Search Results (475)

Background: BDE-47, a pervasive environmental pollutant detected in >90% of human serum samples, is increasingly linked to metabolic disorders. This study investigates the specific impact of BDE-47 exposure on the gut microbiota in prediabetic mice and evaluates the efficacy of therapeutic interventions in mitigating these effects. Objectives: To determine whether BDE-47 exposure induces diabetogenic dysbiosis in prediabetic mice and to assess whether dietary interventions, such as grape exosomes and an antioxidant cocktail, can restore a healthy microbiota composition and mitigate diabetes risk. Methods: In this study, a prediabetic mouse model was established in 54 male SPF-grade C57BL/6J mice through a combination of high-sugar and high-fat diet feeding with streptozotocin injection. Oral glucose tolerance tests (OGTT) were conducted on day 7 and day 21 post-modeling to assess the establishment of the model. The criteria for successful model induction were defined as fasting blood glucose levels below 7.8 mmol/L and 2 h postprandial glucose levels between 7.8 and 11.1 mmol/L. Following confirmation of model success, a 3 × 3 factorial design was applied to allocate the experimental animals into groups based on two independent factors: BDE-47 exposure and exosome intervention. The BDE-47 exposure factor consisted of three dose levels—none, high-dose, and medium-dose—while the exosome intervention factor included three modalities—none, Antioxidant Nutrients Intervention, and Grape Exosomes Intervention. Fresh fecal samples were collected from mice two days prior to sacrifice. Cecal contents and segments of the small intestine were collected and transferred into 1.5 mL cryotubes. All sequences were clustered into operational taxonomic units (OTUs) based on defined similarity thresholds. To compare means across multiple groups, a two-way analysis of variance (ANOVA) was employed. The significance level was predefined at α = 0.05, and p-values < 0.05 were considered statistically significant. Bar charts and line graphs were generated using GraphPad Prism version 9.0 software, while statistical analyses were performed using SPSS version 20.0 software. Results: The results of 16S rDNA sequencing analysis of the microbiome showed that there was no difference in the α diversity of the intestinal microbiota in each group of mice (p > 0.05), but there was a difference in the Beta diversity (p < 0.05). At the gate level, the abundances of Proteobacteria, Campylobacterota, Desulfobacterota, and Fusobacteriota in the medium-dose BDE-7 group were higher than those in the model control group (p < 0.05). The abundance of Patellar bacteria was lower than that of the model control group (p < 0.05). The abundances of Proteobacteria and Campylobacterota in the high-dose BDE-7 group were higher than those in the model control group (p < 0.05). The abundance of Planctomycetota and Patescibacteria was lower than that of the model control group (p < 0.05), while the abundance of Campylobacterota in the grape exosome group was higher than that of the model control group (p < 0.05). The abundance of Patescibacteria was lower than that of the model control group (p < 0.05), while the abundance of Firmicutes and Fusobacteriota in the antioxidant nutrient group was higher than that of the model control group (p < 0.05). However, the abundance of Verrucomicrobiota and Patescibacteria was lower than that of the model control group (p < 0.05). At the genus level, the abundances of Bacteroides and unclassified Lachnospiraceae in the high-dose BDE-7 group were higher than those in the model control group (p < 0.05). The abundance of Lachnospiraceae NK4A136_group and Lactobacillus was lower than that of the model control group (p < 0.05). The abundance of Veillonella and Helicobacter in the medium-dose BDE-7 group was higher than that in the model control group (p < 0.05), while the abundance of Lactobacillus was lower (p < 0.05). The abundance of genera such as Lentilactobacillus and Faecalibacterium in the grape exosome group was higher than that in the model control group (p < 0.05). The abundance of Alloprevotella and Bacteroides was lower than that of the model control group (p < 0.05). In the antioxidant nutrient group, the abundance of Lachnospiraceae and Hydrogenophaga was higher than that in the model control group (p < 0.05). However, the abundance of Akkermansia and Coriobacteriaceae UCG-002 was significantly lower than that of the model control group (p < 0.05). Conclusions: BDE-47 induces diabetogenic dysbiosis in prediabetic mice, which is reversible by dietary interventions. These findings suggest that microbiota-targeted strategies may effectively mitigate the diabetes risk associated with environmental pollutant exposure. Future studies should further explore the mechanisms underlying these microbiota changes and the long-term health benefits of such interventions. Full article

