Why do some children suffer adverse vaccine events while others escape injury? What can be done to limit risk of injury by vaccination? Current CDC (Centers for Disease Control and Prevention) vaccine protocol beginning within 12 hours of birth does not factor gut microbiota as crucial to immune response. Recent study results suggest polymerase chain reaction stool testing be implemented pre-vaccination in order to determine microbiota diversity and potentially assess risk of injury.

A study published in Pediatrics, July 2014, Stool Microbiota and Vaccine Responses of Infants, details the novel finding that Bifidobacteria are associated with greater vaccine response. Bifidobacteria are well-studied and known to have a reciprocal, anti-inflammatory relationship with the host immune system. Along with Lactobacillus, these Actinobacteria are poised to become leading probiotic adjuvants in order to increase vaccine effectiveness. Such adjuvants and probiotic therapy may prove to reduce risk of vaccine injury.

Ample data show that microbiota diversity is positively associated with health in adults. But, according to this study, diversity is not always healthy for infants.

The study found increased diversity of infant microbiota associated with systemic inflammation and reduced vaccine response. Increased populations of microbes such as Clostridia and E. coli and lowered Bifidobacteria were found to reduce vaccine response.

But what if such increased diversity also increases risk of vaccine injury? There are no studies examining this relationship. Yet studies reveal gut-brain mechanisms that can lead to brain and central nervous system (CNS) injury.

The healthy breastfed infant gut is known to be up to 90% Bifidobacteria, comprising several different strains. Gut dysbiosis in adults is generally a matter of overgrown Proteobacteria such as E. coli and reduced or absent commensals such as butyrate-producing Clostridia. Crucial to diversity is a balance of microbes.

Fundamental to the discussion is re-examination of scientific dogma that the womb and fetal gastrointestinal tract are sterile. We now know placental transmission of microbes is a fact and meconium is teeming with life. Children are born at least partially colonized.

A new Washington University paper published in August 2014 illustrates the point, detailing the gut microbe assembly of preterm infants. Patterned progression of bacterial populations in the preterm infant gut reveals gestational age as the overriding factor in colonization. The sequence occurs as follows: first Bacilli flourish, then Gammaproteobacteria such as E. coli become abundant and, finally, Clostridia. Bifidobacteria then flourish with breastfeeding. Environmental factors such as c-section vs. vaginal birth and antibiotics do not affect this progression, though may slow it down. This shows that the dynamic nature of the gut microbiota should be taken into account when carrying out studies on infants.

Current vaccine protocol for preterm infants is to treat as full-term when weighing more than 2.2 lbs. Perhaps preterm infants are at greater risk of autism because gut flora are predominantly Gammaproteobacteria at birth and this triggers an adverse immune response upon vaccination. Protective Bifidobacteria and potentially protective strains of Clostridia are not yet developed at birth.

One other issue needing further exploration is that levels of protective Bifidobacteria vary in populations throughout the world, based on ancestral diet and genes regulating host glycans. If data were to show differences between Western cohorts and other cohorts, this might mean some groups are more prone to vaccine injuries. Data on a wide range of vaccine responses is urgently needed to help inform CDC protocols.

Also on the topic of group differences, Mayo Clinic is busy pondering why Somali Americans respond to rubella vaccination with doubled antibodies.  Could it be their gut bacteria? And maternal microbes are now considered influential in fetal blood-brain barrier permeability without consideration of fetal gut microbes.

It appears the CDC immunization schedule should be reviewed to promote vaccine safety and reflect new knowledge based on microbial interaction with the host immune system.