Search Results (281)

The intricate connections between plants and the microbial populations that surround them are crucial for plant development and resilience, but little is known about the evolutionary processes influencing these partnerships. Less is known about how pathogenic and beneficial microbes coevolve with their plant hosts over ecological and evolutionary timeframes, despite the fact that several studies identify rhizosphere and endophytic microbes that support nutrient acquisition, disease resistance, and stress tolerance. Using molecular, ecological, and evolutionary investigations from soil, rhizosphere, and endosphere habitats, this review summarizes current findings on microbial coevolution in plant–microbe systems. We look at the endosymbiotic processes that underlie the development of organelles, the mechanisms of mutualism and antagonism, and the eco-evolutionary feedbacks that affect plant health and agricultural output. The inadequate comprehension of intraspecific microbial diversity, the application of laboratory coevolution experiments to field settings, and the long-term effects of climate change on the evolutionary dynamics of plants and microbiomes are some of the major knowledge gaps. When pathogenic and beneficial microbes apply selective pressures to one another and their common host, coevolution takes place. This results in mutual genetic and physiological adaptations, such as modifications to host immunity, microbial virulence, or competitive tactics, which influence the way the two types interact over time. We conclude that understanding plants as holobiont-integrated units of hosts and their microbiomes offers fresh chances to develop microbiome-based approaches to sustainable agriculture, such as coevolutionary breeding programs, precision biofertilizers, and resilient cropping systems. Full article

Obesity is a highly complex, multifactorial disease influenced by dynamic interactions among genetic, epigenetic, environmental, and behavioral determinants that explicitly position genetics as the core. While advances in multi-omic integration have revolutionized our understanding of adiposity pathways, translation into personalized clinical nutrition remains a critical challenge. This review systematically consolidates emerging insights into the molecular and nutrigenomic architecture of obesity by integrating data from large-scale GWAS, functional epigenomics, nutrigenetic interactions, and microbiome-mediated metabolic programming. The primary aim is to systematically organize and synthesize recent genetic and genomic findings in obesity, while also highlighting how these discoveries can be contextualized within precision nutrition frameworks. A comprehensive literature search was conducted across PubMed, Scopus, and Web of Science up to July 2024 using MeSH terms, nutrigenomic-specific queries, and multi-omics filters. Eligible studies were classified into five domains: monogenic obesity, polygenic GWAS findings, epigenomic regulation, nutrigenomic signatures, and gut microbiome contributions. Over 127 candidate genes and 253 QTLs have been implicated in obesity susceptibility. Monogenic variants (e.g., LEP, LEPR, MC4R, POMC, PCSK1) explain rare, early-onset phenotypes, while FTO (polygenic) and MC4R (monogenic mutations as well as common polygenic variants) represent major loci across populations. Epigenetic mechanisms, dietary composition, physical activity, and microbial diversity significantly recalibrate obesity trajectories. Integration of genomics, functional epigenomics, precision nutrigenomics, and microbiome science presents transformative opportunities for personalized obesity interventions. However, translation into evidence-based clinical nutrition remains limited, emphasizing the need for functional validation, cross-ancestry mapping, and AI-driven precision frameworks. Specifically, this review systematically identifies and integrates evidence from genomics, epigenomics, nutrigenomics, and microbiome studies published between 2000 and 2024, applying structured inclusion/exclusion criteria and narrative synthesis to highlight translational pathways for precision nutrition. Full article