Aquatic fungi serve as core ecological engines in freshwater ecosystems, driving organic matter decomposition and energy flow to sustain environmental balance. Wetlands, with their distinct hydrological dynamics and nutrient-rich matrices, serve as critical habitats for these microorganisms. As an internationally designated Ramsar Site, Yunnan Dashanbao Black-Necked Crane National Nature Reserve in China not only sustains endangered black-necked cranes but also harbors a cryptic reservoir of aquatic fungi within its peat marshes and alpine lakes. This study employed high-throughput sequencing to characterize fungal diversity and community structure across 12 understudied wetland sites in the reserve, while analyzing key environmental parameters (dissolved oxygen, pH, total nitrogen, and total phosphorus). A total of 5829 fungal operational taxonomic units (OTUs) spanning 649 genera and 15 phyla were identified, with Tausonia (4.17%) and Cladosporium (1.89%) as dominant genera. Environmental correlations revealed 19 genera significantly linked to abiotic factors. FUNGuild functional profiling highlighted saprotrophs (organic decomposers) and pathogens as predominant trophic guilds. Saprotrophs exhibited strong associations with pH, total nitrogen, and phosphorus, whereas pathogens correlated primarily with pH. These findings unveil the hidden diversity and ecological roles of aquatic fungi in alpine wetlands, emphasizing their sensitivity to environmental gradients. By establishing baseline data on fungal community dynamics, this work advances the understanding of wetland microbial ecology and informs conservation strategies for Ramsar sites. Full article

Protists represent a major component of eukaryotic diversity within the soil microbiome, playing critical roles in mediating carbon and nitrogen cycling and influencing nutrient availability and soil health. Their diversity is shaped by multiple factors, including temperature, pH, organic matter content, and land use. In this study, we investigated the protist diversity in rhizosphere soils from both wild and cultivated date palm varieties. Our results identified nitrate, nitrite, calcium, and carbon content as key soil factors significantly correlated with protist diversity. Only 9.2% (42) of operational taxonomic units (OTUs) were shared across all soil samples, suggesting that these taxa possess traits enabling adaptation to extreme environmental conditions. The dominant protist families belonged to Rhizaria, Alveolata, Amoebozoa, and Archaeplastida, primarily comprising bacterial consumers, alongside taxa from Stramenopiles, Opisthokonta, Hacrobia, and Excavata. At the class level, Filosa-Sarcomonadea, Colpodea, Variosea, Tubulinea, and Chlorophyceae were the most abundant. Filosa-Sarcomonadea and Colpodea were positively correlated with bacterial and fungal genera, suggesting their role as consumers, while Variosea showed a negative correlation with bacteria, reflecting predator-prey dynamics. Notably, the protist community composition in wild date palm rhizosphere soils was distinct from that in cultivated soils, with Opisthokonta being particularly abundant, likely reflecting adaptation to drought conditions. Overall, this study highlights the significant differences in protist diversity and community structure between wild and cultivated date palm ecosystems. Full article

