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Call for Papers: Omics and Metabolic Networks in Microbial Xenobiotic Degradation and Detoxification

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This Special Issue aims to bring together cutting-edge research and reviews that integrate omics data, metabolic network analysis, and ecological perspectives to elucidate microbial mechanisms involved in xenobiotic degradation and detoxification. Contributions will highlight novel enzymes and pathways, microbial community dynamics, metabolic engineering strategies, and real-world applications in environmental remediation and industrial biotechnology.
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The genetic repertoire of deep-sea microbiome: From sequence to structure and function

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Highlights • 502M nonredundant genes from 2,138 deep-sea samples reveal unprecedented diversity • Deep-sea microbes’ DNA maintenance genes rapidly evolve with specialized properties • Deep-sea protein fold catalog with 392 novel domains aids structure-guided mining • A structure-mined deep-sea helicase enhances nanopore DNA sequencing speed
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Association between secondhand smoke exposure and ocular microbiome changes in children

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Highlights • Secondhand smoke (SHS) exposure significantly alters the ocular surface microbiome (OSM) in children aged 3–18 years. • Microbial diversity is significantly reduced on ocular surface in SHS-exposed children. • Beneficial commensal taxa are depleted in SHS-exposed children. • Environmental stress-related metabolic pathways and immune-related pathways are significantly altered in SHS-exposed children.
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Resistance patterns and gene expression profiles of Arcobacter butzleri under exposure to selected antibiotics and disinfectants

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Highlights • Disinfectants trigger adaptive, strain-specific responses in Arcobacter butzleri. • Overexpression of AMR and virulence genes in A. butzleri. • Antibiotics induced limited transcriptomic changes.
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TRIM21 induces selective autophagy of viruses and bacteria

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Highlights • Antibodies direct viruses and bacteria for post-infection xenophagy • TRIM21 regulates ADX via its ubiquitination activity • ADX protects against pathogenic Salmonella infection in vivo
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Mucin modulates phage infection dynamics and biofilm formation in enteropathogenic Yersinia enterocolitica

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Highlights • Mucin modulates phage-host dynamics in Yersinia enterocolitica. • Temperature and nutrient availability further shape phage infection outcomes. • Bacterial pre-exposure to mucin leads to 2-log increase in phage titers. • Mucin supplementation reduces biofilm formation in all tested conditions. • Phage-resistant variants carry mutations in metabolism, quorum sensing, antimicrobial resistance genes.
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Hyocholic acids shape neonatal immune tolerance and microbiota assembly

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Highlights • HCAs dominate meconium (>50%) as primary bile acids produced by fetal CYP3A7 • HCAs shape intestinal immune tolerance by promoting Treg cells and suppressing Th17 cells • High neonatal HCAs protect against gastrointestinal disorders and infections
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