Search Results (2,165)

Refrigerated, ready-to-eat (RTE) vegetable foods are widely consumed. Microorganisms may proliferate in these foods during cold chain breaks, increasing the risks for food spoilage and foodborne disease. Despite the increasing use of novel non-thermal preservation technologies, the comprehensive impact of these hurdles on the broad taxonomic structural dynamics of the food microbiota during temperature abuse remains poorly understood. To address this gap, we determined the impact of bacteriocin AS-48 and a high hydrostatic pressure (HHP) treatment, both individually and in combination, on the microbial load and bacterial diversity of a refrigerated vegetable cream upon temperature abuse. Counts of aerobic mesophilic bacteria (37 °C, 24 h) increased significantly (p < 0.05) in controls during temperature abuse, but not in samples treated with bacteriocin, HHP or both. Amplicon-sequencing analysis indicated that the initial microbiota of control samples was composed mainly of Pseudomonadota (74.50%), followed by Bacillota (21.19%) and Actinobacteriota (3.69%). Bacillota became the predominant group during refrigerated storage (87.21 to 99.48%). After temperature abuse, control samples had lower relative abundances of Bacillota during storage and higher relative abundances of Pseudomonadota, Bacteroidota and Actinobacteriota. All treated samples (irrespective of the treatment) showed lower relative abundances of Bacillota during storage compared to untreated controls without temperature abuse. Genus Bacillus was the predominant group in the control samples during storage. Acinetobacter was associated with temperature abuse. In conclusion, both enterocin AS-48 and HHP can be effective hurdles, not only by preventing bacterial proliferation but also by influencing the dynamics of the microbial community associated with spoilage in vegetable creams exposed to inappropriate temperature conditions. Full article

Rice–crab coculture, as China’s third-largest integrated farming model, is pivotal for sustainable Chinese mitten crab aquaculture. This study conducted untargeted metabolomics and 16S rRNA gene sequencing on gut contents of crabs from rice fields and ponds, integrating metabolic and microbial profiles. We aimed to reveal the chemical traits of rice-field Chinese mitten crab linked to gut microbiota, providing scientific guidance for optimizing culture practices and developing microbial additives. Both groups were dominated by the phyla Firmicutes, Proteobacteria, and Bacteroidota, but the phylum Bdellovibrionota was not detected in group R. A total of 1271 distinct amplicon sequence variants (ASVs) were identified, which were annotated to 649 genera. At the ASV level, the Chao1 index for the R group (197.12 ± 17.88) was notably lower compared to the P group (288.75 ± 30.59) (p < 0.01). In contrast, the Shannon index for the R group (3.90 ± 0.06) was significantly greater than that of the P group (3.70 ± 0.06) (p < 0.01). The PCA plot demonstrated a distinct discrimination between the groups. The P group had more microbial species but was dominated by Candidatus_Bacilloplasma, resulting in uneven distribution. In contrast, the R group had fewer species but a more balanced distribution. Among 3531 metabolites identified in both groups, 865 differed significantly. Compared to P, 736 metabolites were significantly upregulated and 129 were significantly downregulated in R. Key metabolic pathways included amino acid, carbohydrate, cofactor and vitamin metabolism, signaling, and xenobiotics biodegradation. Group R had higher levels of L-leucine, L-phenylalanine, L-tyrosine, 2-amino-1-phenylethanol, choline, and pyrophaeophorbide a, which correlated with genera like Candidatus_Hepatoplasma and Aeromonas (p < 0.05), suggesting better nutritional value, flavor, and metabolic health in rice-field crabs. Full article

