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Deep Learning Enables Multiobjective Engineering of T7 Bacteriophage Specificity

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Deep learning reveals and redesigns the multifunctional targeting landscape of the T7 phage receptor‑binding protein. Comparing four model architectures, the study engineers phages optimized for 26 tasks, showing that complex specificities can be tuned with few mutations. Multiobjective models uncover principles of phage biology and offer a general strategy for optimizing multifunctional proteins.
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Cyclic DEAPA Exposure Drives Disinfection Resistance in Salmonella Typhimurium

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Cyclic exposure to the biocide DEAPA selects Salmonella Typhimurium variants with sharply increased tolerance to disinfection, heat, and gentamicin. Adaptive evolution produced multidrug‑tolerant strains carrying mutations across metabolic, signaling, transport, and motility genes, revealing broad cellular rewiring and highlighting risks for food‑processing sanitation.
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How Phylogeny and Environment Shape Glycoside Hydrolase Multidomain Architecture

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Phylogeny strongly constrains glycoside hydrolase multidomain architecture across bacterial genera, while environmental factors fine‑tune domain organization in cosmopolitan lineages. Analysis of 158k GH proteins using domain‑adjacency networks reveals conserved lineage‑specific patterns and highlights accessory domains as key drivers of microbial functional adaptation.
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Repeat‑Driven Plasmid Deletions Cause Within‑Patient Carbapenem Heteroresistance in Klebsiella pneumoniae

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A single‑patient study shows how repeat‑associated deletion of a blaNDM‑1 resistance module in Klebsiella pneumoniae produced divergent carbapenem phenotypes among otherwise closely related isolates. Stable genomes, a validated 10.5‑kb plasmid deletion, and growth differences highlight how structural plasmid variation can drive clinically relevant heteroresistance.
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Geroprotective Probiotic and 5‑AVAB Metabolite Counteract Inflammaging to Extend Healthspan

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A study maps age‑related gut microbiome shifts and introduces MicroAge, a microbiome‑based aging clock. It identifies  Bifidobacterium   pseudocatenulatum as a geroprotective species depleted with age. In mice, supplementation restored intestinal balance, reduced systemic inflammaging, improved cognition and motor function, and extended healthspan. Its metabolite  5-aminovaleric acid betaine (5-AVAB)  reproduced many benefits.
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Clostridia Consortia Reverse Colitis via Tryptophan‑Driven Microbiome and Immune Modulation

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Defined human Clostridia consortia 17‑mix and 11‑mix reverse established colitis in multiple murine IBD models. Beyond SCFA and IL‑10 pathways, these live biotherapeutic products suppress resident pathobionts and activate anti‑inflammatory AhR signaling via bacterial tryptophan metabolites, revealing IL‑10‑independent mechanisms of microbiome‑based therapy.
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Age‑Stratified Gut Microbiome Variation in a Taiwanese Population

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Gut microbiome diversity and composition differed across predefined age groups in a Taiwanese cohort. Several age‑associated genera showed partial agreement across complementary analytic methods. Adult gut microbiome profiles could predict chronological age, though only with modest accuracy, underscoring both biological signal and methodological limits.
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