Search Results (182)

Drought stress poses a significant threat to olive cultivation in Mediterranean regions. This study investigated the resilience and functional adaptation of root-associated and rhizosphere soil microorganisms of four olive cultivars under contrasting water regimes (irrigated vs. drought) across seasons. Using a combination of amplicon-targeted metagenomics, phylogenetic analysis, and text mining of the scientific literature, we identified a conserved core microbiome and revealed that drought stress significantly alters the structure of root-associated—but not rhizosphere soil—bacterial communities. Potential functional profiling indicated that drought conditions enriched for genes involved in stress response pathways, including branched-chain amino acid transport, glutathione S-transferase activity, thioredoxin reductase, and chemotaxis. Text mining co-occurrence networks highlighted strong associations between some key bacterial genera and plant growth-promoting functions like phytohormone production and biocontrol. Furthermore, we identified Solirubrobacter, Microvirga, and Pseudonocardia as the primary contributors to these drought-resilience functions. The stability of the soil microbiome suggests functional redundancy, whereas the restructuring of the root endophytic compartment indicates active plant selection for beneficial microbes. Our findings provide a foundation for developing tailored microbial consortia (SynComs) to enhance drought tolerance in olive trees and support sustainable agriculture in water-limited environments. Full article

Accurate genome binning is essential for resolving microbial community structure and functional potential from metagenomic data. However, existing approaches—primarily reliant on tetranucleotide frequency (TNF) and abundance profiles—often perform sub-optimally in the face of complex community compositions, low-abundance taxa, and long-read sequencing datasets. To address these limitations, we present MBGCCA, a novel metagenomic binning framework that synergistically integrates graph neural networks (GNNs), contrastive learning, and information-theoretic regularization to enhance binning accuracy, robustness, and biological coherence. MBGCCA operates in two stages: (1) multimodal information integration, where TNF and abundance profiles are fused via a deep neural network trained using a multi-view contrastive loss, and (2) self-supervised graph representation learning, which leverages assembly graph topology to refine contig embeddings. The contrastive learning objective follows the InfoMax principle by maximizing mutual information across augmented views and modalities, encouraging the model to extract globally consistent and high-information representations. By aligning perturbed graph views while preserving topological structure, MBGCCA effectively captures both global genomic characteristics and local contig relationships. Comprehensive evaluations using both synthetic and real-world datasets—including wastewater and soil microbiomes—demonstrate that MBGCCA consistently outperforms state-of-the-art binning methods, particularly in challenging scenarios marked by sparse data and high community complexity. These results highlight the value of entropy-aware, topology-preserving learning for advancing metagenomic genome reconstruction. Full article

This study evaluated the effects of adding a Saccharomyces cerevisiae fermentation product (SCFP) to adult cat diets on palatability, intestinal health, nutrient digestibility, immune parameters, and the fecal microbiome over 42 days. Sixty-three healthy Domestic Short-hair cats were randomized to three diets: a control diet (CD) without SCFP, or the same diet containing 1.0% or 2.0% SCFP, targeting daily intakes of 150 or 300 mg/kg body weight, respectively. Body weight and blood parameters remained within reference ranges across all groups. Stool quality was largely not affected, although compared with controls, SCFP-supplemented cats had slightly firmer stools at day 21, and increased fecal pH. Shotgun metagenomic sequencing revealed that microbiome diversity remained steady in SCFP-fed cats, whereas diversity in the control group declined over time. Fecal immunoglobulin A concentrations were lower in cats supplemented with SCFP at 150 mg/kg BW by the end of the study, and positive shifts in the circulatory leukocyte profile were observed at both inclusion levels. Apparent total tract macronutrient digestibility did not differ among groups. Palatability tests showed diets with SCFP were generally preferred, indicating a potential benefit for commercial feline feeds, particularly at the 150 mg/kg BW level, which was preferred over 300 mg/kg BW. Overall, these findings suggest that SCFP can act as a functional ingredient in feline nutrition to maintain microbial diversity and enhance diet acceptance without compromising digestibility. Full article

