Search Results (3,179)

Organic manure and grass mulching are widely recognized as modifiers of soil microbial communities and nutrient dynamics; however, the combined effects of these practices on nitrogen fractionation and microbial functionality in orchard ecosystems remain poorly understood. This study conducted a comprehensive evaluation of soil nitrogen fractions, enzymatic activity, microbial diversity and functional traits in walnut orchards under three management practices: organic manure (OM), grass mulching combined with manure (GM), and chemical fertilization (CF) in China’s Loess Plateau. The results revealed that OM and GM significantly enhanced soil nutrient pools, with GM elevating total nitrogen by 1.96-fold, soil organic carbon by 97.79%, ammonium nitrogen by 128%, and nitrate nitrogen by 54.56% relative to CF. Furthermore, the OM significantly increased the contents of total hydrolysable nitrogen, amino sugar nitrogen, amino acid nitrogen, ammonia nitrogen, hydrolysable unidentified nitrogen, non-acid-hydrolyzable nitrogen compared to the CF and GM treatments. Meanwhile, ASN and AN had significant effects on mineral and total nitrogen. The OM and GM had higher activities of leucine aminopeptidase enzymes (LAP), α-glucosidase enzyme, β-glucosidase enzyme (βG), and N-acetyl-β-D-glucosidase enzyme (NAG). Microbial community analysis revealed distinct responses to different treatments: OM and GM enhanced bacterial Shannon index, while suppressing fungal diversity, promoting the relative abundance of copiotrophic bacterial phyla such as Proteobacteria and Chloroflexi. Moreover, GM favored the enrichment of lignocellulose-degrading Ascomycota fungi. Functional annotation indicated that Chemoheterotrophy (43.54%) and Aerobic chemoheterotrophy (42.09%) were the dominant bacterial metabolic pathways. The OM significantly enhanced the abundance of fermentation-related genes. Additionally, fungal communities under the OM and GM showed an increased relative abundance of saprotrophic taxa, and a decrease in the relative abundances of potential animal and plant pathogenic taxa. The Random forest model further confirmed that βG, LAP, and NAG, as well as Basidiomycota, Mortierellomycota, and Ascomycota served as pivotal mediators of soil organic nitrogen fraction. Our findings demonstrated that combined organic amendments and grass mulching can enhance soil N retention capacity, microbial functional redundancy, and ecosystem stability in semi-arid orchards. These insights support the implementation of integrated organic management as a sustainable approach to enhance nutrient cycling and minimize environmental trade-offs in perennial fruit production systems. Full article

Artificial (technical) snow production is an increasingly common practice in alpine regions, yet little is known about its role in shaping microbial communities at the molecular level. In this study, we combined culture-based methods with high-throughput 16S rRNA gene sequencing and functional trait prediction (FAPROTAX) to investigate bacterial communities across the full technical snowmaking cycle in one of Polish ski resorts. The molecular profiling revealed that technical snow harbors dominant taxa with known cold-adaptation mechanisms, biofilm-forming abilities, and stress tolerance traits (e.g., Brevundimonas, Lapillicoccus, Massilia, with a relative abundance of 2.95, 2.14, 3.38 and 5.61%, respectively). Functional inference revealed a consistent dominance of chemoheterotrophy (up to 38% in relative abundance) and aerobic chemoheterotrophy (up to 36%), with localized enrichment of fermentation (6.9% in cannon filter and 6.5% in sediment) and aromatic compound degradation (3.7% in source waters, 3.8% in cannon filter and 4.6% in sediment). Opportunistic and potentially pathogenic genera (e.g., Acinetobacter, Flavobacterium, Nocardia) persisted in sediments (7.4%, 21.4% and 3.5%) and meltwater (34.9% and 2.31% for the latter two), raising concerns about their environmental reintroduction. Our findings indicate that technical snowmaking systems act as selective environments not only for microbial survival but also for the persistence of molecular traits relevant to environmental resilience and potential pathogenicity. Our study provides a molecular ecological framework for assessing the impacts of snowmaking on alpine ecosystems and underscores the importance of monitoring microbial functions in addition to taxonomic composition. Full article

