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Search Results (196)

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Keywords = symbiotic microbiome

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15 pages, 1360 KiB  
Systematic Review
Prebiotics Improve Blood Pressure Control by Modulating Gut Microbiome Composition and Function: A Systematic Review and Meta-Analysis
by Abdulwhab Shremo Msdi, Elisabeth M. Wang and Kevin W. Garey
Nutrients 2025, 17(15), 2502; https://doi.org/10.3390/nu17152502 - 30 Jul 2025
Viewed by 364
Abstract
Background: Ingestion of dietary fibers (DFs) is a safe and accessible intervention associated with reductions in blood pressure (BP) and cardiovascular mortality. However, the mechanisms underlying the antihypertensive effects of DFs remain poorly defined. This systematic review and meta-analysis evaluates how DFs influence [...] Read more.
Background: Ingestion of dietary fibers (DFs) is a safe and accessible intervention associated with reductions in blood pressure (BP) and cardiovascular mortality. However, the mechanisms underlying the antihypertensive effects of DFs remain poorly defined. This systematic review and meta-analysis evaluates how DFs influence BP regulation by modulating gut microbial composition and enhancing short-chain fatty acid (SCFA) production. Methods: MEDLINE and EMBASE were systematically searched for interventional studies published between January 2014 and December 2024. Eligible studies assessed the effects of DFs or other prebiotics on systolic BP (SBP) and diastolic BP (DBP) in addition to changes in gut microbial or SCFA composition. Results: Of the 3010 records screened, nineteen studies met the inclusion criteria (seven human, twelve animal). A random-effects meta-analysis was conducted on six human trials reporting post-intervention BP values. Prebiotics were the primary intervention. In hypertensive cohorts, prebiotics significantly reduced SBP (−8.5 mmHg; 95% CI: −13.9, −3.1) and DBP (−5.2 mmHg; 95% CI: −8.5, −2.0). A pooled analysis of hypertensive and non-hypertensive patients showed non-significant reductions in SBP (−4.5 mmHg; 95% CI: −9.3, 0.3) and DBP (−2.5 mmHg; 95% CI: −5.4, 0.4). Animal studies consistently showed BP-lowering effects across diverse etiologies. Prebiotic interventions restored bacterial genera known to metabolize DFs to SCFAs (e.g., Bifidobacteria, Akkermansia, and Coprococcus) and increased SCFA levels. Mechanistically, SCFAs act along gut–organ axes to modulate immune, vascular, and neurohormonal pathways involved in BP regulation. Conclusions: Prebiotic supplementation is a promising strategy to reestablish BP homeostasis in hypertensive patients. Benefits are likely mediated through modulation of the gut microbiota and enhanced SCFA production. Full article
(This article belongs to the Special Issue Probiotics and Prebiotics: Past, Present and Future)
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25 pages, 3717 KiB  
Article
A Prebiotic Diet Containing Galactooligosaccharides and Polydextrose Attenuates Hypergravity-Induced Disruptions to the Microbiome in Female Mice
by Robert S. Thompson, Shelby Hopkins, Tel Kelley, Christopher G. Wilson, Michael J. Pecaut and Monika Fleshner
Nutrients 2025, 17(15), 2417; https://doi.org/10.3390/nu17152417 - 24 Jul 2025
Viewed by 443
Abstract
Background/Objectives: Environmental stressors, including spaceflight and altered gravity, can negatively affect the symbiotic relationship between the gut microbiome and host health. Dietary prebiotics, which alter components of the gut microbiome, show promise as an effective way to mitigate the negative impacts of stressor [...] Read more.
