I wrote an opinion piece called 'Applying the core microbiome to understand host-microbe systems', which I was luckily enough to publish in one of my fave journals, Journal of Animal Ecology. This idea stemmed from a discussion with reviewers of a paper I had submitted, where each of the reviewers and editors had a very specific (and often different) idea of what the core microbiome meant. The core microbiome has traditionally pertained to what are likely to be functional microbes within a microbial community, but given with a bit of imagination we can link almost any trait to 'function' (commonness, stability, keystoneness, etc), as well as the fact that 'function' has numerous definitions (although these can be split into two major conceptual groups, as nicely summarized by Klaassen 2018), this has lead to the concept of the core microbiome being extremely widely applied (at least in ecological fields), yet not very well defined. This lack of definition makes it relatively unpopular with pure microbiologists, I believe, who apply it far less frequently than ecologists, and generally think of the core in terms of functional genes rather than key taxonomic units. I had a look through the host-microbe special issues of Molecular Ecology and Journal of Animal Ecology from 2018 before I wrote the piece, and found 14 articles, out of all published across the two special issues, applied or referred to the core microbiome. I reckon that was about a third of all papers.
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