Search Results (5,844)

We applied flow cytometry (FCM) to monitor microbial dynamics during grape must fermentation at the winery scale. Experiments were performed on Pinot Noir grapes using three distinct winemaking protocols: inoculation with active dried yeast, Pied-de-Cuve, and spontaneous fermentation. FCM enabled the assessment of yeast viability and metabolic activity, as well as the detection and monitoring of viable bacterial populations during alcoholic fermentation. Amplicon-based DNA sequencing was performed to characterize the associated microbial communities and evaluate protocol-specific effects. Trends identified by amplicon sequencing were partially mirrored by patterns observed in unsupervised FCM analysis. Overall, our results indicate that FCM is a practical tool for monitoring microbial dynamics during fermentation, providing near–real-time information that can support monitoring strategies and risk management in winemaking. Full article

Escherichia coli O157:H7 is a pathogenic bacterium that causes severe intestinal infections characterized by inflammation and disruption of the intestinal barrier. Probiotic lactic acid bacteria (LAB) from milk can support intestinal health and combat enteric pathogens; however, the potential of feline milk-derived LAB against E. coli O157:H7 infection remains unclear. In this study, Pediococcus acidilactici (P. acidilactici) M22, isolated from feline milk, was evaluated for probiotic activity in vitro and in vivo in a C57BL/6 mouse model of Escherichia coli O157:H7 infection. In vitro assays demonstrated that M22 significantly inhibited the adhesion of Escherichia coli O157:H7 to intestinal epithelial cells. For in vivo assessment, C57BL/6 mice were orally administered M22 prior to infection with E. coli O157:H7. Protective effects were evaluated by monitoring body weight loss, colon length, disease activity index (DAI), myeloperoxidase (MPO) activity, cytokine levels, tight junction protein expression, oxidative stress markers, and gut microbiota composition. M22-treated mice exhibited significantly less body weight loss and lower DAI scores than infected controls. M22 also prevented colon shortening, indicating reduced colonic damage. Probiotic treatment attenuated neutrophil infiltration and mucosal inflammation, as evidenced by decreased colonic MPO activity, reduced levels of pro-inflammatory cytokines, and elevated anti-inflammatory IL-10. Additionally, M22 preserved intestinal barrier function by upregulating tight junction proteins and mitigating infection-induced histopathological changes. M22 supplementation enhanced antioxidant defenses in colonic tissue (lower malondialdehyde, higher superoxide dismutase and glutathione), indicating reduced oxidative stress. Furthermore, gut microbiota analysis (16S rRNA sequencing) revealed that M22 counteracted infection-induced dysbiosis, restoring microbial diversity and a healthy composition (enrichment of beneficial commensals and suppression of harmful bacteria). By safeguarding intestinal integrity and homeostasis, M22 emerges as a promising next-generation probiotic for improving intestinal health in companion animals. Full article

Faced with the challenge of reducing food waste, transforming discarded fruit into functional ingredients useful for the food industry is a valuable solution. Ingredients from fruit such as persimmons, which are rich in indigestible carbohydrates and bioactive compounds with antiradical capacity, could positively impact on the health of certain population groups due to their potential prebiotic effect. This study aimed to select the most suitable drying conditions and milling intensity for obtaining powdered persimmon ingredients with a prebiotic-like effects observed in vitro for postmenopausal women, and to evaluate this effect by considering the stimulation of health-promoting bacterial growth and short-chain fatty acids (SCFAs) production. First, the effect of the drying method (hot air drying at 60 and 70 °C, and freeze-drying) and grinding intensity on antiradical capacity, particle size, and the release of bioactive antiradical components into the intestinal lumen after an in vitro gastrointestinal digestion was determined. Next, the effect of these conditions on the microbiota composition of postmenopausal women was preliminary assessed in a batch colonic fermentation experiment for 24 h. The results showed that the ingredient dried with air at 70 °C had the highest phenol and flavonoid content, suffered the least degradation during in vitro gastrointestinal digestion and promoted the differential growth of fiber-degrader genera. Consequently, this was the ingredient selected as the most suitable. Lastly, the impact of this ingredient on the microbiota composition of 4 postmenopausal women has been evaluated in a long-term study using the Simulator of the Human Intestinal Microbial Ecosystem (SHIME^®) coupled to high throughput sequencing. The growth stimulation of health-associated bacteria, such as Akkermansia muciniphila, Faecalibacterium prausnitzii or Phascolarctobacterium faecium, and the promotion of beneficial metabolic pathways, such as the sugar uptake-specific phosphotransferase system, sugar metabolism and propionate and isobutyrate production, were detected along 14 days of persimmon powder supplementation. A holistic framework for promoting human health while advancing environmental sustainability is represented by the combination of sustainable by-product valorization and microbiota-targeted functional food development. Full article