Background/Objectives: Environmental stressors, including spaceflight and altered gravity, can negatively affect the symbiotic relationship between the gut microbiome and host health. Dietary prebiotics, which alter components of the gut microbiome, show promise as an effective way to mitigate the negative impacts of stressor exposure. It remains unknown, however, if the stress-protective effects of consuming dietary prebiotics will extend to chronic altered-gravity exposure. Methods: Forty female C57BL/6 mice consumed either a control diet or a prebiotic diet containing galactooligosaccharides (GOS) and polydextrose (PDX) for 4 weeks, after which half of the mice were exposed to 3 times the gravitational force of Earth (3g) for an additional 4 weeks. Fecal microbiome samples were collected weekly for 8 weeks, sequenced, and analyzed using 16S rRNA gene sequencing. Terminal physiological endpoints, including immune and red blood cell characteristics, were collected at the end of the study. Results: The results demonstrate that dietary prebiotic consumption altered the gut microbial community structure through changes to β-diversity and multiple genera across time. In addition, consuming dietary prebiotics reduced the neutrophil-to-lymphocyte ratio (NLR) and increased red blood cell distribution width (RDW-CV). Importantly, the prebiotic diet prevented the impacts of altered-gravity on β-diversity and the bloom of problematic genera, such as Clostridium_sensu_stricto_1 and Turicibacter. Furthermore, several prebiotic diet-induced genera-level changes were significantly associated with several host physiological changes induced by 3g exposure. Conclusions: These data demonstrate that the stress-protective potential of consuming dietary prebiotics extends to environmental stressors such as altered gravity, and, potentially, spaceflight. Full article
(This article belongs to the Special Issue Advances in Gut Microbial Genomics and Metabolomics in Human Health)
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13 pages, 1791 KiB  
Article
Hydrogen Gas Inhalation Improved Intestinal Microbiota in Ulcerative Colitis: A Randomised Double-Blind Placebo-Controlled Trial
by Takafumi Maruyama, Dai Ishikawa, Rina Kurokawa, Hiroaki Masuoka, Kei Nomura, Mayuko Haraikawa, Masayuki Orikasa, Rina Odakura, Masao Koma, Masashi Omori, Hirotaka Ishino, Kentaro Ito, Tomoyoshi Shibuya, Wataru Suda and Akihito Nagahara
Biomedicines 2025, 13(8), 1799; https://doi.org/10.3390/biomedicines13081799 - 23 Jul 2025
Viewed by 314
Abstract
Background/Objective: Dysbiosis is implicated in the pathogenesis of ulcerative colitis. Hydrogen has been reported to promote intestinal microbiota diversity and suppress ulcerative colitis progression in mice models. In this study, we investigated changes in the intestinal microbiota, therapeutic effects, and safety of [...] Read more.
Background/Objective: Dysbiosis is implicated in the pathogenesis of ulcerative colitis. Hydrogen has been reported to promote intestinal microbiota diversity and suppress ulcerative colitis progression in mice models. In this study, we investigated changes in the intestinal microbiota, therapeutic effects, and safety of hydrogen inhalation in patients with ulcerative colitis. Methods: In this randomised, double-blind, placebo-controlled trial, 10 active patients with ulcerative colitis (aged ≥20 years; Lichtiger’s clinical activity index, 3–10; and Mayo endoscopic subscores ≥1) participated, and they were assigned to either a hydrogen or air inhalation group (hydrogen and placebo groups, respectively). All patients inhaled gas for 4 h every day for 8 weeks. Subsequently, we performed clinical indices and microbiota analyses using the metagenomic sequencing of stool samples before and after inhalation. Results: There was significant difference in the sum of the Mayo endoscopic subscores before and after inhalation in the clinical assessment indices. The hydrogen group showed higher α-diversity (p = 0.19), and the variation in β-diversity was markedly different, compared to the placebo group, in intestinal microbiota analysis (p = 0.02). Functional gene analysis revealed 115 significant genetic changes in the hydrogen group following treatment. No inhalation-related adverse events were observed. Conclusions: Hydrogen inhalation appeared to improve intestinal microbiota diversity; however, no clear therapeutic effect on ulcerative colitis was observed. Further studies are needed, and hydrogen inhalation may possibly lead to a logical solution combined with microbiome therapy, such as faecal microbiota transplantation, with fewer adverse events. Full article
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15 pages, 1833 KiB  
Article
Comparative Analysis of Gut Microbiota Responses to New SN-38 Derivatives, Irinotecan, and FOLFOX in Mice Bearing Colorectal Cancer Patient-Derived Xenografts
by Katarzyna Unrug-Bielawska, Zuzanna Sandowska-Markiewicz, Magdalena Piątkowska, Paweł Czarnowski, Krzysztof Goryca, Natalia Zeber-Lubecka, Michalina Dąbrowska, Ewelina Kaniuga, Magdalena Cybulska-Lubak, Aneta Bałabas, Małgorzata Statkiewicz, Izabela Rumieńczyk, Kazimiera Pyśniak, Michał Mikula and Jerzy Ostrowski
Cancers 2025, 17(13), 2263; https://doi.org/10.3390/cancers17132263 - 7 Jul 2025
Viewed by 471
Abstract
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 [...] Read more.
