High microbiome diversity constricts the prevalence of human and animal pathogens in the plant rhizosphere worldwide

One Earth, Год журнала: 2024, Номер 7(7), С. 1301 - 1312

Опубликована: Июль 1, 2024

Язык: Английский

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Long-term storage of rainwater: assessing the efficacy of disinfection methods on water quality and pathogenic species dynamics

Environmental Research, Год журнала: 2025, Номер 271, С. 121066 - 121066

Опубликована: Фев. 7, 2025

Язык: Английский

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DCiPatho: deep cross-fusion networks for genome scale identification of pathogens

Briefings in Bioinformatics, Год журнала: 2023, Номер 24(4)

Опубликована: Май 30, 2023

Abstract Pathogen detection from biological and environmental samples is important for global disease control. Despite advances in pathogen using deep learning, current algorithms have limitations processing long genomic sequences. Through the cross-fusion of cross, residual neural networks, we developed DCiPatho accurate based on integrated frequency features 3-to-7 k-mers. Compared with existing state-of-the-art algorithms, can be used to accurately identify distinct pathogenic bacteria infecting humans, animals plants. We evaluated both learned unlearned species genomics metagenomics datasets. an effective tool genomic-scale identification pathogens by integrating k-mers into networks. The source code publicly available at https://github.com/LorMeBioAI/DCiPatho.

Язык: Английский

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Differential responses of selectively bred mussels (Perna canaliculus) to heat stress—survival, immunology, gene expression and microbiome diversity

Frontiers in Physiology, Год журнала: 2024, Номер 14

Опубликована: Фев. 15, 2024

New Zealand’s green-lipped mussel ( Perna canaliculus ) is an ecologically and economically important species. Marine heatwaves are increasing in frequency around NZ’s coastline, these events correlated with increased stress mortality of some aquaculture This study aimed to identify general biomarkers heat P. assess whether responses differed between genetically distinct selectively bred mussels. We exposed three families mussels (families A, B C) seawater temperature regimes the laboratory: 1) a “control” treatment (ambient 12°C), 2) 26°C challenge subsequent recovery period, 3) sustained no recovery. investigated survival, immune response (hemocyte concentration viability, oxidative total antioxidant capacity), hemocyte gene expression gill microbiome during challenges. In heat-stress treatment, family A had highest survival rate (42% compared 25% 5% for C B, respectively). Gene levels significantly shifted thermal families, more dissimilar than C. Family substantially genes impacted by timepoint other while very little genes/pathways that responded stress. Genes related shock proteins (e.g., AIF1, CTSC, TOLL8, CASP9, FNTA, AHCY, CRYAB, PPIF) were upregulated all Microbiome species-richness before heat-stress, having distinctly different flora families. Microbial diversity changed similarly prolonged species Vibrio Campylobacter Our highlights use non-lethal sampling hemocytes as diagnostic tool explore mussels, predict their ocean warming. approach can potential thermotolerant candidates further selective breeding, which may increase resilience industry warming ocean.

Язык: Английский

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Evolution and distribution of antibiotic resistance genes in submerged macrophytes and biofilm systems: From seasonal monitoring to mesocosm experiments

Journal of Environmental Management, Год журнала: 2024, Номер 367, С. 121947 - 121947

Опубликована: Июль 27, 2024

Язык: Английский

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The diversity and risk of potential pathogenic bacteria on the surface of glaciers in the southeastern Tibetan Plateau

The Science of The Total Environment, Год журнала: 2024, Номер 945, С. 173937 - 173937

Опубликована: Июнь 15, 2024

Язык: Английский

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Deciphering the impact of organic loading rate and digestate recirculation on the occurrence patterns of antibiotics and antibiotic resistance genes in dry anaerobic digestion of kitchen waste

Water Research, Год журнала: 2024, Номер 261, С. 122005 - 122005

Опубликована: Июнь 27, 2024

Язык: Английский

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Environmental risks in swine biogas slurry-irrigated soils: A comprehensive analysis of antibiotic residues, resistome, and bacterial pathogens

Environment International, Год журнала: 2024, Номер 191, С. 108954 - 108954

Опубликована: Авг. 16, 2024

Simple anaerobic digestion is insufficient to completely remove residual parent antibiotics and antibiotic resistance genes (ARGs) from animal manure. ARG prevalence in swine biogas slurry-irrigated soils threatens human health. However, comprehensive analysis of residues, high-resolution gene profiles, pathogenic microbiomes very limited. Here, we comprehensively determined the antibiotics, resistome, potential pathogens distribution these soils, using high-performance liquid chromatography-tandem mass spectrometry, high-throughput quantitative PCR, 16S rRNA sequencing. The results revealed a significant enrichment tetracyclines fluoroquinolones ARGs with prolonged slurry irrigation, total 12 175 unique ARGs, 9 mobile genetic elements (MGEs) detected. Quantification veterinary residues (especially chlortetracycline) showed correlations multiple ARGs. abundance MGEs was highest denoting tight link between application spread resistance. presence 50 bacterial genera, including 13 multidrug resistance, identified. Variation partitioning, combined hierarchical partitioning analysis, indicated that Firmicutes, MGEs, were key drivers shaping profiles soils. findings offer insights into mechanisms residue agricultural practice underscoring necessity sustainable soil management mitigate

Язык: Английский

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Exploring the antibiotic resistance genes removal dynamics in chicken manure by composting

Bioresource Technology, Год журнала: 2024, Номер 410, С. 131309 - 131309

Опубликована: Авг. 17, 2024

Prolonged antibiotic usage in livestock farming leads to the accumulation of resistance genes animal manure. Composting has been shown as an effective way removing from manures, but specific mechanisms remain unclear. This study used time-series sampling and metagenomics analyse resistome types their bacterial hosts chicken manures. significantly altered physicochemical properties microbiome composition, reduced by 65.71 %, mobile genetic elements 68.15 % horizontal gene transfer frequency. Source tracking revealed that Firmicutes, Actinobacteria, Proteobacteria are major involved events. reduces risk targeting pathogens such Staphylococcus aureus. Structural equation modelling confirmed composting changing pH pathogen abundance. demonstrates is strategy for mitigating manure, thereby supporting One Health initiative.

Язык: Английский

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Fecal microbiota reveal adaptation of herbivores to the extreme environment of the Qinghai–Tibet Plateau

Grassland Research, Год журнала: 2024, Номер 3(2), С. 155 - 170

Опубликована: Март 27, 2024

Abstract Background Gut microbiota is pivotal in regulating hosts' biological processes and maintaining homeostasis, but knowledge about its role wild herbivores extreme environments remains limited. Methods bacteria fungi were sequenced ruminant (Chiru Yak) nonruminant (Kiang) on the Qinghai–Tibet Plateau, their community structure, co‐occurrence networks, functions, assembly mechanisms investigated using multivariate ecological statistical methods. Results Kiang had lower gut microbial diversity than Chiru Yak. Bacterial host‐specific exclusivity was greater that of fungi. In addition to evidence glycan biosynthesis carbohydrate metabolism, a high Firmicutes/Bacteroidetes ratio low animal pathogen abundance, suggesting better adaptation plateau's harsh environment. Additionally, members tended co‐occur rather co‐exclude all herbivores. Different network complexity stability patterns observed between bacterial fungal communities. Furthermore, primarily controlled by stochastic dispersal limitation drift, whereas deterministic homogeneous selection except Chiru. Conclusions On Yak exhibit more diverse metabolic functions Kiang, are divergent these

Язык: Английский

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