Notopterygium incisum is not only a traditional Chinese medicine but also an endemic herb. Artificial domestication and large-scale cultivation are crucial for resolving the crisis of wild resources and the supply-demand imbalance of N. incisum, yet current techniques have failed to stably provide the herb medicine in good quality. Metagenomic analyses revealed significant differences in the rhizomicrobiota between wild and cultivated N. incisum, particularly in microbial composition, gene functions, and community assembly. The rhizomicrobiota of the wild N. incisum from 3 different sites with an altitude drop over 1400 m had a similar composition when being compared with the cultivated samples. The wild N. incisum had higher abundances of beneficial microbes, particularly Hyphomicrobiales (Rhizobiales) (21.27% on average). In contrast, the rhizosphere microbial communities of the cultivated N. incisum showed a high prevalence of functional genes involved in the pathways of DNA repair and recombination proteins, replication and repair, peptidases and inhibitors, DNA replication proteins, and transfer RNA biogenesis. The co-occurrence networks analysis indicated that the stability of the wild samples' network remained significantly more robust when nodes were proportionally removed, as the wild samples' network had approximately the same positive and negative links while the cultivated samples' network had nearly all positive links and many fewer connectors. This is related to the conclusion that wild N. incisum exhibits superior efficacy, as reported in previous studies. Additionally, it can be observed from the sampling images that the root surface of wild N. incisum has more pronounced tiny protrusions, which may be associated with rhizobial attachment, thereby enhancing the nitrogen fixation process. Importantly, the observed shifts in rhizosphere microbial communities, particularly the enrichment of beneficial rhizobia in wild plants, are closely linked to enhanced accumulation of bioactive secondary metabolites such as coumarins and volatile oils. These microbiome-driven differences are likely associated with the superior medicinal quality of wild N. incisum compared to cultivated counterparts, highlighting the pivotal role of rhizosphere microbes in shaping therapeutic efficacy.

Carrot production regions worldwide incur enormous annual economic losses due to postharvest white mold caused by Sclerotinia sclerotiorum. Biological control is a promising approach for controlling postharvest pathogens. This study investigated the biocontrol efficacy of using Bacillus velezensis JR4 against Sclerotinia rot and its potential mechanisms of action. The results showed that the JR4 strain achieved 91.1% inhibition of S. sclerotiorum in a dual-culture assay. B. velezensis JR4 was able to produce extracellular enzymes such as protease, cellulase, and chitinase. Applying JR4 bacterial suspension at 1 × 10[8] CFU mL[- 1] on postharvest carrots infected with the pathogen reduced rot incidence by 65.4% and lesion length by 80.6% on day 5. The same concentration increased the levels of total phenolics and total flavonoids, as well as the activity of defense-related enzymes, including peroxidase (POD), polyphenol oxidase (PPO), and phenylalanine ammonia-lyase (PAL). It also increased the expression of three defense-related genes in postharvest carrots over four days. Compared to untreated carrots, it exhibited lower levels of cell membrane permeability, malondialdehyde (MDA), superoxide anion (O2[-]), and hydrogen peroxide (H2O2). Furthermore, the cell-free culture filtrate of JR4 showed minimal to no toxicity on WI-38 and Vero cells across all concentrations. The results suggest that B. velezensis JR4 could be an effective and sustainable biocontrol agent for controlling white mold in postharvest carrots. However, further safety assessments are needed for its successful application.

This study integrated environmental DNA (eDNA) metabarcoding, conventional bacteriology, histopathology, water quality variables, and remote sensing indices to investigate how environmental gradients are associated with pathogen-associated taxa communities and influence Nile tilapia (Oreochromis niloticus) health in Kitchener Drain, Northern Egypt. Physicochemical analyses revealed elevated nutrient concentrations, chlorophyll-a (59.21-226.35 µg L[-][1]), with localized hypoxia (dissolved oxygen as low as 2.14 mg L[-][1] in site 2). High-throughput 16S rRNA metabarcoding revealed microbial communities dominated by Actinobacteriota (27.35%) and Proteobacteria (26.73%), with beta-diversity patterns driven primarily by species turnover, indicating strong environmental filtering along the pollution gradient. eDNA metabarcoding detected pathogen-associated taxa, including Mycobacterium, Legionella, Burkholderiaceae, Erysipelothrix, Leptospira, and Flavobacterium, many of which were not recovered by culture-based methods. Cross-database integration of SILVA (v138) and GTDB (r214) references identified 256 ASVs assigned to pathogen-associated taxa across 32 genera, with the dual-database strategy detecting 20-52% additional pathogen-associated ASVs relative to either database alone. Spearman correlation was examined for the 27 taxa with physicochemical parameters; phosphate, chlorophyll-a, dissolved oxygen, and BOD came up most often. Spearman correlation analysis revealed two perfect taxon-environment associations: a positive correlation between G_Pseudomonas and nitrate (ρ = + 1.00) and a negative correlation between G_Acinetobacter and chlorophyll-a (ρ = - 1.00). Both associations were nominally significant before multiple-testing correction (uncorrected p = 0.017); however, neither remained statistically significant after correction for multiple comparisons. These findings were therefore interpreted as exploratory associations rather than evidence of environmental drivers or causal relationships. Integration of remote sensing indices (NDWI, NDTI, NDCI, CDOM, NDVI) and water variables aids in identification of the surrounding environment associated with the presence of species. Culture-dependent analyses identified Aeromonas spp. as the dominant intestinal isolate and the only genus consistently observed by both approaches, suggesting selective host filtering between environmental and gut-associated communities. Histopathological examination revealed epithelial necrosis, villous atrophy, and goblet cell hyperplasia, with the most severe lesions at sites of highest organic loading. This approach can aid as a database for further future work, and for establishing more advanced models of pathogen-associated eDNA distributions and targeted fish-health surveillance, and for maintaining biodiversity.