Reliable identification of seafood species is critical for fisheries management and product authentication, especially when morphological characteristics are lost during processing. In this study, a multiplex PCR system was developed to distinguish seven cuttlefish species (six Sepia spp. and Sepiella inermis) commercially distributed in the Korean seafood market. Species identity was first confirmed by amplifying a mitochondrial cytochrome c oxidase subunit I (COI) fragment (~658 bp) using universal primers (LCO1490/HCO2198), showing 99–100% sequence similarity to corresponding GenBank reference sequences. Analysis of genetic variation based on a 530 bp aligned region demonstrated complete interspecific differentiation without shared haplotypes among species. The number of haplotypes per species ranged from 5 to 21, with haplotype diversity values between 0.667 and 1.000. An extended COI fragment (~1200 bp) was further analyzed to identify diagnostic interspecific variation for marker development. Seven diagnostic single-nucleotide polymorphism (SNP) sites were identified and used to design species-specific forward primers with diagnostic nucleotides positioned at the 3′ termini. Distinct amplicons (220–1099 bp) were generated and clearly resolved by agarose gel electrophoresis. Because simultaneous amplification of all seven primer pairs reduced amplification efficiency, the assay was divided into two multiplex sets. Under optimized conditions (56 °C), each species produced a single expected band without cross-amplification. This multiplex PCR system provides a rapid and sequencing-free approach for reliable species discrimination and can be effectively applied to fisheries monitoring and seafood authentication in commercial supply chains. Full article

Nile tilapia (Oreochromis niloticus) is a major aquaculture species worldwide, yet bacterial infections remain a critical constraint to production sustainability. Although pathogen-associated dysbiosis has been widely described, most studies have focused exclusively on bacterial communities, overlooking the multi-kingdom nature of the intestinal microbiota. This study evaluated the impact of experimental Providencia vermicola infection on both prokaryotic and microeukaryotic intestinal communities under controlled conditions. Using 16S (V3–V4) and 18S (V9) rRNA amplicon sequencing, we compared healthy and infected fish and assessed taxonomic, structural, and predicted functional changes. Infection was associated with significant compositional shifts, including increased relative abundances of Bacteroidota and Proteobacteria and decreased relative abundances of Fusobacteriota and Patescibacteria. Concomitantly, microeukaryotic groups such as Protalveolata, Nematozoa, and Phragmoplastophyta were significantly reduced. Functional prediction revealed metabolic pathway reconfiguration consistent with infection-associated ecological disturbance. Together, these results suggest that the pathogen challenge is associated with coordinated changes in the intestinal microbiota as an integrated system across multiple microbial kingdoms rather than as isolated bacterial shifts. This study supports ecosystem-level interpretations of dysbiosis and highlights the importance of incorporating cross-domain analyses into health assessment strategies in aquaculture species. Full article

Ayu (Plecoglossus altivelis) is an East Asian amphidromous river fish, yet seasonal microbiota dynamics remain unclear. We investigated ayu in the Dajing Stream (Zhejiang Province, China) by synchronously sampling water microbiota (H), gut content microbiota (N), and gut tissue-associated microbiota (C) across four seasons. Each season, four fish were collected, and an overlapping pooling strategy (abc/abd/bcd) generated three composite replicates for C and N (n = 3 composites/season); water was collected as three field replicates (n = 3/season), yielding 36 samples (12 per niche). Using 16S rRNA amplicon sequencing and COI barcoding of stomach contents, we observed the clearest seasonal differentiation in H and seasonal variation in N consistent with diet shifts, whereas C was comparatively stable. COI signals indicated a diet dominated by aquatic insects in spring/summer, which shifted toward smaller prey (e.g., rotifers) in winter. Together, these results highlight strong niche partitioning and season-linked shifts in water and gut content communities relative to the more stable tissue-associated microbiota. These findings should be interpreted as exploratory and require validation in larger individual-level studies. Full article

