The 100 most-cited articles in Frontiers in Microbiology, 2024

Nanoparticles play a crucial role in the field of nanotechnology, offering different properties due to their surface area attributed to their small size. Among them, silver nanoparticles (AgNPs) have attracted significant attention due to their antimicrobial properties, with applications that date back from ancient medicinal practices to contemporary commercial products containing ions or silver nanoparticles. AgNPs possess broad-spectrum biocidal potential against bacteria, fungi, viruses, and Mycobacterium, in addition to exhibiting synergistic effects when combined with certain antibiotics. The mechanisms underlying its antimicrobial action include the generation of oxygen-reactive species, damage to DNA, rupture of bacterial cell membranes and inhibition of protein synthesis. Recent studies have highlighted the effectiveness of AgNPs against various clinically relevant bacterial strains through their potential to combat antibiotic-resistant pathogens. This review investigates the proteomic mechanisms by which AgNPs exert their antimicrobial effects, with a special focus on their…

Pseudomonas aeruginosa , a Gram-negative bacterium, is recognized for its adaptability and opportunistic nature. It poses a substantial challenge in clinical settings due to its complicated antibiotic resistance mechanisms, biofilm formation, and capacity for persistent infections in both animal and human hosts. Recent studies revealed a potential zoonotic transmission of P. aeruginosa between animals, the environment, and human populations which highlights awareness of this microbe. Implementation of the One Health approach, which underscores the connection between human, animal, and environmental health, we aim to offer a comprehensive perspective on the current landscape of P. aeruginosa management. This review presents innovative strategies designed to counteract P. aeruginosa infections. Traditional antibiotics, while effective in many cases, are increasingly compromised by the development of multidrug-resistant strains. Non-antibiotic avenues, such as quorum sensing inhibition, phage therapy, and nanoparticle-based treatments, are emerging as promising alternatives. However,…

Phosphorus (P) is an important nutrient for plants, and a lack of available P greatly limits plant growth and development. Phosphate-solubilizing microorganisms (PSMs) significantly enhance the ability of plants to absorb and utilize P, which is important for improving plant nutrient turnover and yield. This article summarizes and analyzes how PSMs promote the absorption and utilization of P nutrients by plants from four perspectives: the types and functions of PSMs, phosphate-solubilizing mechanisms, main functional genes, and the impact of complex inoculation of PSMs on plant P acquisition. This article reviews the physiological and molecular mechanisms of phosphorus solubilization and growth promotion by PSMs, with a focus on analyzing the impact of PSMs on soil microbial communities and its interaction with root exudates. In order to better understand the ability of PSMs and their role in soil P transformation and to provide prospects for research on PSMs promoting plant P absorption. PSMs mainly activate insoluble P through the secretion of organic acids, phosphatase…

Overuse of antibiotics is accelerating the antimicrobial resistance among pathogenic microbes which is a growing public health challenge at the global level. Higher resistance causes severe infections, high complications, longer stays at hospitals and even increased mortality rates. Antimicrobial resistance (AMR) has a significant impact on national economies and their health systems, as it affects the productivity of patients or caregivers due to prolonged hospital stays with high economic costs. The main factor of AMR includes improper and excessive use of antimicrobials; lack of access to clean water, sanitation, and hygiene for humans and animals; poor infection prevention and control measures in hospitals; poor access to medicines and vaccines; lack of awareness and knowledge; and irregularities with legislation. AMR represents a global public health problem, for which epidemiological surveillance systems have been established, aiming to promote collaborations directed at the well-being of human and animal health and the balance of the ecosystem. MDR bacteria such as E. coli ,…

Clarifying the relationship between soil microorganisms and the plant-soil system is crucial for encouraging the sustainable development of ecosystems, as soil microorganisms serve a variety of functional roles in the plant-soil system. In this work, the influence mechanisms of significant soil microbial groups on the plant-soil system and their applications in environmental remediation over the previous 30 years were reviewed using a systematic literature review (SLR) methodology. The findings demonstrated that: (1) There has been a general upward trend in the number of publications on significant microorganisms, including bacteria, fungi, and archaea. (2) Bacteria and fungi influence soil development and plant growth through organic matter decomposition, nitrogen, phosphorus, and potassium element dissolution, symbiotic relationships, plant growth hormone production, pathogen inhibition, and plant resistance induction. Archaea aid in the growth of plants by breaking down low-molecular-weight organic matter, participating in element cycles, producing plant growth hormones, and…

Plant-microbe interactions are pivotal for ecosystem dynamics and sustainable agriculture, and are influenced by various factors, such as host characteristics, environmental conditions, and human activities. Omics technologies, including genomics, transcriptomics, proteomics, and metabolomics, have revolutionized our understanding of these interactions. Genomics elucidates key genes, transcriptomics reveals gene expression dynamics, proteomics identifies essential proteins, and metabolomics profiles small molecules, thereby offering a holistic perspective. This review synthesizes diverse microbial-plant interactions, showcasing the application of omics in understanding mechanisms, such as nitrogen fixation, systemic resistance induction, mycorrhizal association, and pathogen-host interactions. Despite the challenges of data integration and ethical considerations, omics approaches promise advancements in precision intervention and resilient agricultural practices. Future research should address data integration challenges, enhance omics technology resolution, explore epigenomics, and…

Bacteria are the most prevalent form of microorganisms and are classified into two categories based on their mode of existence: intracellular and extracellular. While most bacteria are beneficial to human health, others are pathogenic and can cause mild to severe infections. These bacteria use various mechanisms to evade host immunity and cause diseases in humans. The susceptibility of a host to bacterial infection depends on the effectiveness of the immune system, overall health, and genetic factors. Malnutrition, chronic illnesses, and age-related vulnerabilities are the additional confounders to disease severity phenotypes. The impact of bacterial pathogens on public health includes the transmission of these pathogens from healthcare facilities, which contributes to increased morbidity and mortality. To identify the most significant threats to public health, it is crucial to understand the global burden of common bacterial pathogens and their pathogenicity. This knowledge is required to improve immunization rates, improve the effectiveness of vaccines, and consider the impact of…

Globally, food security has become a critical concern due to the rise in human population and the current climate change crisis. Usage of conventional agrochemicals to maximize crop yields has resulted in the degradation of fertile soil, environmental pollution as well as human and agroecosystem health risks. Nanotechnology in agriculture is a fast-emerging and new area of research explored to improve crop productivity and nutrient-use efficiency using nano-sized agrochemicals at lower doses than conventional agrochemicals. Nanoparticles in agriculture are applied as nanofertilizers and/or nanopesticides. Positive results have been observed in terms of plant growth when using nano-based agricultural amendments. However, their continuous application may have adverse effects on plant-associated rhizospheric and endospheric microorganisms which often play a crucial role in plant growth, nutrient uptake, and disease prevention. While research shows that the application of nanoparticles has the potential to improve plant growth and yield, their effect on the diversity and function of…

Inflammatory periodontal diseases associated with the accumulation of dental biofilm, such as gingivitis and periodontitis, are very common and pose clinical problems for clinicians and patients. Gingivitis is a mild form of gum disease and when treated quickly and properly is completely reversible. Periodontitis is an advanced and irreversible disease of the periodontium with periods of exacerbations, progressions and remission. Periodontitis is a chronic inflammatory condition that damages the tissues supporting the tooth in its socket, i.e., the gums, periodontal ligaments, root cementum and bone. Periodontal inflammation is most commonly triggered by bacteria present in excessive accumulations of dental plaque (biofilm) on tooth surfaces. This disease is driven by disproportionate host inflammatory immune responses induced by imbalance in the composition of oral bacteria and changes in their metabolic activities. This microbial dysbiosis favors the establishment of inflammatory conditions and ultimately results in the destruction of tooth-supporting tissues. Apart microbial…

The imbalance of microbial composition and diversity in favor of pathogenic microorganisms combined with a loss of beneficial gut microbiota taxa results from factors such as age, diet, antimicrobial administration for different infections, other underlying medical conditions, etc. Probiotics are known for their capacity to improve health by stimulating the indigenous gut microbiota, enhancing host immunity resistance to infection, helping digestion, and carrying out various other functions. Concurrently, the metabolites produced by these microorganisms, termed postbiotics, which include compounds like bacteriocins, lactic acid, and hydrogen peroxide, contribute to inhibiting a wide range of pathogenic bacteria. This review presents an update on using probiotics in managing and treating various human diseases, including complications that may emerge during or after a COVID-19 infection.

Loop-mediated isothermal amplification (LAMP) is a novel method for nucleic acid detection known for its isothermal properties, high efficiency, sensitivity, and specificity. LAMP employs 4 to 6 primers targeting 6 to 8 regions of the desired sequence, allowing for amplification at temperatures between 60 and 65°C and the production of up to 10 9 copies within a single hour. The product can be monitored by various methods such as turbidimetry, fluorometry, and colorimetry. However, it faces limitations such as the risk of non-specific amplification, challenges in primer design, unsuitability for short gene sequences, and difficulty in multiplexing. Recent advancements in polymerase and primer design have enhanced the speed and convenience of the LAMP reaction. Additionally, integrating LAMP with technologies like rolling circle amplification (RCA), recombinase polymerase amplification (RPA), and CRISPR-Cas systems has enhanced its efficiency. The combination of LAMP with various biosensors has enabled real-time analysis, broadening its application in point-of-care testing (POCT).…

Antibiotic resistance is a growing global problem that requires innovative therapeutic approaches and strategies for administering antibiotics. One promising approach is combination therapy, in which two or more drugs are combined to combat an infection. Along this line, the combination of antimicrobial peptides (AMPs) with conventional antibiotics has gained attention mainly due to the complementary mechanisms of action of AMPs and conventional antibiotics. In this article, we review both in vitro and in vivo studies that explore the synergy between AMPs and antibiotics. We highlight several mechanisms through which synergy is observed in in vitro experiments, including increasing membrane permeability, disrupting biofilms, directly potentiating antibiotic efficacy, and inhibiting resistance development. Moreover, in vivo studies reveal additional mechanisms such as enhanced/modulated immune responses, reduced inflammation, and improved tissue regeneration. Together, the current literature demonstrates that AMP-antibiotic combinations can substantially enhance efficacy of…

Biofertilizers based on plant growth promoting rhizobacteria (PGPR) are nowadays gaining increasingly attention as a modern tool for a more sustainable agriculture due to their ability in ameliorating root nutrient acquisition. For many years, most research was focused on the screening and characterization of PGPR functioning as nitrogen (N) or phosphorus (P) biofertilizers. However, with the increasing demand for food using far fewer chemical inputs, new investigations have been carried out to explore the potential use of such bacteria also as potassium (K), sulfur (S), zinc (Zn), or iron (Fe) biofertilizers. In this review, we update the use of PGPR as biofertilizers for a smarter and more sustainable crop production and deliberate the prospects of using microbiome engineering-based methods as potential tools to shed new light on the improvement of plant mineral nutrition. The current era of omics revolution has enabled the design of synthetic microbial communities (named SynComs ), which are emerging as a promising tool that can allow the formulation of biofertilizers based on…

Recent studies have indicated that gut microbiota-mediated oxidative stress is significantly associated with intestinal diseases such as colorectal cancer, ulcerative colitis, and Crohn's disease. The level of reactive oxygen species (ROS) has been reported to increase when the gut microbiota is dysregulated, especially when several gut bacterial metabolites are present. Although healthy gut microbiota plays a vital role in defending against excessive oxidative stress, intestinal disease is significantly influenced by excessive ROS, and this process is controlled by gut microbiota-mediated immunological responses, DNA damage, and intestinal inflammation. In this review, we discuss the relationship between gut microbiota and intestinal disease from an oxidative stress perspective. In addition, we also provide a summary of the most recent therapeutic approaches for preventing or treating intestinal diseases by modifying gut microbiota.

