. Author manuscript; available in PMC: 2025 Dec 11.

Published in final edited form as: Nat Rev Clin Oncol. 2025 Jun 27;22(9):627–639. doi: 10.1038/s41571-025-01049-3

TABLE 1 |.

Ecology terms translated to the management of the microbiota in oncology

Ecology term	Definition adapted to the microbiota of patients with cancer	Application to the management of microbiota in patients with cancer
Biodiversity	The variety of microbial species present in a complex microbiota population. A higher biodiversity is often associated with superior outcomes, although this view is not fully accurate.	Biodiversity indices, such as those proposed by Shannon¹¹⁶ and Simpson¹¹⁷, can be easily calculated from microbiome profiling data and provide a summary metric of the state of microbiota in a patient. Tracking how biodiversity changes (for example, through daily faecal sample analysis) can inform oncologists about microbial resilience and potential vulnerabilities during treatment.
Disturbance	Events that disrupt microbiota composition and function, such as antibiotic use, exposure to chemotherapy or dietary changes.	Treatments used for the management of patients with cancer, especially prophylactic antibiotics and chemotherapy, often shift microbiota composition and function. Monitoring disturbances can guide timely interventions to restore the microbiota, such as faecal microbiota transplantation¹⁰⁴.
Resilience	The ability of the intestinal microbiota to recover from disturbances, maintaining or quickly regaining its original state.	Resilience can be the objective of clinical interventions using designed mixtures of commensals that not only recover microbial functions damaged by cancer treatment but also form a population that can persist upon future disturbances.
Adaptive management	A strategic approach that involves continuously monitoring and adjusting interventions on the basis of the current state and dynamics of the microbiota. This strategy might be used to optimize treatment outcomes in patients with cancer.	Real-time microbiota monitoring enables precision interventions, such as modifying antibiotic regimens or administering defined microbial consortia to improve response to cancer treatment.
Functional redundancy	The presence of multiple microbial species that perform similar functions within a host. Redundancy can ensure that essential functions are preserved even if some species are lost owing to disturbances.	Oncologists can leverage functional redundancy to maintain beneficial ecosystem services (for example, butyrate production for gut barrier integrity) despite fluctuations in microbial composition. This principle supports targeted interventions that enhance key microbial functions.
Ecosystem services	The key functions and benefits that microbiota provide to the host, including nutrient absorption, protection against pathogens and modulation of the immune system.	Specific microbiota-derived metabolites (such as short-chain fatty acids or tryptophan derivatives) influence immune responses and treatment efficacy. Cancer treatments that affect the microbiota can compromise their ability to deliver services to the host.
Trophic interactions	The feeding relationships between different microbial species, which influence the flow of nutrients and energy through the microbiota, and are crucial for maintaining its balance and function.	Cancer treatments can disrupt trophic interactions, with unintended consequences such as the expansion of opportunistic pathogens. Understanding these interactions can guide microbiota-based interventions.
Niche	The specific role or function of a microbial species within the microbial ecosystem. Each species occupies a niche that includes not only what it does but also how it responds to other microbes and the physical environment.	Certain microbes, such as Akkermansia muciniphila, are linked to enhanced responses to immune-checkpoint inhibitors²⁵. Identifying and supporting their niches could help to optimize treatment strategies.