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
(This article belongs to the Section Cancer Therapy)
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23 pages, 5783 KiB  
Article
Achnatherum inebrians Bacterial Communities Associated with Epichloë gansuensis Endophyte Infection Under Low-Concentration Urea Treatment: Links to Plant Growth and Root Metabolite
by Yuanyuan Jin, Zhenjiang Chen, Kamran Malik and Chunjie Li
Microorganisms 2025, 13(7), 1493; https://doi.org/10.3390/microorganisms13071493 - 26 Jun 2025
Viewed by 341
Abstract
Despite chemical exchange often serving as the first step in plant–microbe interactions, the specialized chemical metabolites produced by grass–Epichloë endophyte symbiosis as mediators of host growth, nutrient acquisition, and modulators of the rhizosphere community under low-nitrogen conditions are areas lacking in knowledge. [...] Read more.
Despite chemical exchange often serving as the first step in plant–microbe interactions, the specialized chemical metabolites produced by grass–Epichloë endophyte symbiosis as mediators of host growth, nutrient acquisition, and modulators of the rhizosphere community under low-nitrogen conditions are areas lacking in knowledge. In this study, we investigated the plant growth-promoting effects of the Epichloë endophyte strain and identified the growth of the Epichloë strain under different types of nitrogen source treatments. In addition to the in vitro test, we evaluated growth performance for Epichloë endophyte–infected plants (E+) and Epichloë endophyte–free plants (E−) in a pot trial under 0.01 mol/L urea treatment. Seedlings from E+ and E− groups were collected to analyze the plant bacterial microbiome and root metabolites. The E. gansuensis endophyte strain was found not to produce indoleacetic acid (IAA), pectinase, or contain ferritin. The nitrogenase gene, essential for nitrogen fixation, was also absent. These results suggest that E. gansuensis endophyte strains themselves do not contain attributes to promote plant growth. Concerning N fertilization, it was observed an increase in the colony diameter of E. gansuensis strain was observed only in the NO3-N (NN) treatment, while inhibition was observed in the urea-N (UN) treatment. E. gansuensis endophyte symbiosis significantly increased tiller number and plant dry weight. Overall, our results suggest that the E+ plants had more root forks and greater average root diameter compared to E− plants under the UN treatment. In a pot experiment using UN, data from 16S rRNA amplicon sequencing revealed that E. gansuensis endophyte infection significantly altered the bacterial community composition in shoot and root, and significantly increased Shannon (p < 0.001) and Chao 1 (p < 0.01) indexes. The relative abundance of Acidobacteriota, Actinomycetota, Cyanobacteriota, Fibrobacterota, Myxococcota, and Patescibacteria in the shoot, and Cyanobacteriota, Pseudomonadota, and Verrucomicrobiota in the root were significantly increased by E. gansuensis endophyte infection. Similarly, E. gansuensis endophyte symbiosis shifted the metabolite composition of the host plants, with the E+ plants showing a higher number of metabolites than the E− plants. In addition, co-metabolism network analysis revealed that the positive relevance between exudates and microorganisms in the root of the E+ plants is higher than that of the E− plants. These findings provide valuable insights into the knowledge of the effects of the symbiotic relationship between host plants and Epichloë endophyte on interspecific interactions of plant microbiome, beneficial for harnessing endophytic symbiosis, promoting plant growth. Full article
(This article belongs to the Section Microbiomes)
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20 pages, 1478 KiB  
Review
Cyanobacteria and Soil Restoration: Bridging Molecular Insights with Practical Solutions
by Matias Garcia, Pablo Bruna, Paola Duran and Michel Abanto
Microorganisms 2025, 13(7), 1468; https://doi.org/10.3390/microorganisms13071468 - 24 Jun 2025
Viewed by 691
Abstract
Soil degradation has been accelerating globally due to climate change, which threatens food production, biodiversity, and ecosystem balance. Traditional soil restoration strategies are often expensive, slow, or unsustainable in the long term. In this context, cyanobacteria have emerged as promising biotechnological alternatives, being [...] Read more.