Bottom sediments play a central role in regulating contaminant dynamics in aquatic systems. They act as both storage sites and reactive zones where contaminants undergo transformation, sequestration, or remobilization. Contaminants primarily enter sediments through anthropogenic activities, including agricultural runoff, industrial effluents, wastewater discharge, urban runoff, and mining operations. This review focuses on six major contaminant groups, including nutrients, heavy metals, pharmaceutical residues, pesticides, polycyclic aromatic hydrocarbons, and microplastics, and examines the mechanistic processes that govern their fate in sediments. The main mechanisms includesorption–desorption on minerals and organic materials, sedimentation, and redox processes that regulate metal immobilization and sulfide formation. The persistence and mobility of contaminants are also influenced by synergistic or antagonistic interactions among pollutants, microbial transformation of organic compounds, and oxidative degradation of microplastics by reactive oxygen species. Contaminants can affect benthic communities by causing toxic effects and oxygen depletion. They also may alter microbial and macrofaunal populations and contribute to bioaccumulation and biomagnification. Ultimately, these insights are important for predicting contaminant behavior and assessing ecological risks, which directly informs the development of effective environmental monitoring programs and sustainable sediment remediation strategies for the long-term protection of aquatic ecosystems. Full article

Precision application of fertiliser nutrients based on soil-available nutrients is a vital means of increasing castor (Ricinus communis L.) productivity. Fertiliser application based on the targeted yield model under inorganic fertilisers alone and Integrated Plant Nutrition System (IPNS) differ from the blanket recommendation practices. Field experiments were conducted in two locations to validate the Soil Test Crop Response (STCR) targeted yield model developed for hybrid castor on non-calcareous Alfisol. The main objective was to determine the effect of inorganic fertilisers and organic manures on microbial populations, enzyme dynamics in soil, and productivity of castor. Experimental field data revealed that combined application of inorganic fertilisers along with 12.5 t ha⁻¹ farmyard manure increased the soil microbial population and enzyme activity in the rhizosphere soils of castor. Castor responded positively with an increase in highest targeted yield level. The highest yield of 2726 and 2695 kg ha⁻¹ were attained in the treatment T₈ (STCR-IPNS −2.75 t ha⁻¹) in both locations, and Treatment T₅ (STCR-NPK alone −2.75 t ha⁻¹) was on par with T₈. The IPNS treatments showed higher percent achievement than the NPK treatments alone. Root length and dry matter production increased significantly with the application of a higher dose of fertiliser along with farmyard manure. Root dry matter production significantly contributed towards the castor seed yield. More soil-beneficial microorganisms and enzyme dynamics were observed in the IPNS treatment. Full article

Marine bacteria possess significant potential for numerous applications including environmental remediation, creation of natural products and medicines, agriculture, and various industrial sectors. In this study, the diversity of bacterial populations in the seawater at the nearshore S1 station which is a frequent red-tide occurrence area in the East China Sea, was characterized using 16S rRNA gene amplicon sequencing analysis. The three predominant phyla in the bacterial communities were identified as Proteobacteria, Actinobacteria, and Bacteroidetes, with the families Rhodobacteraceae, Mycobacteriaceae, and Flavobacteriaceae as the dominant groups, respectively. The bacterial community composition at the S1 station significantly differed from those of the other five investigated coastal sites, and demonstrated its own unique taxonomic associations with the Rhodobacteraceae as the keystone species. Functional prediction through KEGG and MetaCyc analyses revealed the presence of an L-tryptophan biosynthesis pathway responsible for indole-3-acetic acid (IAA) production. By using the targeted isolation of cultivable bacterial strains, a novel red-pigmented bacterium, designated S1-TA-50, which produced IAA metabolites, was recovered from the S1 station. It was identified as a potential novel species within the genus Sulfitobacter in the family Rhodobacteraceae. This bacterium demonstrated notable antibacterial activity against four model pathogenic strains and also acted as a new microalgae growth-promoting bacterium with substantial IAA production after bacterial culture optimization. This study contributes to the accumulation of scientific knowledge regarding the dynamics of marine bacterial ecosystems in nearshore eutrophic environments and facilitates a better understanding of phycosphere bacterial roles in coastal ecosystems, as well as the comprehensive utilization of microbial resources. Full article

