The Epidemics of Chronic Diseases also comes from an Unhappy Microbiota Roughed up by Conventional Medicine’s Irrational Standards of Care

As microbiota destroying toxins, fast foods, shower chlorine, pesticides, antibiotics and other pharmaceutical drugs have increased, so have the epidemics of chronic diseases. In this blog-article, i will first show that there exists more than a  strong correlation between lost ancestral gut bacteria among humans and the skyrocketing rise in epidemic diseases (Section A). I will conclude on how Holistic Medicine can help to mitigate and even solve this mainstream medical phenomenon  (Section B).


The losses of particular bacterial species of our ancestral microbiota have altered the context in which immunological, metabolic and cognitive development occur in early life, which results in increased disease. Over succeeding generations, there has been a major shift in the microbiota equilibrium and diversity. The millennial Generation and more and more adults of the preceding generation have been progressively losing microbial diversity. As a consequence, the microbiota are less able to signal to the innate immune important codes. With lifestyle assaults against the “milieu intérieur”, aggressive opportunistic microorganisms have prevailed triggering havoc in both the immune system as well as in the brain. With these shifts in the equilibria, the adaptive immune system becomes less tolerogenic and more reactogenic, especially in babies who come to Earth without Holistic natural birthing environment. All of this feeds the current epidemics of autoimmune and inflammatory diseases, including with prolonged latency.


Section A

Is the Correlation between Microbiota assaults and the Chronic Disease Epidemic causative ?

This epidemic of chronic disease first started in the developed and industrial world and has spread like cancer to the entire world as most countries have imported different aspects of the American model of “convenient” corporate drug-based medicine and fast foods.

These include the rises in cases of autism, lupus, chronic fatigue, obesity, asthma, hay fever, food allergies, inflammatory bowel disease, juvenile (type 1) diabetes and cancer among many others pathologies.

Microbiota Basics

One of the big medical revolutions of the 21st century is the identificataion of the gut’s microbiome and how its genome affects human eukariotic genes. In our intestines, we humanes house trillions of microbes, in particular archae, bacteria, virus and fungi, all of which are beneficial if the diversity, the balance and the composition have evolved holistically over the last 2 billions years. As humans evolved in synergy with the bacterial environment, so did these critters. Our mitochondria has been determined to actually be a parasitic bacteria that got attached to your cell. Like with many other bacteria all throughout our body, the bacteris that evolved into what is today the mitochondria was quite beneficial for both the human host and the bacteria. In a similar way, all of our other bacteria (mouth, skin, gut etc) have been selected over long time periods in order to optimize the microbiota-human synergy, in conformity with evolutionary mechanism. 1. ( )

The Crucial Period. Early Life and Before

Baby delivering is the crucial period during which the adult microbiome becomes established 2, ( ) In early life, the context is set for the important developmental decisions that are required for the immune system to distinguish between what is self and what is not self, for metabolic organs to partition how much energy to expend or to save, and for the brain to determine how to respond socially to a person who might be either a friend or a foe.


. An important concept for all of these sites concerns the timing of developmental windows11. At which point in life are the major immunological decisions made and when does the developmental window close? Although there is unlikely to be an absolute answer, as this window is probably to some degree specific to each individual, there probably will be a time-gradient of opportunity to permit interventions.
even with full resolution of the microbiota composition, the damage to other physiological processes, such as the immune system, has already occurred. We know that severe infections during early childhood stunt the height trajectory of children, from which recovery is limited. Similarly, exposure to therapeutic antibiotic doses early in life may cause profound and sustained microbiota perturbations, which can lead to altered immunity 8.

Causes of the disappearing microbiota

However, this developmental equilibrium has been disrupted by elements of modern life that have led to the loss of crucial microbial taxa, and to the loss of their roles in shaping human physiology 1,3.
First, strong evidence is emerging for the importance of vertical transmission of the key microbiota taxa from mother to child4.

Such a pattern of transmission suggests that if there are extinctions of microbial taxa in one generation, this loss would be passed down to the next generation, unless there are opportunities for the missing taxa to be regained by horizontal transmission3.

One example of a cause of decreased vertical transmission of the microbiota is the caesarean section epidemic. In the United States, one-third of babies are born by caesarean section. For such traumatic births, the intergenerational transfer of microorganisms, which is a conserved feature of essentially all animals, is diminished.

Another example affecting the intergenerational transfer of the microbiota is the widespread use of antibiotics during pregnancy.
A third, given baby formula milk instead of mother’s macrobiota rich milk. and the feeding of formula milk as a replacement for breast milk. Formula milk includes the macronutrients that are necessary for healthy infant growth, but it almost completely lacks many of the micronutrients, such as particular oligosaccharides, that foster the survival of inherited and beneficial microbiota. The composition of breast milk seems to have evolved to favour (select for) those microorganisms that have a well-established commensal relationship, having been passed down over the millennia.
Over sanitation, from chlorine has reduced consdieratly horizontal transmission of the microbiota.

Other Major factors include antibiotic exposures of infants,
Exposure to antibiotics may have the greatest impact on the early life microbiota — due to both the extent and timing of their use. The importance of intergenerational transmission of the microbiota amplifies the effects of prenatal events, such as the antibiotics given to a mother during pregnancy and just at birth (and even later, as they are excreted in milk).

Evidence is accumulating that antibiotic use by young women before pregnancy could also be contributing to health problems in their children.

The microbiotat is not uniformly resilient against conventional medicine’s assaults

the microbiota is not uniformly resilient 5. ( ) In young children in particular, (antibiotic) insults may change the development of the ‘adult’ microbiota, and not allow its normal maturation 6.
Antibiotics not only temporarily perturb the microbiota, but can also lead to the extinction of some microbial taxa, with additive effects on host physiology.