Soil degradation has been accelerating globally due to climate change, which threatens food production, biodiversity, and ecosystem balance. Traditional soil restoration strategies are often expensive, slow, or unsustainable in the long term. In this context, cyanobacteria have emerged as promising biotechnological alternatives, being the only prokaryotes capable of performing oxygenic photosynthesis. Moreover, they can capture atmospheric carbon and nitrogen, release exopolysaccharides (EPSs) that stabilize the soil, and facilitate the development of biological soil crusts (biocrusts). In recent years, the convergence of multi-omics tools, such as metagenomics, metatranscriptomics, and metabolomics, has advanced our understanding of cyanobacterial dynamics, their metabolic potential, and symbiotic interactions with microbial consortia, as exemplified by the cyanosphere of Microcoleus vaginatus. In addition, recent advances in bioinformatics have enabled high-resolution taxonomic and functional profiling of environmental samples, facilitating the identification and prediction of resilient microorganisms suited to challenging degraded soils. These tools also allow for the prediction of biosynthetic gene clusters and the detection of prophages or cyanophages within microbiomes, offering a novel approach to enhance carbon sequestration in dry and nutrient-poor soils. This review synthesizes the latest findings and proposes a roadmap for the translation of molecular-level knowledge into scalable biotechnological strategies for soil restoration. We discuss approaches ranging from the use of native biocrust strains to the exploration of cyanophages with the potential to enhance cyanobacterial photosynthetic activity. By bridging ecological functions with cutting-edge omics technologies, this study highlights the critical role of cyanobacteria as a nature-based solution for climate-smart soil management in degraded and arid ecosystems. Full article
(This article belongs to the Special Issue Omics Research in Microbial Ecology)
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25 pages, 800 KiB  
Review
Microbial Solutions in Agriculture: Enhancing Soil Health and Resilience Through Bio-Inoculants and Bioremediation
by Rahul Kumar, Beatrice Farda, Amedeo Mignini, Rihab Djebaili, Leonard Koolman, Alivia Paul, Subhankar Mondal, Joy M. Joel, Aditi Pandit, Periyasamy Panneerselvam, Marika Pellegrini and Debasis Mitra
Bacteria 2025, 4(3), 28; https://doi.org/10.3390/bacteria4030028 - 24 Jun 2025
Cited by 1 | Viewed by 847
Abstract
Soil microbes are important for maintaining agricultural ecosystems by promoting nutrient cycling, plant growth, and soil resilience. Microbial-based inoculants, such as bio-inoculants and bioremediation agents, have been identified as suitable means to promote soil health, reduce environmental deterioration, and achieve sustainable agriculture. Bio-inoculants, [...] Read more.
Soil microbes are important for maintaining agricultural ecosystems by promoting nutrient cycling, plant growth, and soil resilience. Microbial-based inoculants, such as bio-inoculants and bioremediation agents, have been identified as suitable means to promote soil health, reduce environmental deterioration, and achieve sustainable agriculture. Bio-inoculants, such as biofertilizers and biopesticides, promote nutrient availability, plant growth, and chemical input dependency reduction. Diverse microbial populations, especially plant growth-promoting bacteria (PGPB), enhance resistance by promoting a symbiotic association with plants and inducing natural resistance against insects. Bioremediation, the second significant microbial intervention, is the use of microorganisms for detoxifying and rehabilitating polluted soils. Methods effectively degrade organic pollutants, immobilize heavy metals, and mitigate the toxic effects of industrial and agricultural pollutants. Recent advances in microbial ecology and biotechnology, such as metagenomics, have transformed the knowledge of microbial soil communities, and tailor-made microbial formulations and monitoring equipment may be developed to maximize their activity. Though promising, environmental heterogeneity, scalability, and lack of field-based evidence constrain their widespread application. Multidimensional applications of microbial solutions in agroecology are explored in this review, with a focus on their potential in maintaining soil health, crop production, and environmental sustainability. It also addresses the application of bioremediation and microbial inoculants in agroecosystems and technological innovations with future research objectives. Microbial innovation to shape the soil microbiome offers a valid tool for addressing global challenges in agriculture, food security, and ecological resilience in the context of climate change. Full article
(This article belongs to the Special Issue Harnessing of Soil Microbiome for Sustainable Agriculture)
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15 pages, 1371 KiB  
Article
Host Plant Dependence of the Symbiotic Microbiome of the Gall-Inducing Wasp Trichagalma acutissimae
by Yingnan Wang, Yuanchen Zhang, Ran Li, Yujian Li, Muha Cha and Xianfeng Yi
Insects 2025, 16(7), 652; https://doi.org/10.3390/insects16070652 - 23 Jun 2025
Viewed by 509
Abstract
Symbiotic bacteria play a pivotal role in the biology and ecology of herbivorous insects, affecting host growth and adaptation. However, the effects of host identity on the symbiotic microbiota of gall-inducing insects remain less explored. In this study, we utilized high-throughput sequencing to [...] Read more.