Microbial communities that develop within biofilms on electrodes are necessary for the proper functioning of the microbial electrochemical system. However, the mechanism through which an exogenous exoelectrogen influences the population dynamics and electrochemical performance of biofilms remains unclear. In this study, we explored the community structure dynamics and electrochemical characteristics of iron mine soil biofilm co-cultured with Shewanella oneidensis MR-1, with the anode as the electron acceptor, and compared the results with those of iron mine soil biofilms alone on the anode. Shewanella oneidensis MR-1 improved the electrochemical activity of microbial biofilms, resulting in a higher maximum power density of 195 ± 8 mW/m² compared with that of iron mine soil (175 ± 7 mW/m²) and Shewanella (88 ± 8 mW/m²) biofilms individually. The co-cultured biofilms could perform near the highest power density for a longer duration than the iron mine soil biofilms could. High-throughput 16S rRNA gene sequencing of the biofilms on the anode indicated that the relative abundance of Pelobacteraceae in the co-culture system was significantly (p = 0.02) increased, while that of Rhodocyclaceae was significantly (p = 0.008) decreased, compared with that in iron mine soil biofilms. After continuing the experiment for two months, the presence of Shewanella oneidensis MR-1 changed the predominant bacteria of the microbial community in the biofilms, and the relative abundance of Shewanella was significantly (p = 0.02) decreased to a level similar to that in iron mine soil. These results demonstrate that Shewanella oneidensis MR-1 could improve the performance of iron mine soil biofilms in electrochemical systems by altering the composition of the functional microbial communities. Full article

This present study investigated the microbial dynamics, physicochemical and functional properties, and sensory characteristics of kefir produced by two different approaches: traditional kefir obtained directly from grains and kefir manufactured through a double-fermentation process in cow milk. For the first fermentation, kefir grains were inoculated in milk at different levels (1%, 3%, and 5% w/v) and incubated at 30 °C for 24 h. The lowest inoculation level promoted the greatest increase in grain biomass, whereas higher inoculation levels produced more pronounced pH decreases. All products maintained stable pH values during refrigerated storage at 4 °C for 15 days. Products derived from initial fermentations with 1% and 3% inoculum were subsequently used in a second fermentation step at two inoculation levels (1% and 10% v/v) to produce double-fermentation kefir products. These products exhibited higher counts of lactic acid bacteria and reduced yeast populations compared with traditional grain kefir. After 15 days of storage, all kefir samples maintained more than 10⁸ CFU/mL of lactic acid bacteria, more than 10⁷ CFU/mL of acetic acid bacteria, and around 10⁵ CFU/mL of yeasts. Protein content was comparable among all kefir products and unfermented milk. The product obtained with 1% grains followed by 10% v/v inoculation showed enhanced biofilm formation that increased during storage and displayed the strongest antimicrobial activity, and was therefore selected for sensory evaluation, where it achieved favorable acceptance by regular kefir consumers. Full article

The Sporulation-Inspired Optimization Algorithm (SIOA) is an innovative metaheuristic optimization method inspired by the biological mechanisms of microbial sporulation and dispersal. SIOA operates on a dynamic population of solutions (“microorganisms”) and alternates between two main phases: sporulation, where new “spores” are generated through adaptive random perturbations combined with guided search towards the global best, and germination, in which these spores are evaluated and may replace the most similar and less effective individuals in the population. A distinctive feature of SIOA is its fully self-adaptive parameter control, where the dispersal radius and the probabilities of sporulation and germination are dynamically adjusted according to the progress of the search (e.g., convergence trends of the average fitness). The algorithm also integrates a special “zero-reset” mechanism, enhancing its ability to detect global optima located near the origin. SIOA further incorporates a stochastic local search phase to refine solutions and accelerate convergence. Experimental results demonstrate that SIOA achieves high-quality solutions with a reduced number of function evaluations, especially in complex, multimodal, or high-dimensional problems. Overall, SIOA provides a robust and flexible optimization framework, suitable for a wide range of challenging optimization tasks. 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

