Mostly Microbes and Infection - by David Ojcius

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.

Highlights • W. chondrophila encodes two Ndk paralogs, unlike most Chlamydiota. • ndk genes are early expressed and protein levels peak during bacterial replication. • WcNdk1 is inclusion-bound, while WcNdk2 localizes to host cell compartments. • AZT inhibits bacterial growth and protects host cells from infection-induced death. • AZT sensitivity is linked to ndk2 presence, implicating WcNdk2 as functional target.

Highlights • Adjunctive oral FMT accelerates antidepressant response as early as week 2 • Superior efficacy persists through 8 weeks with no additional side effects • FMT reshapes gut microbes, with donor strains coexisting in recipients • Benefits are mediated by elevated bile acids and reduced systemic inflammation

Highlights • YprA-family helicases are a central hub in the prokaryotic defense system network • YprA phylogeny analysis identifies a distinct class of defense systems called ARMADA • ARMADA protects bacteria against diverse phages and synergizes with Druantia III • ARMADA, Druantia III, and Zorya II co-occur in phage-like integrated elements

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.

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

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.