Newborn baby digestive tract

From MicrobeWiki, the student-edited microbiology resource

Before birth, the digestive tract of the fetus is sterile, but within hours of birth, the baby acquires a complex collection of microorganisms which populate the mouth—then eventually the full length of the tract will be colonized. The development of specific microorganisms is influenced by the exposure to certain factors such as maternal microbiota, environmental contact, mode of delivery and the infant’s diet.

The Niche: Newborn Baby Digestive Tract

The newborn baby digestive tract includes the esophagus, stomach, small intestine, large intestine, and rectum. Although the mouth is not considered part of the digestive tract, it plays a critical role in food breakdown and provides access for microbes to enter and colonize the infant’s digestive tract. Beyond the mouth, the esophagus serves as a passage for the microbes to progress further down the digestive tract, pass the stomach and into the intestines where the microbes can establish and initiate colonization. The intestinal layer consists of a protective mucus layer, which is made up of glycoproteins that serve as potential attachment sites for the microbes. It is the surface of the mucus at the entrance of the villi, where the microbes are normally found (T). Of all the parts of the digestive tract, the intestines are where the majority of the microflora resides. The microbes can exit the digestive tract through the rectum and the anus via feces.

Physical Conditions

The pH of an infant’s stomach ranges approximately from 2 to 5. Initially the pH of the stomach is less acidic, but the presence of microbes, such as Streptococcus and Lactobacillus, and their metabolic activities create a more acidic environment. However, further down the digestive tract the acidity of the environment decreases.


The infant’s stomach is a well-oxygenated area because air swallowed with food arrives in the stomach within moments of ingestion. The facultative anaerobes established in the stomach utilize the available oxygen, resulting in an oxygen-reduced environment for the obligate anaerobic microbes in the intestines.

Factors Affecting the Microflora Composition

The mode of delivery determines the nature of microbes ingested by the infant. Through normal vaginal birth, an infant is exposed to the mother’s vaginal and fecal flora, which results in the colonization of Lactobacillus, Bifidobacterium, Escherichia coli, and Enterococcus. However, an infant delivered by Caesarian section is exposed to a different assortment of microbes, such as Clostridium and Streptococcus, which are acquired from the tools used. These microbes can establish and colonize rapidly within the sterile digestive tract, because there are no pre-existing microbes to compete with. Microbes are able to communicate with their environment as well as others by quorum sensing. Quorum sensing serves as a defense mechanism against colonization by new strains of bacteria (T).


The microflora composition of the infant digestive tract is largely influenced by the dietary intake of the infant. For example, in breast-fed infants, Staphylococcus aureus colonies are found. S. aureus is normally transferred from the mother’s nipple during breast feeding as well as through mouth contact. Differences can be observed in the development of microflora between breast-fed and formula-fed infants, which are shown in the table below.

Breast-Fed Infants Formula-Fed Infants
The digestive tract is colonized by primarily Bifidobacteria. The digestive tract is colonized predominantly of Bacteroides with some Bifidobacteria; but over time the difference in the number of colonies of the two genera decreases.
Human milk has antimicrobial factors that lower the growth of facultative anaerobes. There exists a more complex flora consisting largely of facultative and obligate anaerobes, such as Enterobacteria, Streptococcus and Clostridium.
Intestinal lumen is acidified more easily because human milk does not serve as an efficient buffer. Intestinal lumen is closer to a neutral pH.
Infants are less prone to infections due to a large amount of Bifidobacteria. Infants are more prone to infections due to the lower amount of Bifidobacteria. This can result in a higher risk of diarrhea and allergies.

Microbial Diversity

Bifidobacterium

Bifidobacterium species colonize in great numbers in the infant digestive tract, regardless if the infant is breast-fed or formula-fed (1). The most common Bifidobacterium species in infants are Bifidobacterium infantis, Bifidobacterium breve, and Bifidobacterium longum. However, Bifidobacterium infantis is specifically unique to the infant’s digestive tract (4). They are gram-positive microbes and are oxygen intolerant; hence, they colonize within the intestines rather than the stomach since the intestines are not well-oxygenated regions like the stomach. Being Gram-positive bacteria, Bifidobacterium infantis have a thick cell wall for extra protection from other residing microbes within the intestines.