This review consolidates recent advancements in microbial biotechnology for sustainable food systems. It focuses on the fermentation processes used in this sector, emphasizing precision fermentation as a source of innovation for alternative proteins, fermented foods, and applications of microorganisms and microbial bioproducts in the food industry. Additionally, it explores food preservation strategies and methods for controlling microbial contamination. These biotechnological approaches are increasingly replacing synthetic additives, contributing to enhanced food safety, nutritional functionality, and product shelf stability. Examples include bacteriocins from lactic acid bacteria, biodegradable microbial pigments, and exopolysaccharide-based biopolymers, such as pullulan and xanthan gum, which are used in edible coatings and films. A comprehensive literature search was conducted across Scopus, PubMed, ScienceDirect, and Google Scholar, covering publications from 2014 to 2025. A structured Boolean search strategy was applied, targeting core concepts in microbial fermentation, bio-based food additives, and contamination control. The initial search retrieved 5677 articles, from which 370 studies were ultimately selected after applying criteria such as duplication removal, relevance to food systems, full-text accessibility, and scientific quality. This review highlights microbial biotransformation as a route to minimize reliance on synthetic inputs, valorize agri-food byproducts, and support circular bioeconomy principles. It also discusses emerging antimicrobial delivery systems and regulatory challenges. Overall, microbial innovations offer viable and scalable pathways for enhancing food system resilience, functionality, and environmental stewardship. Full article

The poultry industry requires sustainable strategies to improve gut health and nutrient utilization while reducing antibiotic use. This study assessed the effects of dietary supplementation with a microencapsulated phytosynbiotic from Yanang (Tiliacora triandra) leaf extract fermented with Pediococcus acidilactici V202 (YEP) on broiler ileal digestibility, microbial viability, and cecal fermentation using an in vitro gastrointestinal simulation model. Six YEP inclusion levels (0–2.5%) were tested. Results revealed significant improvements in ileal dry matter and gross energy digestibility and enhanced survival and proliferation of beneficial lactic acid bacteria in the ileum. Increased gas production, lactic acid, and volatile fatty acid concentrations, including acetate, propionate, and butyrate, indicated that cecal fermentation was enhanced in a dose-dependent manner. Moderate YEP levels optimized fermentation speed and butyrate synthesis, while higher levels enhanced total gas and acetate production. YEP also shifted the cecal microbiota toward a healthier profile, enhancing Lactobacillaceae counts and the Lactobacillaceae-to-Enterobacteriaceae ratio. Overall, protective microencapsulation, synergistic phytochemical interactions, and balanced nutrient supply had positive effects at the gut level. Thus, the data highlight YEP as a promising synbiotic feed additive that can enhance nutrient utilization, microbial balance, and gut health in broilers, warranting future in vivo validation. Full article

Broiler chickens are commonly reared in closed housing systems with limited exposure to sunlight, thereby relying entirely on dietary sources of vitamin D. The hydroxylated metabolite 25-hydroxycholecalciferol [25(OH)D₃] has been proposed as a more potent form than native vitamin D₃ (cholecalciferol). This study evaluated the effects of dietary supplementation with vitamin D₃ alone or in combination with 25(OH)D₃ on growth performance, bone characteristics, and cecal microbiota in Ross 308 broilers. A total of 952 one-day-old male chicks were allocated to four treatments: a negative control (no vitamin D₃), a positive control (vitamin D₃ according to Ross 308 specifications), and a positive control supplemented with 25(OH)D₃ at 1394 or 2788 IU/kg, in a randomized design with 17 replicates per treatment and 14 birds per replicate. Over a 40-day feeding trial, diets containing vitamin D₃ (positive control) or supplemented with 25(OH)D₃ significantly improved final body weight, weight gain, average daily gain, and feed conversion ratio compared with the negative control (p < 0.01), with no significant differences among the positive control and 25(OH)D₃-supplemented groups, with a clear linear dose-dependent response. Although tibia ash and bone-breaking strength were not significantly affected, linear responses indicated a slight numerical trend toward improved skeletal mineralization with increasing 25(OH)D₃. Microbiota analysis indicated that 25(OH)D₃ affected cecal microbial ecology: low-dose inclusion showed reduced species richness and evenness, whereas high-dose inclusion restored richness to levels comparable to the positive control and enriched taxa associated with fiber fermentation and bile acid metabolism while reducing Lactobacillus dominance. In conclusion, supplementation with 25(OH)D₃ in addition to vitamin D₃ enhanced growth performance and selectively shaped the cecal microbiota of broilers, with suggestive benefits for bone mineralization. These findings highlight 25(OH)D₃ as a more potent source of vitamin D than cholecalciferol alone and support its practical use in modern broiler nutrition to improve efficiency, skeletal health, and microbial balance. Full article

