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Microbiomes are generally conceived of as one element of a pair – their partner being the habitat they occupy. I call this common scientific practice “pair-thinking”. Research into antimicrobial resistance and its underlying anthropogenic drivers highlight the growing footprint occupied by mobile genetic elements (MGEs). Furthermore, these MGEs are known to circulate widely between microbiomes. Using a pluralistic framework anchored within a processual microbial ontology, these observations point to a reframing of microbiomes as networked and collective, thus challenging pair-thinking. Such a shift has implications for the future of microbiome research, from conceptual and methodological perspectives, and exposes the impacts of anthropogenic forces on the evolution of microbiomes and the functions they carry out.