In order to assess the spreading of tick-borne bacteria and protozoa in a protected area largely frequented by people and in which numerous domestic and wild animals live, molecular analyses were carried out in ticks collected from fallow deer (Dama dama) to detect Anaplasma phagocytophilum, Borrelia sp., Coxiella burnetii, Francisella tularensis, Hepatozoon sp., and piroplasms. A total of 148 tick pools, for a total of 475 ticks collected from fallow deer and identified as female adult Ixodes ricinus, were submitted to DNA extraction and different PCR assays. One hundred and two (68.92%) pools were positive for one or more pathogens: three (2.02%) for C. burnetii, 21 (14.19%) for Borrelia sp., 35 (23.64%) for piroplasms, and 87 (58.78%) for A. phagocytophilum. All tick pools were negative for F. tularensis and Hepatozoon sp. Sixty-seven (45.27%) pools were positive for only one investigated pathogen, whereas in 35 (23.64%) pools DNA of two or more pathogens were found. Sequencing analyses identified 28 piroplasm amplicons as Theileria sp. OT3 and seven amplicons as possible Theileria cervi. Sequencing of the 21 Borrelia amplicons identified six samples as B. miyamotoi and eight as B. lusitaniae, whereas seven amplicons had 100% homology with a Borrelia sp. found in France and 99.37% with a B. theileri strain detected in Zambia. Monitoring tick-borne pathogens in ticks is pivotal to assess the spread of these microorganisms, the evolution of their epidemiology, and the risk of infections for animals and humans. Full article

Soil salinity severely constrains strawberry production by disrupting ion homeostasis and provoking oxidative injury. This study investigated whether soluble silicon (Si) and activated carbon (AC) act to enhance salt tolerance in strawberry (Fragaria × ananassa). Under NaCl stress, plants showed pronounced growth inhibition, increased Na⁺ accumulation and a deteriorated K⁺/Na⁺ balance, accompanied by elevated reactive oxygen species (ROS) and lipid peroxidation. In contrast, combined AC + Si treatment consistently provided the strongest protection, improving seedling vigor and survival. Relative to NaCl alone, AC + Si increased shoot and root fresh weight by 67.5% and 78.5%, reduced shoot Na⁺ by 59.1%, and lowered shoot H₂O₂ and MDA by 62.6% and 66.5%, respectively, indicating marked improvement in ion–redox homeostasis. Beyond plant responses, AC-containing treatments alleviated salt-induced increases in soil electrical conductivity, coinciding with a clear restructuring of the rhizosphere bacterial community and enrichment of putatively beneficial taxa. Transcriptome profiling further supported coordinated reprogramming of ion transport, redox control and stress-responsive signaling pathways under the AC + Si regime. Collectively, the results indicated that Si and AC co-application enhances strawberry salt tolerance through an integrated soil–plant–microbiome mechanism that stabilizes ion homeostasis and reinforces redox homeostasis. Full article

This study investigates the impact of inoculating seeds with bacterial endophytes isolated from Vitis amurensis Rupr. on endophytic community composition in Arabidopsis thaliana (L.) Heynh. Ten bacterial isolates of the genera Agrobacterium, Bacillus, Curtobacterium, Erwinia, Frondihabitans, Gordonia, Pantoea, Pseudomonas, Sphingomonas, and Xanthomonas were applied to seeds and some visible phenotypic effects were observed on plant growth after two weeks. High-throughput sequencing of 16S rRNA revealed that the native endophytic microbiome of A. thaliana was dominated by Gammaproteobacteria, Actinomycetes, Bacteroidia, and Alphaproteobacteria. The key families were Microscillaceae, Chitinophagaceae, Rhizobiaceae, Rhodanobacteraceae, Nocardioi-daceae, Nocardiaceae, Xanthomonadaceae, Devosiaceae, Microbacteriaceae, Crocinitomi-caceae, Pseudomonadaceae, Solimonadaceae, Comamonadaceae, Caulobacteraceae, and Micrococcaceae. Arabidopsis seed inoculation with Agrobacterium sp. R8SCh-B12, Curtobacterium sp. P7SA-B3, and Gordonia aichiensis P6PL2 significantly reduced alpha diversity (Shannon index) and altered beta diversity relative to controls, indicating strong community restructuring. These three isolates, along with Pseudomonas sp. R8SCh-B2, Sphingomonas sp. RA62c-B5, Xanthomonas sp. R7SCh-B6, and Bacillus velezensis AMR25, successfully colonized the plant tissues, as evidenced by significant increases in genus-specific amplicon sequence variants, ASVs (up to 17,820-fold for Curtobacterium sp. ASV33). In contrast, Pantoea sp. P7SCH-B5, Erwinia sp. R8SCh-B3, and Frondihabitans sp. RA62c-B2 failed to colonize A. thaliana, despite being applied to the seeds, suggesting the existence of mechanisms restraining colonization. These findings demonstrate that only a subset of grapevine-derived endophytes can effectively colonize A. thaliana, and that successful colonization correlates with significant shifts in the native microbiome, even in the absence of overt phenotypic changes. This emphasizes the importance of strain-specific compatibility in plant–endophyte interactions. Thus, we report the first descriptions of several novel endophytes that colonized Arabidopsis plants and establish a convenient model to investigate plant–bacterial interactions. Full article