The rumen is a complex anaerobic fermentation ecosystem in which microbial communities undergo dynamic changes during host development, influencing fermentation efficiency, hydrogen utilization, and methane (CH4) production. However, how rumen maturation reshapes hydrogen redistribution and the associated microbial interactions remains poorly understood. This study compared rumen fermentation characteristics, microbial communities (bacteria, archaea, fungi, and protozoa), and Gibbs free energy profiles between 0.5-year-old and 2-year-old goats to elucidate age-related changes in hydrogen metabolism. Adult goats exhibited significantly higher concentrations of dissolved methane (dCH4), dissolved hydrogen (dH2), and total short-chain fatty acids (SCFAs), including acetate, propionate, and butyrate, than young goats (P < 0.05). Thermodynamic analyses indicated that glucose fermentation and methanogenesis were energetically feasible under rumen conditions (ΔG < 0), while age-related differences in Gibbs free energy (ΔG) suggested altered hydrogen partitioning during rumen maturation. The mature rumen was characterized by enrichment of carbohydrate-fermenting microorganisms, particularly Segatella, Anaeroplasma, and the anaerobic fungus Cyllamyces, which were positively associated with glucose conversion pathways, metabolic hydrogen, and SCFA production. In contrast, younger goats showed enrichment of amino acid metabolism pathways together with microbial taxa associated with early rumen development, including Christensenellaceae_R-7_group and Caecomyces. The archaeal community also shifted with age, with significantly higher abundances of Methanosphaera and Methanosarcina in adult goats, consistent with enhanced hydrogen utilization through methanogenic pathways. Functional predictions further revealed enrichment of carbohydrate and energy metabolism in adult goats, whereas amino acid metabolism predominated in young goats. These findings demonstrate that rumen maturation is accompanied by coordinated changes in microbial community structure, metabolic hydrogen redistribution, and thermodynamic characteristics, resulting in a transition from amino acid-oriented metabolism in young goats to a more specialized carbohydrate-fermenting ecosystem in adults. This integrated analysis identifies key microbial groups involved in hydrogen turnover and may provide new insights into the microbial mechanisms underlying rumen maturation, offering potential targets for improving feed efficiency and mitigating methane emissions in ruminants.

Although autochthonous probiotic application is considered standard for the host-specific environment, the allochthonous probiotics also deliver valuable physiological or therapeutic benefits during their transit period before being eliminated naturally. This study evaluated the probiotic and bio-functional attributes of seven zoo feline-derived Levilactobacillus brevis strains for their potential application in companion animals or functional food industry. In vitro methods were employed to assess their survival under simulated gastrointestinal tract (GIT) conditions, safety profiles (hemolytic activity, DNase activity, and antibiotic susceptibility), and bio-functional potential (antimicrobial, antioxidant, and hypocholesterolemic activities). All strains exhibited high survival in the presence of lysozyme (69.0-96.7%), gastric juice (60.7-91.3%), and bile concentrations (up to 78.4-92.2% at 1.8% bile). The isolates displayed strong hydrophobicity (41.7-85.5%) and auto-aggregation properties (29.8-75.2%), and no signs of toxicity (non-hemolytic and DNase negative). Significant variations were noticed among strains with reference to their probiotic and bio-functional properties (p < 0.05). Furthermore, the strains secreted antioxidant metabolites capable of scavenging 2, 2-diphenyl-1-picrylhydrazyl (62-72%), hydroxyl (54-65%), and superoxide (57-69%) radicals. Among selected isolates, strain Lb I (L. brevis MZ400640) demonstrated the strongest antagonistic activity against both Gram-positive and Gram-negative pathogens. The bile salt hydrolase (BSH) gene was conserved across all seven isolates, confirming their ability to deconjugate major mammalian bile salts, sodium glycoholate and taurocholate. Out of the 14 parameters evaluated, strain Lb VII (L. brevis MW450245) exhibited most robust overall performance highlighting the potential of Lb VII as a functional probiotic feed additive to promote health and manage hypercholesterolemia in companion animals.