Despite growing recognition of the role of the gut microbiome in host health and in modulating pathogen activity, the dynamic and reciprocal relationship between enteric viruses and the gut microbial ecosystem remains insufficiently defined and requires further exploration. This comprehensive review examines the bidirectional interplay between the gut microbiome and enteric viral infections by addressing (i) viruses associated with gastrointestinal alterations, (ii) how enteric viral infections alter the composition and function of the gut microbiome, (iii) how the gut microbiome modulates viral infectivity and host susceptibility, and (iv) current microbial-based approaches for preventing or treating enteric viral infections. Gastrointestinal viral infections induce gut microbiome dysbiosis, marked by reductions in beneficial bacteria and increases in potentially pathogenic populations. Specific gut microorganisms can modulate host susceptibility, with certain bacterial genera increasing or decreasing infection risk and disease severity. Pattern recognition receptors in the intestinal epithelium detect microbial signals and trigger antimicrobial peptides, mucus, and interferon responses to control viral replication while maintaining tolerance to commensal bacteria. The gut microbiome can indirectly facilitate viral infections by creating a tolerogenic environment, suppressing antiviral antibody responses, and modulating interferon signaling, or directly enhance viral replication by stabilizing virions, promoting host cell attachment, and facilitating coinfection and viral recombination. In turn, commensal gut bacteria can inhibit viral entry, enhance host antiviral responses, and strengthen mucosal barrier function, contributing to protection against gastrointestinal viral infections. Probiotics and fecal microbiota transplantation constitute potential microbial-based therapeutics that support antiviral defenses, preserve epithelial integrity, and restore microbial balance. In conclusion, the role of the gut microbiome in modulating enteric viral infections represents a promising area of future investigation. Therefore, integrating microbiome insights with virology and immunology could enable predictive and personalized strategies for prevention and treatment. Full article

The field of bacterial systems biology is rapidly advancing beyond static genomic analyses, and moving toward dynamic, integrative approaches that connect genetic variation with cellular function. This review traces the progression from genome-wide association studies (GWAS) to multi-omics frameworks that incorporate transcriptomics, proteomics, and interactome mapping. We emphasize recent breakthroughs in high-resolution transcriptomics, including single-cell, spatial, and epitranscriptomic technologies, which uncover functional heterogeneity and regulatory complexity in bacterial populations. At the same time, innovations in proteomics, such as data-independent acquisition (DIA) and single-bacterium proteomics, provide quantitative insights into protein-level mechanisms. Experimental and AI-assisted strategies for mapping protein–protein interactions help to clarify the architecture of bacterial molecular networks. The integration of these omics layers through quantitative trait locus (QTL) analysis establishes mechanistic links between single-nucleotide polymorphisms and systems-level phenotypes. Despite persistent challenges such as bacterial clonality and genomic plasticity, emerging tools, including deep mutational scanning, microfluidics, high-throughput genome editing, and machine-learning approaches, are enhancing the resolution and scope of bacterial genetics. By synthesizing these advances, we describe a transformative trajectory toward predictive, systems-level models of bacterial life. This perspective opens new opportunities in antimicrobial discovery, microbial engineering, and ecological research. Full article

Food waste (FW) sourced from treatment facilities is predominantly in solid form, with low water content and high variations in organic content. High organic content in FW is ideal in anaerobic digestion for bioenergy applications, but proper monitoring during start-up operations should be employed to avoid imbalance in the acidogenic/methanogenic population due to volatile fatty acid (VFA) accumulation in the system. The seed inoculum (5 L) in each horizontal anaerobic reactor (HAR) was fed with food waste without effluent flow (filling-up phase) until it reached the final working volume of 10 L (continuous phase). The pH, alkalinity, chemical oxygen demand (COD), VFA, biogas production, methane concentration, and microbial community dynamics were set as stability indicators during reactor operation. The results revealed that introducing fluctuations in FW concentrations does not negatively affect the biogas production (1.7 ± 0.2 L/L_R/d) and methane concentration (59.0 ± 2.5%). Acclimatization of the methanogenic and bacterial population was also observed. This study aimed to evaluate the influence of fluctuating FW concentrations on the process performance of horizontal anaerobic reactors, focusing on process stability, microbial dynamics, and biogas output during filling-up and continuous phases. Full article

