An increasing number of microorganisms are classified as 'pathobionts' (i.e., organisms that can cause harm under certain circumstances) but there exist no universally used criteria for this definition. In particular, the term is often used for categorizing disease-associated taxa without proof of 'causality'. This creates confusion and distracts from explicitly searching for beneficial functions of these organisms that they may in fact have. Here, we discuss why this term in its current use, and its apparent simplicity, may obscure the complexity of microbe–host and microbe–microbe interactions that define (the status of) the gut ecosystem. Pathobionts can cause or promote disease only when specific genetic or environmental conditions are altered in the host.Conditions under which pathobionts exhibit virulence include impaired host immune defenses and altered microbiota composition.Several microorganisms classified as pathobionts can also exert beneficial functions on their host in different scenarios.Currently the term 'pathobiont' does not comprise a well-defined concept and should therefore be revised. In this opinion article, we suggest an alternative terminology.