Dietary patterns greatly affect periodontitis, a chronic inflammatory disease that compromises both dental and systemic health. According to the emerging evidence, periodontal risk is more strongly associated with the overall dietary quality, especially fiber density intake, than any one micronutrient. While the average intake in industrialized countries is only half of the recommended 30 g day⁻¹, high-fiber diets such as the Mediterranean diet, the Dietary Approaches to Stop Hypertension (DASH), and whole-food plant-based diets are consistently associated with a 20–40% lower periodontitis prevalence. Dietary fiber plays a central role in regulating immune responses, strengthening tissue barriers, improving metabolic homeostasis, and shaping a healthy microbiome through its microbial fermentation products: short-chain fatty acids (SCFAs). This makes it a biologically rational and clinical evidence-supported strategy for the prevention and management of periodontitis. Integrating high-fiber diet recommendations into routine periodontal care and public health policies could be a crucial step towards more comprehensive oral and systemic health management. This narrative review elaborates on the mechanistic, observational, and intervention data highlighting the role of dietary fiber, especially SCFAs, in periodontal health. Full article

Fermented beverages have been highlighted for their beneficial effects on health, especially due to the presence of probiotic microorganisms. This study aimed to develop and characterize a beverage fermented from the aqueous extract of licuri (Syagrus coronata) with grains of milk kefir and water kefir. Physical–chemical properties, microbial viability, storage stability, and in vitro resistance to the gastrointestinal tract (GIT), as well as microbiological safety and identification of isolated bacteria, were evaluated. The grains were fermented in licuri for 24 and 48 h, and the samples were compared with their respective controls. The analyses revealed that the licuri drink favored the growth of kefir grains, maintaining adequate microbial viability (>7 log CFU mL⁻¹ for lactic acid bacteria and >4 log CFU mL⁻¹ for yeasts), with good resistance to GIT (>60%) and physical–chemical properties for 20 days. The bacterial isolate was identified as Lacticaseibacillus paracasei, with a satisfactory safety profile. Licuri extract is therefore a promising matrix for the development of non-dairy functional beverages with potential probiotic properties. Full article

The microbial community in a recirculating aquaculture system (RAS) is pivotal in fish health, contributing significantly to the productive performance during the growing-out phase. Classical and molecular methods using PCR for species-specific amplifications have traditionally been used for bacterial community surveillance. Unfortunately, these approaches mask the real bacterial diversity and abundance, population dynamics, and prevalence of pathogenic bacteria. In this study, we explored the use of Oxford Nanopore Technology to characterize the microbiota and functional metagenomics in a commercial freshwater RAS. Intestine samples from Atlantic salmon (Salmo salar (85 ± 5.7 g)) and water samples from the inlet/outlet water, settling tank, and biofilters were collected. The full-length 16S rRNA gene was sequenced to reconstruct the microbial community, and bioinformatic tools were applied to estimate the functional potential in the RAS and fish microbiota. The analysis showed that bacteria involved in denitrification processes were found in water samples, as well as metabolic pathways related to hydrogen sulfide metabolism. Observations suggested that fish classified as sick exhibited decreased microbial diversity compared with fish without clinical symptomatology (p < 0.05). Proteobacteria were predominant in ill fish, and pathogens of the genera Aeromonas, Aliivibrio, and Vibrio were detected in all intestinal samples. Notably, Aliivibrio wodanis was detected in fish showing abnormal clinical conditions. Healthy salmon showed higher contributions of pathways related to amino acid metabolism and short-chain fatty acid fermentation (p < 0.05), which may indicate more favorable fish conditions. These findings suggest the utility of nanopore sequencing methods in assessing the microbial community in RASs for salmon aquaculture. Full article