A wadi ecosystem, a wetland characterized by seasonal water flow, is a unique freshwater environment typically found in semi-arid and arid regions. This study investigates the seasonal and spatial dynamics of environmental properties and microbial plankton communities at Wadi Saiysad in Taif City, Saudi Arabia. Using flow cytometry, three distinct picoplankton populations were observed: Synechococcus and heterotrophic prokaryotes classified as low (LNA) or high (HNA) nucleic acid content. Surface freshwater samples were collected from three distinct sites, representing habitats with actively flowing water, biodiverse communities, and human-influenced areas. Interestingly, no significant differences among stations were observed, suggesting that the sampled stretch of Wadi Saiysad receives similar nutrient inputs. Seasonal water temperature reached 24.5 ± 0.57 °C in summer and the pH ranged from neutral to slightly alkaline. Nutrient analyses revealed that Wadi Saiysad is eutrophic and limited by phosphorus. Phytoplankton biomass was dominated by nanoplankton, particularly in summer (46.60 ± 5.33%), while Synechococcus increased significantly with a maximum abundance of 1.32 × 10⁴ cells mL⁻¹ during the cooler months. HNA prokaryotes displayed marked seasonal variation (1.95 × 10⁴–1.78 × 10⁵ cells mL⁻¹) compared to LNA prokaryotes (2.05–8.17 × 10⁴ cells mL⁻¹). This study highlights the urgent need for monitoring and managing the nutrient inputs in Wadi Saiysad to protect its biodiversity and support sustainable use. Full article

Traditional fermentation models often oversimplify kinetics by treating microbial populations as physiologically homogeneous. To address this, we introduce a novel framework that explicitly incorporates cellular fitness by distinguishing the metabolically active subpopulation (“productive cells”) responsible for biosynthesis. This approach integrates established growth models (First Order Plus Dead Time and Logistic) with a modified Luedeking–Piret model (MALP), which introduces a new differential equation to dynamically quantify productive cells. This modeling study relies exclusively on experimental data available in the literature; no new experimental work was conducted. Validated against four diverse fermentation systems from published datasets, the MALP model demonstrated superior predictive accuracy, achieving coefficients of determination (R² > 0.97) for metabolite kinetics. Sensitivity analysis identified time-delay and maintenance-associated parameters as dominant factors governing system behavior. The key contribution of this work is a mechanistic equation that universally captures the real-world dynamics of metabolite production, providing a more realistic and robust framework for modeling heterogeneous bioprocesses. Full article

Due to the regulated nature and purity standards of the bioprocess and biotechnology industries, the sector has seen comparatively less sustainable practices than other chemical industries have. The achievement of sustainability in microbial fermenter design requires that quantitative tools with links between process parameters and end-environmental outcomes are employed. This review begins with environmentally friendly metrics such as process mass intensity, water and energy intensity, and related indicators that act as a template for resource usage and waste generation assessment. The objective of this paper is to highlight the primary focus on computational fluid dynamics (CFD) applied to bioprocesses in aerated stirred bioreactors using Escherichia coli (E. coli). Second, the objective of this paper is to explore state-of-the-art CFD models and methods documented in the existing literature, providing a fundamental foundation for researchers to incorporate CFD modelling into biotechnological process development, while making these concepts accessible to non-specialists and addressing the research gap of linking CFD outputs with sustainability metrics and life cycle assessment techniques. Impeller rotational models such as sliding mesh are an accurate and commonly used method of modelling the rotation of stirring. Multiple different turbulence models are applied for the purpose of stirred bioreactors, with the family of k-ε models being the most used. Multiphase models such as Euler-Euler models in combination with population balance models and gas dispersion models to model bubble size distribution and bubble characteristics are typically used. Full article