Search Results (288)

Background: Prebiotics are selectively used by host microorganisms to promote health. Because effective prebiotic doses (1.5–30 g/day) often require inconvenient delivery formats, this study aims to explore whether capsule-compatible doses of galacto-oligosaccharides (GOS) can effectively modulate the gut microbiome. Methods: The impact of Bimuno^® GOS (Reading, UK) at 0.5, 0.75, 1.83, and 3.65 g on the adult gut microbiome was assessed using the ex vivo SIFR^® technology (n = 8), a clinically validated, bioreactor-based technology. Results: The GOS were rapidly fermented and significantly increased beneficial Bifidobacterium species (B. adolescentis, B. bifidum, and B. longum), even at the lowest tested dose. In doing so, GOS strongly promoted SCFA production, particularly acetate (significant from 0.5 g) and butyrate (significant from 0.75 g). Gas production only mildly increased, likely as Bifidobacterium species do not produce gases. Based on the ability of the SIFR^® technology to cultivate strictly anaerobic, hard-to-culture gut microbes, unlike in past in vitro studies, we elucidated that GOS also enriched specific Lachnospiraceae species. Besides Anaerobutyricum hallii, this included Bariatricus comes, Blautia species (B. massiliensis, Blautia_A, B. faecis), Oliverpabstia intestinalis, Mediterraneibacter faecis, and Fusicatenibacter species. Finally, GOS also promoted propionate (significant from 0.75 g), linked to increases in Phocaeicola vulgatus. Conclusions: GOS displayed prebiotic potential at capsule-compatible doses, offering greater flexibility in nutritional product formulation and consumer convenience. Notably, the strong response at the lowest dose suggests effective microbiome modulation at lower levels than previously expected. Full article

Microbes perform diverse and vital functions in animals, plants, and humans, and among them, plant-associated microbiomes, especially endophytes, have attracted growing scientific interest in recent years. Numerous plant species thriving in diverse environments have been shown to host endophytic microbes. While endophytic bacteria commonly colonize plant tissues such as stems, roots, and leaves, seed-associated endophytes generally exhibit lower diversity compared to those in other plant compartments. Nevertheless, seed-borne microbes are of particular importance, as they represent the initial microbial inoculum that influences a plant’s critical early developmental stages. The seed endophytic microbiome is of particular interest due to its potential for vertical transmission and its capacity to produce a broad array of phytohormones, enzymes, antimicrobial compounds, and other secondary metabolites. Collectively, these functions contribute to enhanced plant biomass and yield, especially under abiotic and biotic stress conditions. Despite their multifaceted roles, seed microbiomes remain underexplored in plant ecology, and their potential benefits are not yet fully understood. This review highlights recent advances in our understanding of the diversity, community composition, mechanisms of action, and agricultural significance of seed endophytic microbes. Furthermore, it synthesizes current insights into how seed endophytes promote plant health and productivity and proposes future research directions to fully harness their potential in sustainable agriculture. Full article

Glycyrrhiza uralensis (G. uralensis), a leguminous plant, is an important medicinal and economic plant in saline–alkaline soils of arid regions in China. Its main bioactive components include liquiritin, glycyrrhizic acid, and flavonoids, which play significant roles in maintaining human health and preventing and adjuvantly treating related diseases. However, the cultivation of G. uralensis is easily restricted by adverse soil conditions in these regions, characterized by high salinity, high alkalinity, and nutrient deficiency. This study investigated the impacts of four multistrain microbial inoculants (Pa, Pb, Pc, Pd) on the growth performance and bioactive compound accumulation of G. uralensis in moderately saline–sodic soil. The aim was to screen the most beneficial inoculant from these strains, which were isolated from the rhizosphere of plants in moderately saline–alkaline soils of the Hexi Corridor and possess native advantages with excellent adaptability to arid environments. The results showed that inoculant Pc, comprising Pseudomonas silesiensis, Arthrobacter sp. GCG3, and Rhizobium sp. DG1, exhibited superior performance: it induced a 0.86-unit reduction in lateral root number relative to the control, while promoting significant increases in single-plant dry weight (101.70%), single-plant liquiritin (177.93%), single-plant glycyrrhizic acid (106.10%), and single-plant total flavonoids (107.64%). Application of the composite microbial inoculant Pc induced no significant changes in the pH and soluble salt content of G. uralensis rhizospheric soils. However, it promoted root utilization of soil organic matter and nitrate, while significantly increasing the contents of available potassium and available phosphorus in the rhizosphere. High-throughput sequencing revealed that Pc reorganized the rhizospheric microbial communities of G. uralensis, inducing pronounced shifts in the relative abundances of rhizospheric bacteria and fungi, leading to significant enrichment of target bacterial genera (Arthrobacter, Pseudomonas, Rhizobium), concomitant suppression of pathogenic fungi, and proliferation of beneficial fungi (Mortierella, Cladosporium). Correlation analyses showed that these microbial shifts were linked to improved plant nutrition and secondary metabolite biosynthesis. This study highlights Pc as a sustainable strategy to enhance G. uralensis yield and medicinal quality in saline–alkali ecosystems by mediating microbe–plant–nutrient interactions. Full article