Acinetobacter baumannii is one of the most common multidrug-resistant pathogens causing nosocomial infections. The prevalence of multidrug-resistant A. baumannii infections is increasing because of several factors, including unregulated antibiotic use. A. baumannii drug resistance rate is high; in particular, its resistance rates for tigecycline and polymyxin—the drugs of last resort for extensively drug-resistant A. baumannii —has been increasing annually. Patients with a severe infection of extensively antibiotic-resistant A. baumannii demonstrate a high mortality rate along with a poor prognosis, which makes treating them challenging. Through carbapenem enzyme production and other relevant mechanisms, A. baumannii has rapidly acquired a strong resistance to carbapenem antibiotics—once considered a class of strong antibacterials for A. baumannii infection treatment. Therefore, understanding the resistance mechanism of A. baumannii is particularly crucial. This review summarizes mechanisms underlying common antimicrobial resistance in A. baumannii , particularly those underlying…

The marine environment has remained a source of novel biological molecules with diversified applications. The ecological and biological diversity, along with a unique physical environment, have provided the evolutionary advantage to the plant, animals and microbial species thriving in the marine ecosystem. In light of the fact that marine microorganisms frequently interact symbiotically or mutualistically with higher species including corals, fish, sponges, and algae, this paper intends to examine the potential of marine microorganisms as a niche for marine bacteria. This review aims to analyze and summarize modern literature data on the biotechnological potential of marine fungi and bacteria as producers of a wide range of practically valuable products (surfactants, glyco-and lipopeptides, exopolysaccharides, enzymes, and metabolites with different biological activities: antimicrobial, antitumor, and cytotoxic). Hence, the study on bioactive secondary metabolites from marine microorganisms is the need of the hour. The scientific novelty of the study lies in the fact that for the…

Arbuscular mycorrhizal fungi (AMF) can penetrate plant root cortical cells, establish a symbiosis with most land plant species, and form branched structures (known as arbuscules) for nutrient exchange. Plants have evolved a complete plant-AMF symbiosis system to sustain their growth and development under various types of abiotic stress. Here, we highlight recent studies of AM symbiosis and the regulation of symbiosis process. The roles of mycorrhizal symbiosis and host plant interactions in enhancing drought resistance, increasing mineral nutrient uptake, regulating hormone synthesis, improving salt resistance, and alleviating heavy metal stress were also discussed. Overall, studies of AM symbiosis and a variety of abiotic stresses will aid applications of AMF in sustainable agriculture and can improve plant production and environmental safety.

The term postbiotic was defined by the International Scientific Association of Probiotics and Prebiotics (ISAPP) as “ a preparation of inanimate microorganisms and/or their components that confers a health benefit on the host .” Although the ISAPP definition is widely cited, some concerns were aired after publication, and alternative definitions of postbiotic, as well as different terms for inactivated microbes, have been previously suggested. This paper addresses questions about the ISAPP definition that have been raised in different forums, including scientific meetings, social media commentary and personal communications. We focus on the rationale, scope, wording, composition and commercial implementation, as well as what is expected of postbiotics regarding safety, efficacy, quantification and mechanisms of action. We hope that exploring these questions will further clarify the definition and its scope and support a common understanding of the concept of postbiotics.

This review examines the role of Pseudomonas spp. bacteria as biocontrol agents against crop diseases, focusing on their mechanisms of action, efficacy, and potential applications in sustainable agriculture. Pseudomonas spp., ubiquitous in soil ecosystems and root microbiomes, have attracted attention for their ability to suppress phytopathogens and enhance plant health through various mechanisms. These include direct competition for nutrients, production of antimicrobial compounds and volatile organic compounds, competition using type VI secretion systems, and indirect induction of systemic resistance. Our review shows that Pseudomonas strains effectively control a wide range of diseases across diverse plant species, with some strains demonstrating efficacy comparable to chemical fungicides. However, the review also highlights challenges in achieving consistent performance when using Pseudomonas inoculants under field conditions due to various biotic and abiotic factors. Strategies to optimize biocontrol potential, such as formulation techniques, application methods, and…

Early and precise detection and identification of various pathogens are essential for epidemiological monitoring, disease management, and reducing the prevalence of clinical infectious diseases. Traditional pathogen detection techniques, which include mass spectrometry, biochemical tests, molecular testing, and culture-based methods, are limited in application and are time-consuming. Next generation sequencing (NGS) has emerged as an essential technology for identifying pathogens. NGS is a cutting-edge sequencing method with high throughput that can create massive volumes of sequences with a broad application prospects in the field of pathogen identification and diagnosis. In this review, we introduce NGS technology in detail, summarizes the application of NGS in that identification of different pathogens, including bacteria, fungi, and viruses, and analyze the challenges and outlook for using NGS to identify clinical pathogens. Thus, this work provides a theoretical basis for NGS studies and provides evidence to support the application of NGS in distinguishing various clinical…

Persistent infection caused by biofilm is an urgent in medicine that should be tackled by new alternative strategies. Low efficiency of classical treatments and antibiotic resistance are the main concerns of the persistent infection due to biofilm formation which increases the risk of morbidity and mortality. The gene expression patterns in biofilm cells differed from those in planktonic cells. One of the promising approaches against biofilms is nanoparticle (NP)-based therapy in which NPs with multiple mechanisms hinder the resistance of bacterial cells in planktonic or biofilm forms. For instance, NPs such as silver (Ag), zinc oxide (ZnO), titanium dioxide (TiO 2 ), copper oxide (Cu), and iron oxide (Fe 3 O 4 ) through the different strategies interfere with gene expression of bacteria associated with biofilm. The NPs can penetrate into the biofilm structure and affect the expression of efflux pump, quorum-sensing, and adhesion-related genes, which lead to inhibit the biofilm formation or development. Therefore, understanding and targeting of the genes and molecular basis of…

Microbial biopolymers have emerged as promising solutions for environmental pollution-related human health issues. Poly-γ-glutamic acid (γ-PGA), a natural anionic polymeric compound, is composed of highly viscous homo-polyamide of D and L-glutamic acid units. The extracellular water solubility of PGA biopolymer facilitates its complete biodegradation and makes it safe for humans. The unique properties have enabled its applications in healthcare, pharmaceuticals, water treatment, foods, and other domains. It is applied as a thickener, taste-masking agent, stabilizer, texture modifier, moisturizer, bitterness-reducing agent, probiotics cryoprotectant, and protein crystallization agent in food industries. γ-PGA is employed as a biological adhesive, drug carrier, and non-viral vector for safe gene delivery in tissue engineering, pharmaceuticals, and medicine. It is also used as a moisturizer to improve the quality of hair care and skincare cosmetic products. In agriculture, it serves as an ideal stabilizer, environment-friendly fertilizer synergist, plant-growth promoter, metal…

The adverse effects of waste generation on the environment and public health have raised global concerns. The utilization of waste as a raw material to develop products with enhanced value has opened up novel prospects for promoting environmental sustainability. Biosurfactants obtained from agro-industrial waste are noteworthy due to their sustainability and environmental friendliness. Microorganisms have been employed to generate biosurfactants as secondary metabolites by making use of waste streams. The utilization of garbage as a substrate significantly reduces the expenses associated with the process. Furthermore, apart from reducing waste and offering alternatives to artificial surfactants, they are extensively employed in bioremediation, food processing, agriculture, and various other industrial pursuits. Bioremediation of heavy metals and other metallic pollutants mitigated through the use of bacteria that produce biosurfactants which has been the more recent research area with the aim of improving its quality and environmental safety. Moreover, the production of…

Soil health is crucial for global food production in the context of an ever-growing global population. Microbiomes, a combination of microorganisms and their activities, play a pivotal role by biodegrading contaminants, maintaining soil structure, controlling nutrients’ cycles, and regulating the plant responses to biotic and abiotic stresses. Microbiome-based solutions along the soil-plant continuum, and their scaling up from laboratory experiments to field applications, hold promise for enhancing agricultural sustainability by harnessing the power of microbial consortia. Synthetic microbial communities, i.e., selected microbial consortia, are designed to perform specific functions. In contrast, natural communities leverage indigenous microbial populations that are adapted to local soil conditions, promoting ecosystem resilience, and reducing reliance on external inputs. The identification of microbial indicators requires a holistic approach. It is fundamental for current understanding the soil health status and for providing a comprehensive assessment of sustainable land…

Plant parasitic nematodes (PPNs) pose a significant threat to global crop productivity, causing an estimated annual loss of US $157 billion in the agriculture industry. While synthetic chemical nematicides can effectively control PPNs, their overuse has detrimental effects on human health and the environment. Biocontrol agents (BCAs), such as bacteria and fungi in the rhizosphere, are safe and promising alternatives for PPNs control. These BCAs interact with plant roots and produce extracellular enzymes, secondary metabolites, toxins, and volatile organic compounds (VOCs) to suppress nematodes. Plant root exudates also play a crucial role in attracting beneficial microbes toward infested roots. The complex interaction between plants and microbes in the rhizosphere against PPNs is mostly untapped which opens new avenues for discovering novel nematicides through multi-omics techniques. Advanced omics approaches, including metagenomics, transcriptomics, proteomics, and metabolomics, have led to the discovery of nematicidal compounds. This review summarizes the status of bacterial and…