Glaciers have been proposed as evolutionary hotspots for microbial evolution; however, direct evidence for glacial microbial population formation and genomic loci undergoing selective sweeps remains limited. To address this knowledge gap, we investigated the genomic diversity, evolutionary pressures, and adaptive strategies of Cryobacterium, a representative genus of glacier environments. Based on recent gene flow analysis, 18 distinct populations of Cryobacterium were identified, each exhibiting clear discontinuities in gene flow and genetic boundaries. Selective pressure analyses revealed purifying selection within populations, maintaining genetic stability, and positive selection between populations, suggesting adaptive divergence from environmental differences. Notably, half of the populations spanned geographically distant glaciers, suggesting widespread dispersal mechanisms such as atmospheric circulation or glacial fauna migrations. We identified 17 genes under strong selective sweeps, involved in metabolic enzymes, transporters, and gene regulation. Based on the reverse ecology principles, these genes (e.g., glucose-6-phosphate dehydrogenase assembly and RNA polymerase-binding gene), are likely to be critical for cold adaptation. This study provided clear genomic evidence of glacial microbial population formation driven by recent gene flow, significantly enhanced our understanding of microbial adaptation in extreme cold ecosystems, and emphasized the importance of deep genomic sequencing in ecological and evolutionary research. Full article

This study aims to reveal the rhizosphere bacteriome patterns, biomarkers, and metabolic functions of dominant plants in the water-level fluctuation zone (WLFZ) of the Three Gorges Reservoir through comparative analyses with the non-rhizosphere bacteriome. The present study showed that a total of 4546–5011 amplicon sequence variants (ASVs) were identified in both rhizosphere and non-rhizosphere soils of Artemisia annua L. and Persicaria lapathifolia (L.) Delarbre. Pseudomonadota and Acidobacteriota were the most abundant bacterial phyla in both rhizosphere and non-rhizosphere bacteriomes. The α-diversity indices of microbial communities in the non-rhizosphere soils were lower than those in the rhizosphere soils associated with the two dominant plant species. Distinctive key biomarkers were successfully identified for both rhizosphere and non-rhizosphere bacterial assemblages, and these biomarkers exhibited a strong plant-specific pattern. Functional annotation revealed that metabolic processes, genetic information processing, and two core functional traits (chemoheterotrophy and aerobic chemoheterotrophy) accounted for the highest relative abundance within the bacteriomes. However, notable discrepancies were observed in the subdominant functional traits between the rhizosphere and non-rhizosphere bacteriomes. Overall, the present study brings novel insight into the plant-microbe interactions in the WLFZ of large reservoirs under the extreme environmental conditions. Full article

As a fast-growing timber tree species with a wide cultivation area, poplar is facing the problem of declining economic benefits under long-term monoculture. Intercropping provides an effective solution. Using Illumina Miseq sequencing, we analyzed soil microbiomes under four patterns: poplar monoculture, and intercropping with amorpha fruticosa, black locust, or cassia seed. The results showed that the Alpha diversity index of intercropping area was significantly higher than that of single planting poplar area under intercropping and monoculture conditions. In the intercropping area, the highest species richness was the intercropping of poplar and black locust, and the lowest was the intercropping of poplar and amorpha fruticosa. The dominant microorganisms in the intercropping mode were Vicinamibacterales, and the fungi were Alternaia and Enterocarpus. In the single planting poplar area, a large number of bacteria gathered in the soil were Dongia and Alphaproteobacteria, and fungi were Fusarium and Mortierella. Functional prediction results showed that the biosynthetic function of ansamycin was the highest in the bacterial community. In the intercropping area, the functional abundance of methanol oxidation, sulfate respiration, sulfate compound respiration, nitrate denitrification, nitrite denitrification, and nitrous oxide denitrification was higher than that in the single planting poplar area. On the contrary, the abundance of methanotrophy function is lower than that of single planting poplar area. In the fungal community, the functional abundance of animal pathogens and the animal pathogen–dung saprotroph–endophyte–plant saprotroph–soil saprotroph–wood saprotroph group in the monoculture poplar area was higher than that in the three intercropping areas. In summary, the intercropping mode of poplar is better than the monoculture mode, and the species richness is the highest when poplar and black locust are intercropped. Therefore, the intercropping pattern of poplar and other tree species improved microbial community. This provides some theoretical guidance for the subsequent solution of continuous cropping obstacles in poplar. Full article