The mycoheterotrophic plant Monotropa uniflora relies on fungal symbionts for carbon and nutrient acquisition. However, its interactions with other microbial groups, beyond ectomycorrhizal fungi, remain unexplored. Here, we characterized bacterial and fungal communities associated with M. uniflora across two compartments: ectomycorrhizospheric soil linked to the mycorrhizal network and the surface-sterilized lower stem endosphere. Microbial community composition was assessed using high-throughput amplicon sequencing of the bacterial 16S rRNA gene and the fungal ITS region. Fungal richness was consistently higher in ectomycorrhizospheric soil than in the stem endosphere, whereas bacterial alpha diversity showed no consistent differences between compartments. Multivariate analyses suggested compartment-associated patterns in both bacterial and fungal community composition. Ectomycorrhizospheric soil was dominated by saprotrophic fungal taxa and bacterial groups with predicted metabolic potential, including taxa associated with iron, sulfur and nitrogen cycling. In contrast, the lower stem endosphere was enriched in bacterial taxa commonly associated with anaerobic and nitrogen-related metabolisms. Functional predictions further suggested an increase of carbon fixation-related pathways in rhizosphere-associated bacterial communities. Together, these results indicate that M. uniflora is associated with distinct and structured microbial assemblages across soil and internal plant compartments, highlighting the predicted functional potential of bacterial communities in nutrient- and carbon-related processes in mycoheterotrophic plant–soil systems alongside fungal partners. Full article

Acinetobacter baumannii remains a significant nosocomial infectious agent, with its ability to acquire antimicrobial resistance posing a global public health concern. Over time, substantial knowledge has been amassed regarding A. baumannii in human clinical cases. Recently, research has shifted to non-human A. baumannii. Therefore, the current work aimed to investigate the occurrence of A. baumannii carrying carbapenem resistance genes in broiler chickens via molecular detection and its public health significance. Two hundred cloacal swabs were collected from broiler chickens and grouped into 40 pools. DNA extraction was conducted on these pools, followed by molecular detection of the A. baumannii bla_OXA-51-like gene. Among the 40 pools, 31 (77.5%) tested positive for the bla_OXA-51-like gene and were further screened for additional carbapenemase genes, including bla_OXA-58, bla_OXA-23, and bla_OXA-24. The bla_OXA-58 gene was identified in eight pools (25.8%), whereas bla_OXA-23 and bla_OXA-24 were not detected. Subsequently, partial DNA sequencing was performed on two PCR amplicons of the A. baumannii bla_OXA-51-like gene derived from broiler chickens, followed by a phylogenetic analysis. The analysis revealed genetic similarity between the A. baumannii sequences obtained in this work and those retrieved from humans, birds, animals, and environmental sources. In conclusion, the occurrence of A. baumannii harboring genes coding for carbapenem resistance in broiler chickens highlights a potential new path of transmission, which may require further investigation to better understand the dynamics of transmission and to guide effective strategies for preventing and controlling A. baumannii infections. Full article

