Search Results (7,162)

Microalgae-based regulation is increasingly recognized as an eco-friendly strategy for improving water quality and nutrient management in intensive aquaculture systems. Although its effects on bacterial communities have been extensively investigated, its ecological impacts on higher trophic levels—particularly eukaryotic plankton communities across different size fractions—remain poorly understood. In this study, two indigenous microalgae species, Nannochloropsis oculata and Thalassiosira weissflogii, were inoculated into shrimp rearing water to elucidate the dynamics and interactions among microalgae, nutrient factors, and eukaryotic plankton communities across the small-sized (0.22–3 μm) and large-sized (>3 μm) fractions. The results revealed significant differences in the composition and diversity of both plankton size fractions under different microalgae treatments. Partial least squares path modeling indicated that microalgae influenced plankton communities both directly and indirectly through nutrient-mediated pathways. According to the neutral community model, microalgae inoculation was associated with an increased contribution of deterministic processes to community assembly. Variance partitioning further revealed that the large-sized community was primarily governed by microalgae, whereas the small-sized community was mainly shaped by rearing time, indicating size-dependent assembly mechanisms. The average variation degree and coefficient of variation, combined with effect-size analyses, indicated that N. oculata inoculation was associated with higher short-term community stability, an effect most pronounced in the large-sized fraction. Overall, these findings demonstrate that microalgal inoculation modulates the structure, assembly processes, and short-term stability of eukaryotic plankton communities, providing new insights into size-dependent, microalgae-driven assembly mechanisms and their potential to stabilize plankton communities for sustainable aquaculture management. Full article

Urban pigeons (Columba livia) are widely distributed synanthropic birds closely associated with environments of intense human activity, raising interest in their role in urban microbial dynamics. Here, we characterized the fecal bacterial microbiota of urban pigeons from northern Mexico using 16S rRNA gene amplicon sequencing (V3–V4). A total of 1479 amplicon sequence variants (ASVs) were identified across five pooled samples. Alpha diversity varied among pools, with observed richness ranging from 228 to 514 ASVs. The bacterial community was dominated by Proteobacteria and Firmicutes, particularly Escherichia–Shigella and Enterococcus. PICRUSt2-based functional predictions suggested a predominance of predicted metabolic pathways related to carbohydrate degradation and energy acquisition. Conservative taxonomic screening identified 58 gut-associated taxa, including 15 bacteria previously reported in association with humans; however, only three (Clostridium perfringens, Enterococcus faecalis, and Proteus mirabilis) showed reported zoonotic associations, all at very low relative abundances (<0.07%). These findings indicate that the fecal bacterial communities characterized in this study were dominated by taxa commonly associated with the avian gastrointestinal tract, whereas taxa that could be conservatively linked to documented zoonotic reports represented only a minor fraction of the detected microbiota. Overall, the results contribute to a more ecologically informed understanding of urban pigeon-associated microbiota within a One Health framework. Full article

Optimizing nitrogen (N) management is essential for sustaining rice productivity and improving soil N retention in paddy ecosystems, yet whether long-term fertilizer postponing (FP) regulates bacterial community assembly and microbial N-cycling potential in a compartment-dependent manner remains unclear. Using soils from an 11-year field experiment, we investigated bacterial communities and eight N-cycling genes in bulk and rhizosphere soils across three rice growth stages. Compared with conventional fertilization (CF), FP significantly increased grain yield, plant N accumulation, soil NH₄⁺-N (8.1%), microbial biomass N (MBN, 4.3%), and urease activity (30.3%). N-cycling genes showed pronounced temporal variation, generally peaking at the heading stage. FP increased the abundance of genes involved in N fixation, nitrification, and denitrification in bulk soil but reduced most N-cycling genes in the rhizosphere. Although bacterial α-diversity was unchanged, FP significantly altered bacterial community composition. Network and redundancy analysis further showed that bacterial community assembly and N-cycling potential were closely associated with soil C and N status. These findings indicate that long-term FP improves rice productivity by enhancing soil N availability and reshaping bacterial community assembly and microbial N-cycling potential in a compartment-dependent manner, providing new insights into the microbial mechanisms underlying sustainable N management in paddy soils. Full article