Legacy sulfur smelting has left behind complex contamination landscapes, yet the spatial structuring of microbial risks and adaptation strategies across soil profiles remains insufficiently understood. Microbial risk genes, including those conferring resistance to antibiotic resistance (ARGs), biocide and metal resistance (BRGs/MRGs), and virulence (VFGs), are increasingly recognized as co-selected under heavy metal stress, posing both ecological and public health concerns. In this study, we integrated geochemical analyses with metagenomic sequencing and functional annotation to jointly characterize the vertical (0–7 m) and horizontal (~2 km) distribution of heavy metals/metalloids, microbial communities, and functional risk genes at a historic smelting site in Zhenxiong, Yunnan. Heavy metals and metalloids such as arsenic (As), chromium (Cr), copper (Cu), and lead (Pb) showed clear accumulation with depth, while significantly lower concentrations were observed in both upstream and downstream locations, revealing persistent vertical and horizontal pollution gradients. Correspondingly, resistance and virulence genes were co-enriched at contaminated sites, suggesting potential co-selection under prolonged stress. LEfSe analysis revealed distinct ecological patterns: vertically, upper layers were dominated by nutrient-cycling and mildly stress-tolerant taxa, while deeper layers favored metal-resistant, oligotrophic, and potentially pathogenic microorganisms; horizontally, beneficial and diverse microbes characterized low-contamination zones, whereas heavily polluted areas were dominated by resistant and stress-adapted genera. These findings provide new insights into microbial resilience and ecological risk under long-term smelting stress. Full article

The degradation of Mediterranean forest ecosystems, such as holm oak forests, has intensified in recent decades due to climate change, forest fires, and deforestation, compromising the natural regeneration of the soil. In this context, it is essential to apply sustainable strategies to restore soil and promote plant growth, thus helping the regeneration of the ecosystem. One of these strategies is the use of plant growth-promoting bacteria (PGPB) in combination with recovered organic waste, such as that from wastewater treatment plants (WWTPs). In this paper, the effects of a biofertilizer formulated from WWTP residue (with and without sterilization), supplemented with two PGPB strains (Bacillus pretiosus and Pseudomonas agronomica), on the growth of holm oak seedlings (Quercus ilex) were evaluated under field conditions. A study was carried out on its nutritional composition, the rhizospheric cenoantibiogram, and its functional and taxonomic microbial diversity. Nine combinations of chemical and biological treatments using irrigation with water as a control were compared. The results showed that treatments with WWTP, especially combined with PGPB strains, promoted greater plant development and a lower seedling mortality rate. The cenoantibiogram exhibited a reduction in the resistance profile in soils treated with biofertilizer, without affecting soil microbial diversity, which remained unaltered across treatments, as confirmed by metagenomic and functional diversity analyses. Overall, this research reinforces the viability of the use of biofertilizers recovered from WWTP as an ecological and effective strategy for the recovery of degraded holm oak forests. Full article

This study aimed to assess the anti-inflammatory properties of mare milk by analyzing immune markers in mice following gavage of mare milk. Metagenomic sequencing was employed to examine variations in the composition and functional profiles of the intestinal microbiota across different experimental groups. Bacterial diversity, abundance, and functional annotations of gut microbiota were evaluated for each group. The results show that, compared to the control group, the mare milk group exhibited a significant decrease in the pro-inflammatory cytokine IL-6 levels and a significant increase in secretory immunoglobulin A (SIgA) levels (p < 0.05). The fermented mare milk group and the pasteurized fermented mare milk group demonstrated a significant downregulation of the pro-inflammatory cytokines TNF-α and IL-1β, along with a significant increase in the anti-inflammatory cytokine IL-10 levels (p < 0.05). Additionally, metagenomic analysis revealed that both the mare milk and fermented mare milk groups were able to regulate the imbalance of the intestinal microenvironment by improving the diversity of the gut microbiota and reshaping its structure. Specifically, the mare milk group enhanced gut barrier function by increasing the abundance of Bacteroides acidifaciens, while the fermented mare milk group increased the proportion of Bacillota and the relative abundance of beneficial bacterial genera such as Faecalibaculum and Bifidobacterium. KEGG pathway annotation highlighted prominent functions related to carbohydrate and amino acid metabolism, followed by coenzyme and vitamin metabolism activities. In conclusion, mare milk and its fermented products demonstrate anti-inflammatory effects, particularly in modulating immune responses and inhibiting inflammatory cascades. Additionally, the administration of mare milk enhances the composition and metabolic activity of intestinal microbiota in mice, supporting intestinal microecological balance and overall gut health, and offering valuable insights for the development of mare milk-based functional foods. Full article

