Search Results (428)

In this study, the distribution patterns of the nitrifying and denitrifying microbiome in a large-scale biofilter (587.24 m³) in a cold freshwater recirculating aquaculture system (RAS) was investigated. Previous studies have revealed that the water quality, nitrification, and denitrification rates in the front (BFF), middle (BFM), and back (BFB) of this biofilter are different. The results showed the highest diversity of the denitrifying microbiome in the BFB, followed by BFF and BFM, whereas nitrifying microbiome diversity remained consistent across different positions. Two genera, Nitrosomonas and Nitrosospira, dominated the nitrifying microbiome, while Pseudomonas, Thauera, Cupriavidus, Dechloromonas, Azoarcus, and Paracoccus comprised the top six denitrifying genera. Principal coordinate analysis indicated a distinct spatial distribution pattern of the denitrifying microbiome but not the nitrifying microbiome. The genera Pseudomonas and Dechloromonas were the biomarkers of the BFF and BFB, respectively. Redundancy analysis showed that nitrite, nitrate, dissolved oxygen, and soluble reactive phosphorus influenced the functional microbiome distribution pattern. Network correlation analysis identified one nitrifying hub (Nitrosospira) in the BFF, five denitrifying hubs (Aromatoleum, Dechloromonas, Paracoccus, Ruegeria, and Thauera) in the BFM, and three denitrifying hubs (Azoarcus, Magnetospirillum, and Thauera) in the BFB. Exclusively negative correlations were found between hubs and its adjacent nodes in the BFF and BFB. This study demonstrates that habitat can shape the distribution patterns of the nitrifying and denitrifying microbiome in the biofilter of the RAS, with the BFF exhibiting greater benefits for the nitrification process. Full article

Metagenomic studies have provided deeper insights into the complex interactions between the skin and its microbiota. However, limited research has been conducted on the skin microbiota of Brazilian women. Given that Brazil ranks as the fourth-largest consumer of cosmetics worldwide, the development of new tools to analyze skin microbiota is crucial for formulating cosmetic products that promote a healthy microbiome. Skin samples were analyzed using the Illumina platform. Biometrology assessments were applied. The results showed pH variations were more pronounced in the older age group, along with higher transepidermal water loss values. Metagenomic analysis showed a predominance of Actinobacteria (83%), followed by Proteobacteria (7%), Firmicutes (9%) and Bacteroidetes (1%). In the older group (36–45 years old), an increase in Actinobacteria (87%) was observed and a decrease in Proteobacteria (6%). Moreover, the results differ from the international literature, since an increase in proteobacteria (13.9%) and a decrease in actinobacteria (46.7%) were observe in aged skin. The most abundant genus identified was Propionibacterium (84%), being the dominant species. Interestingly, previous studies have suggested a decline in Cutibacterium abundance with aging; although there is no significant difference, it is possible to observe an increasing trend in this genus in older skin. These studies can clarify many points about the skin microbiota of Brazilian women, and these findings could lead to the development of new cosmetics based on knowledge of the skin microbiome. Full article

Ultrafine bubbles (UFBs) represent an emerging technology with unique physicochemical properties. This study investigated the effects of air-filled UFBs infused in drinking water on gut microbiota composition and the associated health markers in Sprague Dawley rats over a 12-week period. Using a two-phase design, UFB concentration was increased from 1.7 × 10⁶ to 6.5 × 10⁹ UFBs/mL at week 7 to assess dose-dependent effects. Administration of UFBs in drinking water induced significant shifts in gut microbiome populations, characterized by increased Bacteroidetes (+122% weeks 8–12) and decreased Firmicutes (−43% weeks 8–12) compared to controls. These microbial shifts coincided with enhanced short-chain fatty acid production (butyrate +56.0%, p ≤ 0.001; valerate +63.1%, p ≤ 0.01) and reduced inflammatory markers (TNF-α −84.0%, p ≤ 0.05; IL-1β −41.0%, p ≤ 0.05; IL-10 −69.8%, p ≤ 0.05). UFB effects demonstrated systematic concentration-dependent threshold responses, with 85.7% of parameters exhibiting directional reversals between low (1.7 × 10⁶ UFBs/mL) and high (6.5 × 10⁹ UFBs/mL) concentration phases rather than linear dose–response relationships. The systematic nature of these threshold effects, with 71.4% of parameters achieving statistical significance (p ≤ 0.05), indicates concentration-dependent biological mechanisms rather than random effects on gut biology. Despite current metagenomic techniques identifying only 25% of the total gut microbiome, the observed changes in characterized species and metabolites demonstrate UFB technology’s therapeutic potential for conditions requiring microbiome modulation, providing new insights into UFB influence on complex biological systems. Full article

