Research in microbial ecology and microbiomics focuses increasingly on ecological questions, such as about resilience, that is, the capacity for a system to return to a stable state following a disturbance.
These questions can and should be framed as part of a much longer history of the concept of “regeneration”: the process of, or capacity to, repair or to return to a “normal” state. We explore this connection by asking: How are microbial communities defined, taxonomically or functionally? Are they individuals or parts of individuals like organs? What is community (or microbiome) function and how can it be regenerated following disturbance? What is the relation between the traditional ecological ideas of resilience, succession, assembly, and restoration and the regeneration of microbial communities? How do we define a normal ecological community? How do we define a pathological or diseased community and how can it be “repaired” or what capacities enable self-repair? Is regeneration a good metaphor for describing microbial community change over time?