Symbiotic bacteria play a pivotal role in the biology and ecology of herbivorous insects, affecting host growth and adaptation. However, the effects of host identity on the symbiotic microbiota of gall-inducing insects remain less explored. In this study, we utilized high-throughput sequencing to investigate the effects of different oak hosts on the structure and diversity of the symbiotic microbial community in the asexual larvae of the gall-inducing wasp Trichagalma acutissimae. Host plant species significantly altered the alpha and beta diversity of symbiotic microbiota of T. acutissimae. At the phylum level, Proteobacteria was the predominant microflora in both groups, with significantly higher abundance in larvae parasitizing Quercus acutissima than in those parasitizing Q. variabilis. Pseudomonas, which has been identified as responsible for tannin decomposition, was the most dominant genus in T. acutissimae larvae infesting both hosts. LEfSe analysis revealed substantial differences in the symbiotic microbial communities between the two hosts while also highlighting some commonalities. Functional prediction analysis indicated no significant difference in the functional roles of symbiotic bacteria between larvae infesting the two hosts. These findings suggest that the symbiotic microbiome of T. acutissimae larvae is influenced by host plant species, yet different microbial compositions may perform similar functions, implying the potential role of symbiotic microbiota in the adaptation to high-tannin oak leaves. This research enhances our understanding of the symbiotic relationship between forest pests and their associated microbes. Full article
(This article belongs to the Section Insect Pest and Vector Management)
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17 pages, 4582 KiB  
Article
Comparative Analysis of Rhizosphere Microbiomes in Different Blueberry Cultivars
by Lifeng Xiao, Qiuyue Zhao, Jie Deng, Lingyan Cui, Tingting Zhang, Qin Yang and Sifeng Zhao
Horticulturae 2025, 11(6), 696; https://doi.org/10.3390/horticulturae11060696 - 17 Jun 2025
Viewed by 799
Abstract
Blueberry growth is closely tied to its rhizosphere’s microbial communities. Recent advancements in high-throughput sequencing and multi-omics technologies have enhanced the investigation of variations in rhizosphere microbial communities and their functional roles across different plant cultivars. In this study, high-throughput sequencing was utilized [...] Read more.
Blueberry growth is closely tied to its rhizosphere’s microbial communities. Recent advancements in high-throughput sequencing and multi-omics technologies have enhanced the investigation of variations in rhizosphere microbial communities and their functional roles across different plant cultivars. In this study, high-throughput sequencing was utilized to assess the rhizosphere microbial diversity in highbush and rabbiteye blueberry groups, encompassing a total of eight cultivars. Notable variations were observed in both bacterial and fungal community diversity. Ten bacterial phyla, each with a relative abundance greater than 1%, constituted 92.32–97.08% of the total abundance across the eight cultivars, with Acidobacteriota, Actinobacteriota, and Pseudomonadota being predominant. Similarly, five major fungal phyla, each exceeding 1% in relative abundance, accounted for 88.18–97.20% of the total abundance, with Ascomycota and Basidiomycota being the most dominant. The results showed that the rhizospheres of blueberries host a variety of plant growth-promoting rhizobacteria (PGPR), including genera such as Burkholderia, Enterobacter, Streptomyces, Arthrobacter, and Pseudomonas. Rabbiteye blueberry cultivars exhibit a greater propensity for accumulating beneficial symbiotic microorganisms compared to highbush cultivars. Notably, the relative abundance of ericoid mycorrhizal fungi, specifically Oidiodendron, is significantly elevated in the cultivars Emerald, Premier, O’Neal, and Brightwell, with the most pronounced increase observed in Emerald. Furthermore, rabbiteye blueberries support a more diverse and abundant array of cultivar-specific fungal communities than their highbush counterparts. Understanding the interaction networks between blueberries and their associated microbes can provide a theoretical foundation for the targeted regulation of rhizosphere microbiomes and offer valuable insights for the management of rhizospheres in other acidophilic crops. Full article
(This article belongs to the Section Fruit Production Systems)
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28 pages, 767 KiB  
Review
Microbiome Markers in Gastrointestinal Disorders: Inflammatory Bowel Disease, Colorectal Cancer, and Celiac Disease
by M. Isabel San-Martin, Alejandro Chamizo-Ampudia, África Sanchiz, Miguel Ángel Ferrero, Honorina Martínez-Blanco, Leandro Benito Rodríguez-Aparicio and Nicolás Navasa
Int. J. Mol. Sci. 2025, 26(10), 4818; https://doi.org/10.3390/ijms26104818 - 17 May 2025
Cited by 1 | Viewed by 977
Abstract
Intestinal microbiota and the host’s immune system form a symbiotic alliance that sustains normal development and function in the human gut. Changes such as dietary habits among societies in developed countries have led to the development of unbalanced microbial populations in the gut, [...] Read more.