Oligosaccharides such as N-acetylglucosamine, glucose, galactose, and certain glycoproteins composing human milk are potential growth factors for Bifidobacterium. A rough range of 50%-90% of human milk oligosaccharides pass through infants undigested. Bifidobacterium is able to break down these undigested sugars and obtain energy and nutrients for growth (2). Bifidobacterium infantis prefer glucose over other oligosaccharides due to the availability and abundance of glucose as well as the lower level of difficulty for them to metabolize glucose. They situate themselves by associating with the intestinal wall, either directly attaching to the epithelium or entrapping themselves in the mucous layer of the epithelium. By situating themselves here, they are able to be in an environment that can help in their metabolic activities. With the assistance of intestinal peptidases such as alpha-glutamyl transpeptidase, aminopeptidase, oligoaminopeptidase, and carboxypeptidase, the food ingested by the infant can be broken down further for the microbe to access and utilize essential components more effectively (3). Effective digestion by the intestinal peptides and hormones within the environment, allows for the microbe to lower their energy expenditure by down-sizing the load and complexity of the essential components.


Increased colonization of Bifidobacterium in the large intestine, and its interaction with Lactobacilli, results in enhanced carbohydrate fermentation (5). Fermentation results in an increased production of acetic acid, butyric acid, and lactic acid, which creates an acidic barrier against pathogenic bacteria. Bifidobacterium infantis interacts with Lactobacillus salivarius to exert immunomodulatory effects on intestinal immune cells that mediate host responses to flagellin and pathogens. They are able to modulate the intestinal epithelium by making Salmonella typhimurium less virulent as well as weakening flagellin-induced pro-inflammatory responses (6). Both species interact to down-regulate the secretion of basal IL-8, but Bifidobacterium infantis specifically inhibits flagellin-induced IL-8 secretion. Flagellin serves as a key activator of pro-inflammatory responses to specifically Salmonella intestinal epithelial cell responses (6). The major point to understand from this is that Bifidobacterium infantis interacts with Lactobacillus salivarius to modulate intestinal epithelial cell responses by limiting IL-8 secretion. While they are interacting to weaken pro-inflammatory responses, they may encounter other microbes such as Bacteroides vulgatus that activate pro-inflammatory gene expression in intestinal epithelial cells (6).

Lactobacillus

Lactobacilli are Gram-positive rods that can be found throughout the digestive tract, but is predominantly present in the large intestine (F). They can infiltrate an infant’s sterile digestive tract by means of contact with the mucosal surface of the mother’s vagina or from the mother’s breast milk (D). Lactobacilli are second only to Bifidobacteria in dominating the microbiota of breast-fed infants. The most common species of Lactobacillus found in infants is Lactobacillus acidophilus (C). Lactobacilli contribute to digestion, stimulate the immune system, and inhibit the growth of pathogens (A). They live in habitats rich in carbohydrates, such as an infant’s digestive tract. Lactobacilli, a member of the lactic acid bacteria group, break down sugars, mainly lactose, into lactic acid using the enzyme β-galactosidase. Sugar metabolism provides nutrients and energy for its growth and survival (E, F). The accumulation of lactic acid lowers the environmental pH, which inhibits the growth of pathogenic bacteria, such as Helicobacter pylori. Lactobacilli can regulate their enzymatic activity to achieve a more suitable or optimal living condition. They can also inhibit growth of other bacteria by competing with them for nutrients and adhesion sites on the epithelial lining of the intestinal wall (A). Lactobacilli are commonly used as probiotics, supplements containing bacteria that are beneficial to humans (C, F).

Clostridium

Clostridia are Gram-positive, spore-forming, obligate anaerobes. Many species of Clostridium are potentially pathogenic, due to their ability to form toxins and spores [G]. Birth by Caesarian section and a formula-based diet, increases colonization of Clostridia in an infant’s gut. Clostridia thrive in the anaerobic environment of the intestines, where they can multiply in great numbers and produce toxins [G]. However, if the environment becomes unfavorable, such as when nutrient availability is low, they can often survive by sporulating. Forming spores is beneficial for the microbes, because by forming them, the microbes can withstand harsh conditions for long periods of time. Then, when the surrounding becomes more favorable, they can proceed into germination and start reproducing again[W].


The most common Clostridium species found in an infant’s gut is Clostridum difficile. Clostridium difficile can colonize in large numbers in the intestines, increasing the production of toxins. These toxins are what causes diarrhea in infants (Mutlu). Mass colonization of Clostridium difficile can be life-threatening to especially infants who are taking antibiotics, because the antibiotics can target potential C. difficile competitors, reducing their colonies. A reduction in their competitors can increase their chances of producing toxins as well as other activities. Another species, Clostridium botulinum, can also be found in the infant digestive tract, but only in infants with botulism.