Gamma-aminobutyric acid (GABA) is the main inhibitory neurotransmitter in the vertebrate central nervous system, known for its role in promoting sleep, reducing anxiety, regulating blood pressure, and modulating stress, cognition, and behavior. Microbial fermentation offers an effective method for GABA production, with certain lactic acid bacteria (LAB) strains recognized as efficient producers. This study assessed the GABA-producing potential of 31 LAB strains, including isolates from traditional Bulgarian foods and plants. The strains were cultivated in an MRS medium supplemented with 1% monosodium glutamate (MSG), and GABA production was quantified using HPLC after derivatization with dansyl chloride. Most strains produced between 200 and 300 mg/L of GABA. However, Levilactobacillus brevis NCTC 13768 showed much higher productivity, reaching 3830.7 mg/L. To further evaluate its capacity, L. brevis NCTC 13768 was cultivated for 168 h in MRS medium with and without MSG. Without MSG, GABA production peaked at 371.0 mg/L during the late exponential phase. In contrast with MSG, GABA levels steadily increased, reaching 3333.6 mg/L after 168 h. RT-qPCR analyses of the glutamic acid decarboxylase (GAD) system showed that the genes of glutamate decarboxylase (gadB), glutamate-GABA antiporter (gadC), and transcriptional regulator (gadR) are significantly overexpressed when the culture reaches the late stationary phase of growth (96 h after the beginning of cultivation). These results identify L. brevis NCTC 13768 as a high-yield GABA producer, with potential applications in the production of fermented functional foods and beverages. Full article

Food waste (FW) presents a critical issue, representing an environmental liability and a largely untapped resource. Its heterogeneity and low valorization rate among main-stream alternative treatments challenge its integration into economically and environmentally sustainable bioprocesses. We explore biorefineries as a solution that can address the complexity of urban food waste through biological strategies capable of converting food waste into valuable products. Exploring the current landscape of FW biorefineries, this study focused on the interplay between feedstock heterogeneity, pretreatment strategies, microbial dynamics, and integration potential. We propose a framework distinguishing between robust fermentations that can use minimally treated FW and tailored fermentations, which require refined media pretreatment and/or supplementation to yield higher-value compounds. Drawing on recent techno-economic and life cycle assessments, this article evaluates process viability and environmental impacts across multiple scales, reinforcing the need for robust analysis to support decision-making. Real-world initiatives and policy frameworks are analyzed to contextualize technological advances within regulatory and infrastructural realities. By linking practical constraints to biochemical and operational strategies, this work outlines how food waste biorefineries can contribute meaningfully to circular economy goals. Instead of treating FW as an intractable problem, it is seen as a versatile feedstock that demands integration, investment, and adaptive process design. Full article

The seafood industry is increasingly adopting intelligent packaging to preserve product quality and improve freshness transparency. This study developed and evaluated a pH-sensitive freshness indicator (FI) for skate sashimi (Zearaja chilensis). This product is consumed at varying stages of fermentation. The FI incorporated bromothymol blue (BTB) and bromocresol purple (BCP) in a polymer matrix. It targeted volatile basic nitrogen (VBN) compounds, with trimethylamine (TMA) as the primary marker. As freshness declined, VBN compounds accumulated in the package headspace and caused a gradual FI color change from yellow to blue through pH variation. ΔE increased from 7.72 on day 2 to 23.52 on day 3. This marked the onset of visible color change and the FI reached full blue by day 7. Headspace solid-phase microextraction (HS-SPME) and gas chromatography–flame ionization detection (GC-FID) quantified monomethylamine (MMA), dimethylamine (DMA) and TMA throughout storage. ΔE correlated strongly with total bacterial count (TBC, r = 0.978), pH (r = 0.901) and TMA (r = 0.888). These results indicate that microbial growth, alkalinity increase and amine production were closely associated with color transitions. The FI reliably tracked freshness loss in skate sashimi. It has potential to enhance consumer transparency and strengthen quality control in the seafood supply chain. Full article

Processing economically and socio-culturally significant Amazonian fruits—andiroba (Carapa guianensis Aubl.), açai (Euterpe oleracea Mart.), and babassu (Attalea speciosa Mart. ex Spreng.)—generates substantial biomass waste, posing critical environmental and waste management challenges. This study explored the valorization of these abundant residual biomasses as sustainable feedstocks for biosurfactant production by bacterium Pseudomonas aeruginosa P23G-02, while simultaneously profiling their nutritional value and broader implications for a circular bioeconomy. Through liquid fermentation, biosurfactants were produced at an approximate yield of 6 mg/mL. The isolated biosurfactants exhibited favorable properties, including emulsification indices of around 60% and surface tension reduction to below 30 mN/m, with the andiroba-derived biosurfactant identified as a rhamnolipid type. Nutritional profiling of the residues revealed significant energy values, reaching up to 656 kcal/100 g, with açai and babassu residues being carbohydrate-rich (exceeding 80%), and andiroba residues exhibiting a high lipid profile (up to 57%). These distinct compositions critically influenced biosurfactant yield. These findings underscore the viability of Amazonian fruit biomass as valuable resources for developing eco-friendly bioproducts and innovative waste management solutions. While highlighting a promising pathway for circular bioeconomy development, future research should address biosafety and explore alternative microbial hosts for applications in sensitive sectors such as food and nutrition. Full article