Nowadays, sustainable agriculture approaches are based on the use of biofertilizers and biopesticides. Tomato ( Solanum lycopersicum L.) rhizosphere could provide rhizobacteria with biofertilizing and biopesticide properties. In this study, bacteria from the rhizosphere of tomato were evaluated in vitro for plant growth promotion (PGP) properties. Five Pseudomonas isolates (PsT-04c, PsT-94s, PsT-116, PsT-124, and PsT-130) and one Bacillus isolate (BaT-68s), with the highest ability to solubilize tricalcium phosphate (TCP) were selected for further molecular identification and characterization. Isolates showed phosphate solubilization up to 195.42 μg mL −1 . All isolates showed phosphate solubilization by organic acid production. The six isolates improved seed germination and showed effective root colonization when tomato seeds were coated with isolates at 10 6 cfu g −1 in axenic soil conditions. Furthermore, the selected isolates were tested for beneficial effects on tomato growth and nutrient status in greenhouse experiments with natural rock phosphate (RP). The results showed that…

Background Colorectal cancer (CRC) is a type of tumor caused by the uncontrolled growth of cells in the mucosa lining the last part of the intestine. Emerging evidence underscores an association between CRC and gut microbiome dysbiosis. The high mortality rate of this cancer has made it necessary to develop new early diagnostic methods. Machine learning (ML) techniques can represent a solution to evaluate the interaction between intestinal microbiota and host physiology. Through explained artificial intelligence (XAI) it is possible to evaluate the individual contributions of microbial taxonomic markers for each subject. Our work also implements the Shapley Method Additive Explanations (SHAP) algorithm to identify for each subject which parameters are important in the context of CRC. Results The proposed study aimed to implement an explainable artificial intelligence framework using both gut microbiota data and demographic information from subjects to classify a cohort of control subjects from those with CRC. Our analysis revealed an association between gut microbiota and this…

Proteus mirabilis is a Gram-negative bacterium with exclusive molecular and biological features. It is a versatile pathogen acclaimed for its distinct urease production, swarming behavior, and rapid multicellular activity. Clinically, P. mirabilis is a frequent pathogen of the human urinary system where it causes urinary tract infections (UTIs) and catheter-associated urinary tract infections (CAUTIs). This review explores the epidemiology, risk factors, clinical manifestations, and treatment of P. mirabilis infections, emphasizing its association with UTIs. The bacterium’s genome analysis revealed the presence of resistance genes against commonly used antibiotics, an antibiotic-resistant phenotype that poses a serious clinical challenge. Particularly, the emergence of extended-spectrum β-lactamases (ESBLs) and carbapenemases resistant P. mirabilis strains. On a molecular level, P. mirabilis possesses a wide array of virulence factors including the production of fimbriae, urease, hemolysins, metallophores, and biofilm formation. This review thoroughly tackles a substantial gap in…

Non-Tuberculous mycobacteria (NTM) are opportunistic environmental bacteria. Globally, NTM incidence is increasing and modeling suggests that, without new interventions, numbers will continue to rise. Effective treatments for NTM infections remain suboptimal. Standard therapy for Mycobacterium avium complex, the most commonly isolated NTM, requires a 3-drug regime taken for approximately 18 months, with rates of culture conversion reported between 45 and 70%, and high rates of relapse or reinfection at up to 60%. New therapeutic options for NTM treatment are urgently required. A survey of ongoing clinical trials for new NTM therapy listed on ClinicalTrials.Gov using the terms ‘ Mycobacterium avium ’, ‘ Mycobacterium abscessus ’, ‘ Mycobacterium intracellulare ’, ‘Non tuberculous Mycobacteria’ and ‘Nontuberculous Mycobacteria’ and a selection criterion of interventional studies using antibiotics demonstrates that most trials involve dose and combination therapy of the guideline based therapy or including one or more of; Amikacin, Clofazimine, Azithromycin and the anti-TB drugs…

Saline soils pose significant challenges to global agricultural productivity, hindering crop growth and efficiency. Despite various mitigation strategies, the issue persists, underscoring the need for innovative and sustainable solutions. One promising approach involves leveraging microorganisms and their plant interactions to reclaim saline soils and bolster crop yields. This review highlights pioneering and recent advancements in utilizing multi-traits Trichoderma and Bacillus species as potent promoters of plant growth and health. It examines the multifaceted impacts of saline stress on plants and microbes, elucidating their physiological and molecular responses. Additionally, it delves into the role of ACC deaminase in mitigating plant ethylene levels by Trichoderma and Bacillus species. Although there are several studies on Trichoderma-Bacillus, much remains to be understood about their synergistic relationships and their potential as auxiliaries in the phytoremediation of saline soils, which is why this work addresses these challenges.

The development of antibiotic resistance compromises the effectiveness of our most effective defenses against bacterial infections, presenting a threat to global health. To date, a large number of research articles exist in the literature describing the case reports associated with extensively drug-resistant (XDR) and multidrug-resistant (MDR) bacterial strains. However, these findings are scattered, making it time-consuming for researchers to locate promising results and there remains a need for a comparative study to compile these case reports from various geographical regions including the Kingdom of Saudi Arabia. Additionally, no study has yet been published that compares the genetic variations and case reports of MDR and XDR strains identified from Saudi Arabia, the Middle East, Central Europe, and Asian countries. This study attempts to provide a comparative analysis of several MDR and XDR case reports from Saudi Arabia alongside other countries. Furthermore, the purpose of this work is to demonstrate the genetic variations in the genes underlying the resistance mechanisms…

In agricultural environments, plants are often exposed to abiotic stresses including temperature extremes, salt stress, drought, and heavy metal soil contamination, which leads to significant economic losses worldwide. Especially salt stress and drought pose serious challenges since they induce ionic toxicity, osmotic stress, and oxidative stress in plants. A potential solution can be the application of bacteria of the Serratia spp. known to promote plant growth under normal conditions Thus the mini-review aims to summarize the current knowledge on plant growth promotion by Serratia spp. (under the conditions of salinity stress, drought, and nutrient deficit) and highlight areas for development in the field. So far, it has been proven that Serratia spp. strains exhibit a variety of traits contributing to enhanced plant growth and stress tolerance, such as phytohormone production, ACC deaminase activity, nitrogen fixation, P and Zn solubilization, antioxidant properties improvement, and modulation of gene expression. Nevertheless, further research on Serratia spp. is needed,…

Metagenomics, Metabolomics, and Metaproteomics have significantly advanced our knowledge of microbial communities by providing culture-independent insights into their composition and functional potential. However, a critical challenge in this field is the lack of standard and comprehensive metadata associated with raw data, hindering the ability to perform robust data stratifications and consider confounding factors. In this comprehensive review, we categorize publicly available microbiome data into five types: shotgun sequencing, amplicon sequencing, metatranscriptomic, metabolomic, and metaproteomic data. We explore the importance of metadata for data reuse and address the challenges in collecting standardized metadata. We also, assess the limitations in metadata collection of existing public repositories collecting metagenomic data. This review emphasizes the vital role of metadata in interpreting and comparing datasets and highlights the need for standardized metadata protocols to fully leverage metagenomic data's potential. Furthermore, we explore future directions of…

A large number of microbial species tend to communicate and produce biofilm which causes numerous microbial infections, antibiotic resistance, and economic problems across different industries. Therefore, advanced anti-biofilms are required with novel attributes and targets, such as quorum sensing communication system. Meanwhile, quorum sensing inhibitors as promising anti-biofilm molecules result in the inhibition of particular phenotype expression blocking of cell-to-cell communication, which would be more acceptable than conventional strategies. Many natural products are identified as anti-biofilm agents from different plants, microorganisms, and marine extracts. Marine algae are promising sources of broadly novel compounds with anti-biofilm activity. Algae extracts and their metabolites such as sulfated polysaccharides (fucoidan), carotenoids (zeaxanthin and lutein), lipid and fatty acids (γ-linolenic acid and linoleic acid), and phlorotannins can inhibit the cell attachment, reduce the cell growth, interfere in quorum sensing pathway by blocking related enzymes, and disrupt…

Amid the growing challenge of antibiotic resistance on a global scale, there has been a notable resurgence in bacteriophage-based treatments, signaling a shift in our approach to managing infections. Bacteriophages (BPs), bacterial predators of nature, present a promising alternative for tackling infections caused by antibiotic-resistant pathogens. This review delves into the intricate relationship between bacteriophages and resistant bacteria, exploring various treatment strategies. Drawing upon both preclinical and clinical studies, the review highlights the effectiveness of bacteriophage therapy, particularly when integrated synergistically with conventional antibiotics. It discusses various treatment approaches for systemic and localized infections, demonstrating the adaptability of bacteriophage therapy across different clinical scenarios. Furthermore, the formulation and delivery of bacteriophages shed light on the various methods used to encapsulate and administer them effectively. It also acknowledges the challenge of bacterial resistance to bacteriophages and the ongoing…

Gut microbiota regulates the immune system, the development and progression of autoimmune diseases (AIDs) and overall health. Recent studies have played a crucial part in understanding the specific role of different gut bacterial strains and their metabolites in different AIDs. Microbial signatures in AIDs are revealed by advanced sequencing and metabolomics studies. Microbes such as Faecalibacterium prausnitzii, Akkermansia muciniphila, Anaerostipes caccae, Bacteroides sp., Roseburia sp., Blautia sp., Blautia faecis, Clostridium lavalense, Christensenellaceae sp., Coprococcus sp., Firmicutes sp., Ruminococcaceae sp., Lachnospiraceae sp., Megamonas sp., Monoglobus sp., Streptococcus pneumoniae and Bifidobacterium sp. help maintain immune homeostasis; whereas, Prevotella copri, Ruminococcus gnavus, Lactobacillus salivarius, Enterococcus gallinarum, Elizabeth menigoseptica, Collinsella sp., Escherichia sp., Fusobacterium sp., Enterobacter ludwigii, Enterobacteriaceae sp., Proteobacteria, Porphyromonas gingivalis, Porphyromonas nigrescens, Dorea sp., and Clostridium sp. cause…

Various traditional management techniques are employed to control plant diseases caused by bacteria and fungi. However, due to their drawbacks and adverse environmental effects, there is a shift toward employing more eco-friendly methods that are less harmful to the environment and human health. The main aim of the study was to biosynthesize silver Nanoparticles (AgNPs) from Rhizoctonia solani and Cladosporium cladosporioides using a green approach and to test the antimycotic activity of these biosynthesized AgNPs against a variety of pathogenic fungi. The characterization of samples was done by using UV–visible spectroscopy, SEM (scanning electron microscopy), FTIR (fourier transmission infrared spectroscopy), and XRD (X-ray diffractometry). During the study, the presence of strong plasmon absorbance bands at 420 and 450 nm confirmed the AgNPs biosynthesis by the fungi Rhizoctonia solani and Cladosporium cladosporioides. The biosynthesized AgNPs were 80–100 nm in size, asymmetrical in shape and became spherical to sub-spherical when aggregated. Assessment of the antifungal activity…