This comprehensive study investigates the spatial distribution of metals in surface water, their accumulation in fish tissues, and their impact on the gut microbiome dynamics of fish in the Qi River, Huanggang City, Hubei Province. Three distinct sampling regions were established: the mining area (A), the transition area (B), and the distant area (C). Our results revealed that metal concentrations were highest in the mining area and decreased with increasing distance from it. The bioaccumulation of metals in fish tissues followed the order of gut > brain > muscle, with some concentrations exceeding food safety standards. Analysis of the gut microbiota showed that Firmicutes and Proteobacteria dominated in the mining area, while Fusobacteriota were more prevalent in the distant area. Heavy metal pollution significantly altered the composition and network structure of the gut microbiota, reducing microbial associations and increasing negative correlations. These findings highlight the profound impact of heavy metal pollution on both fish health and the stability of their gut microbiota, underscoring the urgent need for effective pollution control measures to mitigate ecological risks and protect aquatic biodiversity. Future research should focus on long-term monitoring and exploring potential remediation strategies to restore the health of affected ecosystems. Full article

Salinization of olive orchards constitutes a front-line agronomic challenge for farmers, consumers, and the scientific community as food security, olive logistics, and land use become more unsustainable and problematic. Plantlets of two olive varieties (var. Kalamon and var. Koroneiki) were tested for their performance under soil saline conditions, in which L-methionine, choline-Cl, and L-proline betaine were applied foliarly to alleviate adverse effects. The ‘Kalamon’ variety ameliorated its photosynthetic rates when L-proline betaine and L-methionine were administered at low saline exposure. The stressed varieties achieved higher leaf transpiration rates in the following treatment order: choline-Cl > L-methionine > L-proline betaine. Choline chloride supported stomatal conductance in stressed var. Kalamon olives without this pattern, which was also followed by var. Koroneiki. Supplementation regimes created a mosaic of responses on varietal water use efficiency under stress. The total phenolic content in leaves increased in both varieties after exogenous application only at the highest levels of saline stress. None of the substances applied to olive trees could stand alone as a tool to mitigate salinity stress in order to be recommended as a solid agronomic practice. The residual exploitation of amino acids by the olive orchard microbiome must also be considered as part of an environmentally friendly, integrated strategy to mitigate salinity stress. Full article

Fecal water syndrome (FWS) in horses is characterized by two-phase defecation, including both solid and liquid phases. While satisfactory explanations for FWS are unavailable, bacterial dysbiosis has been suggested as a contributing or causative factor. The objectives of this study were to determine whether fecal bacterial dysbiosis is associated with FWS in horses in the midwestern USA. Fecal samples were collected from horses with FWS and from unaffected horses at the same location. In total, 16S rRNA amplicon libraries produced from fecal bacterial DNA were sequenced using the Illumina sequencing platform. Significant differences in beta diversity were detected between affected and control horses (p = 7 × 10⁻⁴, F = 1.51), and differential abundance testing identified several features enriched in affected and control horses. These results agree with prior work regarding specific features in the bacterial microbiome associated with FWS, including Alloprevotella spp., and suggest fecal dysbiosis is associated with FWS. Full article