Alterations of gut microbiota are common in chronic kidney disease (CKD) and contribute to increased uremic toxins including indoxyl sulfate (IS), p-cresyl sulfate (pCS) and trimethylamine N-oxide (TMAO), which are linked to cerebrovascular disease risk. This study examined the kidney–gut–brain axis in CKD mice and in dialysis patients. Male and female mice with adenine-induced CKD were fed a high-amino-acid (HAA) diet to increase precursors of gut-derived uremic toxins. A subgroup of mice received antibiotics in drinking water to suppress gut microbiota and evaluate its role in toxin generation. Behavior tests, gut microbiome composition and brain histology for cerebral microhemorrhages were analyzed. CKD mice had higher serum levels of creatinine, cystatin C and gut-derived toxins, a 2.5-fold increase in brain microhemorrhages, and decreased locomotor activity. The HAA diet significantly increased serum TMAO but not IS and pCS, and all three toxins were reduced by antibiotic therapy. Sex differences were observed; in male animals, higher TMAO was associated with increased brain microhemorrhages, whereas in female mice, pCS was associated with brain microhemorrhage burden. The suppression of toxins with antibiotics improved working memory in male animals. Gut microbiota analysis revealed the expansion of Lactobacillus and Ileibacterium in CKD mice. The HAA diet and antibiotics altered gut microbiota composition without changing alpha diversity. The human study utilized biobanked serum samples and a retrospective review of brain imaging scans in a hemodialysis patient cohort; TMAO levels were associated with increased lobar microbleeds. Our study supports a role for bacterial-derived uremic toxins in the kidney–gut–brain axis and cerebral microhemorrhage formation in CKD. Full article

Trachoma, caused by Chlamydia trachomatis (Ct), persists as a major cause of preventable blindness despite the global SAFE strategy. Understanding how Ct genovars and genovariants influence infection dynamics and clinical outcomes is crucial for sustaining elimination efforts and informing vaccine development. A four-year longitudinal study was conducted in a trachoma-endemic region of Tanzania across multiple rounds of mass drug administration (MDA) with azithromycin. Ct infections were genotyped by ompA sequencing to identify genovars and genovariants. Associations between genetic variants, bacterial load, and clinical signs of trachoma were assessed. Following MDA, a shift in Ct genovar prevalence occurred from genovar B to genovar A. Genovar B was associated with more severe clinical signs, including follicles, papillae, and scarring, whereas genovar A infections exhibited higher bacterial loads. Among 121 individuals with recurrent infections, 94% were re-infected with the same genovar, indicating limited protective immunity and incomplete clearance despite MDA coverage exceeding 60%. The genovariants B2, B9, and A2 predominated, with an A → T amino acid substitution in B9 potentially modifying antigenic recognition. Post-MDA, normalized genovariant diversity increased, suggesting ongoing transmission or strain reintroduction. Distinct genovar-associated clinical and immunological patterns underscore the need to elucidate genovar-specific virulence and immune evasion mechanisms. These findings provide key insights for optimizing trachoma control and advancing vaccine development. Full article

Continuous cropping obstacles (CCOs) severely disrupt the soil physical structure, nutrient cycling, and microbial community balance, leading to decreased crop productivity. However, the effects of soil amendment interventions on bacterial, fungal, and archaeal communities in foxtail millet (Setaria italica (L.) P. Beauvois.) systems are not well comprehended. Selected physical, chemical, biological soil amendment and crop rotations were evaluated for their effects on rhizosphere soil microbial diversity, composition, network characteristics, community assembly processes, niche breadth, and multi-functionality. High-throughput sequencing of 16S rRNA and ITS regions demonstrated that earthworm castings significantly enhanced archaeal Chao1, Shannon diversity, and multi-functionality. Meanwhile, Bacillus mucilaginosus enhanced fungal diversity, and B. subtilis promoted bacterial network complexity. In continuous cropping soil alone, microbial communities exhibited low diversity and were predominantly governed by ecological drift. In contrast, soil amendment treatments shifted assembly toward deterministic processes, including homogeneous and heterogeneous selection. However, the analysis demonstrated greater complexity and niche width in bacterial communities than in fungal or archaeal communities, with keystone modules driven by Actinomycetota, Ascomycota, and Halobacteriota. Structural equation modeling indicated that soil physicochemical properties directly mediated rhizosphere soil microbial alpha diversity, which in turn positively influenced multi-functionality. Overall, organic amendments and microbial inoculants were associated with increases in microbial diversity, network stability, and functionality in this pot experiment, suggesting that such practices may help mitigate CCOs and sustainably improve foxtail millet productivity in dryland agricultural systems. Full article

