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Predicting antimicrobial resistance for precision medicine

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Summary Antibiotics are among medicine’s greatest successes, but resistance evolution threatens their continued efficacy. Decades of research have deepened our understanding of the mechanisms and evolutionary dynamics of antimicrobial resistance. More recently, advances in machine learning (ML) and artificial intelligence (AI) show promise in predicting antimicrobial resistance in pathogens based on rapid whole-genome sequencing and other accessible data. In this perspective, we highlight advances in understanding the mechanisms and spread of antimicrobial resistance. We discuss how this knowledge, coupled with ML- and AI-based approaches, can inform the prediction of resistance and a precision-medicine strategy that targets pathogenic bacteria specifically, thereby limiting resistance evolution and collateral damage to the microbiome. These accurate predictions of bacterial vulnerabilities will enable the adaptation of classical antimicrobial treatments with adjuvants, as well as the ...
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Genome-Based Taxonomy and Provirus Identification in Halococcus from Hypersaline Environments

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Highlights • Halococci differ from other haloarchaea by their thick cell wall structure. • Currently no viruses are known to infect Halococci. • Seven novel Halococcus strains were characterized and the genomes sequenced. • The novel Halococcus strains contain predicted anti-viral defence mechanisms. • Detected proviruses indicate that Halococci are infected by viruses in nature.
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Gut microbiota-derived lysine phenylacetylation impairs mitochondrial function and is alleviated by SIRT3

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Highlights • Lysine phenylacetylation (Kpaa) is a diet- and gut microbiota-derived PTM • Kpaa is enriched in mitochondria and regulated by SIRT3 • High Kpaa impairs mitochondrial function and correlates with MASH • K481 phenylacetylation of HSP60 leads to the mitochondrial unfolded protein response
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Meta-analysis reveals microbiome signatures for colorectal cancer that are universal across age groups and sequencing methods

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Highlights • Gut microbiome CRC signature is universal across age groups and sequencing approaches • Tumor-enriched microbes are concordant with fecal CRC signatures • Increasing dietary fiber intake reduces the microbiome CRC signature score • Fusobacterium subspecies show biogeographic variation in CRC enrichment
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Microbial drivers of soil health: Integrating physical, chemical and biological properties for food security under climate change

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Highlights • Climate stressors restructure soil microhabitats, reassembling microbial guilds that regulate C–N–P cycling and resilience. • Cross-domain feedbacks link pore architecture and soil chemistry to microbiome functions and emergent soil health outcomes. • Rhizosphere mechanisms (exudates, siderophores, ACC deaminase, ISR, AMF/N-fixing symbioses) provide actionable leverage points under stress. • Integrative indicators connect physical, chemical, and biological metrics to soil multifunctionality for monitoring under climate extremes. • Emerging tools (meta-omics, 3D imaging, spectroscopy, isotopic tracing, in situ sensors) enable mechanistic diagnosis and decision support.
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CBASS limits bacteriophage production while maintaining cell viability in Pseudomonas aeruginosa

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Highlights • CBASS antagonizes phage replication while preserving cell viability in P. aeruginosa • 3′,3′-cGAMP-activated CapV targets diverse phages and overcomes CBASS inhibitors • CBASS-sensitive phages transcribe and replicate their genome • CBASS activity limits packaged phage DNA, reducing virion production
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Pathogenesis and Genome Characterization of Translucent Post-larvae Disease-Causing Vibrio parahaemolyticus in Litopenaeus vannamei

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Highlights • Isolated TPD-causing V. parahaemolyticus strain P40.49 from infected shrimp. • Experimental infection confirmed the pathogenicity of the TPD-causing strain P40.49. • Whole genome sequencing confirmed the presence of ∼69 kbp TPD-associated plasmid. • The shrimp stomach and intestine tissues are ideal for early TPD detection (6 hpi). • Four unique TPD-associated genes may serve as additional markers for TPD detection.
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