Streptococcus

Streptococci are spherical, Gram-positive, facultative anaerobic bacteria found in the neonatal intestinal tract. It is one of the initial microbes that colonize the digestive tract after birth. This anaerobe utilizes the oxygen present creating a reduced environment which allows for growth of obligate anaerobic bacteria (Parracho et al., 2007). Streptococci also ferment sugars into lactic acid. Streptococcus agalactiae is known as Group B Streptococci (GBS) and is known to cause meningitis and sepsis in infants (Bohnsack et al., 200.

Escherichia coli

Current Research

To define the microbial ecology within the infant digestive tract that exists today involved many years of research. Studies have shown that human adults have specific microbes living in their digestive tract, but one question remained unanswered- how did the microbes get there? In order to answer this question, a long journey of studying the infant digestive tract began. Even today, establishing the microbial make-up of the infant digestive tract is ongoing. Various microbes have been found, but their specific activities and influences on the infant are not fully known. It has been evident that microbes within the digestive tract are essential for neonatal nutrition, metabolism, and health; however, how the microbes are doing this as well as what they are using is still a mystery. Fortunately, more molecular biological methods are being developed as well as dietary supplements that are increasingly being applied to study the microbial ecology of the infant digestive tract. Below are some of many ongoing research on newborn baby digestive tract.

Probiotics and Prebiotics

Differences in adult digestive tract microflora and that of the infant are evident, but what factors are involved in causing the change is still being studied. The possibility that dietary supplements may influence the microflora composition in the infant's digestive tract has been raised, and probiotics and prebiotics are helpful for conducting such research.


What are probiotics and prebiotics?

Probiotics are live microbial food supplements that beneficially affects the host by improving its intestinal microbial balance. Probiotics are useful and effective in conducting research only if the following conditions are met:


  • must exert a beneficial effect on the host
  • must be non-pathogenic and non-toxic.
  • must have large number of viable cells
  • must be able to survive and metabolize in the digestive tract, especially the intestines
  • must stay viable during storage and use
  • must be capable to isolate from the same species as its intended host


Prebiotics are non-digestible food ingredient that beneficially affects the host by selectively stimulating the growth and the activity of specific number of bacterial species already residing in the intestines. Prebiotics are useful and effective in conducting research only if the following conditions are met:


  • not hydrolyzed or absorbed in the upper part of the digestive tract
  • must be a selective substrate for microbes present in the intestines
  • selective substrate must stimulate growth of microbes and provide energy for microbes
  • must be able to alter microflora composition to that of a healthier one

The Research with Probiotics

Several studies have been conducted using probiotics. The main question in this study is to see if probiotics given to infants can be utilized as bacteriotherapy. For example, will probiotics of specific bacterial strain be effective in reducing or preventing activities of other bacterial species? In other words, can probiotics modulate or influence microbial ecology of the infant's digestive tract?

Several factors were established and were used as the baseline for this study. Robinson and Thompson showed in their study that Lactobacillus acidophilus supplement given to formula-fed infants was thought to improve weight gain (R). Another study showed that Lactobacillus casei promoted recovery from acute diarrhea in children (use Isolauri et al reference). With these two results as well as the fact that infantile diarrhea is caused by Escherichia coli, Salmonella, and Shigella, Gonzalez et al used a mixture of both Lactobacillus species. This mixture would be used as bacteriotheraphy against the three diarrhea-causing microbes.

The results showed that Lactobacillus casei in conjunction with live oral rotavirus vaccine to infants, resulted in an elevated response in rotavirus-specific immunoglobulin M- secreting cells as well as an improvement in function of antirotavirus immunoglobulin A seroconversion (use Isolauri et al references). The other strain, Lactobacillus acidophilus, was involved in immune response, of which it was effective against bacterially induced gastroenteritis. The compilation of all the observations made throughout the study, as well as the results above, shows that the probiotics containing the two Lactobacillus strains (L. acidophilus and L. casei), definitely helped modulate the infant microflora. This can be seen by the probiotics reducing gastroenteritis; thus, decreasing the number and their activities of the diarrhea-causing microbes in infants (E.coli, Salmonella, and Shigella). Overall, the probiotics reduced diarrhea and gastroenteritis in infants.

References

[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.

Edited by [Coco Chin , Jeremy Dayrit , Hanaah Fannin , Angela Ho , Chon Ieng , Min-jeong Suh ], students of Rachel Larsen