The aquatic plant Wolffia globosa and the probiotic Limosilactobacillus reuteri KUB-AC5 have been proposed as candidate synbiotic components targeting gut microbiota modulation. In this study, we investigated the effects of W. globosa supplementation, alone or in combination with L. reuteri KUB-AC5, on the gut microbiota and health status in healthy adult dogs. For a 28-day feeding trial, 24 healthy dogs were randomly assigned to three dietary treatment groups: control, prebiotic (PRE; 3.5% W. globosa powder), and synbiotic (SYN, 3.5% W. globosa powder combined with L. reuteri KUB-AC5 at 1 × 10⁸ CFU/day). No significant differences were observed in body weight, body condition score, fecal consistency, feed intake, or blood parameters among groups (p > 0.05). Although overall gut microbial diversity remained unchanged, linear discriminant analysis effect size analysis revealed the selective enrichment of specific bacterial taxa. The PRE group exhibited higher relative abundances of Parabacteroides merdae, Romboutsia lituseburensis, Subdoligranulum variabile, and Phocaeicola sartorii, whereas the SYN group showed increased levels of Escherichia coli and Terrisporobacter glycolicus and reduced levels of Anaerobiospirillum succiniciproducens and Campylobacter upsaliensis (p < 0.05). In conclusion, W. globosa, alone or combined with L. reuteri KUB-AC5, was safely used to modulate gut bacterial composition as a potential functional ingredient. Full article

Unraveling rhizosphere microbial assembly and plant–microbe co-adaptation is essential for understanding how fragile mountain ecosystems respond to environmental stress. This study investigated the rhizosphere bacterial communities of Carex enervis C. A. Mey, a dominant species in arid and semi-arid alpine meadows, along an altitudinal gradient from 1160 to 1860 m. By integrating high-throughput sequencing, iCAMP-based community assembly analysis, niche differentiation assessment, and partial least squares path modeling, we examined associations among macro-environmental gradients, rhizosphere soil conditions, bacterial community assembly, and ammonium nitrogen availability. The results revealed a dual-track assembly pattern. Macro-environmental heterogeneity, particularly in elevation and precipitation, was associated with rare microbial diversity primarily through heterogeneous selection. In contrast, abundance-weighted patterns suggested homogeneous selection of core dominant microbial groups in the rhizosphere. Within several dominant genera, closely related taxa showed divergent covariation patterns rather than uniform responses along the environmental gradient, suggesting potential fine-scale differentiation in environmental responses. Path analysis further indicated that enzyme-based rhizosphere activity proxies were associated with the relative abundance of microbial response groups and with the availability of ammonium nitrogen. These findings suggest that the rhizosphere conditions of Carex enervis are associated with bacterial assembly patterns, fine-scale taxon differentiation, and nutrient-related soil variables along the elevational gradient. This study provides new insight into plant–microbe co-adaptation in arid and semi-arid mountain ecosystems. Full article

Although microbial remediation is a promising strategy for PAH pollution control, its field application remains a significant challenge. PAH-degrading microbial consortia were enriched from contaminated sites in Nanjing. High-throughput sequencing was applied to analyze the community structure and functional characteristics of bacteria and fungi, and the phenanthrene degradation performance of free consortia and sodium alginate-activated carbon-immobilized composite beads was systematically evaluated. Results showed that the distance from the pollution source was the key factor driving the differentiation of microbial community structure. For bacteria, sites closer to the pollution source showed significantly lower bacterial diversity and richness, while an opposite trend was observed for fungi. Proteobacteria (40–87%) and Ascomycota (51–88%) were the dominant phyla of bacterial and fungal communities, respectively. Despite significant differences in genus-level community composition among samples, the functional gene abundance related to PAHs metabolism was highly similar across all consortia. The immobilized composite beads achieved a significantly higher phenanthrene degradation efficiency (94.70–99.26%) compared with free consortia (65.84–85.78%). The embedding material had a significant effect on degradation performance, while nutrient sources showed no significant impact on the degradation efficiency. This study provides theoretical support for the application of immobilized microbial technology in PAH-contaminated site remediation. Full article