Sepsis is a syndrome precipitated by immune dysregulation in response to infection, and represents a pivotal factor in global mortality attributed to diseases. The recent consensus delineates sepsis as a perilous state of organ dysfunction arising from the host's maladaptive reaction to infection. It masks the complexity and breadth of the immune mechanisms involved in sepsis, which is characterized by simultaneous hyperinflammation and immunosuppression. Sepsis is highly correlated with the dysregulation of immune response, which is mainly mediated by various immune cells and their interactions. This syndrome can lead to a plethora of complications, encompassing systemic inflammatory response, metabolic disturbances, infectious shock, MODS, and DIC. Furthermore, more research studies have been conducted on sepsis in the past few years. The pathological characteristics of sepsis have been improved or treated by targeting signaling pathways like NF-B, JAK-STAT, PI3K-Akt, and p38-MAPK. Combined drug therapy is better than single drug therapy for sepsis. This article will review the…

Although aboveground biodiversity has been extensively studied, the impact of nutrient enrichment on soil microbial populations remains unclear. Soil microorganisms serve as important indicators in shaping soil nutrient cycling processes and are typically sensitive to nutrient additions. For this, we employed a factorial combination design to examine the impact of nutrient additions on the composition and function of soil bacteria in a temperate steppe. Nitrogen addition promoted the growth of copiotrophic bacteria (Proteobacteria, Firmicutes, and Bacteroidota) but inhibited the growth of oligotrophic bacteria (Acidobacteria, Chloroflexi, and Verrucomicrobiota). Phosphorus addition alleviated phosphorus deficiency, resulting in a decrease in the abundance of phoD-harboring bacteria (Actinobacteria and Proteobacteria). Significant enhancement of soil bacterial alpha diversity was observed only in treatments with added phosphorus. Changes in NO 3 − -N, NH 4 + -N, available phosphorus, and dissolved organic carbon resulting from nutrient addition may have a greater impact on microbial…

The diagnosis and treatment of bacterial infections in the medical and public health field in the 21st century remain significantly challenging. Artificial Intelligence (AI) has emerged as a powerful new tool in diagnosing and treating bacterial infections. AI is rapidly revolutionizing epidemiological studies of infectious diseases, providing effective early warning, prevention, and control of outbreaks. Machine learning models provide a highly flexible way to simulate and predict the complex mechanisms of pathogen-host interactions, which is crucial for a comprehensive understanding of the nature of diseases. Machine learning-based pathogen identification technology and antimicrobial drug susceptibility testing break through the limitations of traditional methods, significantly shorten the time from sample collection to the determination of result, and greatly improve the speed and accuracy of laboratory testing. In addition, AI technology application in treating bacterial infections, particularly in the research and development of drugs and vaccines, and the application of…

The plastisphere, a unique microbial biofilm community colonizing plastic debris and microplastics (MPs) in aquatic environments, has attracted increasing attention owing to its ecological and public health implications. This review consolidates current state of knowledge on freshwater plastisphere, focussing on its biodiversity, community assembly, and interactions with environmental factors. Current biomolecular approaches revealed a variety of prokaryotic and eukaryotic taxa associated with plastic surfaces. Despite their ecological importance, the presence of potentially pathogenic bacteria and mobile genetic elements (i.e., antibiotic resistance genes) raises concerns for ecosystem and human health. However, the extent of these risks and their implications remain unclear. Advanced sequencing technologies are promising for elucidating the functions of plastisphere, particularly in plastic biodegradation processes. Overall, this review emphasizes the need for comprehensive studies to understand plastisphere dynamics in freshwater and to support effective management strategies to…

Mycotoxins are secondary metabolites produced during the growth, storage, and transportation of crops contaminated by fungi and are physiologically toxic to humans and animals. Aflatoxin, zearalenone, deoxynivalenol, ochratoxin, patulin, and fumonisin are the most common mycotoxins and can cause liver and nervous system damage, immune system suppression, and produce carcinogenic effects in humans and animals that have consumed contaminated food. Physical, chemical, and biological methods are generally used to detoxify mycotoxins. Although physical methods, such as heat treatment, irradiation, and adsorption, are fast and simple, they have associated problems including incomplete detoxification, limited applicability, and cause changes in food characteristics (e.g., nutritive value, organoleptic properties, and palatability). Chemical detoxification methods, such as ammonification, ozonation, and peroxidation, pollute the environment and produce food safety risks. In contrast, bioenzymatic methods are advantageous as they achieve selective detoxification and are environmentally…

Introduction The oral microbial group typically represents the human body’s highly complex microbial group ecosystem. Oral microorganisms take part in human diseases, including Oral cavity inflammation, mucosal disease, periodontal disease, tooth decay, and oral cancer. On the other hand, oral microbes can also cause endocrine disorders, digestive function, and nerve function disorders, such as diabetes, digestive system diseases, and Alzheimer’s disease. It was noted that the proteins of oral microbes play significant roles in these serious diseases. Having a good knowledge of oral microbes can be helpful in analyzing the procession of related diseases. Moreover, the high-dimensional features and imbalanced data lead to the complexity of oral microbial issues, which can hardly be solved with traditional experimental methods. Methods To deal with these challenges, we proposed a novel method, which is oral_voting_transfer, to deal with such classification issues in the field of oral microorganisms. Such a method employed three features to classify the five oral microorganisms,…

Phosphorus (P) is a critical nutrient for plant growth, yet its uptake is often hindered by soil factors like clay minerals and metal oxides such as aluminum (Al), iron (Fe), and calcium (Ca), which bind P and limit its availability. Phosphate-solubilizing bacteria (PSB) have the unique ability to convert insoluble P into a soluble form, thereby fostering plant growth. This study aimed to assess the efficacy of inoculation of Bacillus megaterium B119 (rhizospheric) and B. subtilis B2084 (endophytic) via seed treatment in enhancing maize yield, grain P content, and enzyme activities across two distinct soil types in field conditions. Additionally, we investigated various mechanisms contributing to plant growth promotion, compatibility with commercial inoculants, and the maize root adhesion profile of these strains. During five crop seasons in two experimental areas in Brazil, Sete Lagoas-MG and Santo Antônio de Goiás-GO, single inoculations with either B119 or B2084 were implemented in three seasons, while a co-inoculation with both strains was applied in two seasons. All treatments…

Legumes are renowned for their distinctive biological characteristic of forming symbiotic associations with soil bacteria, mostly belonging to the Rhizobiaceae familiy, leading to the establishment of symbiotic root nodules. Within these nodules, rhizobia play a pivotal role in converting atmospheric nitrogen into a plant-assimilable form. However, it has been discerned that root nodules of legumes are not exclusively inhabited by rhizobia; non-rhizobial endophytic bacteria also reside within them, yet their functions remain incompletely elucidated. This comprehensive review synthesizes available data, revealing that Bacillus and Pseudomonas are the most prevalent genera of nodule endophytic bacteria, succeeded by Paenibacillus, Enterobacter, Pantoea, Agrobacterium, and Microbacterium. To date, the bibliographic data available show that Glycine max followed by Vigna radiata, Phaseolus vulgaris and Lens culinaris are the main hosts for nodule endophytic bacteria. Clustering analysis consistently supports the prevalence of Bacillus and Pseudomonas as the most abundant nodule…

Globally, ~8%-12% of couples confront infertility issues, male-related issues being accountable for 50%. This review focuses on the influence of gut microbiota and their metabolites on the male reproductive system from five perspectives: sperm quality, testicular structure, sex hormones, sexual behavior, and probiotic supplementation. To improve sperm quality, gut microbiota can secrete metabolites by themselves or regulate host metabolites. Endotoxemia is a key factor in testicular structure damage that causes orchitis and disrupts the blood-testis barrier (BTB). In addition, the gut microbiota can regulate sex hormone levels by participating in the synthesis of sex hormone-related enzymes directly and participating in the enterohepatic circulation of sex hormones, and affect the hypothalamic-pituitary-testis (HPT) axis. They can also activate areas of the brain that control sexual arousal and behavior through metabolites. Probiotic supplementation can improve male reproductive function. Therefore, the gut microbiota may affect male reproductive function and behavior; however,…

Introduction Salinization damages soil system health and influences microbial communities structure and function. The response of microbial functions involved in the nutrient cycle to soil salinization is a valuable scientific question. However, our knowledge of the microbial metabolism functions in salinized soil and their response to salinity in arid desert environments is inadequate. Methods Here, we applied metagenomics technology to investigate the response of microbial carbon (C), nitrogen (N), phosphorus (P), and sulfur (S) cycling and the key genes to salinity, and discuss the effects of edaphic variables on microbial functions. Results We found that carbon fixation dominated the carbon cycle. Nitrogen fixation, denitrification, assimilatory nitrate reduction (ANRA), and nitrogen degradation were commonly identified as the most abundant processes in the nitrogen cycle. Organic phosphorus dissolution and phosphorus absorption/transport were the most enriched P metabolic functions, while sulfur metabolism was dominated by assimilatory sulfate reduction (ASR), organic sulfur…

Understanding the response of microbial communities and their potential functions is essential for sustainability of agroecosystems under long-term continuous cropping. However, limited research has focused on investigating the interaction between soil physicochemical factors and microbial community dynamics in agroecosystems under long-term continuous cropping. This study probed into the physicochemical properties, metabolites, and microbial diversity of tobacco rhizosphere soils cropped continuously for 0, 5, and 20 years. The relative abundance of bacterial genera associated with nutrient cycling (e.g., Sphingomonas ) increased while potential plant pathogenic fungi and beneficial microorganisms showed synergistic increases with the duration of continuous cropping. Variations in soil pH, alkeline nitrogen (AN) content, and soil organic carbon (SOC) content drove the shifts in soil microbial composition. Metabolites such as palmitic acid, 3-hydroxypropionic acid, stearic acid, and hippuric acid may play a key role in soil acidification. Those results enhance our ability to predict…

The gut microbiota is a complex and diverse community of microorganisms that colonizes the human gastrointestinal tract and influences various aspects of human health. These microbes are closely related to enteric infections. As a foreign entity for the host, commensal microbiota is restricted and regulated by the barrier and immune system in the gut and contributes to gut homeostasis. Commensals also effectively resist the colonization of pathogens and the overgrowth of indigenous pathobionts by utilizing a variety of mechanisms, while pathogens have developed strategies to subvert colonization resistance. Dysbiosis of the microbial community can lead to enteric infections. The microbiota acts as a pivotal mediator in establishing a harmonious mutualistic symbiosis with the host and shielding the host against pathogens. This review aims to provide a comprehensive overview of the mechanisms underlying host-microbiome and microbiome-pathogen interactions, highlighting the multi-faceted roles of the gut microbiota in preventing enteric infections. We also discuss the applications of…