Background: Developments in biology, genetics, soil science, plant breeding, engineering, and agricultural microbiology are driving advances in soil microbiology and microbial biotechnology. Material and methods: The literature for this review was collected by searching leading scientific databases such as Embase, Medline/PubMed, Scopus, and Web of Science. Results: Recent advances in soil microbiology and biotechnology are discussed, emphasizing the role of microorganisms in sustainable agriculture. It has been shown that soil and plant microbiomes significantly contribute to improving soil fertility and plant and soil health. Microbes promote plant growth through various mechanisms, including potassium, phosphorus, and zinc solubilization, biological nitrogen fixation, production of ammonia, HCN, siderophores, and other secondary metabolites with antagonistic effects. The diversity of microbiomes related to crops, plant protection, and the environment is analyzed, as well as their role in improving food quality, especially under stress conditions. Particular attention was paid to the diversity of microbiomes and their mechanisms supporting plant growth and soil fertility. Conclusions: The key role of soil microorganisms in sustainable agriculture was highlighted. They can support the production of natural substances used as plant protection products, as well as biopesticides, bioregulators, or biofertilizers. Microbial biotechnology also offers potential in the production of sustainable chemicals, such as biofuels or biodegradable plastics (PHA) from plant sugars, and in the production of pharmaceuticals, including antibiotics, hormones, or enzymes. Full article

The oral–gut microbiota axis is a relatively new field of research. Although most studies have focused separately on the oral and gut microbiota, emerging evidence has highlighted that the two microbiota are interconnected and may influence each other through various mechanisms shaping systemic health. The aim of this review is therefore to provide an overview of the interactions between oral and gut microbiota, and the influence of diet and related metabolites on this axis. Pathogenic oral bacteria, such as Porphyromonas gingivalis and Fusobacterium nucleatum, can migrate to the gut through the enteral route, particularly in individuals with weakened gastrointestinal defenses or conditions like gastroesophageal reflux disease, contributing to disorders like inflammatory bowel disease and colorectal cancer. Bile acids, altered by gut microbes, also play a significant role in modulating these microbiota interactions and inflammatory responses. Oral bacteria can also spread via the bloodstream, promoting systemic inflammation and worsening some conditions like cardiovascular disease. Translocation of microorganisms can also take place from the gut to the oral cavity through fecal–oral transmission, especially within poor sanitary conditions. Some metabolites including short-chain fatty acids, trimethylamine N-oxide, indole and its derivatives, bile acids, and lipopolysaccharides produced by both oral and gut microbes seem to play central roles in mediating oral–gut interactions. The complex interplay between oral and gut microbiota underscores their crucial role in maintaining systemic health and highlights the potential consequences of dysbiosis at both the oral and gastrointestinal level. Some dietary patterns and nutritional compounds including probiotics and prebiotics seem to exert beneficial effects both on oral and gut microbiota eubiosis. A better understanding of these microbial interactions could therefore pave the way for the prevention and management of systemic conditions, improving overall health outcomes. Full article