Fungi are the most poorly described kingdom of Eukarya. Fundamental questions about their species diversity, their distributions, and their biotic interactions remain largely unanswered, despite fungi playing important roles in the ecology and biogeochemistry of terrestrial ecosystems. To assess some of these data gaps, we intensively surveyed club and coral fungi in a temperate Australian forest in the Upper Lane Cove Valley, Sydney, Australia, over a period of two years. Specimens identified as Clavulinopsis, Ramaria, or Ramariopsis based on morphology were then assigned to operational taxonomic units (OTUs) using the criterion of 97% identity across the entire rDNA internal transcribed spacer (ITS) region. Based on this criterion and ITS-based phylogenies, we identified 80 OTUs in these genera of club and coral fungi within the survey area. Of these OTUs, only 11.25% could be assigned a species name based on BLASTn matches to full-length ITS sequences, suggesting that almost 90% of OTUs were novel taxa, or are yet to be represented in DNA databases. Specimens that were morphologically similar to well-known Northern Hemisphere species were shown to be distinct upon DNA sequencing. Accumulation curves suggest that our surveys only recovered about half of the species in the target genera, and seven times the effort would be required to sample to exhaustion. In summary, even in a small area of less than 100 km², there is evidence for multiple undescribed, cryptic, and undiscovered species. This highlights the fundamental work that remains to be completed in fungal taxonomy and biology. Full article

Microbiome data analysis is essential for understanding the role of microbial communities in human health. However, limited data availability often hinders research progress, and synthetic data generation could offer a promising solution to this problem. This study aims to explore the use of machine learning (ML) to enrich an unbalanced dataset consisting of microbial operational taxonomic unit (OTU) counts of 148 samples, belonging to 61 patients. In detail, 34 samples are from 16 adenomatous polyps (AP) patients, while 114 samples are from 46 colorectal cancer (CRC) patients. Synthesis of AP and CRC samples was conducted using the Synthetic Data Vault Python library, employing a Gaussian Copula synthesiser. Subsequently, the synthesised data quality was evaluated using a logistic regression model in parallel with an optimised support vector machine algorithm (polynomial kernel). The data quality is considered good when neither of the two algorithms can discriminate between real and synthetic data, showing low accuracy, F1 score, and precision values. Furthermore, additional statistical tests were employed to confirm the similarity between real and synthetic data. After data validation, layer-wise relevance propagation (LRP) was performed on a deep learning classifier to extract important OTU features from the generated dataset, to discriminate between CRC patients and those affected by AP. Exploiting the acquired features, which correspond to unique bacterial taxa, ML classifiers were trained and tested to estimate the validity of such microorganisms in recognising AP and CRC samples. The simplified version of the original OTU table opens up opportunities for further investigations, especially in the realm of extensive data synthesis. This involves a deeper exploration and augmentation of the condensed data to uncover new insights and patterns that might not be readily apparent in the original, more complex form. Digging deeper into the simplified data may help us better grasp the biological or ecological processes reflected in the OTU data. Transitioning from this exploration, the synergy of ML and synthetic data enrichment holds promise for advancing microbiome research. This approach enhances classification accuracy and reveals hidden microbial markers that could prove valuable in clinical practice as a diagnostic and prognostic tool. Full article

The rumen microbiome impacts beef cattle feed efficiency, a key economic factor in production systems. This study investigated the rumen microbiome of Charolais bulls with divergent residual feed intake-expected progeny difference (RFI-EPD) values to identify microbial taxa associated with feed efficiency. Forty Charolais bulls were evaluated for feed intake and growth over 60 days, and RFI values were determined. The 10 most efficient (NegRFI) and 10 least efficient (PosRFI) bulls were selected for microbiome analysis. Rumen fluid samples were collected and analyzed via 16S rRNA gene sequencing. Microbial analysis revealed no significant differences in alpha or beta diversity between groups, but differential abundance analysis identified 20 operational taxonomic units (OTUs) as more prevalent in NegRFI bulls, while 15 OTUs were more abundant in PosRFI bulls. Two OTUs from the key genus Prevotella showed different relative abundances in the two RFI-EPD groups. NegRFI bulls had a higher relative abundance of Prevotella OTU 109358, while PosRFI bulls had more Prevotella OTU 626329. Additionally, OTUs from Ruminococcus, a genus involved in fiber degradation and volatile fatty acid (VFA) production, were more abundant in NegRFI bulls. In contrast, PosRFI bulls had a higher abundance of OTUs from Oscillospira and F16, both linked to butyrate production. The results of this study support the need for further exploration into the role of microbial taxa associated with feed efficiency. A deeper understanding of the functional profile of the microbiota could aid in the development of microbiome-informed strategies to enhance nutrient utilization and performance in beef cattle. Full article

