Now that we know the microbiome exists and is largely responsible for our digestion, immunity, and assimilation and production of nutrients, we are charged with learning about its optimal manifestation. How is it created? What are the ingredients to a healthy microbiome? Are there some more critical and some less critical steps?
As I describe here, it turns out the steps may be as simple as following the evolutionary order of operations.
- Eat right
- Birth vaginally in your place of dwelling
A new study in Cell Host & Microbe (don’t you love that there are actually journals with these titles?) points a finger at the hubris involved in positioning surgical birth and bottle-feeding as “separate but equal” alternatives.
Fecal samples of 98 Swedish infants over the first year of life revealed the following:
- Mode of deliver impacts the infant’s microbiome. As has been previously demonstrated, C-section birth results in infant colonization with: “skin and oral microbes, but also bacteria from the surrounding environment during delivery.” Specifically, “Bacteroides, in particular B. ovatus/B. xylanisolvens, B. thetaiotaomicron, B. uniformis, and B. vulgatus/B. dorei, were less prevalent or missing in the C-section-delivered newborns compared to vaginally born infants, and this difference remained at 4 and 12 months.” The microbiota of C-section babies contained higher proportions of antibiotic-resistance genes and these babies overlapped with their mother’s stool patterns only 41% of the time rather than 72% in the vaginal births (which were potentially still contaminated by the hospital microbiome according to this study).
Breastfeeding and bottle-feeding impact the infant’s microbiome differently. Exclusively breast-fed infants had increased levels of taxa that are used as probiotics such as L. johnsonii/L.gasseri, L. paracasei/L. casei, and B. longum. Four-month old formula-fed infants had elevated levels of Clostridium difficile, Granulicatella adiacens, Citrobacter spp., Enterobacter cloacae, Bilophila wadsworthia, in agreement with previous studies.
The changes to the microbiome in the first year are non-random and highly orchestrated for specific nutrient production. The authors state:
“Our results underscore the role of the gut microbiota for the production of essential amino acids and vitamins for the growing infant. While the infant gut microbiota acquired significant capacity to produce amino acids and vitamins after four months of life, the increase in transporters capacity indicates that the newborn’s microbiome is poised to the upcoming change in the intestinal environment and progression to a mature profile. Intriguingly, considering evidence that the gut microbiota may affect behavior, many functions of the developing gut microbiome linked to the metabolism of vitamins, iron, and amino acids are also required for normal brain development (Lozoff et al., 1987), thus adding to the possibility that the gut microbiota might affect behavior.”
- The cessation of breastfeeding rather than the introduction of solid food is what directs the transition to a more adult-looking microbiome.
It Happens This Way For A Reason
Suzanne Humphries, MD, take us on a tour in this video series about the design behind the infant immune system – that babies are born into a “clamped-down” immunologic state which breastfeeding serves to template over the first two years. She explores the importance of full cord blood transfer, and the wrong-headedness of provoking adult-like immune responses through vaccines. Medicine has had a way of treating infants and babies like mini-adults. Perhaps awareness of the microbiome development will force us to acknowledge the mother-infant dyad and the uniqueness therein.
This above study, unsurprisingly, did not control for the influence of vaccination on the infant’s microbiome. There has been shamefully scant literature examining the effects of vaccines on our native ecology and no research on the role of microbiota in increased vulnerability to injury. This may be related to the fact that true scientific acknowledgement of the microbiome and our enmeshment with the microbial world undermines the entire premise of vaccination.
Despite acknowledgement that:
“…no comprehensive studies have been undertaken to examine the gastrointestinal microbiota in relation to vaccine administration and if there is a discernible alteration in the community following vaccine administration,”
a handful of studies indicate that:
- “At greatest risk of intestinal injury by rotavirus are those with a microbial predisposition high in LPS-producers as viral infectivity is most virulent in presence of LPS and other sugars in the cell wall of certain bacteria” – Keith Bell referencing this study.
- Cholera vaccine significantly increases gram negative bacteria (1)
- Regarding the flu vaccine: “We find that LAIV vaccination reverses normal bacterial clearance from the nasopharynx and significantly increases bacterial carriage densities of the clinically important bacterial pathogens Streptococcus pneumoniae and Staphylococcus aureus” (2)
- Bifidobacter or the absence of may dictate vaccine response.
- With over 90 serotypes of pneumococcus identified, the Prevnar vaccine targets 7 resulted in shifts in nasopharyngeal colonies toward different strains associated with pathology including ear infections. The authors state:
“…we observed an increase in culture-proven S. aureus carriage in the original randomized controlled trial, as well as further increases in culture-proven S. aureus and H. influenzae carriage observed in surveillance studies 3–5 years after PCV-7 implementation in the Netherlands.”
Even the vitamin K shot with its whopping megadose of synthetic K1, propylene glycol, and polysorbate 80, was noted to impact gene expression. The authors state:
We observed enriched levels of genes for vitamin K2 (menaquinone) synthesis in newborns, which correlated with the high abundance of Bacteroides and Escherichia/Shigella.
The Microbiome Is Real And It’s Here To Stay
Medical interventions and pharmaceuticals of all kinds must be subject to study of their microbiota-based effects. Risks associated with these interventions must also be stratified along individual microbiota profiles. Because this is not being done and has not been done, we must proceed with extreme caution, defaulting always to the power of the evolutionary principle which demands that we honor our connectivity to the natural world and to the wisdom of our own biology.
In the words of Rene Dubos:
“We are beginning, in fact, to witness the appearance of man-made diseases caused by the rapid changes in human ecology brought about by the new therapeutic procedures.”
His words echo like a gentle commentary, now turned into a threat under the weight of our disconnection from these foundational concepts. Let’s get back to basics and help our new mothers do the same.
“© Kelly Brogan MD. This work is reproduced and distributed with the permission of Kelly Brogan MD.