The Story of our Microbiome

Any good author knows how to adeptly use metaphors in telling stories.  Sometimes in medicine we view metabolic processes through the lens of metaphors.  We may look at the cardiovascular system as a pumping station or a transport highway.  We may look at the immune system as the armed services defending the body.  We take these metaphors for granted forgetting that history did not always use the same metaphors especially when our understanding of the body’s physiology was lacking or even misguided.

            As we learn more about the microbiome, the collection of billions of bacteria and other organisms in our GI tract, our current metaphors both helps and hinder our understanding.  No one metaphor fully encapsulates the intricate interplay between these microbes and our bodies.  Nicolae Morar and Brendan J. M. Bohannan offer an enlightening examination of 5 current metaphors in the June 2019 edition of the Quarterly Review of Biology. My quick summary follows here.

            The “organ” metaphor views the mass of microbes as an organ which can be targeted or transplanted. Specific probiotics can be prescribed.  A complete transplant may be recommended to rid oneself of Clostridium difficile infection. However, true organs are more static whereas the microbiome constantly changes. 

            The “immune system” framework considers this microbial collection as a part of the immune system.  This is supported by comparisons of vaginal birthed versus C section children and how their gut bacteria differ.  It is also supported by the dependence by the immune system on the microbiome for its strength.  This metaphor misses the metabolic contributions of the bacteria to our daily functioning.

            The “superorganism” view considers the microbiome and the human body as part of a larger organism. This considers the effects of missing bacterial niches on our health.  However, the heritability influence required for this view to predominate has not been upheld in studies. 

            A “holobiont” metaphor proposes that humans and bacteria evolved together with the microbes fulfilling specific roles in metabolism and function.  This view has contributed more to the rise of probiotics, but again falls short in requiring inheritance of bacteria from one generation to the next. 

            Finally, the “ecosystem” view considers the microbiome as a more dynamic entity fluctuating between different states.  This view fails to adequately recognize clear connections between the microbes and their human host. 

            Each of these metaphors compete for the story of our microbiome.  Scientists prefer viewing systems through single metaphors, but the microbiome may not succumb to the scientists wishes in this case.  Each metaphor allows us to find and use various therapies like fecal transplants or probiotics. 

            For a functional medicine doctor like myself, keeping an open mind to potential therapies and possible root causes for patients is nothing new.  On the other hand, I do like simplicity in understanding and explaining our therapies to patients.  For now, I will have to be content with a variety of story metaphors in helping patients restore their health.  Even so, I can hope for our understanding of this amazing interplay between microbes and our bodies to grow in the coming years of research. 


Nicolae Morar, Brendan J. M. Bohannan. The Conceptual Ecology of the Human Microbiome. The Quarterly Review of Biology, 2019; 94 (2): 149 DOI: 10.1086/703582


Thanks to Science Daily where a fuller summary can be found:

University of Chicago Press Journals. “A pluralistic approach to thinking about the human microbiome.” ScienceDaily. ScienceDaily, 5 June 2019. <>.


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