Due to limited land resources and traditional farming practices, continuous cassava cropping is common in China. This practice leads to soil degradation, including reduced fertility, imbalanced microbial communities, and lower crop yields. In this study, we investigated the impacts of continuous cassava cropping (CC) and cassava–maize rotation (RC) systems on soil physicochemical properties, microbial community composition, and functional gene abundance related to carbon and nitrogen cycling. The RC system consists of a five-year rotation cycle: cassava is planted in the first year, followed by two consecutive years of maize, and then, cassava is planted again in the last two years. The soil type is classified as Haplic Acrisols with a clay loam texture in this research. Soil samples from both cropping systems were analyzed for physicochemical properties and enzyme activities, and the results showed significant decreases in soil pH, available nitrogen, available phosphorus, and available potassium in CC. Using metagenomic sequencing, 1,280,928 and 1,224,958 unigenes were identified under RC and CC, respectively, with differences in microbial taxonomic and functional profiles. Bacteria accounted for 89.257% of the soil community in RC, whereas the proportion was 88.72% in CC. The proportions of eukaryota and viruses in RC were 0.031% and 0.006%, respectively; in contrast, their proportions were 0.04% and 0.02% in CC, respectively. Cassava–maize rotation promoted the metabolic activities of soil microbes, leading to a significant enhancement in functional genes related to nitrogen and carbon cycling, such as nasA, nasD, nrtC, coxA, porA, and frdA. This shows that microbial activity and nutrient cycling improved in the crop rotation system. Thus, these findings highlight the importance of crop rotation for maintaining soil health, enhancing microbial functions, and improving sustainable cassava production. This study provides valuable insights into the management of cassava agroecosystems and the mitigation of the adverse effects of continuous cropping. Full article

Groundwater, a critical source of drinking water, plays an essential role in global biogeochemical cycles, yet its microbial ecosystems remain insufficiently characterized, particularly in pristine karst aquifers. This study conducted high-resolution profiling of microbial communities and environmental parameters in two representative alpine karst aquifers in Slovenia: Idrijska Bela and Krajcarca. Monthly groundwater samples from the Krajcarca spring and Idrijska Bela borehole over a 14-month period were analyzed using whole-metagenome sequencing (WMS), UV-Vis spectroscopy, inductively coupled plasma mass spectrometry (ICP-MS), and isotopic analysis. The results revealed stable hydrochemical conditions with clear spatial differences driven by bedrock composition and groundwater residence time. Bacterial communities displayed strong correlations with hydrochemical parameters, while archaeal communities exhibited temporal stability. Functional gene profiles mirrored bacterial patterns, emphasizing the influence of environmental gradients on metabolic potential. No significant temporal changes were detected across two sampling campaigns (2016–2023), highlighting the resilience of these aquifers. This work establishes a valuable baseline for understanding pristine groundwater microbiomes and informs future monitoring and water quality management strategies. Full article

Bacterial endophytes have emerged as critical components of plant microbiomes, offering multifaceted benefits ranging from growth promotion to stress resilience. This review synthesizes two decades of research, from 2004 to 2024, on bacterial endophyte identification and applications, highlighting advances in both traditional culture-based techniques and modern omics approaches. The review also focuses on interactions between these microorganisms and their host plants, emphasizing their roles in biocontrol, phytoremediation, and nanoparticle biosynthesis. While significant progress has been made in characterizing cultivable bacterial endophytes, challenges persist in accessing unculturable species and understanding strain-specific functional mechanisms. The integration of metagenomics, metatranscriptomics, and metabolomics has begun unraveling this hidden diversity, revealing novel metabolic pathways and plant–microbe communication systems. There have been limitations in endophyte isolation protocols and field applications, and therefore a need exists for standardized frameworks to bridge lab-based discoveries with agricultural practices. Cutting-edge multi-omics techniques, such as genomics, transcriptomics, metabolomics, proteomics, and phenomics, should be used more in future research to clarify the mechanistic underpinnings of plant–endophyte interactions to thoroughly profile the microbial communities and unlock their functional potential under diverse environmental conditions. Overall, bacterial endophytes present viable paths toward sustainable farming methods, supporting food security and crop resilience in the face of environmental difficulties by providing a transformative opportunity for next-generation agriculture, mitigating climate-related agricultural stressors, reducing dependence on synthetic agrochemicals, and enhancing crop productivity. Full article