Intestinal microbiota and the host’s immune system form a symbiotic alliance that sustains normal development and function in the human gut. Changes such as dietary habits among societies in developed countries have led to the development of unbalanced microbial populations in the gut, likely contributing to the dramatic increase in inflammatory diseases in the last few decades. Recent advances in DNA sequencing technologies have tremendously helped to characterize the microbiome associated with disease, both in identifying global alterations and discovering specific biomarkers that potentially contribute to disease pathogenesis, as evidenced by animal studies. Beyond bacterial alterations, non-bacterial components such as fungi, viruses, and microbial metabolites have been implicated in these diseases, influencing immune responses and gut homeostasis. Multi-omics approaches integrating metagenomics, metabolomics, and transcriptomics offer a more comprehensive understanding of the microbiome’s role in disease pathogenesis, paving the way for innovative diagnostic and therapeutic strategies. Unraveling the metagenomic profiles associated with disease may facilitate earlier diagnosis and intervention, as well as the development of more personalized and effective therapeutic strategies. This review synthesizes recent and relevant microbiome research studies aimed at characterizing the microbial signatures associated with inflammatory bowel disease, colorectal cancer, and celiac disease. Full article
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13 pages, 1102 KiB  
Review
Innovative Approaches for Engineering the Seed Microbiome to Enhance Crop Performance
by Piao Yang, Ling Lu, Abraham Condrich, Gavin A. Muni, Sean Scranton, Shixiang Xu, Ye Xia and Shuai Huang
Seeds 2025, 4(2), 24; https://doi.org/10.3390/seeds4020024 - 14 May 2025
Viewed by 938
Abstract
Seed science is the comprehensive study of seeds. It encompasses their biology, production, technology, genetics, physiology, ecology, and applications in agriculture and conservation. Seed science has undergone transformative advancements through the integration of microbial technologies, with beneficial microorganisms emerging as critical tools for [...] Read more.
Seed science is the comprehensive study of seeds. It encompasses their biology, production, technology, genetics, physiology, ecology, and applications in agriculture and conservation. Seed science has undergone transformative advancements through the integration of microbial technologies, with beneficial microorganisms emerging as critical tools for enhancing germination, seedling vigor, and crop resilience. Research demonstrates that microbial treatments improve nutrient uptake, hormonal regulation, and stress tolerance while establishing early symbiotic relationships with plants. This review synthesizes recent advances in understanding the roles of beneficial microbes in seed science, focusing on their impact on seed germination, seedling growth, and plant health. We explore the composition and transmission of seed microbiomes, highlighting the vertical transfer of microbes from parent plants to seeds and the influence of environmental factors on microbial community structure. The review also discusses innovative approaches to seed microbiome engineering. Particular attention is given to seed biopriming with plant growth-promoting bacteria (PGPB), which has shown significant potential in improving germination rates, seedling vigor, and crop productivity. Specific microbial strains, such as Trichoderma species and Pseudomonas fluorescens, are discussed with emphasis on their mechanisms of action in enhancing plant performance. The review also addresses the impact of breeding on seed microbiomes and explores emerging research directions, including the development of tailored microbial inoculants and the investigation of intracellular seed bacteria. By synthesizing these findings, this review aims to provide a comprehensive summary of the current state of seed microbiome research and its implications in seed science for sustainable agriculture. Full article
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18 pages, 4183 KiB  
Article
Synergistic Recruitment of Symbiotic Fungi by Potting and Scleroderma bovista Inoculation Suppresses Pathogens in Hazel Rhizosphere Microbiomes
by Cheng Peng, Yuqing Li, Hengshu Yu, Hongli He, Yunqing Cheng, Siyu Sun and Jianfeng Liu
Microorganisms 2025, 13(5), 1063; https://doi.org/10.3390/microorganisms13051063 - 2 May 2025
Viewed by 486
Abstract
This study explored how potted treatments (with and without Scleroderma bovista inoculation) shape rhizosphere microbial diversity in hazel across five soils using split-root cultivation. Three treatments (control, split-root, split-root with S. bovista) were analyzed for root growth and microbial dynamics. S. bovista [...] Read more.