Rhizosphere microorganisms mediate the material exchange and chemical cycling between plant roots and soil. However, the response mechanisms of the rhizosphere microbial community, especially its co-occurrence patterns, to thinning remain poorly understood. We investigated the rhizosphere microbial communities of Pinus massoniana under different thinning intensities, including control (CK, 0%), light-intensity thinning (LIT, 10%), moderate-intensity thinning (MIT, 30%), and high-intensity thinning (HIT, 50%). Basic taxonomic information was obtained through high-throughput sequencing, while R software was utilized to identify thinning-sensitive operational taxonomic units (tsOTUs), construct co-occurrence networks, and perform other statistical analyses. Although no discernible patterns were observed in α-diversity changes, the Kruskal–Wallis test indicated that season was the primary factor driving α-diversity variation. Meanwhile, thinning intensity significantly shaped the rhizosphere microbial community structures, with each intensity harboring a specific tsOTUs subset. Although the top three modules of the meta-co-occurrence networks in summer and winter exhibited consistent tsOTU composition, winter triggered changes in network connectivity. Regardless of summer or winter, the number of network nodes under MIT was the highest. Additionally, after thinning, the relative abundances of most keystone taxa declined; however, MIT facilitated the enrichment of certain keystone taxa. Collectively, thinning profoundly shapes microbial community composition and network characteristics. Moderate thinning intensity may represent the optimal thinning intensity for the studied P. massoniana plantations. Full article

Since 2017, a fishing ban in the Chishui River (China) has reduced human disturbances, yet the early-stage recovery of fish resources remains unquantified. Here, we applied environmental DNA (eDNA) metabarcoding to assess fish diversity and restoration status across its upper, middle, and lower reaches. An analysis of operational taxonomic units (OTUs) revealed higher unique than shared OTUs among reaches, indicating significant spatial partitioning of fish communities. The upper reaches exhibited the highest diversity due to reduced human activity, attributed to greater species richness, while the middle and lower reaches showed similar community structures. Key findings include the following: (1) the detection of rare endemic species (Schizothorax) and non-native Oreochromis DNA, suggesting invasion risks; (2) the investigation revealed a predominance of small-bodied fish species, indicating that large-bodied fish populations in the Chishui River (China) remained relatively scarce; (3) the recovery of demersal fish DNA from surface waters, confirming eDNA’s broad detection capacity. The results indicate that the fishing ban has contributed to the partial recovery of the fish community in the Chishui River (China). However, risks of biological invasion (e.g., Oreochromis species) remain, and large-bodied fish are still relatively scarce. To ensure effective conservation, it is critical to strengthen the monitoring and evaluation of the fishing ban’s effectiveness and implement timely measures to prevent invasive species proliferation. Full article

Intestinal diseases in nursery pigs harm health and performance and drive antimicrobial resistance. This study evaluated whether early probiotic inoculation helps piglets to cope with weaning-related gut challenges. The probiotic, containing Lacticaseibacillus rhamnosus, Enterococcus lactis, Bifidobacterium longum subsp. infantis, and Bifidobacterium breve, was given orally to newborn piglets daily until day 4 and then every other day until weaning at day 28 (at 4 × 10⁹ CFU/dose). The control piglets received a placebo. The results showed that the probiotic pigs had reduced fecal alpha-diversity on day 7 but greater Shannon diversity on day 28 (feces) and day 23 (intestinal contents) compared to those of the control pigs. Beta-diversity analysis showed microbial differences between the groups on day 35. Most zOTUs (zero-radius operational taxonomic units) found to significantly differentiate the two treatment groups were found pre weaning. Bifidobacterium breve, Ligilactobacillus salivarius, as well as Clostridium ramosum were significantly more abundant in the feces of the probiotic pigs more than once. The probiotic pigs had higher expression levels of mucin 2 (MUC2); solute carrier family 5, member 8 (SLC5A8); and interleukin 8 (IL-8) post weaning. In the early post-weaning period, the probiotic pigs had less diarrhea as well as lower cadaverine levels in digesta than the control pigs. In conclusion, early probiotic inoculation may induce lasting immunomodulation via microbial antigen changes, enhancing resilience during challenges, like weaning. Notably, the effects persisted beyond weaning and probiotic cessation. Full article

