Apparently, there is a « microbe revolution » going on these days. Without being a specialist at all, I see it as a critical step in modern biology in the sense that it gets us facing the choice between two roads ahead.
The first option is obviously to expand the notion of what is an individual, from one nuclear DNA and its expression to multispecies DNA and its interconnection. This consists in trying to maintain (save?) the reductionist paradigm of Neo-Darwinism*, which is in essence a neo-mechanism.
But this option raises questions such as where is the physical limit between holobionts, since microbes can come in and out of my body and even of my cells? And why should we consider the host-microbes interactions as a part of one larger individual while we’re leaving the other interactions outside the holobiont at the same time? Ultimately, why not considering a whole ecosystem, or even the biosphere, as one big holobiont? And in this case, what would be the space left for selection and competition as the drivers of evolution? These could be serious epistemological issues, in my opinion.
On the other hand, we could go the other way and expand the notion of environment (or rather ecosystem) to the very inside of organisms. This is a much risky and foggy direction, but it looks so much more exciting at the same time. And to be honest, I see it as a moral emergency that we change our view on nature in a time when we are turning the world into a desert for living diversity.
This second option is for me a revolution in a much more deep sense, because it breaks away from the so-called « modern synthesis » of the genomic era, when any questions had to be answered by a gene locus and a more or less deterministic biosynthetic pathway. But it requires that we turn away from the all-mighty paradigm of selfish individuals or/and genes and start considering a world where relations are prior to entities, that is a constructivist and pluralistic world saturated of polysemous signalling activities, where the « me » and the « non-me » are becoming pretty blurred, negotiable, relative.
This may not fit into our rather fantastic vision of science as the production of unequivocal and permanent causal relations emerging through technological and statistical processes, but it could be a still more exciting and moving challenge : questioning the unending possibilities and modalities of coexistence in a pluralistic universe.
* Read for example Bordenstein S R & Theis K R, 2015. Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes, PLoS Biol 13(8).