Consumers are increasingly concerned about the flavor quality of poultry meat, yet the relationship between inosine monophosphate (IMP), intramuscular fat (IMF), and the gut microbiota remains largely unclear. This study aimed to characterize the cecal microbiota associated with IMP/IMF deposition in Daheng broilers selectively bred for high-IMP/IMF levels (High group) and low levels (Control group). A two-stage microbiome analysis strategy was applied. Initially, 16S rRNA gene sequencing was conducted to assess microbial diversity and composition. Significant differences were observed between groups in alpha diversity indices (Chao1 and Faith_PD) and beta diversity (p < 0.05). LEfSe analysis identified 55 differentially abundant taxa (LDA > 3, p < 0.05), primarily within the Phylum bacteroidota. To achieve species-level and functional insights, whole-metagenome shotgun sequencing was performed. Taxonomic profiling of 62,443 microbial species revealed significant beta diversity differences (p < 0.05), with 120 dominant species differentially enriched (LDA > 3, p < 0.05), including 77 species in the High group such as Merdivivens faecigallinarum. Enriched functional genes were mainly involved in methane metabolism, starch and sucrose metabolism, and the nucleoside phosphate metabolic process. A total of 882 metagenome-assembled genomes (MAGs) were reconstructed and integrated with 19,628 publicly available chicken MAGs, resulting in 2609 non-redundant genomes, including 52 novel ones. These findings suggest that cecal microbial composition and function are associated with IMP/IMF levels in broilers, providing candidate bacterial species and functional pathways for further validation through gavage-based intervention and multi-omics analysis. Full article

Low-dose carrot rhamnogalacturonan-I (cRG-I) has shown consistent modulatory effects on the gut microbiota and immune function in humans. In this study we investigated its effects on the microbial composition and metabolite production of the gut microbiota of small (5–10 kg), medium-sized (10–27 kg), and large (27–45 kg) dogs, using inulin and xanthan as comparators. Fecal samples from six dogs of each size group were evaluated. Overall microbiome composition, assessed using metagenomic sequencing, was shown to be driven mostly by dog size and not treatment. There was a clear segregation in the metabolic profile of the gut microbiota of small dogs versus medium-sized and large dogs. The fermentation of cRG-I specifically increased the levels of acetate/propionate-producing Phocaeicola vulgatus. cRG-I and inulin were fermented by all donors, while xanthan fermentation was donor-dependent. cRG-I and inulin increased acetate and propionate levels. The responses of the gut microbiota of different sized dogs to cRG-I were generally consistent across donors, and interindividual differences were reduced. This, together with the significant increase in P. vulgatus during fermentation in both this study and an earlier human ex vivo study, suggests that this abundant and prevalent commensal species has a core capacity to selectively utilize cRG-I. Full article

Background/Objectives: Celiac disease (CD) is an autoimmune disorder characterized by small intestinal enteropathy triggered by gluten ingestion, often associated with gut dysbiosis. The most effective treatment is strict adherence to a gluten-free diet (GFD), which alleviates symptoms. This study uniquely integrates taxonomic, functional, and resistance profiling to evaluate the gut microbiota of women with CD on a GFD. Methods: To evaluate the long-term impact of a GFD, this study analyzed the gut microbiota of 10 women with CD on a GFD for over a year compared to 10 healthy controls with unrestricted diets. Taxonomic diversity (16S rRNA gene sequencing and the analysis of α and β-diversity), metabolic functionality (Biolog EcoPlates^®), and antibiotic resistance profiles (Cenoantibiogram) were assessed. Results: Metagenomic analysis revealed no significant differences in taxonomic diversity but highlighted variations in the abundance of specific bacterial genera. Women with CD showed increased proportions of Bacteroides, Streptococcus, and Clostridium, associated with inflammation, but also elevated levels of beneficial genera such as Roseburia, Oxalobacter, and Paraprevotella. Despite no significant differences in metabolic diversity, higher minimum inhibitory concentrations (MICs) in women in the healthy control group suggest that dietary substrates in unrestricted diets may promote the proliferation of fast-growing bacteria capable of rapidly developing and disseminating antibiotic resistance mechanisms. Conclusions: These findings indicate that prolonged adherence to a GFD in CD supports remission of gut dysbiosis, enhances microbiota functionality, and may reduce the risk of antibiotic resistance, emphasizing the importance of dietary management in CD. Full article