The current proceedings summarize the presentations delivered during the third International Electronic Conference on Microbiology (ECM 2025), which was held online from 1 to 3 April 2025, via the SciForum platform. This virtual event brought together researchers from around the world to share recent advances in microbiological sciences. The ECM 2025 highlighted recent developments across a broad spectrum of microbiological research, including antimicrobial resistance, gut microbiota, infectious diseases, and environmental microbiomes. Participants shared their work through online presentations and abstracts, with selected submissions invited for full publication. The event fostered global collaboration, promoted open-access science, and showcased innovative tools for studying and managing microbial systems in health, agriculture, and industry. The multidisciplinary program was organized into several thematic sessions: S1. Gut Microbiota and Health Disease. S2. Foodborne Pathogens and Food Safety. S3. Antimicrobial Agents and Resistance. S4. Emerging Infectious Diseases. S5. Microbiome and Soil Science. S6. Microbial Characterization and Bioprocess. S7. Microbe–Plant Interactions. This conference report presents summaries of the contributions made by participating authors over the three-day event. Full article

Suckling is crucial for piglet intestinal development and gut health, as it improves resilience during the challenging weaning phase and promotes subsequent growth. IPS, comprising Na⁺/K⁺ ions, whey protein, and glucose, has been shown to have positive effects on animal growth and intestinal health. The objectives of this study were to assess the impact of IPS consumption on the growth performance, immunity, intestinal growth and development, and microbiota structure of suckling piglets. A total of 160 newborn piglets were randomly divided into control and IPS groups, with IPS supplementation starting from 2 to 8 days after birth and continuing until 3 days before weaning. The findings revealed that IPS boosted the body weight at 24 days by 3.6% (p < 0.05) and improved the body weight gain from 16 to 24 days by 15.7% (p < 0.05). Additionally, the jejunal villus height and villus height to crypt depth ratio in the IPS group were notably increased to 1.08 and 1.31 times (p < 0.05), respectively, compared to the control group. Furthermore, IPS elevated the plasma levels of IgA and IgM, reduced the plasma levels of blood urea nitrogen (BUN), and enhanced the content of secretory immunoglobulin A (SIgA) in the jejunal mucosa of suckling piglets. Furthermore, IPS upregulated the mRNA expression of tight junction proteins GLP-2, ZO-1, and Claudin-1 in jejunal tissue, while downregulating the regulatory genes in the Toll-like pathway, including MyD88 and TLR-4 (p < 0.05). The analysis of gut microbiota indicated that IPS altered the relative abundance of gut microbes, with an increase in beneficial bacteria like Alloprevotella and Bacteroides. In conclusion, this study demonstrates that IPS supplementation enhances weaning weight, growth performance, immune function, and intestinal development in piglets, supporting the integration of IPS supplementation in the management of pre-weaning piglets. Full article

Fusaric acid (FSA) is a mycotoxin produced by pathogenic Fusarium species that inhibits the growth of various beneficial microbes. In this study, we investigated the molecular mechanisms by which Trichoderma harzianum NJAU4742 (Th), a beneficial fungus, responds to FSA-induced stress. Here, by combining a transcriptome analysis, a gene knockout, and physiological data measurements, our study investigated the molecular mechanisms underlying the response of Trichoderma harzianum NJAU4742 (Th) to FSA stress. The results showed that FSA can induce severe oxidative stress in Th, and an aldehyde dehydrogenase (Thaldh3) in Th plays a critical role in alleviating FSA stress. Deleting Thaldh3 significantly decreased the γ-aminobutyrate (GABA) content, causing more severe oxidative damage in Th. Furthermore, we also provide evidence demonstrating that Thaldh3 alleviates FSA stress by enhancing the activities of key enzymes involved in the tricarboxylic acid cycle and ATP content. A pot experiment showed that an enhanced tolerance to FSA increased the Th biomass, strengthening its antagonistic capacity against pathogens and reducing the disease index in tomatoes. In conclusion, these observations provide new insight into the role of beneficial microbes in promoting plant health. Full article

Soil salinization poses a critical threat to global agriculture, necessitating innovative strategies for sustainable remediation. This review synthesizes advances in leveraging plant–microbe interactions to remediate saline–alkali soils, focusing on oilseed crops—Brassica napus, Glycine max, Arachis hypogaea, Helianthus annuus, and Sesamum indicum—as keystone species for ecosystem restoration. These crops exhibit unique adaptive strategies, including root architectural plasticity and exudate-mediated recruitment of stress-resilient microbiomes (Proteobacteria, Actinobacteria, and Ascomycota), which collectively stabilize soil structure and enhance nutrient cycling, ion homeostasis, and soil aggregation to mitigate soil salinity and alkalinity. Emerging technologies further amplify these natural synergies: nanomaterials optimize nutrient delivery and microbial colonization, while artificial intelligence (AI) models predict optimal plant growth-promoting rhizobacteria (PGPR) combinations and simulate remediation outcomes. This integration establishes a roadmap for precision microbiome engineering, offering scalable strategies to restore soil health and ensure food security in saline–alkali ecosystems. Full article

