What plankton and whales can teach us about the human microbiome


Imagine all the diverse creatures of the ocean’s plankton population were to disappear due to climate change, ocean acidification, micro plastics, etc. This would have devastating consequences for all the higher species that depend on plankton, largely via filter-feeding. Populations of jellyfish and whales, for instance, would suffer, as they rely on plankton to survive.

What if, in our plankton-depleted ocean, we artificially restore jellyfish or whales—what would happen to them? They would likely survive a short time by consuming other creatures, but would likely again die because there is no plankton.

In other words, plankton represents a keystone collection of species that make life for higher creatures on the food chain possible. Without plankton, there are no jellyfish and no whales.

The same principle applies in the human microbiome: There are keystone species that, by their presence and production of metabolites and biofilms, permit the proliferation of other species. Without these keystone species, other bacterial species are less likely to survive.

I highlight this issue because I believe that this explains some fundamental uncertainties in our understanding of the human microbiome. For example, if your mother passed the species Bifidobacteria infantis onto you as a newborn as you passed through the birth canal or in breastfeeding, this species stays with you for years, perhaps a lifetime (until, of course, you are given a course of antibiotics, you are exposed to glyphosate or other herbicides, etc.). But if you take Bifidobacteria infantis later in life as a probiotic, it likely will not persist for more than a few days to weeks—but why? I believe it parallels the situation in which we restore jellyfish but fail to restore plankton: Keystone species were not restored. If we were to introduce Bifidobacteria infantis into a microbiome that includes keystone species that support the proliferation of Bifidobacteria infantis, we might then allow this species persist for a long time.

Problem: We do not yet know what species/strains are among those that serve this keystone, or foundational, function. I believe that Akkermansia muciniphila and Lactobacillus reuteri are among those keystone species, as they have such spectacular features that modify the persistence and behavior of other species. The science is evolving but remains incomplete. But I believe this explains why we can take the many species in a commercial probiotic yet virtually none of the species/strains contained take up more than a few weeks residence, then disappear.

I also believe that the probiotic of the future will not contain just a haphazard collection of species (with no strain specified!), but will need to contain the several crucial keystone species whose presence supports the proliferation of dozens, even hundreds, of other species. In other words, the key may not be the number of species/strains contained in a probiotic, but the inclusion of keystone species. Just as first restoring plankton allows jellyfish and whales to thrive once again, so restoring the keystone species to your microbiome may allow all the other species/strains to thrive to support your health.

Stay tuned, as I believe we may be just months or a couple of years away from such important insights.



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