Choledochal cyst (CC), a congenital biliary anomaly, is associated with recurrent infections, chronic inflammation, and an increased risk of malignancy. Although emerging evidence implicates the biliary microbiome in disease pathophysiology, its developmental dynamics in pediatric CC remain unclear. Using deep metagenomic sequencing and comprehensive functional annotation, this study characterized age-dependent changes in the biliary microbiome of 201 pediatric CC patients stratified into infancy (<1 year), early childhood (1–5 years), and later childhood (5–12 years). We found that while the taxonomic composition and alpha diversity of the microbiota remained conserved across age groups, profound functional remodeling occurred with host development. A core set of microbial species(Bacteroidota, Actinomycetota, Bacillota, and Pseudomonadota) and functional pathways was shared across all ages; however, early childhood (1–5 years) exhibited the greatest number of unique functional genes, metabolic pathways, and carbohydrate-active enzymes, identifying this period as a critical window for microbial metabolic adaptation. Age-specific patterns were also evident in clinically relevant traits: infants (<1 year) harbored the most unique antibiotic resistance and virulence factor genes, whereas the resistome and virulome became more streamlined in older children. These findings establish a paradigm of “taxonomic conservation coupled with functional remodeling” in the CC microbiome and highlight age as a key determinant of microbial community function. This study offers novel insights into the microbial dynamics underlying CC progression and suggests potential age-specific targets for future therapeutic strategies. Full article

To investigate the effects of mixed forests on soil bacterial characteristics in the Yellow River Delta, pure forests of Ailanthus altissima, Ulmus pumila, Robinia pseudoacacia, and Fraxinus velutina (hereafter Aa, Up, Rp, and Fv, respectively) and mixed forests of Aa-Rp, Up-Rp, Fv-Rp, and Ma (Melia azedarach)-Fv were selected as the research objects. High-throughput sequencing technology was employed to analyze the structure, diversity, and function of bacterial communities in this region. The results showed that Acidobacteria, Proteobacteria, and Actinobacteria were the dominant microbial groups. The relative abundance of Acidobacteria was reduced by mixed patterns of Up-Rp, Fv-Rp and Ma-Fv, and the abundance of Proteobacteria was increased in Ma-Fv. The Chao1, ACE and Shannon indices of Aa-Rp and Fv-Rp were increased, while the Chao1 and ACE indices of Up-Rp and Ma-Fv were decreased. Functional prediction revealed that chemoheterotrophic and aerobic chemoheterotrophic bacteria had the highest abundance, with mixed forests exerting variable effects on different functional bacterial groups. In conclusion, mixed forest management exerts a significant influence on shaping bacterial community structure, regulating its diversity, and facilitating the directional enrichment of functional bacteria, which is conducive to enhancing the stability and sustainability of plantations. Full article

Tea cultivar genotype plays a critical role in shaping rhizosphere microbiome assembly, yet the underlying mechanisms remain poorly understood. This study employed a controlled pot experiment with five widely cultivated Chinese tea cultivars (Camellia sinensis) to investigate how cultivar-specific variation influences rhizosphere microbial communities and their assembly processes. Rhizosphere soil microbiomes (bacterial and fungal communities) and metabolomes were characterized using 16S rRNA and ITS2 amplicon sequencing combined with untargeted metabolomics. Significant differences in rhizosphere metabolite composition, primarily organic acids, fatty acids, and carbohydrates, were observed among cultivars, which corresponded to distinct bacterial and fungal community structures. Redundancy analysis (RDA) revealed that rhizosphere metabolites explained 19.87% of bacterial and 21.63% of fungal community compositional variation, second only to soil physicochemical properties. Neutral community model and modified stochasticity ratio analyses indicated that microbial assembly across cultivars was predominantly deterministic, and rhizosphere metabolite profiles were strongly correlated with microbial community structure. Notably, arbuscular mycorrhizal fungi made up about 11% of the fungal communities in minimally fertilized pot systems, contrasting sharply with their near-absence in conventionally managed systems plantations. These findings demonstrate that tea cultivar genotype significantly shapes rhizosphere microbiome assembly through metabolic differentiation, providing a theoretical foundation for integrating microbiome considerations into tea breeding programs and developing cultivar-specific management strategies. Full article

