Volume 1 Issue 1 (2025)

Microorganisms, including bacteria, archaea, fungi, and viruses, have evolved intricate molecular mechanisms to regulate gene expression, transduce signals, and adapt to environmental stresses. This review synthesizes recent advances (2022–2025) in microbial molecular biology, focusing on conserved and taxon-specific strategies in gene regulation, signal transduction cascades, molecular adaptation to niche environments, stress response pathways, and core cellular processes. We highlight cross-taxon similarities in regulatory modules, such as two-component systems in bacteria and archaea, RNA-based regulation in fungi and viruses, and stress-induced chromatin remodeling in eukaryotic microbes. Additionally, we discuss how these mechanisms contribute to microbial survival in extreme habitats, host-pathogen interactions, and biogeochemical cycling. Understanding these conserved and divergent molecular processes provides insights into microbial evolution and offers potential targets for antimicrobial development and biotechnological applications.

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Microbial genomics and functional genetics have undergone transformative advances over the past decade, driven by breakthroughs in genome sequencing technologies, multi-omics profiling, and gene-function validation tools. This review synthesizes recent progress (2022–2025) in microbial genome sequencing, functional genomics, transcriptomics, proteomics, metabolomics, and gene-function discovery, highlighting their integration to unravel microbial biology at unprecedented resolution. We discuss how high-throughput sequencing has expanded the microbial genomic landscape, enabling the characterization of uncultured taxa via metagenomics and single-cell genomics. Furthermore, we explore how multi-omics approaches (transcriptomics-proteomics-metabolomics) have facilitated the annotation of novel genes, elucidation of metabolic pathways, and identification of genotype-phenotype relationships in diverse microbial systems—from extremophiles to host-associated microbiomes. We also address technical challenges and emerging solutions in gene-function validation, such as CRISPR-based tools and synthetic biology approaches, and their applications in ecological research and biotechnology. Finally, we outline future directions for microbial genomics, including the integration of artificial intelligence with multi-omics data to accelerate gene discovery and predict microbial behavior. This review underscores the pivotal role of microbial genomics and functional genetics in advancing our understanding of microbial diversity, ecology, and evolution, while unlocking new opportunities for biotechnological innovation.

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Host–microbe and microbe–microbe interactions are fundamental to life on Earth, governing processes ranging from host health and disease to ecosystem function. Over the past decade, advances in molecular biology, multi-omics, and imaging technologies have unraveled the complex molecular mechanisms underlying these interactions, revealing how microbes communicate, compete, and cooperate with each other and their hosts. This review synthesizes recent progress (2022–2025) in understanding the molecular basis of symbiosis, pathogenicity, immune modulation, microbiome interactions, and microbial communication. We discuss how symbiotic microbes establish beneficial relationships with hosts via molecular signaling, nutrient exchange, and immune modulation, while pathogenic microbes employ virulence factors, immune evasion strategies, and host cell manipulation to cause disease. Additionally, we explore the dynamic interactions within microbial communities, including quorum sensing, metabolic cross-feeding, and competitive exclusion, and their impact on host health and environmental processes. We also highlight emerging technologies enabling the study of these interactions at unprecedented resolution, and address current challenges and future directions in the field. This review underscores the pivotal role of molecular mechanisms in shaping host–microbe and microbe–microbe interactions, and their potential for translating basic research into novel therapeutics, probiotics, and environmental management strategies.

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Microbial communities (microbiomes) are integral to all ecosystems, driving critical molecular functions that shape host health and environmental processes. Recent advances in multi-omics technologies, functional genomics, and computational modeling have transformed our ability to decode the molecular mechanisms underlying microbiome function, unravel the drivers of microbiome dynamics, and quantify microbial contributions to host physiology and environmental biogeochemistry. This review synthesizes key progress (2022–2025) in microbiome molecular function research, focusing on three core themes: (1) functional analysis of microbial communities, including the characterization of metabolic pathways, signaling networks, and functional redundancy; (2) molecular drivers of microbiome dynamics, such as host-microbe signaling, environmental cues, and horizontal gene transfer (HGT); and (3) microbial contributions to host physiology (e.g., metabolism, immune regulation) and environmental processes (e.g., nutrient cycling, bioremediation). We highlight emerging technologies enabling high-resolution functional profiling and discuss current challenges in linking taxonomic composition to molecular function. Finally, we outline future directions for translating functional microbiome research into therapeutic, agricultural, and environmental applications. This review underscores the central role of molecular functions in defining microbiome impacts, providing a framework for advancing our understanding of microbiome biology and harnessing microbial functions for global challenges.

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Antimicrobial resistance (AMR) in Gram-negative bacteria poses a severe global health threat, with metabolic reprogramming emerging as a key driver of resistance development. This study integrated transcriptomic and metabolomic analyses to investigate metabolic alterations associated with cephalosporin resistance in Escherichia coli and Klebsiella pneumoniae. Results revealed upregulation of central carbon metabolism pathways, including glycolysis and the tricarboxylic acid cycle, alongside enhanced biosynthesis of branched-chain amino acids and fatty acids in resistant strains. Transcriptomic data identified overexpression of genes encoding metabolic enzymes (e.g., pyruvate kinase, isocitrate dehydrogenase) and efflux pump components, suggesting a coordinated metabolic-efflux network. Metabolomic profiling confirmed accumulation of key metabolites (e.g., pyruvate, succinate, valine) that contribute to energy production and cell wall modification. These findings highlight the critical role of metabolic regulation in AMR and provide potential targets for developing novel antimicrobial strategies.

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