Potato (Solanum tuberosum L.) is a vital food security and cash crop in Eritrea, yet bacterial and fungal pathogens responsible for 15–30% yield losses remain molecularly uncharacterized across its production systems. Here, we present the first nationwide amplicon-based metagenomic survey of potato pathogen communities, sampling 81 farms across 14 sub-regions spanning four agroclimatic regions during July–August 2023. High-throughput amplicon sequencing targeting the bacterial 16S rRNA V3–V4 region and fungal ITS1–ITS2 loci revealed pronounced geographic heterogeneity in community composition and alpha diversity. Pseudomonas spp. were ubiquitous, with a peak relative abundance of 32.5% in Dekemhare. Dominant fungi included Alternaria spp. (14.3% in Berik), Fusarium spp. (highest diversity 53.8% in Adi Kuala), Botrytis cinerea (36.9% in Adi Keih), and Rhizoctonia solani (44.4% in Adi Tekeliezan). Bacterial Shannon diversity averaged 5.67; fungal, 4.70. Weighted UniFrac PCoA accounted for 56.5% of bacterial community variance along PC1, confirming distinct geographic clustering. Potential pathogen-associated taxa of Pseudomonas, Alternaria, Fusarium, and Colletotrichum were detected in every asymptomatic sample examined, demonstrating the inadequacy of visual-only disease surveillance. These findings establish the first molecular baseline for potato-associated taxon diversity in Eritrea, providing the empirical foundation for region-specific integrated disease management and evidence-based seed certification protocols. Full article

Pectinolytic bacteria of the Pectobacteriaceae family constitute an important group of plant pathogens. Apart from infected plants, they are regularly found in aquatic environments. Pectinolytic isolates were selected, during 3 years, from water of naturally eutrophic lakes and from the rhizosphere of waterside plants in a site protected from direct agricultural inputs. A total of 89 isolates were assigned to Enterobacterales including the genera Dickeya (62%) and Pectobacterium (13%). In contrast to previous reports showing the prevalence of Pectobacterium species in river water, the Dickeya isolates were largely preponderant in lake water. Six Dickeya and four Pectobacterium species were isolated from water including D. oryzae, D. lacustris, D. parazeae, P. quasiaquaticum and P. aquaticum and, at a low frequency, D. chrysanthemi, D. aquatica, D. zeae, P. brasiliense, and P. versatile. The most common species isolated from plant rhizosphere was D. chrysanthemi. Notably, the rhizosphere of Solanum dulcamara harbored the highest number and diversity of Dickeya and Pectobacterium isolates. Members of different species and/or genera were found in the same water sample or plant rhizosphere, indicating that they can cohabit in close environments. Despite noticeable individual variations, the water strains have a pathogenic potential similar to that of other strains of the same species. Full article

Curcumin (Cur), a polyphenol with excellent antioxidant and anti-inflammatory properties, is widely used in aquaculture. However, its low water solubility limits bioavailability. This study first investigated the effects of a highly water-soluble and bioavailable valine-curcumin (Val-Cur) on growth performance, antioxidant capacity, inflammatory factor expression and gut microbiota in juvenile largemouth bass. A total of 450 healthy largemouth bass (initial weight 12.00 ± 0.45 g per fish) were randomly divided into six groups: the basal diet group (CK), the group supplemented with 60 mg/kg of curcumin (Cur), and groups that were fed with 15, 30, 60, and 120 mg/kg of Val-Cur. Each group had three replicates (25 fish per replicate). After 8 weeks, compared with both the CK and Cur groups, 30–60 mg/kg Val-Cur displayed significantly increased growth rates, specific growth rates, and protein conversion efficiency, and significantly decreased the feed conversion ratio. Quadratic regression analysis indicated that the optimal supplementation level was approximately 51.62 mg/kg Val-Cur. The Cur and Val-Cur between 30 and 60 mg/kg groups also displayed significantly improved serum biochemical indicators (↑HDL-C, ALB, LZM, CAT and SOD, and ↓MDA). These groups also promoted the expression of intestinal anti-inflammatory factors (TGF-β1 and IL-10) and physical barrier genes (Claudin1, Occludin and Claudin4). In terms of regulating the intestinal microbiota, both Cur and Val-Cur significantly reduced the bacterial diversity (↓Sobs, Chao1 and PD indices) and increased the evenness of bacterial distribution (↑Simpson, Shannon and Pielou indices). In addition, the abundance of some potential pathogens (e.g., Plesiomonas, Plesiomonas shigelloides, and Pseudomonas fluorescens) significantly decreased, while the abundance of beneficial bacteria (e.g., Faecalibaculum, Faecalibaculum rodentium and Lactobacillus murinus) significantly increased. Pearson’s correlation analysis showed that the increase in the abundance of beneficial bacteria was positively correlated with improvement in growth performance, serum biochemical and antioxidant capacity indicators. In summary, Val-Cur exerted superior biological effects at lower dietary inclusion levels than Cur. This study laid a theoretical foundation for elucidating the mechanism of Val-Cur in improving fish immunity and promoting the application of water-soluble curcumin in aquaculture. Full article