The desert ecosystem harbors a resilient microbial community that sustains plant life under extreme stress. Understanding the endophytic microbiota of desert flora provides key insights into how these microorganisms enable plant survival and maintain ecological balance in arid landscapes. To date, the endophytic bacterial communities of dominant desert plants in the Arabian Peninsula have not been comprehensively characterized. Here, we investigated the endophytic microbiota of five co-adapted desert species, namely, Schweinfurthia papilionacea, Sesuvium verrucosum, Ochtocloa compressa, Helianthemum nummularium, and Convolvulus arvensis. These plants coexist in hyper-arid habitats and exhibit exceptional tolerance to drought, salinity, and nutrient scarcity. We hypothesized that, despite their phylogenetic divergence, these plants host functionally convergent microbial communities shaped by desert selection pressures. Using 16S rRNA gene amplicon sequencing, we obtained 3.4 million high-quality reads from 25 samples. Clustering at 97% similarity revealed 35 phyla and 17 dominant genera, highlighting notable microbial richness and ecological complexity. Alpha-diversity indices showed comparable species richness across hosts, while beta-diversity indicated community differentiation driven by environmental filtering. The dominant phyla included Pseudomonadota, Actinomycetota, Cyanobacteriota, and Bacillota, reflecting microbial adaptation to extreme desert conditions. Functional pathway prediction revealed enrichment of genes associated with DNA repair and protein turnover, suggesting metabolic flexibility and enhanced survival under stress. Overall, this study provides a comparative metagenomic insight into the endophytic bacterial communities of five desert plant species, uncovering a consistent pattern of functional convergence across diverse hosts. The findings suggest the presence of shared functional traits among the endophytic microbiota examined here, offering preliminary evidence for microbial contributions to plant resilience in arid environments. Full article

Background/Objectives: Medication-related osteonecrosis of the jaw (MRONJ) is a rare but severe complication of antiresorptive therapy for osteoporosis. This study investigated bacterial adhesion and microbial composition on two suture materials and their potential impact on early wound healing following tooth extraction in patients receiving antiresorptive therapy. Methods: In this prospective exploratory clinical study with partially randomized allocation, female patients undergoing antiresorptive therapy were evaluated for clinical parameters, including the Mombelli Plaque Index (MPI), Mombelli Bleeding Index (MBI), oral smear analysis, and Early Wound Healing Score (EHS). Suture samples (Vicryl and Monocryl, Ethicon, Germany) were removed after 10 days, measured, and weighed. Bacterial DNA was isolated and quantified by qPCR targeting the albumin and 16S rRNA genes. In addition, 16S rRNA gene amplicon sequencing was performed to assess the microbial community composition. Statistical and bioinformatic analyses were conducted to compare materials and evaluate the clustering patterns. Results: Fifty-two suture samples were analyzed. Vicryl exhibited significantly higher 16S rRNA gene copy numbers than Monocryl, indicating increased bacterial colonization, whereas albumin gene copy numbers were significantly higher in Monocryl. The suture weight correlated primarily with albumin gene copy numbers. Amplicon sequencing revealed no material-dependent differences in the microbial composition; instead, samples clustered predominantly by patient, particularly in split-mouth cases. The wound healing outcomes based on the EHS were comparable between materials. Conclusions: Although Vicryl and Monocryl differ in bacterial load and host material deposition, the microbial community composition is primarily patient-specific and the clinical healing outcomes are similar. Surgical management and patient-related factors appear more critical than suture material selection. Full article