Pharmaceuticals, recognized for their life-saving potential, have emerged as a concerning class of micropollutants in the environment. Even at minute concentrations, chronic exposure poses a significant threat to ecosystems. Various pharmaceutically active micropollutants (PhAMP), including antibiotics, analgesics, and hormones, have been detected in underground waters, surface waters, seawater, sewage treatment plants, soils, and activated sludges due to the absence of standardized regulations on pharmaceutical discharge. Prolonged exposureof hospital waste and sewage treatment facilities is linked to the presence of antibiotic-resistant bacteria. Conventional water treatment methods prove ineffective, prompting the use of alternative techniques like photolysis, reverse osmosis, UV-degradation, bio-degradation, and nano-filtration. However, commercial implementation faces challenges such as incomplete removal, toxic sludge generation, high costs, and the need for skilled personnel. Research gaps include the need to comprehensively identify and understand various types of…

The review aimed to investigate the diversity of oral microbiota and its influencing factors, as well as the association of oral microbiota with oral health and the possible effects of dysbiosis and oral disorder. The oral cavity harbors a substantial microbial burden, which is particularly notable compared to other organs within the human body. In usual situations, the microbiota exists in a state of equilibrium; however, when this balance is disturbed, a multitude of complications arise. Dental caries, a prevalent issue in the oral cavity, is primarily caused by the colonization and activity of bacteria, particularly streptococci. Furthermore, this environment also houses other pathogenic bacteria that are associated with the onset of gingival, periapical, and periodontal diseases, as well as oral cancer. Various strategies have been employed to prevent, control, and treat these disorders. Recently, techniques utilizing microbiota, like probiotics, microbiota transplantation, and the replacement of oral pathogens, have caught the eye. This extensive examination seeks to offer a…

Bifidobacteriumspecies are essential members of a healthy human gut microbiota. Their presence in the gut is associated with numerous health outcomes such as protection against gastrointestinal tract infections, inflammation, and metabolic diseases. Regular intake ofBifidobacteriumin foods is a sustainable way of maintaining the health benefits associated with its use as a probiotic. Owing to their global acceptance, fermented dairy products (particularly yogurt) are considered the ideal probiotic carrier foods. As envisioned in the definition of probiotics as “live organisms,” the therapeutic functionalities ofBifidobacteriumspp. depend on maintaining their viability in the foods up to the point of consumption. However, sustainingBifidobacteriumspp. viability during the manufacture and shelf-life of fermented dairy products remains challenging. Hence, this paper discusses the significance of viability as a prerequisite forBifidobacteriumspp. probiotic functionality. The paper focuses on the stress factors that influenceBifidobacteriumspp. viability during the manufacture and shelf…

The infant gut microbiota undergoes significant changes during early life, which are essential for immune system maturation, nutrient absorption, and metabolic programming. Among the various microbial metabolites, short-chain fatty acids (SCFAs), primarily acetate, propionate, and butyrate, produced through the fermentation of dietary fibers by gut bacteria, have emerged as critical modulators of host-microbiota interactions. SCFAs serve as energy sources for colonic cells and play pivotal roles in regulating immune responses, maintaining gut barrier integrity, and influencing systemic metabolic pathways. Recent research highlights the potential neuroprotective effects of SCFAs in pediatric populations. Disruptions in gut microbiota composition and SCFA production are increasingly associated with a range of pediatric health issues, including obesity, allergic disorders, inflammatory bowel disease (IBD), and neurodevelopmental disorders. This review synthesizes current knowledge on the role of microbiota-derived SCFAs in pediatric health, emphasizing their contributions from gut…

Cancer is the most common cause of human death worldwide, posing a serious threat to human health and having a negative impact on the economy. In the past few decades, significant progress has been made in anticancer therapies, but traditional anticancer therapies, including radiation therapy, surgery, chemotherapy, molecular targeted therapy, immunotherapy and antibody-drug conjugates (ADCs), have serious side effects, low specificity, and the emergence of drug resistance. Therefore, there is an urgent need to develop new treatment methods to improve efficacy and reduce side effects. Antimicrobial peptides (AMPs) exist in the innate immune system of various organisms. As the most promising alternatives to traditional drugs for treating cancers, some AMPs also have been proven to possess anticancer activities, which are defined as anticancer peptides (ACPs). These peptides have the advantages of being able to specifically target cancer cells and have less toxicity to normal tissues. More and more studies have found that marine and terrestrial animals contain a large amount of ACPs.…

The revival of the transmission dynamics of mosquito-borne diseases grants striking challenges to public health intensified by climate change worldwide. This inclusive review article examines multidimensional strategies and challenges linked to climate change and the epidemiology of mosquito-borne diseases such as malaria, dengue, Zika, chikungunya, and yellow fever. It delves into how the biology, pathogenic dynamics, and vector distribution of mosquitoes are influenced by continuously rising temperatures, modified rainfall patterns, and extreme climatic conditions. We also highlighted the high likelihood of malaria in Africa, dengue in Southeast Asia, and blowout of Aedes in North America and Europe. Modern predictive tools and developments in surveillance, including molecular gears, Geographic Information Systems (GIS), and remote sensing have boosted our capacity to predict epidemics. Integrated data management techniques and models based on climatic conditions provide a valuable understanding of public health planning. Based on recent data and expert ideas, the objective of…

Global climate change poses a significant threat to plant growth and crop yield and is exacerbated by environmental factors, such as drought, salinity, greenhouse gasses, and extreme temperatures. Plant growth-promoting rhizobacteria (PGPR) help plants withstand drought. However, the mechanisms underlying PGPR–plant interactions remain unclear. Thus, this study aimed to isolate PGPR, Bacillus megaterium strains CACC109 and CACC119, from a ginseng field and investigate the mechanisms underlying PGPR-stimulated tolerance to drought stress by evaluating their plant growth-promoting activities and effects on rice growth and stress tolerance through in vitro assays, pot experiments, and physiological and molecular analyses. Compared with B. megaterium type strain ATCC14581, CACC109 and CACC119 exhibited higher survival rates under osmotic stress, indicating their potential to enhance drought tolerance. Additionally, CACC109 and CACC119 strains exhibited various plant growth-promoting activities, including phosphate solubilization, nitrogen fixation, indole-3-acetic acid production,…

Large-scale outbreaks of virus-associated severe diarrhea have occurred in pig populations since 2010. To investigate the prevalence and genetic evolution of the diarrhea-associated viruses responsible for the outbreaks, we tested 1,791 diarrhea samples collected from 213 pig farms in five provinces in southern China between 2021 and 2023. The test results showed that porcine epidemic diarrhea virus (PEDV) was the most frequently detected virus. The prevalence rates ranged from 47.40 to 52.22% in samples and 76.06% (162/213) in pig farms. Porcine rotavirus (PoRV) was the second common virus, with prevalence rates ranging from 25.81 to 50.81% in samples and 72.77%(155/213) in pig farms. Porcine delta coronavirus (PDCoV) was the third common virus, with prevalence rates ranging from 16.33 to 17.48% in samples and 38.50% (82/213) in pig farms. The detection rates of both transmissible gastroenteritis virus (TGEV) and porcine acute diarrheal syndrome coronavirus (SADS-CoV) were very low, less than 1.01% in samples and less than 3.76% in pig farms. In this study, we found SADS-CoV only…

This study investigated the microbial community in three-color sauce-flavor Daqu (black, yellow, and white) throughout their maturation processes, together with their physicochemical factors, culturable microbes, flavor components, and fermenting vitalities. Results from high-throughput sequencing revealed distinct microbial diversity, with more pronounced variations in bacterial community than in fungal community. Firmicutes and Ascomycota emerged as the most dominant bacterial and fungal phyla, respectively, during maturation. Genus-level analysis identified Kroppenstedia, Virgibacillus, and Bacillus as dominant bacteria in black Daqu, yellow Daqu, and white Daqu, severally, while Thermoascus was shared as the core dominant fungi for these Daqu. Physicochemical factors, particularly acidity, were found to exert a significant impact on microbial community. Kroppenstedtia was the key bacteria influencing the color formation of these Daqu. Furthermore, correlations between dominant microbes and flavor compounds highlighted their role in Daqu quality. Molds (Aspergillus, Rhizomucor,…

Rosacea is an inflammatory skin disease involving diverse symptoms with a variable clinical progress which can severely impact the patient's quality of life as well as their mental health. The pathophysiological model of rosacea involves an unbalanced immune system predisposed to excessive inflammation, in addition to vascular and nervous alterations, being certain cutaneous microorganisms' triggers of the symptoms onset. The gut-skin axis explains a bidirectional interaction between skin and gut microbiota in some inflammatory skin diseases such as atopic dermatitis, psoriasis, or rosacea. The introduction and consolidation of the next-generation sequencing in recent years has provided unprecedented information about the microbiome. However, the characterization of the gut and skin microbiota and the impact of the gut-skin axis in patients with rosacea has been little explored, in contrast to other inflammatory skin diseases such as atopic dermatitis or psoriasis. Furthermore, the clinical evolution of patients with rosacea is not always adequate and it is common for them to…

The microbiota, intensely intertwined with mammalian physiology, significantly impacts health, productivity, and reproductive functions. The normal microbiota interacts with the host through the following key mechanisms: acting as a protective barrier against pathogens, maintain mucosal barrier integrity, assisting in nutrient metabolism, and modulating of the immune response. Therefore, supporting growth and development of host, and providing protection against pathogens and toxic substances. The microbiota significantly influences brain development and behavior, as demonstrated by comprehensive findings from controlled laboratory experiments and human clinical studies. The prospects suggested that gut microbiome influence neurodevelopmental processes, modulate stress responses, and affect cognitive function through the gut-brain axis. Microbiota in the gastrointestinal tract of farm animals break down and ferment the ingested feed into nutrients, utilize to produce meat and milk. Among the beneficial by-products of gut microbiota, short-chain fatty acids (SCFAs) are particularly…

Oral health is critical for total body health and well-being; however, little improvement in oral health status has occurred in the U.S. over the past 20 years. Tooth decay and gum disease remain highly prevalent, with more than 90% and 50% of adults suffering from these conditions, respectively. To combat this lack of improvement, alternative approaches to dental care are now being suggested. One such alternative therapy is probiotics for oral care. In the oral cavity, probiotic strains have been shown to reduce levels of oral pathogens, inhibit the formation of dental caries, and reduce the levels of bacteria that cause halitosis. However, as the oral care probiotic market expands, many products contain bacterial species and strains with no documented health benefits leading to confusion and mistrust among consumers and clinicians. This confusion is enhanced by the regulatory status of probiotic products which puts the onus of safety and efficacy on the manufacturer rather than a central regulatory body. The overarching goal of this review is to provide consumers and clinicians…