Nanomaterials have emerged as a transformative technology in agricultural science, offering innovative solutions to improve plant–microbe interactions and crop productivity. The unique properties, such as high surface area, tunability, and reactivity, of nanomaterials, including nanoparticles, carbon-based materials, and electrospun fibers, render them ideal for applications such as nutrient delivery systems, microbial inoculants, and environmental monitoring. This review explores various types of nanomaterials employed in agriculture, focusing on their role in enhancing microbial colonization and soil health and optimizing plant growth. Key nanofabrication techniques, including top-down and bottom-up manufacturing, electrospinning, and nanoparticle synthesis, are discussed in relation to controlled release systems and microbial inoculants. Additionally, the influence of surface properties such as charge, porosity, and hydrophobicity on microbial adhesion and colonization is examined. Moreover, the potential of nanocoatings and electrospun fibers to enhance seed protection and promote beneficial microbial interactions is investigated. Furthermore, the integration of nanosensors for detecting pH, reactive oxygen species, and metabolites offers real-time insights into the biochemical dynamics of plant–microbe systems, applicable to precision farming. Finally, the environmental and safety considerations regarding the use of nanomaterials, including biodegradability, nanotoxicity, and regulatory concerns, are addressed. This review emphasizes the potential of nanomaterials to revolutionize sustainable agricultural practices by improving crop health, nutrient efficiency, and environmental resilience. Full article

Identifying natural alternatives to conventional chemical fertilizers is critical to preventing the widespread soil degradation and environmental damage caused by modern agriculture. Microbe-based biofertilizers have emerged as promising candidates due to their natural ability to improve nutrient bioavailability and promote plant growth. However, how biofertilizers affect the soil microbiome remains unclear. To investigate the impact of biofertilizer application on soil microbiome, LNP-1, a strain of Bacillus subtilis, was used as a biofertilizer in conjunction with no fertilizer, organic fertilizer, and chemical fertilizer for the cultivation of cabbage. Soil samples were collected and analyzed using next-generation sequencing to determine microbial abundance and diversity. Our results showed that LNP-1 supplementation not only improved cabbage yield significantly but also improved soil microbe diversity, a key indicator of soil health. Overall, soils treated with LNP-1 showed the enrichment of microbes involved in nutrient cycling and plant growth when compared to untreated groups. Notably, the yield of organically fertilized cabbage plants increased by 39.7% when treated with LNP-1. These results therefore demonstrate the potential for using biofertilizers to establish a more well-rounded, multifunctional soil microbiome to reduce reliance on chemical inputs and achieve high crop yield sustainably. Full article

Viticulture is vital to Italy’s agricultural sector, since it significantly contributes to the global wine industry. Microflora and microfauna are considered important factors for soil quality, improving grapevine growth, and promoting resistance to biotic and abiotic stresses. This study examined the impact of selected Trichoderma strains (T. harzianum M10 and T. afroharzianum T22) and their secondary metabolite 6-pentyl-α-pyrone (6PP) on the soil microbiome, the metabolome, and physiological changes of grapevines. Before treatment application, low levels of plant-parasitic nematodes (Rotylenchulus spp., Xiphinema pachtaicum) were found in the soil, together with pathogens (Fusarium spp., Neonectria spp.) and beneficial microbes (Clonostachys rosea, Pseudomonas spp.). Metagenomic analysis revealed significant treatment impacts in the soil microbiome, with T22 and 6PP treatments increasing Proteobacteria abundance, while slight variations of fungal communities and no significant differences in nematofauna were found. Metabolomic analysis showed that treatments induced grapevines to produce antioxidant secondary metabolites able to boost plant defense against abiotic and biotic stresses and increase nutraceutical grapes’ value. Finally, T22 treatment increased the grapes’ winemaking value, raising their Brix grade. Our results demonstrate that microbial or metabolite-based treatments could affect the soil microbiome composition, grapevine health and resilience, and grapes’ oenological and nutraceutical properties. Full article