Marine fungi are pivotal components of coastal ecosystems, facilitating essential biogeochemical cycling and trophic dynamics. However, the complex mechanisms governing their spatiotemporal community patterns in tropical–subtropical coasts remain largely unexplored. In this study, we characterized marine fungal diversity across a comprehensive seasonal cycle (spring (March), summer (June), autumn (August), and winter (December)) at 21 representative sites along the Leizhou Peninsula, China. These sites were strategically selected to encompass a broad range of dissolved inorganic nitrogen (DIN) gradients. Fungal community composition was characterized via high-throughput sequencing of the internal transcribed spacer 2 (ITS2) region, followed by functional guild profiling using the FUNGuild database. A total of 8777 amplicon sequence variants (ASVs) were identified, encompassing a broad taxonomic breadth of 10 phyla and 358 genera. Ascomycota, Basidiomycota, and Chytridiomycota emerged as the predominant phyla across all samples. Our results revealed significant spatiotemporal heterogeneities: seasonal succession fundamentally reshaped community composition, with DIN exerting its most pronounced influence during the winter. Furthermore, fungal functional structures exhibited distinctive clustering across regions defined by DIN enrichment levels. Co-occurrence network analysis revealed a highly modular and robust architecture, characterized by predominantly positive interactions and dense inter-taxon connectivity. These findings underscore the synergistic influence of temporal dynamics and DIN enrichment in shaping marine fungal community assembly and functional compositions. Our study provides critical baseline insights into the ecological resilience of coastal mycobiota in the South China Sea. Full article

In this study, we compared the bacterial diversity of two independent snow and ice sampling campaigns conducted in 2015–2016 and 2018–2019 at Dome C, Concordia Station, Antarctica. Using 16S rRNA gene amplicon sequencing, we analysed 81 samples and, after quality filtering and rarefaction, obtained approximately 3.8 million high-quality reads. Alpha diversity analyses revealed comparable richness between the two sampling periods, while community evenness was higher in 2018–2019. In contrast, all beta diversity metrics consistently showed significant differences in community composition between years, while beta dispersion analyses indicated distinct levels of heterogeneity within the year. The results of the Raup-Crick null model (R0) analyses showed that the observed differences did not deviate from random expectations under the applied null hypothesis. Overall, these results indicate pronounced interannual variability in bacterial assemblages at Concordia Station and suggest that temporal changes in community composition are consistent with assembly processes dominated by episodic inputs and limited persistence under extreme environmental conditions. This study implements previous investigations by providing a comparative temporal perspective and contributes to a better understanding of microbial dynamics in one of the most isolated and low-biomass environments on Earth. Full article

This study aimed to explore the efficacy of oral supplementation with 11 probiotic strains, combined in the strain mix Probatech™ (Centro Sperimentale del Latte S.r.l Strada Provinciale per Merlino, 326839 Zelo Buon Persico (LO), Italy) and delivered through the food supplement PROBAFLOR and how it plays a positive role in maintaining normal intestinal function, providing benefits in healthy adult subjects. A 16-week, randomized, double-blind, placebo-controlled clinical study was conducted starting with 60 participants. Participants were randomly assigned to either the probiotic or placebo group. Participants were asked to provide one faecal sample at the beginning of the study, another one after 12 weeks of supplementation and the final one after 16 weeks. Amplicon 16S rRNA gene sequencing and GC-MS Short-Chain Fatty Acid (SCFA) profiling were performed on the faecal samples. Participants filled out questionnaires to assess their gastrointestinal health and psychological well-being. The overall mean GIQLI scores increased in both groups over time. The increases were significant within both groups but not between groups. Following the administration of PROBAFLOR, Shannon and Simpson diversity indices showed a significant increase at day 90 (week 12) (p < 0.05), demonstrating that the intervention effectively enhanced gut microbiota diversity. A shift in the intestinal microbiota towards SCFA-producing families and genera was observed. Moreover, the change in total and single SCFAs was significantly different between probiotic and placebo groups at the end of the supplementation period. Once-daily consumption of the PROBAFLOR probiotics formula regulated gut microbiota balance by modulating SCFA production. It may be beneficial for gut health, improving defecation habits and satisfaction, normalizing stool frequency, and promoting bacterial metabolism. Full article