This study explored how potted treatments (with and without Scleroderma bovista inoculation) shape rhizosphere microbial diversity in hazel across five soils using split-root cultivation. Three treatments (control, split-root, split-root with S. bovista) were analyzed for root growth and microbial dynamics. S. bovista inoculation consistently enhanced root parameters (number, tips) in all soils. Potted treatments (with and without S. bovista inoculation) altered microbial features (OTU/ASV), with only 0.9–3.3% of features remaining unchanged. At the class level, potting increased Agaricomycetes abundance while reducing Sordariomycetes, a trend amplified by S. bovista. Potting decreased species richness estimates (ACE and Chao1), while both treatments lowered diversity index (Shannon index). Potted treatments without S. bovista inoculation drove stronger shifts in species composition than inoculation. Findings reveal potting and S. bovista synergistically recruit symbiotic fungi via root exudates, establishing disease-suppressive communities that selectively inhibit pathotrophic fungi (particularly plant pathogen Coniothyrium and fungal parasite Cladobotryum) while roughly maintaining non-pathogenic saprotrophic microbes essential for organic matter decomposition. This work provides insights for optimizing hazel orchard management and ectomycorrhizal agent development. Full article
(This article belongs to the Section Plant Microbe Interactions)
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15 pages, 6286 KiB  
Article
Unique Microbial Characterisation of Oesophageal Squamous Cell Carcinoma Patients with Different Dietary Habits Based on Light Gradient Boosting Machine Learning Classifier
by Shun Liu, Zhifeng Lin, Zhimin Huang, Menglin Yu, Zheng Lin and Zhijian Hu
Nutrients 2025, 17(8), 1340; https://doi.org/10.3390/nu17081340 - 14 Apr 2025
Viewed by 650
Abstract
Objectives: The microbiome plays an important role in cancer, but the relationship between dietary habits and the microbiota in oesophageal squamous cell carcinoma (ESCC) is not clear. The aim of this study is to explore the complex relationship between the microbiota in [...] Read more.
Objectives: The microbiome plays an important role in cancer, but the relationship between dietary habits and the microbiota in oesophageal squamous cell carcinoma (ESCC) is not clear. The aim of this study is to explore the complex relationship between the microbiota in oesophagal tissue and dietary habits in ESCC patients. Methods: 173 ESCC patients were included. The method of 16S rRNA sequencing was used to analyze microbial composition and diversity. The LEfSe and Boruta methods were used to screen important microbes, and the LightGBM algorithm distinguished microbes associated with different dietary habits. PICRUST2 and DESeq2 predicted microbial function and screened differential functions. The Pearson test was used to analyze correlations between microbes and functions, and SPARCC microbial symbiotic networks and Cytoscape were used to determine microbial interactions. Results: Significant differences in microbial composition were observed among ESCC patients with different dietary habits. LEfSe and Boruta identified three, six, and two significantly different bacteria in the FF/FP, FF/PF, and FF/PP groups, respectively, with AUC values of 0.683, 0.830, and 0.715. PICRUST2 and DESeq2 analysis revealed 3, 11, and 5 significantly different metabolic pathways in each group. Eubacterium_B sulci was positively correlated with PWY-6285, PWY-3801, and PWY-5823. PWY-6397 was positively correlated with undefinded (Fusobacterium_C). Microbial network analysis confirmed unique microbial characteristics in different diet groups. Conclusions: Different dietary habits lead to alterations in Eubacterium_B sulci and undefinded (Fusobacterium_C) and related functional pathways. Full article
(This article belongs to the Section Nutrition and Public Health)
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24 pages, 2146 KiB  
Review
Unraveling the Intricacies of Powdery Mildew: Insights into Colonization, Plant Defense Mechanisms, and Future Strategies
by Chun-Mei Gan, Ting Tang, Zi-Yu Zhang, Mei Li, Xiao-Qiong Zhao, Shuang-Yu Li, Ya-Wen Yan, Mo-Xian Chen and Xiang Zhou
Int. J. Mol. Sci. 2025, 26(8), 3513; https://doi.org/10.3390/ijms26083513 - 9 Apr 2025
Cited by 1 | Viewed by 1321
Abstract
Powdery mildew, a debilitating phytopathogen caused by biotrophic fungi within the order Erysiphales, endangers crop yields and global food security. Although traditional approaches have largely emphasized resistant cultivar development and chemical control, novel strategies are necessary to counter the advent of challenges, [...] Read more.
