Multi-Omics Applications in Systems Microbiology: From Microbial Function to Biological Discovery

Systems microbiology increasingly relies on multi-omics strategies to study microbial communities, their functional activity, and their interactions with hosts and environments. The combined use of metagenomics, metatranscriptomics, metabolomics, proteomics, and related approaches is expanding the field beyond descriptive profiling toward more complete biological interpretation. These approaches are helping researchers connect community structure with metabolism, ecological behavior, immune modulation, and system-level function across diverse microbial settings.Despite this progress, important challenges remain in experimental design, harmonized measurement, biological validation, and the translation of multi-omics findings into robust microbiological insight. There is a growing need for studies that show how multi-omics can be applied effectively in real biological systems, generate testable hypotheses, and clarify microbial mechanisms in health, disease, agriculture, and environmental contexts.This Research Topic aims to highlight biologically driven applications of multi-omics in systems microbiology, with emphasis on discovery, validation, and functional interpretation rather than on algorithm development alone. We welcome contributions that use integrated omics to advance understanding of microbial communities, microbial functions, and microbe–host or microbe–environment relationships across experimental, ecological, agricultural, clinical, and translational settings.To gather further insights into the value of multi-omics in systems microbiology, we welcome articles addressing, but not limited to, the following themes:• Multi-omics studies revealing microbial metabolic, ecological, and functional dynamics• Applications of integrated omics to microbe-host interactions, colonization, and immune responses• Multi-omics approaches in infectious disease, environmental microbiology, and host-associated microbiomes• Single-cell, spatial, and longitudinal omics applications in microbial systems• Experimental frameworks linking omics profiles to phenotype, function, or mechanism• Biomarker discovery and translational microbiome applications supported by multi-omics evidence• Multi-omics-guided studies in synthetic biology, microbial engineering, and community design• FAIR data resources, reference datasets, and reproducible workflows that support biological reuse and interpretation• Case studies showing how integrated omics improves hypothesis generation, validation, or microbiological insightWe particularly welcome submissions where the main contribution is biological, experimental, or translational insight enabled by multi-omics, along with the introduction of a new computational integration algorithm or transformer-based framework.Article types considered include Original Research, Reviews, Methods, Mini Reviews, Perspectives, and Opinion articles. Topic editors: APOORV TIWARI, Khalid Raza Source: https://www.frontiersin.org/research-topics/79638/multi-omics-applications-in-systems-microbiology-from-microbial-function-to-biological-discovery