Temperature fluctuations caused by climate change and global warming pose a threat to fish. The burbot (lota lota) population is particularly sensitive to increased water temperature, but the systematic impacts of high-temperature exposure on their liver and intestinal health remain unclear. In January of 2025, we collected wild adult burbot individuals from the Ussuri River (water temperature: about 2 °C), China. The burbot were exposed to 2 °C, 7 °C, 12 °C, 17 °C, and 22 °C environments for 96 h; then, the liver and intestinal contents were subsequently collected for histopathology observation, immunohistochemistry, biochemical index assessment, and transcriptome/16S rDNA sequencing analysis. There was obvious liver damage including hepatocyte necrosis, fat vacuoles, and cellular peripheral nuclei. Superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GSH-Px) activities were elevated and subsequently decreased. Additionally, the malondialdehyde (MDA) level significantly increased with increasing temperature. These results indicate that 7 °C (heat stress temperature), 12 °C (tipping point for normal physiological metabolism status), 17 °C (tipping point for individual deaths), and 22 °C (thermal limit) are critical temperatures in terms of the physiological response of burbot during their breeding period. In the hepatic transcriptome profiling, 6538 differentially expressed genes (DEGs) were identified, while KEGG enrichment analysis showed that high-temperature stress could affect normal liver function by regulating energy metabolism, immune, and apoptosis-related pathways. Microbiomics also revealed that acute heat stress could change the intestinal microbe community structure. Additionally, correlation analysis suggested potential regulatory relationships between intestinal microbe taxa and immune/apoptosis-related DEGs in the liver. This study revealed the potential impact of environmental water temperature changes in cold habitats in winter on the physiological adaptability of burbot during the breeding period and provides new insights for the ecological protection of burbot in the context of global climate change and habitat warming. Full article

Microplastic particles (MPs) are an emerging global pollutant of increasing concern due to their widespread occurrence, persistence, and multifaceted impact on aquatic ecosystems. This study provides a comprehensive review of peer-reviewed literature from 2011 to 2025, analysing the presence, distribution, and microbiological associations of MPs in surface waters across five continents. The findings confirm that MPs are present in both marine and freshwater systems, with concentrations varying by region, hydrology, and proximity to anthropogenic sources. Polyethylene and polypropylene were identified as the most common polymers, often enriched in river mouths, estuaries, and aquaculture zones. A key focus of this review is the plastisphere—microbial biofilms colonizing MPs—which includes both environmental and pathogenic bacteria such as Vibrio, Pseudomonas, and Acinetobacter. Notably, MPs serve as vectors for the spread of antibiotic resistance genes (ARGs), including sul1, tetA and ermF, and β-lactamase genes like blaCTX-M. This highlights their role in enhancing horizontal gene transfer and microbial dissemination. The results emphasize the need for standardized monitoring protocols and further interdisciplinary research. In light of the One Health approach, understanding the microbial dimension of MP pollution is essential for managing risks to environmental and public health. Full article

Background: Early neurovascular unit (NVU) impairment plays a critical role in the pathogenesis of diabetic retinopathy (DR), often preceding clinically detectable changes. Butyrate, a short-chain fatty acid (SCFA) derived from gut microbiota, has shown promising metabolic and anti-inflammatory effects. Methods: This study investigated the protective potential of oral butyrate supplementation in a mouse model of early type 2 diabetes mellitus (T2DM) induced by a high-fat diet and streptozotocin. Mice (C57BL/6J) received sodium butyrate (5 g/L in drinking water) for 12 weeks. Retinal NVU integrity was assessed using widefield swept-source optical coherence tomography angiography (WF SS-OCTA), alongside evaluations of systemic glucose and lipid metabolism, hepatic steatosis, visual function, and gut microbiota composition via 16S rRNA sequencing. Results: Butyrate supplementation significantly reduced body weight, fasting glucose, serum cholesterol, and hepatic lipid accumulation. Microbiome analysis demonstrated a partial reversal of gut dysbiosis, characterized by increased SCFA-producing taxa (Ruminococcaceae, Oscillibacter, Lachnospiraceae) and decreased pro-inflammatory, lipid-metabolism-related genera (Rikenella, Ileibacterium). KEGG pathway analysis further revealed enrichment in microbial lipid metabolism functions (fabG, ABC.CD.A, and transketolase). Retinal vascular and neurodegenerative alterations—including reduced vessel density and retinal thinning—were markedly attenuated by butyrate, as revealed by WF SS-OCTA. OKN testing indicated partial improvement in visual function, despite unchanged ERG amplitudes. Conclusions: Butyrate supplementation mitigates early NVU damage in the diabetic retina by improving glucose and lipid metabolism and partially restoring gut microbial balance. This study also underscores the utility of WF SS-OCTA as a powerful noninvasive tool for detecting early neurovascular changes in DR. Full article

