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Health Protocols

Maintaining a Healthy Microbiome

Establishing and Shaping the Microbiome

The infant microbiome plays a foundational role in educating the immune system and is therefore an important determinant of lifelong health (Dominguez-Bello 2016). Its composition is shaped by multiple factors, including mode of birth, human genetic factors, geography and culture, diet and lifestyle, physiology, illnesses, surroundings, and contact with other people and pets (van der Meulen 2016; Turnbaugh 2007; Song 2013; Goodrich 2014; Yatsunenko 2012; Tasnim 2017). In addition, the use of medications such as antibiotics and proton pump inhibitors can influence the microbiome (van der Meulen 2016).

Our first exposure to the microbiome is at birth (Falana 2015; Koboziev 2014). During vaginal delivery, the newborn becomes colonized with microorganisms that originate from the maternal birth canal and skin (Knight 2017; Krajmalnik-Brown 2012; Koboziev 2014). Compared with babies born vaginally, the microbiomes of those born by C-section have been found to have more microbes that originate from the mother's skin and fewer microbes that originate from the vaginal canal (Krajmalnik-Brown 2012; Dominguez-Bello 2016; Rutayisire 2016). Bifidobacterium bacteria, as well as Lactobacillus species, are especially important early colonizers of the infant gut, where they help guide the development of a healthy microbiome and the maturation of the immune system (Koboziev 2014; Mueller 2015).

The mother's vaginal microbiome is critical in establishing the initial gut microbiome in the newborn during birth, and it helps shape immune system maturation and metabolism. This microbiome transmission from the mother to the newborn occurs during a critical period of the newborn brain development. Environmental factors, such as maternal stress during pregnancy, can change the vaginal microbiome and its transmission to the infant, and may affect neurological development of the infant later in life (Jasarevic, Rodgers 2015; Jasarevic, Howerton 2015; Jasarevic 2017).

Breastfeeding is another opportunity for the transfer of Lactobacillus and Bifidobacterium species, as well as other bacterial species, to the infant (Soto 2014; Mueller 2015; Urbaniak 2012). In addition, certain prebiotic carbohydrates found in human breast milk (called human milk oligosaccharides) support the growth of Bifidobacterium species, which are important in the infant's gut, where they promote the healthy development and function of the intestinal mucosal surface and the immune system (Knight 2017; Mueller 2015).

Human Milk Oligosaccharides
Breast milk provides all of the nutrients required for a newborn's healthy growth and development. It also contains an array of biologically active compounds that protect and support the newborn during early immune, cognitive, and metabolic development (Martin 2016; Kulinich 2016; Castanys-Munoz 2016). These are well known to include maternal immune components such as antibodies, immune cells, and cytokines—chemicals needed for immune signaling (Witkowska-Zimny 2017; Cabinian 2016). Only recently has the importance of specialized breast milk oligosaccharides in establishing a healthy gut microbiome and balanced immune function been appreciated (Kulinich 2016; Donovan 2016).

Human milk oligosaccharides are a complex mixture of small indigestible carbohydrates that promote the growth of beneficial gut bacteria. In particular, Bifidobacterium species, abundant in the intestines of healthy breastfed infants, are able to ferment these oligosaccharides (Donovan 2016; O'Callaghan 2016). By supporting the presence of beneficial bacteria, human milk oligosaccharides enhance the establishment of normal intestinal barrier function and mucosal immunity. Findings from laboratory and animal studies also suggest human milk oligosaccharides may directly impact mucosal and immune maturation and function, and exert direct antimicrobial actions against infection-causing microorganisms (Donovan 2016; Ackerman 2017).

The differences in microbiome composition between babies born vaginally versus by C-section may explain the increased risks of allergies and asthma, obesity, type 1 diabetes, and neurodevelopmental disorders associated with C-section birth (Ho 2015; Moya-Perez 2017). Introducing C-section-born infants to vaginal microbes by swabbing them with maternal vaginal fluids at birth is a new strategy being explored to help establish a healthy microbiome (Dominguez-Bello 2016). Formula feeding also disrupts the healthy infant microbiome and has been associated with an increased risk for immunologic and metabolic disorders later in life. Even small amounts of supplemental formula can alter the gut microbial populations (Mueller 2015).

The infant gut microbiome undergoes changes in the first two to four years of life and then becomes more similar to the one found in adults (Chan 2013). Changes in diet and the body contribute to this shift in the microbial profile. Exposure to animals, such as pets, during these younger years is associated with a lower risk of allergies. Microbial patterns can also be altered by antibiotic use, microbes in the surroundings, and illness (Xu 2015; Francino 2015; Ojima 2016).

After this time of rapid diversification and expansion, the microbiome becomes relatively stable, and changes are more gradual (Knight 2017; Krajmalnik-Brown 2012). The relationship between aging and the microbiome is still being explored, but evidence suggests gut microbial profiles of the elderly are different from those of younger adults and are correlated with measures of frailty, poor diet, and health problems (Claesson 2011; Claesson 2012).

While a healthy microbiome is generally resistant to changes in its environment, and returns to the previous state afterwards (Lloyd-Price 2016), it is nonetheless susceptible to certain disrupting factors. Antibiotics, for example, can have dramatic effects on the microbiome, and the ability to recover to the pre-antibiotic microbial balance differs between individuals. Changes in eating habits can also cause profound and rapid alteration in the microbiome that can be brief or persistent. Hormonal cycles, travel, illness, and aging are other examples of factors that shape the microbiome (Krajmalnik-Brown 2012; D'Argenio 2015; Xu 2015; Zapata 2015).