Multispecies Interactions and Microbial Ecologies

Microbial communities form intricate networks of interaction that span across taxa, environments and hosts. In natural and engineered systems, bacteria, archaea, fungi and viruses engage in metabolic cross-feeding, chemical signalling and spatial structuring to establish stable or dynamic consortia. These multispecies interactions regulate nutrient cycling, influence host development and immunity, and drive community resilience under stress. Advances in multi-omic profiling, high-resolution imaging and computational ecology have revealed that microbial ecologies are not merely sums of individual species but emergent systems in which interkingdom partnerships and competition shape functional outcomes. From rhizosphere consortia that boost plant productivity to gut microbiota that calibrate human physiology, the holobiont concept has reframed organisms as composite entities. Manipulation of these networks through synthetic consortia, probiotics or ecological engineering holds promise for sustainable agriculture, bioremediation and novel therapeutic strategies. Yet understanding the context-dependence of interactions and the rules governing community assembly remains a key challenge for translating basic insights into real-world applications.

Research from Nature Portfolio

Recent studies have articulated a broad social-science and humanities agenda for microbiome research, underscoring the need for dialogue between natural scientists, policymakers and lay publics to ensure ethically and culturally informed interventions. This work highlights how collective identities and regulatory frameworks shape the uptake of microbiome technologies and calls for participatory models that integrate lived experience with biological data.

Parallel research has explored the shift from an antibiotic-dominated worldview towards more probiotic, ecological perspectives. By deploying participatory metagenomics in domestic settings, researchers have enabled non-expert households to visualise and interpret their own kitchen microbiomes. This approach has illuminated the sensory, emotional and cultural dimensions of human–microbe relations, and proposes new metaphors and visual tools for engaging publics in adaptive microbiopolitics.

Multispecies Interactions and Microbial Ecologies publication trend

The graph below shows the total number of articles in multispecies interactions and microbial ecologies across all publications each year (not limited to Nature Index journals).

Technical terms

Microbiome: The collective genomes and ecological functions of microbial communities in a defined habitat.

Metagenomics: The sequencing and analysis of genetic material recovered directly from environmental samples.

Dysbiosis: A state of microbial imbalance associated with disease or environmental disturbance.

Holobiont: A host organism and its associated microbial communities considered as a single ecological unit.

Multispecies interactions: The dynamic relationships among diverse microbial taxa and their hosts that influence ecosystem structure and function.

References

1. Setting the agenda for social science research on the human microbiome. Humanities and Social Sciences Communications (2020).
2. Unsettling antibiosis: how might interdisciplinary researchers generate a feeling for the microbiome and to what effect?. Humanities and Social Sciences Communications (2018).
3. Making the microbiome public: Participatory experiments with DNA sequencing in domestic kitchens. Transactions of the Institute of British Geographers (2019).
4. Multispecies entanglements in the virosphere: Rethinking the Anthropocene in light of the 2019 coronavirus outbreak. The Anthropocene Review (2020).
5. “You can’t manage what you can’t measure”: Regenerative agriculture, farming by numbers, and calculability in soil microbiopolitics. Environment and Planning E Nature and Space (2024).