Microbiome research has predominantly focused on correlating microbial abundance profiles with host phenotypes and environmental factors, yet clear evidence of causality remains elusive. This gap necessitates a shift towards research designs that elucidate causal relationships and provide insights into taxon-function relationships, rather than merely correlating microbiome profiles with external factors. The role of species composition in microbial community functions is context-dependent, and a significant gap exists in understanding the taxon-function decoupling (TFD) pattern. This decoupling is particularly pronounced in environments subjected to anthropogenic pressures, such as chemical contaminants and antibiotics, compared to natural ecosystems. Functional redundancy (FR) within microbiomes, which may explain this decoupling, is not well understood. Positive interactions within microbiomes, such as horizontal gene transfer (HGT), cross-feeding, and quorum sensing, are crucial for understanding FR. However, the impact of antagonistic interactions on FR remains underexplored. Molecular Omics and metabolic computational models offer promising avenues to investigate these complex microbial interactions.

This research topic aims to integrate experimental and computational approaches to achieve a comprehensive understanding of the functional redundancy underlying taxon-function decoupling patterns in microbial ecosystems, particularly under natural versus anthropogenic conditions. The primary objective is to delineate the mechanisms that govern positive and antagonistic interactions within microbiomes and their contributions to functional redundancy. By leveraging advanced omics technologies and computational models, the research seeks to predict, quantify, and validate microbial metabolic abilities, thereby moving from a descriptive taxon scope to a function-oriented phase in microbiome research.

To gather further insights into the boundaries and limitations of this research, we welcome articles addressing, but not limited to, the following themes:

- Mechanisms of horizontal gene transfer (HGT) in microbial communities
- Cross-feeding interactions and their impact on functional redundancy
- Quorum sensing and its role in microbial community stability
- The influence of anthropogenic factors on taxon-function decoupling
- Computational models for predicting microbial metabolic functions
- Empirical validation of computational predictions using novel experimental techniques
- The role of antagonistic interactions in shaping microbial community structure and function
- Metabolite exchange and its implications for microbial interactions and ecosystem stability

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Frontiers in Microbiomes

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