Polyhydroxyalkanoate (PHA) bioplastics are produced from wastewater as a carbon recovery strategy. However, the tuneable characteristics of PHAs and wastewater biorefinery potential have not been comprehensively reviewed. The aim of this study is to review the main challenges and strategies for carbon recovery from wastewater feedstocks via PHA production, assessing potential target biopolymer applications. Diverse PHA-accumulating prokaryotes metabolize organic pollutants present in wastewater through different metabolic pathways, determining the biopolymer characteristics. The synthesis of PHAs using mixed microbial cultures with wastewater feedstocks derived from municipal, agro-industrial, food processing, lignocellulosic biomass processing and biofuel production activities are described. Acidogenic fermentation of wastewater feedstocks and mixed microbial culture enrichment are key steps in order to enhance PHA productivity and determine biopolymer properties towards customized bioplastics for specific applications. Biorefinery of PHA copolymers and extracellular polysaccharides (EPSs), including alginate-like polysaccharides, are alternatives to enhance the value-chain of carbon recovery from wastewater. PHAs and EPSs exhibit a wide repertoire of applications with distinct safety control requirements; hence, coupling biopolymer production demonstrations with target applications is crucial to move towards full-scale applications. This study discusses the relationship between the metabolic basis of PHA synthesis and composition, wastewater type, and target applications, describing the potential to maximize carbon resource valorisation. Full article

Fermented fruit juices are considered functional beverages because they contain bioactive compounds derived from plant materials and produced by the microorganisms involved in fermentation. The composition of these beverages can vary depending on the strain used. This study aimed to determine the effect of different microorganisms conducting lactic acid fermentation on the chemical composition and bioactive component content of naturally cloudy fermented pear and plum juices. The process used Lactiplantibacillus plantarum K7 bacteria, which were isolated during sauerkraut fermentation, as well as Lachancea thermotolerans PYCC6375 and Lachancea fermentati PYCC5883 yeast cultures, which have poor ethanol fermentation capabilities. The pH, acidity, sugars (HPLC), free amino nitrogen, selected organic acids (HPLC), color (CIELAB), polyphenols (HPLC), volatiles (GC-MS), aroma-active volatiles (GC-MS-O), and sensory characteristics were analyzed. The fermented juices obtained were rich in organic acids (of plant and microbial origin), polyphenols, and had a reduced sugar content (with polyols replacing glucose and fructose), as well as a low alcohol content (<0.2%). At the same time, all three microorganisms significantly enhanced the fruity aroma of the juices. Lachancea yeasts proved to be a viable alternative to lactic acid bacteria for producing fermented juices and were significantly better suited to fermenting plum juices. The highest polyphenol content and highest consumer preference rating were obtained with plum juices fermented with L. fermentati yeast. Full article

Lignocellulosic agro-forestry residues (LARs), such as rice straw, sugarcane bagasse, and wood wastes, are abundant and low-cost feedstocks for polyhydroxyalkanoate (PHA) bioplastics. However, their complex cellulose–hemicellulose–lignin matrix requires integrated valorization strategies. This review presents a dual-framework approach: “pretreatment–co-substrate compatibility” and “pretreatment–microbial platform matching”, to align advanced pretreatment methods (including deacetylation–microwave integration, deep eutectic solvents, and non-sterilized lignin recovery) with engineered or extremophilic microbial hosts. A “metabolic interaction” perspective on co-substrate fermentation, encompassing dynamic carbon flux allocation, synthetic consortia cooperation, and one-pot process coupling, is used to elevate PHA titers and tailor copolymer composition. In addition, we synthesize comprehensive kinetic analyses from the literature that elucidate microbial growth, substrate consumption, and dynamic carbon flux allocation under feast–famine conditions, thereby informing process optimization and scalability. Microbial platforms are reclassified as broad-substrate, process-compatible, or product-customized categories to emphasize adaptive evolution, CRISPR-guided precision design, and consortia engineering. Finally, next-generation techno-economic analyses, embracing multi-product integration, regional adaptation, and carbon-efficiency metrics, are surveyed to chart viable paths for scaling LAR-to-PHA into circular bioeconomy manufacturing. Full article