Wastewater treatment has evolved from a pollution-control strategy to a resource recovery platform that supports circular economy principles and sustainable environmental management. Microbial communities play central roles in nutrient cycling, organic matter degradation, carbon sequestration and the removal of emerging contaminants throughout wastewater treatment processes. This review synthesizes current knowledge on microbial community dynamics in domestic, industrial and agricultural wastewater treatment systems, emphasizing their functional roles in biological nutrient removal, enhanced biological phosphorus removal and resource recovery. Recent advances in metagenomics, metatranscriptomics, metaproteomics, fluorescence in situ hybridization (FISH) and artificial intelligence have significantly improved the characterization and monitoring of wastewater microbiomes, enabling more efficient process optimization and predictive management. The review also discusses the growing importance of wastewater surveillance for monitoring antimicrobial resistance genes, pathogenic microorganisms and contaminants of emerging concern, highlighting their implications for environmental and public health. Emerging technologies, including bio-electrochemical systems, microbial fuel cells, immobilized microbial consortia and anaerobic resource recovery platforms, demonstrate considerable potential for improving energy efficiency and reducing greenhouse gas emissions while enhancing nutrient recovery. Despite substantial technological progress, challenges remain regarding large-scale implementation, operational stability, standardization of multi-omics approaches and integration of biological and engineering processes. Future wastewater treatment facilities are expected to function as integrated biorefineries that simultaneously recover water, nutrients, energy and valuable bioproducts while minimizing environmental impacts. Continued advances in microbial ecology, systems biology, artificial intelligence and process engineering will be essential for developing resilient, low-carbon wastewater treatment systems that support sustainable resource management and public health protection.

The human gut microbiota plays a central role in shaping host immunity, metabolic homeostasis and resistance to infection. Beyond microbial metabolites, increasing evidence highlights the importance of microbial and probiotic-derived proteins as key mediators of host-microbe communication. These proteins participate in immune signalling, epithelial barrier regulation and competitive interactions with intestinal pathogens. This review synthesizes current knowledge on the protein biochemistry of gut microbes and probiotics, emphasizing their mechanisms of immune modulation and roles in host-pathogen interactions. We discuss surface-associated proteins, secreted effectors, peptides and extracellular vesicle associated proteins that influence innate and adaptive immune responses. Furthermore, we explore how probiotic strains counteract pathogenic microbes through protein-mediated mechanisms and immune training. Finally, we highlight translational implications, emerging technologies and future directions for protein focussed microbiome research. This integrative perspective aims to advance the mechanistic understanding of gut microbiota-immune interactions and inform the development of next generation probiotic and therapeutic strategies.