The fermented feed used in broiler production has gained significant attention for its potential to improve growth performance, enhance gut health, and modulate gut microbiota. This review synthesized findings on the effects of both solid and liquid fermented feed in broilers. Fermentation processes enhance nutrient bioavailability; reduce anti-nutritional factors; and generate beneficial metabolites, such as short-chain fatty acids, which contribute to gut health. Incorporating fermented feed in broiler diets has been shown to improve weight gain, the feed conversion ratio, and nutrient absorption by promoting favorable gut morphology changes, including an increased villus height and villus height-to-crypt depth ratios. Additionally, fermented feed fosters a beneficial microbial environment by increasing lactic acid bacteria populations while reducing pathogenic microbes. Fermentation also modulates gut immunity by regulating cytokine production and stimulating immune cell activity. However, challenges such as inconsistent effects on feed intake and growth during the early production stages underscore the need for optimizing fermentation protocols tailored to broiler production systems. Although the implementation of liquid fermented feed presents logistical challenges, research suggests it can significantly improve feed digestibility. Advances in precision fermentation techniques and multi-strain inoculant use hold promise for further improving fermented feed efficacy. Future research should focus on assessing the long-term impacts, economic viability, and environmental sustainability of fermented feed in commercial poultry systems. Overall, fermented feed offers a promising strategy to enhance productivity and sustainability in broiler farming while reducing the reliance on conventional feed additives. This review reflects the body of knowledge at the time of writing. Full article

The growing interest in health-promoting diets has brought fermented foods into the spotlight due to their unique microbial compositions and bioactive metabolites. Fermented foods and their beneficial microbiota are expected to stimulate the overall industry’s expansion over the next few years as their beneficial health effects become established. This narrative review explores the evolving dynamics of fermented food microbiota and their interactions with the gut microenvironment, emphasizing strategic pathways to enhance human health. Fermented foods, both industrially produced and traditionally prepared, serve as carriers of beneficial microorganisms such as lactic acid bacteria, yeasts, and certain fungi that transform food substrates into bioactive compounds including short-chain fatty acids (SCFAs), exopolysaccharides, and bioactive peptides. Simultaneously, their bioactive metabolites are the subject of passionate investigation by the scientific community, uncovering novel beneficial aspects that have not been elucidated until now. These metabolites contribute to improved gut barrier function, modulation of immune responses, and overall metabolic health. Notably, microbial fermentation can reshape the intrinsic properties of food, offering therapeutic potential beyond basic nutrition. The interactions between food-derived microbes and the host gut microbiota suggest a synergistic mechanism influencing gastrointestinal and systemic health outcomes. Nevertheless, there remains a significant gap in the comprehensive evaluation of the existing literature in this specific research area. Further research is needed to standardize fermented food formulations, validate the effects of individual microbial strains, and optimize their application in personalized nutrition and functional food development. Accordingly, this review highlights the association between the microbiota of fermented foods and their metabolites with the gut microenvironment, emphasizing their potential health-promoting properties. Full article

Urban soils are subject to intense anthropogenic disturbance, often resulting in biodiversity loss and reduced ecosystem functionality. However, rhizospheric microbial communities help maintain critical soil-ecosystem services, supporting urban soil resilience. This study evaluated the diversity of culturable bacteria associated with the rhizospheres of Pennisetum clandestinum and Pseudelephantopus spicatus in green areas of Medellín, Colombia, under contrasting levels of anthropic pressures. Rhizospheric and non-rhizospheric soils were sampled near automotive mechanic sites, and bacterial communities were assessed through plate counting and morphological characterization. Alpha, beta, and rarefaction diversity indices were applied to evaluate culturable morphotypes. P. clandestinum supported a more diverse and complex rhizospheric microbiome, particularly in non-exposed soils, while P. spicatus hosted less diverse communities under similar conditions. Diversity indices effectively distinguished microbial patterns, demonstrating the utility of culture-based methods for microbial community assessment. As a first step in microbial bioprospecting workflows, these methods allow for the rapid screening of culturable diversity and support decision-making for the selection of promising environments, plant species, and microbial isolates. This approach can inform urban soil threats, the promotion of beneficial plant–microbe interactions, and the identification of bioindicator species for soil health monitoring in a framework for the management of green areas. Full article