De-Extinction and the Microbiome

by Ben Novak

Current research on microbiomes reveals that an organism’s microbiota are co-evolved with the host species, but not to a point of specificity that is problematic between related organisms (such as one kind of pigeon in relation to another). While genetic and epigenetic factors play between the host organism and the microbiota — determining which microbes successfully colonize the gut and other organs — the ultimate dictating force of the composition of an organism’s microbiome is diet and environment.

For de-extinction purposes, the microbiome of the living species used to engineer the extinct species is the microbiome that the revived extinct species will first inherit. In thinking of pigeons, there have been many pigeons born and raised in captivity that were fostered by surrogate parents (such as Victorian crested pigeon chicks raised by nicobar pigeons and nicobar pigeon chicks raised by rock pigeons). In these cases the chicks were exposed to the microbiome of a different species, yet developed normally and were healthy. The chicks were introduced to their own species’ flocks successfully. It works so well that it is a standard practice. This shows us that microbiomes between related species are compatible. Since environment and diet change microbiomes, we can expect that when introducing the extinct species into its former habitat and giving it its former diet, the microbiome will change and become similar to the original microbiome of the extinct species. Evidence for these fluctuations in microbiomes is well documented in research being published on microbiota.

When human beings travel around the world, their gut flora change in composition, shifting the ratios of different microbial species and even introducing new species. Several research groups have noted differences in microbiomes between human populations around the world. These differences reveal that being human is not dependent on a specific set of microbes. No one would say that pygmies in the Congo are an incompatible species separate from Europeans solely due to their microbiome. Strains of lab mice have had their microbiomes manipulated, and in some cases sterilized for experiments, yet they are still mice and not something “new” or “different”. Thus in reference to de-extinction, the microbiome of a newly created extinct species is not a determining factor in deciding how to classify the extinct species. If the passenger pigeon had not gone extinct, its microbiome today would be different than it was in the 1800s, due to climate change and the introduction of new plants into North American forests, as well as exposure to feral rock pigeons.

Microbiomes of revived species will affect the biology of the species, but are in no way a major obstacle for de-extinction, rather a topic that requires creative research and thinking. Microbiome research is part of the considerations of our de-extinction efforts. Based on the science of microbiomes, we do not expect the differences in the microbiome of the new passenger pigeon from the historical microbiome to inhibit the reproduction and successful reintroduction of new passenger pigeons to the wild.