AUTHOR=Fernández-Gómez Paula , Leong Dara , Berg Gabriele , Brennan Fiona , Caruso Tancredi , Charles Trevor C. , Cocolin Luca S. , Lange Lene , McAuliffe Olivia , Maguin Emmanuelle , O’Sullivan Orla , Sanz Yolanda , Sarand Inga , Sessitsch Angela , Smidt Hauke , Brereton Nicholas , Candela Marco , Kenny John , Kostic Tanja , Mahony Jennifer , Wagner Martin , Cotter Paul D. 

TITLE=Harnessing agri-food system microbiomes for sustainability and human health

JOURNAL=Frontiers in Science

VOLUME=Volume 3 - 2025

YEAR=2025

URL=https://www.frontiersin.org/journals/science/articles/10.3389/fsci.2025.1575468

DOI=10.3389/fsci.2025.1575468

ISSN=2813-6330

ABSTRACT=Food system microbiomes include complex microbial networks that range from soil and marine environments to primary agriculture, farming, food processing, and distribution, and which influence human and environmental health. Advances in “omics” technologies, such as metagenomics, metatranscriptomics, metaproteomics, metabolomics, and culturomics, and their integration have deepened our understanding of microbiome dynamics and interactions. This growing knowledge is being leveraged to develop microbiome-based solutions enabling more sustainable food systems. This review explores microbiome interconnections along the food system and how this and other knowledge relating to microbiomes can be harnessed to, among other things, enhance crop resilience and productivity, improve animal health and performance, refine management practices in fishing and aquaculture, or prolong shelf life and reduce food spoilage during distribution. The often-overlooked role of bacteriophages on shaping microbiomes is discussed, as is the impact of diet on the human gut microbiota and, in turn, health. Despite advances, knowledge remains incomplete in particular areas and targeted experimental approaches are necessary to fill these gaps—going beyond merely predicting microbiome functionality. Ultimately, the ideal development of microbiome-based innovations in food systems will require collaboration between stakeholders and regulators to ensure safety, efficacy, and widespread adoption, unlocking its full potential to improve the health of animals, humans and the environment globally.