Introduction: Antimicrobial resistance (AMR) is a global health problem that requires early and effective treatments to prevent the indiscriminate use of antimicrobial drugs and the outcome of infections. Mass Spectrometry (MS), and more particularly MALDI-TOF, have been widely adopted by routine clinical microbiology laboratories to identify bacterial species and detect AMR. The analysis of AMR with deep learning is still recent, and most models depend on filters and preprocessing techniques manually applied on spectra. Methods: This study propose a deep neural network, MSDeepAMR, to learn from raw mass spectra to predict AMR. MSDeepAMR model was implemented for Escherichia coli, Klebsiella pneumoniae, and Staphylococcus aureus under different antibiotic resistance profiles. Additionally, a transfer learning test was performed to study the benefits of adapting the previously trained models to external data. Results: MSDeepAMR models showed a good classification performance to detect antibiotic resistance. The AUROC of the model was above 0.83 in most cases studied, improving the…

Introduction Endophytes are colonizers of healthy plants and they normally exhibit biocontrol activities, such as reducing the occurrence of plant diseases and promoting plant growth. The endophytic bacterium Bacillus halotolerans Q2H2 (Q2H2) was isolated from the roots of potato plants and was found to have an antagonistic effect on pathogenic fungi. Methods Q2H2 was identified by morphological observations, physiological and biochemical identification, and 16S rRNA gene sequence analysis. Genes related to the anti-fungal and growth-promoting effects were analyzed using whole-genome sequencing and comparative genomic analysis. Finally, we analyzed the growth-promoting and biocontrol activities of Q2H2 in potato plants using pot experiments. Results Antagonism and non-volatile substance plate tests showed that Q2H2 had strong antagonism against Fusarium oxysporum , Fusarium commune , Fusarium graminearum , Fusarium brachygibbosum , Rhizoctonia solani and Stemphylium solani . The plate test showed that Q2H2 had the ability to produce proteases, cellulases, β-1,3-glucanase, dissolved…

The growing threat of antimicrobial resistance (AMR) has underlined the need for a sustained supply of novel antimicrobial agents. Endophyte microorganism that reside within plant tissues as symbionts have been the source of potential antimicrobial substances. However, many novel and potent antimicrobials are yet to be discovered from these endophytes. The present study investigates the potential of endophytic fungi as a source of novel bioactive chemicals with antibacterial capabilities. These fungi synthesize secondary metabolites such as polyketides and peptides via polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) pathways. Notable substances, like prenylated indole alkaloids and fumaric acid, have shown promising antibacterial and antifungal properties against multidrug-resistant infectious agents. This review also emphasizes the symbiotic link between endophytes and their host plants, which is critical for secondary metabolite production. The study focuses on the significance of isolation methods for endophytes and proposes their use in for sustainable…

Plants establish specific interactions with microorganisms, which are vital for promoting growth and resilience. Although advancements in microbiome modulation technologies show great potential for sustainable agriculture, several challenges have hindered the wider application of plant microbiomes in the field. These challenges may include inconsistent microbial colonization, competition with native microbiota, and environmental variability. Current strategies, while promising, often yield inconsistent results in real-world agricultural settings, highlighting the need for more refined approaches. Agricultural practices and plant genotypes significantly influence the composition and function of plant-associated microbiota. A data-driven strategy that incorporates genomic profiling, environmental assessments, and optimized delivery systems is essential for selecting effective microbial strains. Additionally, refining farming practices, such as crop rotation, intercropping, and reduced tillage, along with robust plant breeding programs, can greatly enhance crop health and productivity.

Background Multidrug-resistant Klebsiella pneumoniae (MDR-KP) poses a significant global health threat due to its involvement in severe infections and high mortality rates. The emergence of MDR strains necessitates the exploration of alternative therapeutic strategies. Methods K. pneumoniae isolates were obtained from human and animal sources. Antibacterial susceptibility testing was performed, followed by the evaluation of essential oil activity through inhibition zone, MIC, and MBC determinations. Checkerboard assays were conducted to assess synergistic effects with amikacin. Gene expression analysis and transmission electron microscopy were employed to elucidate the mechanisms of action. Molecular docking studies were performed to identify potential binding targets of bioactive compounds. Results Klebsiella pneumoniae was isolated from 25 of the100 samples examined, representing a prevalence rate of 25%. All isolates were found to be multidrug-resistant. Tea tree and thyme essential oils exhibited potent antibacterial activity and synergistic effects with amikacin. Notably, these…

Background: Flavivirus pose a continued threat to global health, yet their worldwide burden and trends remain poorly quantified. We aimed to evaluate the global, regional, and national incidence of three common flavivirus infections (Dengue, yellow fever, and Zika) from 2011 to 2021. Methods: Data on the number and rate of incidence for the three common flavivirus infection in 204 countries and territories were retrieved from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2021. The estimated annual percent change (EAPC) was calculated to quantify the temporal trend during 2011-2016, 2016-2019, and 2019-2021, respectively. Results: In 2021, an estimated 59,220,428 individuals were infected globally, comprising 58,964,185 cases of dengue, 86,509 cases of yellow fever, and 169,734 cases of Zika virus infection. The age-standardized incidence rate (ASIR) of the three common flavivirus infections increased by an annual average of 5.08% (95% CI 4.12 to 6.05) globally from 2011 to 2016, whereas decreased by an annual average of -8.37% (95% CI -12.46 to -4.08) per…

Bacteria and fungi tend to coexist within biofilms instead of in planktonic states. Usually, such communities include cross-kingdom microorganisms, which make them harder to remove from abiotic surfaces or infection sites. Additionally, the produced biofilm matrix protects embedded microorganisms from antibiotics, disinfectants, or the host immune system. Therefore, classic therapies based on antibiotics might be ineffective, especially when multidrug-resistant bacteria are causative factors. The complexities surrounding the eradication of biofilms from diverse surfaces and the human body have spurred the exploration of alternative therapeutic modalities. Among these options, bacteriophages and their enzymatic counterparts have emerged as promising candidates, either employed independently or in synergy with antibiotics and other agents. Phages are natural bacteria killers because of mechanisms of action that differ from antibiotics, phages might answer worldwide problems with bacterial infections. In this review, we report the attempts to use bacteriophages in combating…

Porcine epidemic diarrhea virus (PEDV) is a single-stranded RNA virus with a capsid membrane that causes acute infectious gastrointestinal disease characterized by vomiting, diarrhea, and dehydration in swine. Piglets are more susceptible to PEDV than adults, with an infection rate reaching 90% and a fatality rate as high as 100%. Moreover, PEDV has a rapid transmission rate and broad transmission range. Consequently, PEDV has caused considerable economic losses and negatively impacted the sustainability of the pig industry. The surface spike (S) glycoprotein is the largest structural protein in PEDV virions and is closely associated with host cell fusion and virus invasion. As such, the S protein is an important target for vaccine development. In this article, we review the genetic variation, immunity, apoptosis-induction function, virulence, vaccine potential, and other aspects of the PEDV S protein. This review provides a theoretical foundation for preventing and controlling PEDV infection and serves as a valuable resource for further research and development of PEDV vaccines.

Leptospirosis, one of the most common global zoonotic infections, significantly impacts global human health, infecting more than a million people and causing approximately 60,000 deaths annually. This mini-review explores effective treatment strategies for leptospirosis, considering its epidemiology, clinical manifestations, and current therapeutic approaches. Emphasis is placed on antibiotic therapy, including recommendations for mild and severe cases, as well as the role of probiotics in modulating the gut microbiota. Furthermore, novel treatment options, such as bacteriophages and newly synthesized/natural compounds, are discussed, and the findings are expected to provide insights into promising approaches for combating leptospirosis.

MicroRNAs (miRNAs) are a class of small non-coding RNAs, typically 20-25 nucleotides in length, that play a crucial role in regulating gene expression post-transcriptionally. They are involved in various biological processes such as plant growth, development, stress response, and hormone signaling pathways. Plants interact with microbes through multiple mechanisms, including mutually beneficial symbiotic relationships and complex defense strategies against pathogen invasions. These defense strategies encompass physical barriers, biochemical defenses, signal recognition and transduction, as well as systemic acquired resistance. MiRNAs play a central role in regulating the plant's innate immune response, activating or suppressing the transcription of specific genes that are directly involved in the plant's defense mechanisms against pathogens. Notably, miRNAs respond to pathogen attacks by modulating the balance of plant hormones such as salicylic acid, jasmonic acid, and ethylene, which are key in activating plant defense mechanisms. Moreover, miRNAs can cross boundaries into fungal…

Background: (MP) decreased significantly. At the beginning of the summer of 2023, there was an increasing trend of MP infection in China and the MP pneumonia (MPP) is surging when it comes to the school season and lasts for several months which has attracted widespread attention. Objective: This study aims to investigate the prevalent characteristics of the MP and the difference between the COVID-19 pandemic and the post in Shanghai, China. Methods: The demographic information and the results of laboratory pathogen detection from July 2021 to May 2024 were collected and analyzed to find out the prevalent characteristics of MP. Two periods, during the COVID-19 pandemic and the post-pandemic, were divided and compared. The P1 genotyping and macrolide resistance-associated gene of 23 s rRNA were detected using the remaining MP-positive samples. Results: During the COVID-19 pandemic, the prevalence of the MP has significantly decreased. Female children are more susceptible to MP infection than the male. The school-aged group (>6 years) had the highest infection rate. The rate of MP P1…

In recent years, overexplorations of ore and the growth of industries are the prime factors in the release of heavy metals in environments. As a result, the food crops and water bodies are contaminated with metals which may have several adverse effects on the health of humans and other living species. These metals and metalloids, such as Zn, Cu, Mn, Ni, Cr, Pb, Cd, and As, upset the biochemical pathways of metabolite synthesis in living organisms and contribute to the etiology of different diseases. Microorganisms include bacteria, archaea, viruses, and many unicellular eukaryotes, which can span three domains of life-Archaea, Bacteria, and Eukarya-and some microorganisms, such as cyanobacteria, have shown high efficiency in the biosorption rate of heavy metals. Cyanobacteria are suitable for bioremediation as they can grow in adverse environments, have a less negative impact on the surrounding environment, and are relatively cheaper to manage. The structure of cyanobacteria has shown no extensive internal-bound membranes, so it can directly employ the physiological mechanisms to…

Airborne fungi and bacteria have been extensively studied by researchers due to their significant effects on human health. We provided an overview of the distribution and sources of airborne pathogenic microbes, and a detailed description of the detrimental effects that these microorganisms cause to human health in both outdoor and indoor environments. By analyzing the large body of literature published in this field, we offered valuable insights into how airborne microbes influence our well-being. The findings highlight the harmful consequences associated with the exposure to airborne fungi and bacteria in a variety of natural and human-mediated environments. Certain demographic groups, including children and the elderly, immunocompromised individuals, and various categories of workers are particularly exposed and vulnerable to the detrimental effect on health of air microbial pollution. A number of studies performed up to date consistently identified Alternaria, Cladosporium, Penicillium, Aspergillus, and Fusarium as the predominant fungal genera in various indoor and outdoor…