Climate change can have a direct impact on the decomposition of organic matter, as well as indirect effects on peatland vegetation (including carnivorous plants) and the microbial communities associated with this environment. The activity of microbes varies depending on the type of peatland they inhabit. Because some microorganisms are highly sensitive, they can be used as indicators of climate change. However, there is still little knowledge of how changes in the temperature of the environment can affect the microbiome of carnivorous plants. The study was conducted to test the following hypotheses: (1) The effect of rising water temperature on the qualitative and quantitative structure of the microbiome of carnivorous peatland plants depends on the type of peatland; (2) habitats with a higher trophic status stimulate the development of microbial communities in the water, but are an unfavourable habitat for the development of the microbiome of plant traps. Irrespective of the type of peatland, the species richness of microorganisms was much higher in the water than in the traps. As the temperature increased, there was an increase in the abundance of bacteria, heterotrophic flagellates, and testate amoebae, which was much more pronounced in the peat bog than in the carbonate fen. Full article

Background: Symbiotic gut microbiota can enhance cancer therapy efficacy, while treatment-induced dysbiosis may reduce effectiveness or increase toxicity. Our preclinical study compared the anticancer effects and impact on fecal microbiota and metabolites of two water-soluble SN-38 derivatives (BN-MePPR and BN-MOA), with those observed after treatment with Irinotecan, and the FOLFOX regimen in NOD scid gamma mice bearing patient-derived colon adenocarcinoma xenografts (CRC PDX). Methods: Five individual experiments with Irinotecan and its derivatives and eight individual experiments with FOLFOX were conducted using eight CRC PDX models. Chemotherapeutics were administered intraperitoneally 4–5 times at 5-day intervals. Fecal samples were collected before and after treatment. Microbiota composition was analyzed by 16S rRNA gene (V3–V4 regions) sequencing. Mass spectrometry was used to quantify short-chain fatty acids (SCFAs) and amino acids (AAs). Results: All treatments significantly inhibited tumor growth versus controls. However, no significant changes were observed in gut microbiota α- and β-diversity between treated and untreated groups. Tumor progression in controls was associated with increased abundance of Marvinbryantia, Lactobacillus, Ruminococcus, and [Eubacterium] nodatum group. FOLFOX-treated mice showed increased Marvinbryantia, Bacteroides, and Candidatus Arthromitus, and decreased Akkermansia. No distinct taxa changes were found in the Irinotecan or derivative groups. SCFA levels remained unchanged across groups, while BN-MePPR, BN-MOA, and Irinotecan all increased AA concentrations. Conclusions: Contrary to earlier toxicological data, these findings indicate a relatively limited impact of the tested chemotherapeutics on the gut microbiome and metabolome, emphasizing the importance of research method selection in preclinical studies. Full article

Rice-field eel (Monopterus albus) slices, an important aquatic product in Southeast Asia, are prone to spoilage and deterioration during cold chain storage. In this study, the effects of a composite preservative (ε-polylysine, Vitamin C (Vc), epigallocatechin gallate (EGCG), and phloretin) on the muscle quality (color, texture, water holding capacity (WHC)) of rice-field eel slices during refrigeration storage at 4 °C for up to 7 days was investigated, and the underlying mechanism was elucidated by the integrated microbiome and metabolomics, in addition to Elisa and Low-Field Nuclear Magnetic Resonance (LF-NMR). After 7 days of storage, the WHC, shear force, and a* decreased by 11.39%, 34.37%, and 49.20% in treated samples, and by 19.18%, 38.38%, and 54.87% in control samples, respectively. The addition of the composite preservative significantly increased Hexokinase, Pyruvate kinase, and Creatine kinase, while it decreased the total viable count (TVC), total volatile basic nitrogen (TVB-N), thiobarbituric acid reactive substance (TBARS), and Lactic acid. Preservative treatment maintained the moisture content of the eel slices during storage and prevented bright red oxymyoglobin from transforming into brown metmyoglobin. Microbiota composition (especially Pseudomonas) and metabolic pathways (including amino acid and its metabolites, nucleotide and its metabolite, and organic acid and its derivatives, etc.) were obviously altered by the preservative treatment. Pseudomonas, tryptophan-aspartic acid (Trp-Asp), D-Glucose 6-phosphate, Succinic Acid, Biliverdin 1, 5-Diaminopentane, and Tyramine, etc., are potential biomarkers for the quality changes of eel slices during refrigeration. These findings provide an in-depth understanding of the improvement of the eel slice quality during refrigeration storage by the composite preservative. Full article

