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The composition and function of microbiomes are critical for most animals and plants, leading some to suggest that hosts and their microbiomes should be considered as single ecological unit—the holobiont. This Open Highlights Collection explores how relationships between hosts and microbes have evolved over time. Open Highlights use recent PLOS Biology research articles as keystones around which to nucleate a short synthesis of up to ten related research articles from other PLOS journals and from the wider Open Access corpus.