Studies in mice have shown that short-term, low-dose antibiotic exposures early in life have long-term effects on host phenotypes, such as adiposity and the levels of immunological mediators7.

Immune effects of the disappearing microbiota

This combination, of a loss of commensals in one generation (for example, owing to antibiotic use or formula milk feeding) and the diminution of both vertical and horizontal transmission, suggests that microbial extinctions become fixed and cumulative across generations3. Therefore, the microbial disappearances are increasing and the loss of diversity is steadily worsening. There is already evidence to support the reality of microbial extinctions9 and of cumulative effects over generations10.

These ideas are particularly relevant to immunology, because early life is the period when the adaptive immune responsiveness of a host develops, and when important decisions regarding responsiveness versus tolerance are made11.

( ) ft In immunology, as in all of developmental biology, context is crucial. Although innate immunity has evolved, in part, to defend against high-grade pathogens, more subtle interactions (for example with commensal microorganisms) and those innate responses requiring amplification benefit from an engaged adaptive immune response. The frontier regulating the development of adaptive immunity may be the most context specific, and carries the greatest long-term consequences.

A growing body of evidence indicates that both the prenatal (maternal) microbiota12 and the early life (infant) microbiota have crucial roles in the later development of adaptive immunity13.

Section B

Holistic Medicine

Vaginal birth, Breastfeedind and Dirt playing are crucial

Pprebiotics and probiotics also.

Avoiding what destroys: chlorine GMO glyphosate, antibiotics….leaky gut….gluten, drugs etc even stress.

With a disordered microbiome, opportunistic organisms may have disproportionate roles, by suppressing developmentally beneficial microbiota taxa..

In Search for a Unified Theory

Although microbiota science and microbiology have taught us a lot with regards to the microbiome, more research is warranted because of the cause consequence issue. Once disease is manifest, any microbial abnormalities that are detected could be a consequence of the disease and/or of the pharmacological agents that are used to treat the disease, rather than its cause. But it could also be its cause, since scientists have shown that they were able to reverse obesity and autism with fecal transplants.

Understanding the threats and stopping the damage to the next generation are the first orders of business. With deeper knowledge of immunological development, for example, we might be able to define the best location, timing and mechanism to intervene.


The remarkable aspect of vertebrate life is not that we respond to pathogens, but that we so easily tolerate the overwhelming numbers of commensal microorganisms that we host.

the interactions of the early life microbiome with the host are setting the immunological tone for the remainder of the host’s lifespan

For immunologists, armed with the discoveries of modern science, it will mean a return to their historical nineteenth century roots in microbiology. with the emergence of the microbiome as an unanticipated force of nature.

With the decline of the ancestral microbiota,

ultimately we will have to restore our lost microbiota to optimize human health and to reverse the disease epidemics that are increasing around the world. This long-term scientific challenge will require immunologists and medical scientists to work in the interstices of microbiology


Reference and Precision Notes

Blaser, M. J. Who are we? Indigenous microbes and the ecology of human diseases. EMBO Rep. 7, 956–960 (2006).

Yatsunenko, T. et al. Human gut microbiome viewed across age and geography. Nature 486, 222–227 (2012).

Blaser, M. J. & Falkow, S. What are the consequences of the disappearing human microbiota? Nat. Rev. Microbiol. 7, 887–894 (2009).
Moeller, A. H. et al. Cospeciation of gut microbiota with hominids. Science 353, 380–382 (2016).

Dethlefsen, L. & Relman, D. A. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc. Natl Acad. Sci. USA 108, 4554–4561 (2011).

Bokulich, N. A. et al. Antibiotics, birth mode, and diet shape microbiome maturation during early life. Sci. Transl. Med. 8, 343ra382 (2016).

Cox, L. M. et al. Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences. Cell 158, 705–721 (2014).

Ruiz, V. E. et al. A single early-in-life macrolide course has lasting effects on murine microbial network topology and immunity. Nat. Comm. (in the press).

Clemente, J. C. et al. The microbiome of uncontacted Amerindians. Sci. Adv. (2015).

Sonnenburg, E. D. et al. Diet-induced extinctions in the gut microbiota compound over generations. Nature 529, 212–215 (2016).

Simon, A. K., Hollander, G. A., McMichael, A. Evolution of the immune system in humans from infancy to old age. Proc. R. Soc. B 282, 20143085 (2015).

Gomez de Agüero, M. et al. The maternal microbiota drives early postnatal innate immune development. Science 351, 1296–1302 (2016).
Show context

Gensollen, T., Iyer, S. S., Kasper, D. L. & Blumberg, R. S. How colonization by microbiota in early life shapes the immune system. Science 352, 539–544 (2016).

Markle, J. G. et al. Sex differences in the gut microbiome drive hormone dependent regulation of autoimmunity. Science 339, 1084–1088 (2013).

Livanos, A. E. et al. Antibiotic-mediated gut microbiome perturbation accelerates development of type 1 diabetes in mice. Nat. Microbiol. 1, 16140 (2016).

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Trained in Conventional Medicine, Traditional Chinese Acupuncture, Naturopathy, oenology and Law, Professor Joubert teaches in different parts of the world how to extend a healthy Lifespan to 120 years and beyond, Pr. Joubert is working on a Documentary and book that redefines Medicine in light of new discoveries, ancient wisdoms, innovative research and holistic science, but he can be nonetheless available to coach patients back to homeostasis, wellbeing & Joie de Vivre. On occasion, Pr Joubert can also coach health professionals to better protect their holistic practice when they must deviate from outdated and irrational “standards of care”. See links on “Contact” and “Mission” (under the “About” link) for details.

Posted in Chronic Diseases and their Reversal with Holistic Savoir-Faire, Microbiota, Microbiome, Intestinal Flora, Cultured Foods & Prebiotics

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