Retrogressive succession alters soil conditions and microbial community dynamics in cold-region wetlands, yet its ecological implications remain understudied. This study explored the structure and function of soil microbial communities across three successional stages: swamp (SP), swamped meadow (SM), and meadow (MW). High-throughput 16S rRNA gene sequencing identified 2852 operational taxonomic units (OTUs), with 1682 shared among all stages (58.85%). Alpha diversity indices, including Shannon, Chao, ACE, and Sobs, were significantly higher in MW, with the Shannon index increasing by approximately 32% compared to SP, indicating enhanced richness and evenness. In contrast, Simpson and Coverage indices were highest in SP. Proteobacteria, Actinobacteriota, and Acidobacteriota were dominant phyla, showing distinct distributions across stages. Beta diversity analysis (PCoA and NMDS) revealed clear separation of microbial communities. Soil organic carbon (SOC), pH, soil water content (SWC), cation exchange capacity (CEC), and bulk density (BD) significantly influenced microbial composition and distribution. Functional prediction using FAPROTAX and BugBase indicated a shift from anaerobic metabolism, nitrogen fixation, and cellulolysis in the SP to aerobic chemoheterotrophy and stress tolerance in MW. These results demonstrate that microbial communities adapt to changing soil environments during retrogressive succession, highlighting their role in ecosystem function and resilience in cold-region wetlands. Full article

Rhizospheres harbor many beneficial microorganisms interacting with the plant ecosystem. However, in agriculture, there is a tendency to remove any plant that is different from that being cultivated. This work aimed to display the root microbial communities of native vegetation growing wild in agricultural soil. Thus, high-throughput sequencing of culture-independent marker genes was performed for bacteria and fungi from these habitats after a period of high environmental temperatures. With respect to bacteria, results revealed a number of Operational Taxonomic Units (OTUs) ranging from 3210 to 3266. With respect to fungi, the results revealed a number of OTUs ranging from 963 to 973. Information on the composition of the rhizosphere microbial communities favours the understanding of their potential functions and their beneficial effects on the sustainability of the agrosystems. Full article

Pinus tabuliformis is a well-recognized woody mycorrhizae host plant growing in North China. EM fungi contribute to the host health and the stability of the forest ecosystem. However, ectomycorrhiae (EM) fungal community associated with this species is less documented. In this study, we examined EM fungal diversity and composition of P. tabuliformis from three sites in Inner Mongolia, China by using Illumina MiSeq sequencing on the rDNA ITS2 region. Our results showed that a total of 105 EM fungal operational taxonomic units (OTUs) were identified from 15 composite root samples, and the dominant lineages were /suillus-rhizopogon, /tomentella-thelephora, /tricholoma, /amphinema-tylospora, /wilcoxina, /inocybe, and /Sebacina. A high proportion of unique EM fungal OTUs (33, 31.4% of total OTUs) were detected, and some abundant OTUs preferred to exist in specific sites. The composition of EM fungal communities was significantly different among the sites, with soil, climatic, and spatial variables being related to the community variations. The EM fungal community assembly was mainly driven by environmental factors in deterministic processes. These findings suggest that this endemic Pinaceae species in China also harbored a rich and distinctive EM fungal community and deterministic processes played more important roles than stochastic in shaping the symbiotic fungal community. Our study improves our understanding of EM fungal diversity and community structure from the perspective of a single host plant that has not been investigated exclusively before. Full article