One of the most pressing challenges facing healthcare today is the rise of biofilm infections and antibiotic-resistant bacteria, which demand entirely new therapeutic strategies beyond conventional antibiotic reliance. A biofilm is a structured community of microorganisms encased in a self-produced extracellular polymeric substance (EPS) matrix, which confers resistance to host immune defenses and antimicrobial agents. Accumulating evidence demonstrates that plant-derived secondary metabolites—including flavonoids, phenolic acids, tannins, terpenoids, and alkaloids—exert potent antibacterial and antibiofilm activities through diverse mechanisms of action. These natural compounds inhibit biofilm formation by disrupting bacterial adhesion, suppressing quorum sensing, degrading the EPS matrix, and impairing bacterial motility. Beyond independent bioactivity, phytochemicals demonstrate significant synergistic potential when combined with conventional antibiotics, revitalizing antimicrobial efficacy against drug-resistant pathogens. Nanoformulation and biogenic carrier technologies further enhance the bioavailability and therapeutic potency of these compounds. Despite these advances, critical challenges persist, including poor bioavailability, physicochemical instability, dose-dependent toxicity, and the risk of resistance development. This review presents a critical and integrative analysis of the pharmacological mechanisms of plant secondary metabolites, with particular emphasis on their role in combating biofilm-associated infections and antibiotic resistance, and discusses translational opportunities including structure–activity relationship (SAR)-guided optimization, high-throughput screening platforms, and advanced drug delivery systems. Collectively, plant secondary metabolites represent a scientifically compelling and clinically relevant pipeline for the development of next-generation antimicrobial and antibiofilm therapeutics. Full article

Stir-frying is an important process for terminating fermentation and improving the flavor of sour shrimp paste. This study investigated the flavor characteristics, volatile profiles, and post-storage microbial community of stir-fried sour shrimp paste. Sensory evaluation demonstrated that it exhibits a well-balanced flavor profile, characterized by fruity, soy sauce, spicy, and salty notes. Based on HS-SPME-GC-MS analysis, a total of 68 volatile compounds were identified, of which 26 made notable contributions to the aroma. Among them, esters were the most diverse group, with ethyl butyrate, ethyl acetate, and ethyl 2-methylbutyrate serving as the main contributors to the fruity aroma. Acids such as butanoic acid, acetic acid, and 2-methylbutanoic acid far exceeded their thresholds, linking to sour and spicy notes. Microbial community analysis revealed that low-abundance fermentative bacteria, such as Vagococcus and Levilactobacillus, remained detectable after storage, whereas Pseudomonas and Acinetobacter were identified as the most probable spoilage organisms. These findings provide a systematic understanding of the unique flavor of stir-fried sour shrimp paste and its potential microbial risks during storage, providing a basis for the application of stir-frying technology. Full article

Packing density regulates the microenvironment of tobacco (Nicotiana tabacum L.) fermentation and may thereby influence microbial activity and product quality. However, its effects on microbial community assembly and quality formation remain poorly understood. This study aimed to clarify how packing density affects flue-cured tobacco quality by shaping microbial communities, functional potential, and ecological interactions. Here, we investigated the effects of three packing densities (60%, 70%, and 80%) on chemical components, aroma compounds, microbial community structure, functional potential, co-occurrence networks, and assembly mechanisms of flue-cured tobacco (cv. Piaohe No. 2) after 10 days of fermentation. Moderate density (70%) achieved the most balanced chemical profile, with appropriate nicotine retention, potassium/chlorine ratio, and sugar/nicotine balance. T70 also exhibited the highest levels of total esters, total ketones, and β-ionone, key contributors to fruity, floral, and woody aromas. Microbial analysis revealed that T70 supported the highest diversity and was characterized by the enrichment of aroma-related bacterial taxa, including Bacillus and lactic acid bacteria, as well as the fungal genus Pichia. In contrast, T60 favored aerobic nicotine degraders, whereas T80 selected for obligate anaerobes associated with off-odor production. Functional predictions and network analysis showed that T70 upregulated fatty acid and carotenoid biosynthesis pathways and exhibited the highest modularity, indicating a compartmentalized, functionally complementary community. Neutral model fitting revealed increasing stochasticity with density, with T70 displaying a mixed assembly regime. Collectively, our findings show that packing density influences tobacco quality by regulating microbial community composition, functional potential, network interactions, and assembly processes. These results provide a scientific basis for optimizing packing density in tobacco processing. Full article