the development of an infant, where, though there are differences between individual babies, the diet of the newborn plays an essential role in the development of its’ microflora (18,19).
Research has found that most breast-fed infants show a gut microbiome dominated by a species known as Bifidobacterium, which have been shown to need Human oligosaccharides (HMOs) to pass into the infant digestive tract (20,21). HMOs are carbohydrates found only in human breast milk. In addition, there are also other beneficial bacteria present in the guts of breast-fed infants, including Lactobacillus, Bacteroides, Streptoccus, etc. (22) Formula-fed infants have been shown to have more diverse species of certain bacteria, and infants exclusively formula-fed are often colonized with more C. difficile, E. coli, B. fragilis, and Lactobacilli than those that are only breastfed (23).
Although earlier studies used to show a reduced presence of the Bifidobacterium in formula-fed infants, recent technological changes have shown their presence in both formula and breast-fed infants (24). When weaning to solid foods from breast milk or from a formula-based diet, the microbiome shows a change towards a more stable form, like that of an adult (19):
Essentially, the first three years of the life of a baby are extremely important in shaping its’ gut microbiome and it’s health, the effects of which could last throughout its life (25).
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