Agricultural soil microbiomes play a crucial role in the modification and maintenance of soil properties such as soil fertility, nutrient availability, and organic matter decomposition. This study assessed the influence of organic and conventional farming practices on soil microbiomes associated with common bean (Phaseolus vulgaris L.) at the field scale in Northern Spain. Metabarcoding techniques were used to compare both microbial communities. Alpha and beta diversity analyses revealed that organic soils supported richer fungal communities with a higher species evenness, whereas conventional soils were abundant in prokaryotes. Taxonomic assignment of the observed Operational Taxonomic Units (OTUs) identified a total of 1141 prokaryotic and 622 fungal taxa. Among these, 200 prokaryotic and 113 fungal OTUs showed significant differences in response to different farming practices. This classification allowed the establishment of a core microbial community associated with the common bean crop, comprising 594 prokaryotic OTUs classified into 11 phyla, and 256 fungal OTUs classified into 11 phyla. Functional analyses indicated that organic farming promoted a broader range of prokaryotic functions related to nitrogen metabolism, stronger positive interactions between fungi and bacteria, a higher abundance of beneficial microorganisms, such as biocontrol fungi and mycorrhizae, and greater overall microbial stability. In contrast, conventional soil showed a higher prevalence of potentially phytopathogenic fungi and more complex, competitive microbial interactions. These results highlight the effect of the farming system on the diversity and microbial composition of the soils associated with bean crops in Northern Spain. While further research in different climatic regions and crop systems is essential, these findings underscore the potential of organic farming to improve soil diversity and enhance microbial network interactions. Full article

Fairy ring fungi are considered keystone species in grasslands due to their strong impact on soil physicochemical properties, but their effect on the associated bacterial community is poorly understood. Here, we analyze shifts in soil bacterial diversity and community composition across fairy rings using Illumina metabarcoding. A total of 254,135 MiSeq reads and between 405 and 1444 operational taxonomic units (OTUs) per soil sample were observed in a montane grassland in the Eastern Pyrenees. We found a strong reduction in all bacterial diversity indices inside the ring-affected zones compared to the outside grassland, especially in the stimulation (current ring) zone. The exception were Firmicutes, the dominant taxa in the grassland, which increased their relative abundance further in fairy ring-affected zones. The recovery of bacterial populations after the fungal front passage highlights the strong resilience of the bacterial communities to this biotic disturbance. Full article

This study aimed to evaluate the effects of different crop cultivation practices on soil chemical properties and microbial communities in the Mu Us Desert, with the goal of optimizing land management and promoting ecological restoration. A one-way randomized block design was used to establish experimental plots for a cereal (Setaria italica, SI), a legume (Glycine max, GM), and a control group with no crops (CK) in the central Mu Us Desert. Soil samples were collected to assess physicochemical properties and to analyze microbial community structures via high-throughput 16S rRNA gene sequencing. Results showed that crop cultivation decreased soil pH while increasing soil organic carbon (SOC), total nitrogen (TN), and available phosphorus (AP), indicating improved soil fertility and reduced soil alkalinity. The composition of soil bacterial communities varied significantly among treatments. Both SI and GM treatments increased the number of operational taxonomic units (OTUs), enhancing bacterial richness and diversity. Proteobacteria and Actinobacteria increased with crop cultivation, whereas Chloroflexi declined. These shifts were largely attributed to changes in pH and nutrient availability. Notably, SI treatment had a stronger positive effect on bacterial richness. Correlation analyses between soil chemical properties and microbial community composition highlighted the potential of crop cultivation to influence soil ecosystem services. These findings provide a scientific basis for sustainable agricultural practices and ecological restoration in arid regions such as the Mu Us Desert. Further studies are warranted to investigate the functional roles of microbial communities under different cropping patterns. Full article