This investigation examines the influence of P. dabryanus density on the growth performance of P. nigromaculatus and the structural and functional dynamics of paddy soil microbial communities within a rice–frog–loach integrated aquaculture system. Field experiments were conducted with five density gradients of P. dabryanus (0.5, 1.0, 1.5, 2.0, and 2.5 × 10⁴ individuals/667 m²), designated as RFLS0.5, RFLS1.0, RFLS1.5, RFLS2.0, and RFLS2.5, respectively. Control treatments included rice monoculture (RM) and rice–frog co-culture (RFS). These findings demonstrated that as the density of loach increased, the weight gain ratio of P. nigromaculatus showed a unimodal pattern, reaching its peak in RFLS1. Metagenomic analysis on paddy soil revealed that the RFLS1 facilitated the enrichment of nitrogen-fixing bacteria (Proteobacteria), while concurrently suppressing proliferation of the potential pathogen Pseudomonas aeruginosa and microbial markers in metal-contaminated environments of Usitatibacter rugosus. Further, functional profiling indicated that RFLS1 group reached a peak activity in amino acid metabolism (14.52 ± 0.09%) and carbohydrate metabolism (14.44 ± 0.06%) and showed a higher proportion of glycosyltransferase (GT) abundance (41.93 ± 0.02%) than other groups. In summary, the optimal stocking density of P. dabryanus in rice–frog–loach integrated systems was determined to be 1.0 × 10⁴ individuals/667 m². This density not only promotes the growth of P. nigromaculatus but also improves the structure of paddy soil microbial communities. Full article

Background/Objectives: Cardiovascular diseases remain the leading cause of global mortality, with the gut microbiome emerging as a critical factor. This study aimed to characterize gut microbiome composition and metabolic pathways in individuals with low cardiovascular risk (LCR) compared to healthy controls to reveal insights into early disease shifts. Methods: We performed shotgun metagenomic sequencing on fecal samples from 25 LCR individuals and 25 matched healthy controls. Participants underwent a comprehensive cardiovascular evaluation. Taxonomic classification used MetaPhlAn 4, and functional profiling employed HUMAnN 3. Results: Despite similar alpha diversity, significant differences in bacterial community structure were observed between groups (PERMANOVA, p < 0.05). The LCR group showed enrichment of Faecalibacterium prausnitzii (p = 0.035), negatively correlating with atherogenic markers, including ApoB (r = −0.3, p = 0.025). Conversely, Fusicatenibacter saccharivorans positively correlated with ApoB (r = 0.4, p = 0.006). Metabolic pathway analysis revealed upregulation of nucleotide biosynthesis, glycolysis, and sugar degradation pathways in the LCR group, suggesting altered metabolic activity. Conclusions: We identified distinct gut microbiome signatures in LCR individuals that may represent early alterations associated with cardiovascular disease development. The opposing correlations between F. prausnitzii and F. saccharivorans with lipid parameters highlight their potential roles in cardiometabolic health. These findings suggest gut microbiome signatures may serve as indicators of early metabolic dysregulation preceding clinically significant cardiovascular disease. Full article

Forest musk deer (Moschus berezovskii Flerov), a critically endangered ruminant species, faces extinction risks, with captive populations further threatened by prevalent digestive and immune disorders. This study utilized comparative metagenomic sequencing to assess intestinal microbiota structure and functional profiles between wild populations in Chongqing and Hunan and captive individuals. Wild populations exhibited a Pseudomonadota-dominated gut microbiota (significantly more abundant than in captive counterparts), enriched with lignin-degrading genera Novosphingobium and Acinetobacter. In contrast, the captive group demonstrated increased abundances of Bacillota/Bacteroidota, alongside abnormal proliferation of Escherichia and Clostridium. Both alpha and beta diversity analyses confirmed significant compositional divergences among the three groups, with wild populations maintaining higher diversity than captive populations. Notably, while substantial disparities in microbial abundance existed between wild populations (attributed to habitat vegetation differences), core microbial diversity and carbohydrate metabolic functions exhibited convergence. Functional analyses marked divergences in metabolic pathways: Captive microbiota showed enrichment in translation and glycan metabolism pathways, whereas wild populations displayed pronounced enrichment in immune regulation and environmental sensing pathways. These findings establish a theoretical foundation for optimizing wild population conservation strategies and developing science-based captive management protocols. Full article