Plants engage in a variety of interactions, including sharing nutrients through common mycorrhizal networks (CMNs), which are facilitated by arbuscular mycorrhizal fungi (AMF). These networks can promote the establishment, growth, and distribution of limited nutrients that are important for plant growth, which in turn benefits the entire network of plants. Interactions between plants and microbes in the rhizosphere are complex and can either be socialist or capitalist in nature, and the knowledge of these interactions is equally important for the progress of sustainable agricultural practice. In the socialist network, resources are distributed more evenly, providing benefits for all connected plants, such as symbiosis. For example, direct or indirect transfer of nutrients to plants, direct stimulation of growth through phytohormones, antagonism toward pathogenic microorganisms, and mitigation of stresses. For the capitalist network, AMF would be privately controlled for the profit of certain groups of plants, hence increasing competition between connected plants. Such plant…

Introduction: Microplastics (MPs) are widely distributed in the environment, causing damage to biota and human health. Due to their physicochemical characteristics, they become resistant particles to environmental degradation, leading to their accumulation in large quantities in the terrestrial ecosystem. Thus, there is an urgent need for measures to mitigate such pollution, with biological degradation being a viable alternative, where bacteria play a crucial role, demonstrating high efficiency in degrading various types of MPs. Therefore, the study aimed to identify bacteria with the potential for MP biodegradation and the enzymes produced during the process. Methods: The methodology used followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) protocol. Results and Discussion: as the main organisms involved in MP biodegradation. Additionally, enzymes such as hydrolases and alkane hydroxylases were emphasized for their involvement in this process. Thus, the potential of bacterial biodegradation is emphasized as a promising pathway to mitigate the…

Endometriosis is classically defined as a chronic inflammatory heterogeneous disorder occurring in any part of the body, characterized by estrogen-driven periodic bleeding, proliferation, and fibrosis of ectopic endometrial glands and stroma outside the uterus. Endometriosis can take overwhelmingly serious damage to the structure and function of multi-organ, even impair whole-body systems, resulting in severe dysmenorrhea, chronic pelvic pain, infertility, fatigue and depression in 5-10% women of reproductive age. Precisely because of a huge deficiency of cognition about underlying etiology and complex pathogenesis of the debilitating disease, early diagnosis and treatment modalities with relatively minor side effects become bottlenecks in endometriosis. Thus, endometriosis warrants deeper exploration and expanded investigation in pathogenesis. The gut microbiota plays a significant role in chronic diseases in humans by acting as an important participant and regulator in the metabolism and immunity of the body. Increasingly, studies have shown that the gut microbiota is closely…

Soil salinization has become a major challenge that severely threatens crop growth and influences the productivity of agriculture. It is urgent to develop effective management measures to improve saline-alkali soil. Thus, in this study, soil properties, microbial communities, and function under desulfurization gypsum (DE), soil amendment (SA), farm manure (FA), and co-application of desulfurization gypsum, soil amendment, and farm manure (TA) in a field experiment were examined by high-throughput sequencing. The results showed that the application of modified materials is an effective approach in improving saline-alkali soil, especially TA treatment significantly increased the content of available phosphorus (AP), available potassium (AK), soil organic matter (SOM), and alkaline hydrolysis nitrogen (AHN) and decreased pH, bulk density (BD), and electrical conductivity (EC). The application of modified materials resulted in notable enhancement in fungal diversity and altered the composition and structure of the fungal community. Conversely, the effect on the bacterial community was…

The demand for lithium-ion batteries (LIBs) has dramatically increased in recent years due to their application in various electronic devices and electric vehicles (EVs). Great amount of LIB waste is generated, most of which ends up in landfills. LIB wastes contain substantial amounts of critical metals (such as Li, Co, Ni, Mn, and Cu) and can therefore serve as valuable secondary sources of these metals. Metal recovery from the black mass (shredded spent LIBs) can be achieved via bioleaching, a microbiology-based technology that is considered to be environmentally friendly, due to its lower costs and energy consumption compared to conventional pyrometallurgy or hydrometallurgy. However, the growth and metabolism of bioleaching microorganisms can be inhibited by dissolved metals. In this study, the indigenous acidophilic chemolithotrophs in a sediment from a highly acidic and metal-contaminated mine pit lake were enriched in a selective medium containing iron, sulfur, or both electron donors. The enriched culture with the highest growth and oxidation rate and the lowest microbial…

The best environment for plant growth and development contains certain essential metabolites. A broad category of metabolites known as "plant biostimulants" (PBs) includes biomolecules such as proteins, carbohydrates, lipids, and other secondary metabolites related to groups of terpenes, specific nitrogen-containing compounds, and benzene ring-conjugated compounds. The formation of biomolecules depends on both biotic and abiotic factors, such as the release of PB by plants, animals, and microorganisms, or it can result from the control of temperature, humidity, and pressure in the atmosphere, in the case of humic substances (HSs). Understanding the genomic outputs of the concerned organism (may be plants or others than them) becomes crucial for identifying the underlying behaviors that lead to the synthesis of these complex compounds. For the purposes of achieving the objectives of sustainable agriculture, detailed research on PBs is essential because they aid in increasing yield and other growth patterns of agro-economic crops. The regulation of homeostasis in the…

Preclinical evidence has firmly established a bidirectional interaction among the lung, gut, and gut microbiome. There are many complex communication pathways between the lung and intestine, which affect each other's balance. Some metabolites produced by intestinal microorganisms, intestinal immune cells, and immune factors enter lung tissue through blood circulation and participate in lung immune function. Altered gut-lung-microbiome interactions have been identified in rodent models and humans of several lung diseases such as pulmonary fibrosis, chronic obstructive pulmonary disease, lung cancer, asthma, etc. Emerging evidence suggests that microbial therapies can prevent and treat respiratory diseases, but it is unclear whether this association is a simple correlation with the pathological mechanisms of the disease or the result of causation. In this review, we summarize the complex and critical link between the gut microbiota and the lung, as well as the influence and mechanism of the gut microbiota on respiratory diseases, and discuss the role of interventions such as…

Background Terminalia chebula Retz, known as the King of Tibet, is considered a functional food in China, celebrated for its antioxidant, immune-modulating, antibacterial, and anti-inflammatory properties. Chebulinic acid, derived from aqueous extracts of Terminalia chebula Retz, is known for its anti-inflammatory properties. However, its potential as an anti- Helicobacter pylori (HP) agent has not been fully explored. Methods Herein, we extracted the main compound from Terminalia chebula Retz using a semi-preparative liquid chromatography (LC) system and identified compound 5 as chebulinic acid through Ultra-high performance liquid chromatography-MS/MS (UPLC–MS/MS) and Nuclear Magnetic Resonance (NMR). To evaluate its role, we conducted minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) assays, scanning electron microscope (SEM) imaging, inhibiting kinetics curves, urea fast test, cell counting kit-8 (CCK-8) assay, western blot analysis, griess reagent system, and molecular docking. Results Our results showed that chebulinic acid effectively…

The fight against bacterial antibiotic resistance must be given critical attention to avert the current and emerging crisis of treating bacterial infections due to the inefficacy of clinically relevant antibiotics. Intrinsic genetic mutations and transferrable antibiotic resistance genes (ARGs) are at the core of the development of antibiotic resistance. However, traditional alignment methods for detecting ARGs have limitations. Artificial intelligence (AI) methods and approaches can potentially augment the detection of ARGs and identify antibiotic targets and antagonistic bactericidal and bacteriostatic molecules that are or can be developed as antibiotics. This review delves into the literature regarding the various AI methods and approaches for identifying and annotating ARGs, highlighting their potential and limitations. Specifically, we discuss methods for (1) direct identification and classification of ARGs from genome DNA sequences, (2) direct identification and classification from plasmid sequences, and (3) identification of putative ARGs from feature selection.

Introduction: Chlorhexidine (CHX) is a commonly used antiseptic in situations of limited oral hygiene ability such as after periodontal surgery. However, CHX is also considered as a possible factor in the emergence of cross-resistance to antibiotics. The aim of this study was to analyze the changes in the oral microbiota and the prevalence of antimicrobial resistance genes (ARGs) due to CHX treatment. Materials and methods: We analyzed the oral metagenome of 20 patients who applied a 0.2% CHX mouthwash twice daily for 4 weeks following periodontal surgical procedures. Saliva and supragingival plaque samples were examined before, directly after 4 weeks, and another 4 weeks after discontinuing the CHX treatment. Results: Alpha-diversity decreased significantly with CHX use. The Bray-Curtis dissimilarity increased in both sample sites and mainly streptococci showed a higher relative abundance after CHX treatment. Although no significant changes of ARGs could be detected, an increase in prevalence was found for genes that encode for tetracycline efflux pumps. Conclusion: CHX treatment…

In view of water and soil getting polluted by Pb(II), Zn(II), and other heavy metals in tailings and acid mine drainage (AMD), we explored the removal effect of sulfate-reducing bacteria (SRB) on Pb(II), Zn(II), and other pollutants in solution and tailings based on the microbial treatment technology. We used the scanning electron microscope-energy dispersive spectroscopy (SEM-EDS), X-ray diffraction (XRD), and X-ray fluorescence (XRF), to reveal the mechanism of SRB treatment of tailings. The results showed that SRB had a strong removal capacity for Zn(II) at 0–40 mg/L; however, Zn(II) at 60–100 mg/L inhibited the growth of SRB. Similarly, SRB exhibited a very strong ability to remove Pb(II) from the solution. At a Pb(II) concentration of 10–50 mg/L, its removal percentage by SRB was 100%. SRB treatment could effectively immobilize the pollutants leached from the tailings. With an increase in the amount of tailings added to each layer, the ability of SRB to treat the pollutants diminished. When 1 cm of tailingssand was added to each layer, SRB had the best effect on tailing sand…

Alginate lyases can fully degrade alginate into various size-defined unsaturated oligosaccharide products by β-elimination. Here, we identified the bifunctional endolytic alginate lyase Aly35 from the marine bacterium Vibrio sp. Strain H204. The enzyme Aly35 is classified into the polysaccharide lyase 7 superfamily and contains two alginate lyase catalytic domains. The relationship and function of the two lyase domains are not well known. Thus, the full-length recombinant enzyme and its truncated proteins Aly35-CD1 (catalytic domain 1), Aly35-CD2 (catalytic domain 2 domain) were constructed. The three enzymes showed similar biochemical characteristics and exhibited temperature and pH stability. Further research showed that Aly35 and Aly35-CD2 can efficiently degrade alginate, polymannuronate (PM) and polyguluronate (PG) into a series of unsaturated oligosaccharides, while Aly35-CD1 exhibits greater PM-degrading activity than that of Aly35-CD2 but can not degraded PG efficiently. The results suggest that the domain (Trp295-His582) is critical for PG-degrading activity, the domain has…