Background/Objectives: Nutrition and the gut microbiota influence treatment tolerance and recovery in patients with colon cancer receiving chemotherapy. This pilot study examined changes in diet quality and fecal microbiota over 6 months of chemotherapy and evaluated longitudinal associations between diet quality and gut microbiota diversity and taxa. Methods: 48 adults with stage II–III colon cancer receiving 5-fluorouracil-based chemotherapy were assessed at baseline and 6 months post-initiation. Diet quality was measured using 3-day dietary recalls to calculate Healthy Eating Index (HEI) scores. Stool samples underwent 16S rRNA sequencing to assess Shannon diversity, Beta and taxonomic composition. Pre–post changes were analyzed using paired tests, and associations between HEI and microbiota measures were evaluated using multivariable linear regression adjusting for demographic and clinical covariates. Results: Diet quality declined during chemotherapy, with reduced intake of fiber, fruits and vegetables, and whole grains. Gut microbial alpha diversity decreased over time. At the phylum level, Actinobacteriota decreased, while Bacteroidota and Proteobacteria increased. At the genus level, only Streptococcus (decreased) and Escherichia (increased) remained significantly altered after multiple testing correction. Higher baseline diet quality and improvements over time were associated with greater microbial diversity and lower Proteobacteria abundance. Diet quality was inversely associated with Streptococcus and Escherichia and positively associated with short-chain fatty acid-producing, fiber-responsive genera (Faecalibacterium, Mediterraneibacter, Ruminococcus_E, Fusicatenibacter). Baseline gut microbiota did not significantly associate with changes in diet quality. Conclusions: Chemotherapy was associated with declines in diet quality, gut microbial alpha diversity, along with shifts in beta diversity and microbial taxa. Higher diet quality appeared protective against microbial disruption, supporting a bidirectional relationship between diet and the gut microbiome during chemotherapy. Nutritional and microbiota-focused approaches warrant further investigation in the context of chemotherapy. Full article

The phyllosphere microbiome is an important component of plant-associated ecosystems, and its structure is susceptible to biotic stress and agricultural interventions. However, the non-target effects of plant-derived pesticides and their nanoformulations on the phyllosphere microbial community remain unclear. By using 16S rRNA amplicon sequencing, we investigated the non-target effects of azadirachtin (Aza) and its nanoformulation (O-carboxymethyl chitosan-loaded azadirachtin, O-cmc-aza) on the phyllosphere microbial community of maize, including Spodoptera frugiperda herbivory stress (Attack) as an additional treatment. The results showed that all three treatments significantly altered the phyllosphere microbial community structure, while the overall microbial diversity indices remained stable. Specifically, the Attack treatment significantly enriched bacterial genera such as Akkermansia and Burkholderia-Caballeronia-Paraburkholderia; the Aza treatment mainly increased the abundance of taxa such as Stenotrophomonas and Herbaspirillum, which have been associated in the literature with plant growth promotion; and the O-cmc-aza treatment specifically enriched microbial groups such as Ralstonia and Sphingomonas, which have been reported to include strains involved in pollutant degradation and nitrogen cycling, while reducing the ACE index but maintaining high community evenness. Our results indicated that azadirachtin and its nanoformulations induced compositional changes in the phyllosphere microbiome, without causing marked decline in microbial diversity. This study provides data support for evaluating plant-derived pesticides and nanoformulations with respect to their non-target effect on phyllosphere microbial communities in green agricultural systems. Full article

Olive orchard soils are a source of microorganisms capable of inhibiting major olive pathogens. In this study, rhizobacteria were isolated and characterized based on plant growth-promoting traits, and soil 16 rRNA gene sequencing analysis was performed to analyze microbial communities at two key olive phenological stages (flowering and fruit formation). Using a culture-dependent approach, a total of 90 bacterial isolates representing distinct colony morphotypes were recovered from olive soils, with 35 during the flowering stage and 55 during the fruit formation stage, indicating a higher cultivable diversity during the latter period. We identified some bacterial strains with antagonistic activity and observed phenology-related shifts in the soil microbiome. Using differential abundance analysis, we identified bacterial taxa that were significantly enriched or depleted during olive fruit formation. Overall, this study demonstrates that olive-associated bacteria harbor antagonistic potential against olive pathogens. The use of bacteria adapted to olive agroecosystems represents a promising strategy for sustainable disease management. Full article