Rice sustains a large global population, making its sustainable production vital for food security. Alternate wetting-and-drying (AWD) irrigation offers a promising approach to reducing water use in rice paddies but can impact grain yields. Plant growth-promoting rhizobacteria (PGPR) can enhance rice productivity under AWD cultivation conditions. This review explores integrating PGPR into AWD systems, focusing on their mechanisms for promoting growth and water stress resilience. It examines diverse microbial communities, particularly bacteria, and their contributions to nutrient acquisition, root development, and other beneficial processes in rice under fluctuating moisture, as well as the influence of AWD on rice’s structural and physiological development. The challenges and opportunities of AWD are also addressed, along with the importance of bacterial selection and interactions with the native soil microbiome. This synthesizes current research to provide an overview of PGPR’s potential to improve sustainable and productive rice cultivation under AWD. Future studies can leverage powerful tools such as e-DNA and NGS for a deeper understanding of these complex interactions. Full article

Calocybe indica (milky mushroom), an edible mushroom with significant nutritional value, shows potential for cultivation in subtropical regions. Investigating the composition and diversity of the microbial community structure of the casing materials of C. indica is of great significance for understanding the stable yield of the mushroom. This study evaluated four casing materials—loamy soil (LS), loamy soil + cow dung (LS + CD), loamy soil + sand (LS + S), and plant ash (PA)—for their effects on mushroom yield, soil physicochemical properties, and microbial dynamics. The results demonstrated that LS + CD significantly enhanced the yield (2078.50 g) and fruiting body quality, with the shortest pinhead formation time (7.67 days) and superior morphological traits (e.g., cap diameter: 10.10 cm). Physicochemical analysis revealed LS + CD’s elevated moisture retention (19.7%), nutrient availability (e.g., available P: 59.63 mg/kg), and microbial biomass (C: 399.22 mg/kg), alongside a distinct microbial community dominated by Basidiomycota and Actinobacteria. Conversely, LS + S exhibited poor performance due to low water retention and nutrient deficiencies. Redundancy analysis highlighted strong correlations between soil nutrients (nitrogen, potassium, phosphorus) and microbial composition, with LS + CD fostering a microbiome conducive to mushroom growth. These findings underscore LS + CD as the optimal casing material for C. indica cultivation, improving both yield and soil health. Future studies should explore the functional roles of key microbes and refine organic amendments for sustainable practices. Full article

The unarmored dinoflagellate Akashiwo sanguinea is a cosmopolitan harmful algal species known for forming intense blooms leading to mass mortality of fish, shellfish, and seabirds. Globally distributed populations of A. sanguinea have been classified into four ribotypes based on their characteristic sequences in LSU rRNA gene and primary geographic distributions. In this study, we compared the bacterial communities co-existing with the six strains of A. sanguinea from China and the USA (belonging to two ribotypes) using high-throughput sequencing of 16S rRNA gene amplicons. Generally, a bacterial microbiome with high diversity was found to be associated with laboratory-cultured A. sanguinea strains from different geographic origins. Based on ribotype classification, the six samples were divided into two groups (ribotype A: AsCHINA; ribotype C: AsUSA) for subsequent comparative analyses of their bacterial communities. Beta diversity analysis revealed a clear separation between the two groups, reflecting significant differences in bacterial community composition between the two ribotypes. Significantly higher abundance of nitrogen-fixing bacteria was found in the AsUSA group, suggesting that ribotype C may benefit from external nitrogen sources provided by their bacterial associates. If this also holds true in natural environments, this nitrogen-fixing partnership likely confers a competitive advantage to ribotype C in oligotrophic offshore waters, and potentially extends bloom duration when environmental nitrogen is depleted. Our study raised the possibility that different ribotypes of A. sanguinea may harbor distinct prokaryotic microbiomes in their phycospheres under stable cultivation conditions. Further comprehensive comparison among more isolates across all four ribotypes is highly necessary to validate this hypothesis. Full article