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Currently we’re living through a revolutionary re-evaluation of the biological definition of human (1). Aggregate data indisputably reveals that we are each not so much individuals as mammalian-microbe ecosystems. In such a landscape, choosing to examine microbes solely through the prism of pathogens is unsatisfactory, restricted and passe.

Actually, microbes tutoring our immunity is a natural dictate of human biology.

  • In utero, we are largely devoid of contact with microbes.
  • Yet how abruptly and permanently that changes as soon as we are born.
  • Immediately post-birth, our skin and mucosal surfaces become colonized by numerous species of microbes.
  • In the process, we change profoundly and for good from mammalian into a mammalian-microbe ecosystem and eventually microbes outnumber mammalian cells by ~10:1 in our bodies.
  • That’s not all. A non-mammalian mix of not just bacteria, fungi, and viruses but also protists and helminths become an indelible part of the human body for life.
  • This process is usually so seamless and uneventful that it largely escapes our notice but slowly and surely a body of knowledge is building up which suggests that the process of microbial colonization of our newborn bodies, both the sequence of species that colonize us as well as their relative abundance and frequency of contact is critical for ‘proper training‘ of our immune system (2, 3, 4).

What could be a more relevant example of an animal that incorporates microbes to train its immunity than the human?

In fact, an increasing number of chronic diseases are more accurately characterized as the outcome of persistent maladjustment between the mammalian and microbial components of the human ecosystem, a maladjustment that results in immune function dysregulation. Examples include allergies, autoimmunities such as rheumatoid arthritis, metabolic syndrome, type II diabetes, obesity, gut imbalances such as IBD (Inflammatory Bowel Diseases) and perhaps even neurodevelopmental and mental disorders such as autism and major depressive disorders (5, 6).

Another premise of the question is that a particular compelling argument would be sufficient to convince an anti-vaccine advocate of the error of their ways. I disagree.

  • Mere facts are unlikely to persuade against entrenched beliefs that are grounded in emotion, not intellect, especially sacrosanct, core beliefs that define a person’s identity.
  • This is especially true for anti-vaccine ideas, especially those that stem from overpowering fears concerning the health of one’s children.
  • Rather, personal accounts of former anti-vaccine advocates who got themselves and their children vaccinated are more likely to change minds about vaccines.
  • Such narratives have a greater chance of resonating emotionally than any sober, rational argument about the benefits of vaccines.
  • Widespread dissemination of such essays would probably be more helpful in helping to change minds.
  • Here are a couple of examples of such changes of heart about vaccines:
    I Used to Be an Anti-Vaxer
    I’m finally getting vaccinated. But not because of your shaming


  1. McFall-Ngai, Margaret, et al. “Animals in a bacterial world, a new imperative for the life sciences.” Proceedings of the National Academy of Sciences 110.9 (2013): 3229-3236. Page on wwu.edu
  2. Valdez, Yanet, Eric M. Brown, and B. Brett Finlay. “Influence of the microbiota on vaccine effectiveness.” Trends in immunology 35.11 (2014): 526-537.
  3. Ahern, Philip P., Jeremiah J. Faith, and Jeffrey I. Gordon. “Mining the human gut microbiota for effector strains that shape the immune system.” Immunity 40.6 (2014): 815-823. Page on els-cdn.com
  4. Sánchez, Borja, et al. “Intestinal microbiota as modulators of the immune system.” Journal of immunology research (2015). http://downloads.hindawi.com/jou…
  5. Weng, M., and W. A. Walker. “The role of gut microbiota in programming the immune phenotype.” Journal of developmental origins of health and disease 4.03 (2013): 203-214. Page on nih.gov
  6. Rook, Graham AW, Christopher A. Lowry, and Charles L. Raison. “Hygiene and other early childhood influences on the subsequent function of the immune system.” Brain research (2014). Hygiene and other early childhood influences on the subsequent function of the immune system