The bioactive compounds and microbial consortia contained in plant-based fermented foods support oral and gut microbiota, host immune function and metabolic resilience. This Review describes the impact of the fermented food microbiome on the oral–gut axis and identifies a strategic roadmap to integrate this edible microbiome into precision nutrition practices to promote health.

Advancing microbiome research beyond well-studied bacterial species is key to understanding the full functional diversity and potential of the human gut microbiome. In this Review, Turnbaugh and colleagues explore the unique metabolism and pathogenic potential of Eggerthella lenta, supporting the feasibility and utility of studying diverse human-associated bacterial species.

In this Review, Vázquez-Torres discusses our current understanding of how the dynamic interplay between microbial competition, host defences and Salmonella enterica serovar Typhimurium countermeasures determines the outcome of infection.

In this study, Wang et al. report that climate change-driven aridification shapes soil properties and plant–microorganism relationships across arid and semi-arid grasslands in China.

In this study, Wu and colleagues demonstrate that long-term nitrogen fertilization acidifies soils, altering soil properties and bacterial community composition in Tibetan alpine grasslands.

This study provides evidence that afforestation and reforestation can increase soil carbon storage and support soil microbial communities, thus highlighting their potential in nature-based climate solutions.

This study suggests that shifts in bioavailable heavy metals during soil remediation reshape microbial physiological traits, thereby increasing microbial carbon use efficiency and enhancing soil carbon storage.

Urban soils must move from providing single, engineered functions to supporting multifunctionality. Managing their microbiomes could simultaneously strengthen climate regulation, water retention, pollutant removal, biodiversity and human health, but only if biological restoration is coupled to risk assessment, long-term monitoring and equitable access.

Microbial interventions offer sustainable opportunities to enhance soil health and ecosystem functioning, but they can also have unintended ecological consequences. This Comment explores their benefits and risks, arguing for a shift in perspective from microbial products as agricultural inputs to tools for ecological restoration.