Search Results (969)

The modern livestock industry incorporates widely used antibiotic growth promoters into animal feed at sub-therapeutic levels to enhance growth performance and feed efficiency. However, this practice contributes to the emergence of antibiotic-resistant pathogens in livestock, which may be transmitted to humans through the food chain, thereby diminishing the efficacy of antibiotics in treating bacterial infections. Current research explores the potential of essential oils from derived medicinal plants as alternative phytobiotics. This review examines modern encapsulation strategies that incorporate essential oils into natural-origin matrices to improve their stability and control their release both in vitro and in vivo. We discuss a range of encapsulation approaches utilizing polysaccharides, gums, proteins, and lipid-based carriers. This review highlights the increasing demand for antibiotic alternatives in animal nutrition driven by regulatory restrictions, and the potential benefits of essential oils in enhancing feed palatability and stabilizing the intestinal microbiome in monogastric animals and ruminants. Additionally, we address the economic viability and encapsulation efficiency of different matrix formulations. Full article

Human milk bacteria contribute to gut microbiome establishment in breastfed infants. Although breastfeeding is recommended throughout infancy, temporal variation in the milk microbiome—particularly beyond solid food introduction—remains understudied. We analyzed 539 milk samples from 83 mother–infant dyads between 1 week and 12 months postpartum using full-length 16S rRNA gene sequencing. The microbiota was dominated by Streptococcus (34%), Cutibacterium (12%), and Staphylococcus (9%), with marked inter-individual variation. Microbiome profiles remained largely stable across lactation, with only six taxa showing temporal fluctuations, including increases in typical oral bacteria such as Streptococcus salivarius, Streptococcus lactarius, Rothia mucilaginosa, and Granulicatella adiacens. Richness and evenness were higher at 1 week compared to 1 month postpartum (p = 0.00003 and p = 0.007, respectively), then stabilized. Beta diversity also remained stable over time. Maternal pre-pregnancy BMI was positively associated with Gemella haemolysans (p = 0.016), while Haemophilus parainfluenzae was more abundant in milk from mothers with allergies (p = 0.003) and those who gave birth in autumn or winter (p = 0.006). The introduction of solid food was linked to minor taxonomic shifts. Overall, the milk microbiome remained robustly stable over the first year of lactation, with limited but notable fluctuations in specific taxa. This study supports the role of human milk as a consistent microbial source for infants and identifies maternal BMI, allergy status, and birth season as key variables warranting further investigation. Full article

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

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

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

Hydrogen sulfide (H₂S) can be produced from the metabolism of foods containing sulfur in the gastrointestinal tract (GIT). At low doses, H₂S regulates the gut microbial community and supports GIT health, but depending on dose, age, and individual health conditions, it may also contribute to inflammatory responses and gut barrier dysfunction. Controlling H₂S production in the GIT is important for maintaining a healthy gut microbiome. However, research on this subject is limited due to the gaseous nature of the chemical and the difficulty of accessing the GIT in situ. In the present ex vivo experiment, we used a single-dose sodium sulfide preparation (SSP) as a H₂S precursor to test the effect of H₂S on the human gut microbiome across different age groups, including breastfed infants, toddlers, adults, and older adults. Metagenomic sequencing and metabolite measurements revealed that the development of the gut microbial community and the production of short-chain fatty-acids (SCFAs) were age-dependent; that the infant and the older adult groups were more sensitive to SSP exposure; that exogeneous SSP suppressed SCFA production across all age groups, except for butyrate in the older adult group, suggesting that H₂S selectively favors specific gut microbial processes. 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

Background/Objectives: Chronic inflammation and Western-style diets elevate colorectal cancer (CRC) risk, particularly in individuals with colitis, a feature of inflammatory bowel disease (IBD). Diets rich in polyphenol-containing functional foods, such as cocoa, may reduce gut inflammation and modulate the gut microbiome. This study investigated the impact of cocoa polyphenol (CP) supplementation on inflammation and microbiome composition in mice with colitis, fed either a healthy or Western diet, before, during, and after the onset of disease. We hypothesized that CPs would attenuate inflammation and promote distinct shifts in the microbiome, especially in the context of a Western diet. Methods: A 2 × 2 factorial design tested the effects of the basal diet (AIN93G vs. total Western diet [TWD]) and CP supplementation (2.6% w/w CocoaVia™ Cardio Health Powder). Inflammation was induced using the AOM/DSS model of colitis. Results: CP supplementation did not reduce the severity of colitis, as measured by disease activity index or histopathology. CPs did not alter gene expression in healthy tissue or suppress the colitis-associated pro-inflammatory transcriptional profile in either of the two diet groups. However, fecal microbiome composition shifted significantly with CPs before colitis induction, with persistent effects on several rare taxa during colitis and recovery. Conclusions: CP supplementation did not mitigate inflammation or mucosal injury at the tissue level, nor did it affect the expression of immune-related genes. While CPs altered microbiome composition, most notably in healthy mice before colitis, these shifts did not correspond to changes in inflammatory signaling. Basal diet remained the primary determinant of inflammation, mucosal damage, and colitis severity in this model. Full article