This study reports the incidental collection and exploratory analysis of a biofilm sample obtained from a water distribution pipeline in the Central Province of Sri Lanka, which had been in continuous service for approximately 50 years. Access to the pipe interior was achieved during a repair operation, providing a rare opportunity to directly sample an aged pipeline under the typical operating conditions of a tropical, developing country. An exploratory research design was adopted to examine the bacterial community composition and was explicitly framed as hypothesis-generating rather than testing predefined hypotheses. Bacterial community composition was analyzed using high-throughput MiSeq sequencing. At the genus level, the community was strongly enriched with Clostridium sensu stricto lineages, notably type 1 (relative abundance of 9.19%), type 12 (8.58%), and type 9 (3.09%). Several other genera, Nitrospira (4.94%), Bacillus (4.60%), Methyloligobacillus (3.75%), Hyphomicrobium (2.14%), and Haliangium (1.82%), occurred at moderate abundances, raising their potential consequences on biological and chemical water quality issues. Given the exploratory nature of the study, these findings represent site-specific biofilm characteristics in an aging drinking water distribution line in Sri Lanka. Although limited to a single biofilm sample, this study provides empirical observations from a rarely accessible environment and identifies knowledge gaps to guide future comprehensive investigations into biofilm dynamics, microbial ecology, and infrastructure management in tropical water distribution systems. Full article

In this study, a Nocardia niigatensis strain was isolated from boron-rich mining soils in the Bigadiç region of Türkiye and comprehensively characterized. The primary aim of this study was to isolate boron-tolerant Nocardia species and evaluate their physiological, enzymatic, and biochemical profiles. Selective isolation techniques were employed to obtain Nocardia isolates, and species-level identification was achieved using both 16S rRNA gene sequencing and MALDI-TOF MS analysis, which consistently confirmed the isolate as N. niigatensis. In addition to molecular identification, the morphological, physiological, and biochemical characteristics of the strain were extensively investigated. The strain demonstrated notable boron tolerance, exhibiting robust growth at concentrations up to 50 mM, highlighting its potential applicability in the bioremediation of boron-contaminated environments. Physiological assays further revealed moderate halotolerance and a mesophilic growth profile, with optimal growth observed at 27–37 °C. Enzymatic screening indicated positive L-glutaminase activity, an enzyme of considerable industrial relevance. Moreover, API ZYM profiling revealed a broad enzymatic spectrum, including esterases, arylamidases, phosphatases, and glucosidases, suggesting substantial metabolic versatility. Antibiotic susceptibility testing showed sensitivity to doxycycline, tobramycin, and erythromycin, whereas resistance was observed against imipenem and several β-lactam antibiotics. Metagenomic analysis of boron-rich soils from two distinct mining sites revealed marked differences in microbial community composition, with variations in Actinobacteria abundance associated with mineral type. Overall, these findings emphasize the adaptive capacity and biotechnological potential of environmental Nocardia strains inhabiting chemically stressful ecosystems, warranting further genomic and metabolomic investigations. Full article

The gut plays a central role in fish nutrition, immunity, and overall health, making it key in aquaculture research. The microbiota, crucial to gut function, is increasingly studied as an indicator of health and nutritional status. This study characterized the gut microbiota of juvenile meagre (Argyrosomus regius) (initial weight 4.6 ± 0.4 g) fed for seven weeks on diets in which fishmeal (FM) and fish oil (FO) were replaced by increased proportions of plant-based ingredients, with the aim of identifying microbial profiles associated with nutritional challenge. Fish were fed a FM/FO control diet (CTRL; 55.1% FM, 11.3% FO), a low FM/FO diet (CD; 15% FM, 7% FO), or a very low FM/FO diet (ED; 5% FM, 5% FO). Next-generation sequencing analysis of gut mucosa and digesta revealed no significant differences in alpha or beta diversity among different dietary groups. Firmicutes dominated all samples, particularly Bacilli, Mycoplasmatales, Mycoplasmataceae, and Mycoplasma. Significant differences were only observed in low-abundance taxa (<1%), with higher abundance of Thermoactinomycetales (p = 7.71 × 10⁻⁴), Thermoactinomycetaceae (p = 7.71 × 10⁻⁴), Kroppenstedtia (p = 1.70 × 10⁻³), and Pseudogracilibacillus (p = 0.039) in challenged groups. This study highlights the potential of low-abundance microbial groups as targets to establish gut health biomarkers in fish. Full article