Powdery mildew, a debilitating phytopathogen caused by biotrophic fungi within the order Erysiphales, endangers crop yields and global food security. Although traditional approaches have largely emphasized resistant cultivar development and chemical control, novel strategies are necessary to counter the advent of challenges, such as pathogen adaptation and climate change. This review fully discusses three principal areas of pathogen effector functions, e.g., the reactive oxygen species (ROS)-suppressive activity of CSEP087, and host susceptibility factors, like vesicle trafficking regulated by Mildew Locus O (MLO). It also briefly mentions the transcriptional regulation of resistance genes mediated by factors, like WRKY75 and NAC transcription factors, and post-transcriptional regulation via alternative splicing (As). In addition, this discussion discusses the intricate interactions among powdery mildew, host plants, and symbiotic microbiomes thereof, highlighting the mechanism through which powdery mildew infections disrupt the foliar microbiota balance. Lastly, we present a new biocontrol approach that entails synergistic microbial consortia, such as combinations of Bacillus and Trichoderma, to induce plant immunity while minimizing fungicide dependency. Through the study of combining knowledge of molecular pathogenesis with ecological resilience, this research offers useful insights towards climate-smart crop development and sustainable disease-management strategies in the context of microbiome engineering. Full article
(This article belongs to the Special Issue The Molecular Basis of Plant–Microbe Interactions)
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17 pages, 564 KiB  
Review
The Interplay Between Nutrition and Microbiota and the Role of Probiotics and Symbiotics in Pediatric Infectious Diseases
by María Slöcker-Barrio, Jesús López-Herce Cid and María José Solana-García
Nutrients 2025, 17(7), 1222; https://doi.org/10.3390/nu17071222 - 31 Mar 2025
Viewed by 898
Abstract
The interplay between nutrition and infectious diseases has been a central theme in health sciences for the last decades due to its great impact on the pediatric population, especially in immunocompromised patients and critically ill children. As conventional treatment and the development of [...] Read more.
The interplay between nutrition and infectious diseases has been a central theme in health sciences for the last decades due to its great impact on the pediatric population, especially in immunocompromised patients and critically ill children. As conventional treatment and the development of antimicrobials for most infections standard treatment is either limited or not possible, alternative treatment options should be explored. Recent research shows that early enteral nutrition and nutritional supplements (such as probiotics and symbiotics) could have a pivotal role in promoting a healthy microbiome and subsequently preventing and improving outcomes for certain pediatric infectious diseases. However, understanding the specific mechanism of action and tailoring nutritional interventions remains a significant challenge. The optimal dose range for different probiotic strains and prebiotics and the most effective combination for each treatment indication needs further investigation and is yet to be defined. Additionally, in the era of personalized medicine, goal- and patient-directed treatment are key to optimizing and improving outcomes and minimizing potential complications and side effects, especially in complex and immunocompromised patients. The main objectives of this narrative review are 1. to explore the relationship and the complex interactions between microbiota and the human immune system; 2. to describe the influence of nutrition on infectious diseases; 3. to evaluate the impact of supplementation with probiotics and symbiotics in the prevention and treatment of the most relevant infections in children; and 4. to identify knowledge gaps and potential research priorities regarding the use of these supplements in pediatric patients. Full article
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