Plant diseases resulting from pathogens and pests constitute a persistent threat to global food security. Pathogenic infections of plants are influenced by environmental factors; a concept encapsulated in the “disease triangle” model. It is important to elucidate the complex molecular mechanisms underlying the interactions among plants, their pathogens and various environmental factors in the disease triangle. This review aims to highlight recent advancements in the application of systems biology to enhance understanding of the plant disease triangle within the context of microbiome rising to become the 4th dimension. Recent progress in microbiome research utilizing model plant species has begun to illuminate the roles of specific microorganisms and the mechanisms of plant–microbial interactions. We will examine (1) microbiome-mediated functions related to plant growth and protection, (2) advancements in systems biology, (3) current -omics methodologies and new approaches, and (4) challenges and future perspectives regarding the exploitation of plant defense mechanisms via microbiomes. It is posited that systems biology approaches such as single-cell RNA sequencing and mass spectrometry-based multi-omics can decode plant defense mechanisms. Progress in this significant area of plant biology has the potential to inform rational crop engineering and breeding strategies aimed at enhancing disease resistance without compromising other pathways that affect crop yield. Full article

Psychological stress and dietary behavior are interdependent forces that greatly influence mental and physical health. Thus, both what and how we eat impact our well-being. Maladaptive eating patterns, such as eating in response to emotional cues rather than physiological hunger, have become increasingly common amid modern stressors and an ultra-processed food environment. This narrative review synthesizes interdisciplinary findings from nutritional psychiatry, microbiome science, and behavioral nutrition to explore how stress physiology, gut–brain interactions, and dietary quality shape emotional regulation and eating behavior. It highlights mechanisms (e.g., HPA-axis dysregulation, blunted interoception, and inflammatory and epigenetic pathways) and examines the evidence for mindful and intuitive eating; phytochemical-rich, whole-food dietary patterns; and the emerging role of precision nutrition. Trauma-informed approaches, cultural foodways, structural barriers to healthy eating, and clinical implementation strategies (e.g., interprofessional collaboration) are considered in the context of public health equity to support sustainable mental wellness through dietary interventions. Ultimately, restoring a healthy relationship with food positions nutrition not only as sustenance but as a modifiable regulator of affect, cognition, and stress resilience, central to mental and physical well-being. Full article

Background/Objectives: Traditional dietary screeners face significant limitations: they rely on subjective self-reporting, average intake estimates, and are influenced by a participant’s awareness of being observed—each of which can distort results. These factors reduce both accuracy and reproducibility. The Guide Against Age-Related Disease (GARD) addresses these issues by applying Assembly Theory to objectively quantify food and food behavior (FFB) complexity. This study aims to validate the GARD as a structured, bias-resistant tool for dietary assessment in clinical and research settings. Methods: The GARD survey was administered in an internal medicine clinic within a suburban hospital system in the southeastern U.S. The tool assessed six daily eating windows, scoring high-complexity FFBs (e.g., fresh plants, social eating, fasting) as +1 and low-complexity FFBs (e.g., ultra-processed foods, refined ingredients, distracted eating) as –1. To minimize bias, patients were unaware of scoring criteria and reported only what they ate the previous day, avoiding broad averages. A computer algorithm then scored responses based on complexity, independent of dietary guidelines. Internal (face, convergent, and discriminant) validity was assessed using Spearman rho correlations. Results: Face validation showed high inter-rater agreement using predefined Assembly Index (A_i) and Copy Number (N_i) thresholds. Positive correlations were found between high-complexity diets and behaviors (rho = 0.533–0.565, p < 0.001), while opposing constructs showed moderate negative correlations (rho = –0.363 to −0.425, p < 0.05). GARD scores aligned with established diet patterns: Mediterranean diets averaged +22; Standard American Diet averaged −10. Full article

Sustainable farmland management is vital for global food security and for mitigating environmental degradation and climate change. While individual practices such as crop rotation and no-tillage are well-documented, this review synthesizes current evidence to illuminate the critical synergistic effects of integrating four key strategies: crop rotation, conservation tillage, organic amendments, and soil microbiome management. Crop rotation enhances nutrient cycling and disrupts pest cycles, while conservation tillage preserves soil structure, reduces erosion, and promotes carbon sequestration. Organic amendments replenish soil organic matter and stimulate biological activity, and a healthy soil microbiome boosts plant resilience to stress and enhances nutrient acquisition through key functional groups like arbuscular mycorrhizal fungi (AMFs). Critically, the integration of these practices yields amplified benefits that far exceed their individual contributions. Integrated management systems not only significantly increase crop yields (by up to 15–30%) and soil organic carbon but also deliver profound global ecosystem services, with a potential to sequester 2.17 billion tons of CO₂ and reduce soil erosion by 2.41 billion tons annually. Despite challenges such as initial yield variability, leveraging these synergies through precision agriculture represents the future direction for the field. This review concludes that a holistic, systems-level approach is essential for building regenerative and climate-resilient agroecosystems. Full article

Traditional type I sourdoughs are being rediscovered and increasingly used in artisanal and industrial bakeries due to the unique taste and texture, potential health benefits, and longer shelf life they confer on to baked products. These unique properties are attributed to the diverse microbial communities of sourdough, comprising both yeasts and bacteria. The traditional preservation method for type I sourdough (i.e., continuous backslopping) may lead, over time, to taxonomic and functional rearrangements of its microbial communities. Consequently, significant deviations in the characteristics of baked products can occur. In this context, this review aims to summarize the recent literature on the long-term preservation and maintenance strategies for type I sourdough and highlight the essential role that microbial biological resource centers (mBRCs) could play in the preservation and sharing of sourdough microbiomes. Specifically, the identification of appropriate preservation methods, implementation of well-defined access and benefit-sharing protocols, and development of microbiome-specific datasets, should be encouraged within the context of mBRCs. These infrastructures are expected to play a pivotal role in preserving the microbiota of fermented foods, serving as a crucial element for innovation and the safeguarding of traditional foods and culinary heritage. Full article

Recent advances in microbiome studies have deepened our understanding of endosymbionts and gut-associated microbiota in host biology. Of those, lepidopteran systems in particular harbor a complex and diverse microbiome with various microbial taxa that are stable and transmitted between larval and adult stages, and others that are transient and context-dependent. We highlight key microorganisms—including Bacillus, Lactobacillus, Escherichia coli, Pseudomonas, Rhizobium, Fusarium, Aspergillus, Saccharomyces, Bifidobacterium, and Wolbachia—that play critical roles in microbial ecology, biotechnology, and microbiome studies. The fitness implications of these microbial communities can be variable; some microbes improve host performance, while others neither positively nor negatively impact host fitness, or their impact is undetectable. This review examines the central position played by the gut microbiota in interactions of insects with plants, highlighting the functions of the microbiota in the manipulation of the behavior of herbivorous pests, modulating plant physiology, and regulating higher trophic levels in natural food webs. It also bridges microbiome ecology and applied pest management, emphasizing S. frugiperda as a model for symbiont-based intervention. As gut microbiota are central to the life history of herbivorous pests, we consider how these interactions can be exploited to drive the development of new, environmentally sound biocontrol strategies. Novel biotechnological strategies, including symbiont-based RNA interference (RNAi) and paratransgenesis, represent promising but still immature technologies with major obstacles to overcome in their practical application. However, microbiota-mediated pest control is an attractive strategy to move towards sustainable agriculture. Significantly, the gut microbiota of S. frugiperda is essential for S. frugiperda to adapt to a wide spectrum of host plants and different ecological niches. Studies have revealed that the microbiome of S. frugiperda has a close positive relationship with the fitness and susceptibility to entomopathogenic fungi; therefore, targeting the S. frugiperda microbiome may have good potential for innovative biocontrol strategies in the future. Full article

Aquaculture is a key food production sector responsible for meeting the nutritional needs of a rapidly growing global population. However, the emergence of disease outbreaks has become a major challenge for the aquaculture industry, resulting in significant economic losses. The use of costly and toxic antibiotics for treatment has a negative impact on the aquatic environment. Consequently, there has been a growing interest in probiotics as a non-antibiotic approach to manage disease outbreaks and improve fish performance. The use of the yeast Saccharomyces cerevisiae (SC) has shown remarkable benefits in aquaculture. In February 2025, a systematic search was conducted based on the Web of Science (WoS) database for the period 2015–2025 to identify relevant studies investigating the beneficial effects of SC in aquaculture. After searching on WoS, 466 documents were found and analyzed using R-bibliometric package for comprehensive analysis to identify research gap, trends, and distribution of global literature that focuses on SC in aquaculture. The most relevant and recent articles were reviewed, summarized and discussed. The yeast SC have shown a wide range of benefits, including improved growth performance, feed efficiency, enhanced diversity of the gut microbiome and immune response. The implementation of SC is becoming a recent trend and its efficacy in aquatic environments has been thoroughly investigated. This review aims to provide a valuable insight into SC as one of the most important aquaculture probiotics. It also emphasizes the need for further research to fully understand its benefits and the way it works. Full article