The role of sediment oxygen demand (SOD) in causing dissolved oxygen (DO) depletion is widely acknowledged, with previous studies mainly focusing on chemical and biological SOD separately. However, the relationship between the putative functions of sediment microbes and SOD, and their impact on DO depletion in overlying water, remains unclear. In this study, DO depletion was observed in the downstream of the Gan River during the summer. Sediments were sampled from three downstream sites (YZ, Down1, and Down2) and one upstream site (CK) as a control. Aquatic physicochemical parameters and SOD levels were measured, and microbial functions were inferred from taxonomic genes through analyses of the 16S rRNA gene. The results showed that DO depletion sites exhibited a higher SOD rate compared to CK. The microbial community structure was influenced by the spatial variation of Proteobacteria, Chloroflexi, and Bacteroidota, with total organic carbon (TOC) content acting as a significant environmental driver. A negative correlation was observed between microbial diversity and DO…

Selenium (Se) is a vital trace element integral to numerous biological processes in both plants and animals, with significant impacts on soil health and ecosystem stability. This review explores how soil microorganisms facilitate Se transformations through reduction, oxidation, methylation, and demethylation processes, thereby influencing the bioavailability and ecological functions of Se. The microbial reduction of Se compounds, particularly the conversion of selenate and selenite to elemental Se nanoparticles (SeNPs), enhances Se assimilation by plants and impacts soil productivity. Key microbial taxa, including bacteria such as Pseudomonas and Bacillu s, exhibit diverse mechanisms for Se reduction and play a substantial role in the global Se cycle. Understanding these microbial processes is essential for advancing soil management practices and improving ecosystem health. This review underscores the intricate interactions between Se and soil microorganisms, emphasizing their significance in maintaining ecological balance and promoting sustainable agricultural practices.

This review aims to comprehensively chronicle the biosynthesis, classification, properties, and applications of bacteriocins produced by Weissella genus strains, particularly emphasizing their potential benefits in food preservation, human health, and animal productivity. Lactic Acid Bacteria (LAB) are a class of microorganisms well-known for their beneficial role in food fermentation, probiotics, and human health. A notable property of LAB is that they can synthesize antimicrobial peptides known as bacteriocins that exhibit antimicrobial action against both closely related and other bacteria as well. Bacteriocins produced by Weissella spp. are known to exhibit antimicrobial activity against several pathogenic bacteria including food spoilage species, making them highly invaluable for potential application in food preservation and food safety. Importantly, they provide significant health benefits to humans, including combating infections, reducing inflammation, and modulating the gut microbiota. In addition to their applications in food fermentation and probiotics, Weissella…

Helicobacter pylori (H. pylori) is a strict microaerophilic bacterial species that exists in the stomach, and H. pylori infection is one of the most common chronic bacterial infections affecting humans. Eradicating H. pylori is the preferred method for the long-term prevention of complications such as chronic gastritis, peptic ulcers, gastric mucosa-associated lymphoid tissue lymphoma, and gastric cancer. However, first-line treatment with triple therapy and quadruple therapy has been unable to cope with increasing antibacterial resistance. To provide an updated review of H. pylori infections and antibacterial resistance, as well as related treatment options, we searched PubMed for articles published until March 2024. The key search terms were “H. pylori”, “H. pylori infection”, “H. pylori diseases”, “H. pylori eradication”, and “H. pylori antibacterial resistance.” Despite the use of antimicrobial agents, the annual decline in the eradication rate of H. pylori continues. Emerging eradication therapies, such as the development of the new strong acid blocker vonoprazan, probiotic…

Microalgae are vital for their photosynthetic abilities, contributing significantly to global oxygen production, serving as a key trophic level in aquatic ecosystems, aiding in biofuel production, assisting in wastewater treatment, and facilitating the synthesis of valuable biochemicals. Despite these advantages, photosynthetic microalgae are sensitive to salt stress, which alters their physiochemical and metabolic status, ultimately reducing microalgal growth. This sensitivity highlights the importance of understanding the impact of elevated salt content on the physiochemical, metabolic, and transcriptomic profiling of Scenedesmus sp., areas that are not yet fully understood. Our findings indicate that elevated salt stress decreases photosynthetic efficiency and increases non-regulated photochemical quenching of photosystem II (PSII). Moreover, PSII-driven linear electron flow (LEF) decreased, whereas photosystem I (PSI)-driven cyclic electron flow (CEF) increased in salt-stressed cells. To better understand the electron flow from PSII to PSI under elevated salt treatment, we…

High lead (Pb) levels in agricultural soil and wastewater threaten ecosystems and organism health. Microbial remediation is a cost-effective, efficient, and eco-friendly alternative to traditional physical or chemical methods for Pb remediation. Previous research indicates that micro-organisms employ various strategies to combat Pb pollution, including biosorption, bioprecipitation, biomineralization, and bioaccumulation. This study delves into recent advancements in Pb-remediation techniques utilizing bacteria, fungi, and microalgae, elucidating their detoxification pathways and the factors that influence Pb removal through specific case studies. It investigates how bacteria immobilize Pb by generating nanoparticles that convert dissolved lead (Pb-II) into less harmful forms to mitigate its adverse impacts. Furthermore, the current review explores the molecular-level mechanisms and genetic engineering techniques through which microbes develop resistance to Pb. We outline the challenges and potential avenues for research in microbial remediation of Pb-polluted habitats, exploring…

As antibiotic resistance increases and antibiotic development dwindles, new antimicrobial agents are needed. Recent advances in nanoscale engineering have increased interest in metal oxide nanoparticles, particularly zinc oxide nanoparticles, as antimicrobial agents. Zinc oxide nanoparticles are promising due to their broad-spectrum antibacterial activity and low production cost. Despite many studies demonstrating the effectiveness of zinc oxide nanoparticles, the antibacterial mechanism is still unknown. Previous work has implicated the role of reactive oxygen species such as hydrogen peroxide, physical damage of the cell envelope, and/or release of toxic Zn 2+ ions as possible mechanisms of action. To evaluate the role of these proposed methods, we assessed the susceptibility of S. aureus mutant strains, Δ katA and Δ mprF , to zinc oxide nanoparticles of approximately 50 nm in size. These assays demonstrated that hydrogen peroxide and electrostatic interactions are not crucial for mediating zinc oxide nanoparticle toxicity. Instead, we found that Zn 2+ accumulates in…

Background: Respiratory syncytial virus (RSV) is a common cause of upper and lower respiratory tract infections. This study aimed to explore the prevalence of respiratory syncytial virus (RSV) and other respiratory viruses in Bulgaria, characterize the genetic diversity of RSV strains, and perform amino acid sequence analyses of RSV surface and internal proteins. Methods: Clinical and epidemiological data and nasopharyngeal swabs were prospectively collected from patients with acute respiratory infections between October 2020 and May 2023. Real-time PCR for 13 respiratory viruses, whole-genome sequencing, phylogenetic, and amino acid analyses were performed. Results: This study included three epidemic seasons (2020-2021, 2021-2022, and 2022-2023) from week 40 of the previous year to week 20 of the following year. Of the 3,047 patients examined, 1,813 (59.5%) tested positive for at least one viral respiratory pathogen. RSV was the second most detected virus (10.9%) after SARS-CoV-2 (22%). Coinfections between RSV and other respiratory viruses were detected in 68 cases, including 14…

Colorectal cancer (CRC) is a common malignancy affecting the gastrointestinal tract worldwide. The etiology and progression of CRC are related to factors such as environmental influences, dietary structure, and genetic susceptibility. Intestinal microbiota can influence the integrity of the intestinal mucosal barrier and modulate intestinal immunity by secreting various metabolites. Dysbiosis of the intestinal microbiota can affect the metabolites of the microbial, leading to the accumulation of toxic metabolites, which can trigger chronic inflammation or DNA damage and ultimately lead to cellular carcinogenesis and the development of CRC. Postbiotics are preparations of inanimate microorganisms or their components that are beneficial to the health of the host, with the main components including bacterial components (e.g., exopolysaccharides, teichoic acids, surface layer protein) and metabolites (e.g., short-chain fatty acids, tryptophan metabolite, bile acids, vitamins and enzymes). Compared with traditional probiotics, it has a more stable chemical structure and higher safety. In…

Background As the field of probiotic research continues to expand, new beneficial strains are being discovered. The Christensenellaceae family and its newly described member, Christensenella minuta , have been shown to offer great health benefits. We aimed to extensively review the existing literature on these microorganisms to highlight the advantages of their use as probiotics and address some of the most challenging aspects of their commercial production and potential solutions. Methods We applied a simple search algorithm using the key words “ Christensenellaceae ” and “ Christensenella minuta ” to find all articles reporting the biotherapeutic effects of these microorganisms. Only articles reporting evidence-based results were reviewed. Results The review showed that Christensenella minuta has demonstrated numerous beneficial properties and a wider range of uses than previously thought. Moreover, it has been shown to be oxygen-tolerant, which is an immense advantage in the manufacturing and production of Christensenella minuta -based biotherapeutics. The results suggest that…

Background: Whole-genome sequencing (WGS) has contributed significantly to advancements in machine learning methods for predicting antimicrobial resistance (AMR). However, the comparisons of different methods for AMR prediction without requiring prior knowledge of resistance remains to be conducted. Methods: using three machine learning algorithms (random forest, support vector machine, and XGBoost) combined with k-mer features extracted from WGS data. Results: A cohort of 339 isolates was used for model construction. The average essential agreement and category agreement of the best models exceeded 90.90% (95%CI, 89.03-92.77%) and 95.29% (95%CI, 94.91-95.67%), respectively; the exceptions being levofloxacin, minocycline and imipenem. The very major error rates ranged from 0.0 to 5.71%. We applied feature selection pipelines to extract the top-ranked 11-mers to optimise training time and computing resources. This approach slightly improved the prediction performance and enabled us to obtain prediction results within 10 min. Notably, when employing these top-ranked 11-mers in an…

Genus Pseudomonas is a large assemblage of diverse microorganisms, not sharing a common evolutionary history. To clarify their evolutionary relationships and classification, we have conducted comprehensive phylogenomic and comparative analyses on 388 Pseudomonadaceae genomes. In phylogenomic trees, Pseudomonas species formed 12 main clusters, apart from the “Aeruginosa clade” containing its type species, P. aeruginosa . In parallel, our detailed analyses on protein sequences from Pseudomonadaceae genomes have identified 98 novel conserved signature indels (CSIs), which are uniquely shared by the species from different observed clades/groups. Six CSIs, which are exclusively shared by species from the “Aeruginosa clade,” provide reliable demarcation of this clade corresponding to the genus Pseudomonas sensu stricto in molecular terms. The remaining 92 identified CSIs are specific for nine other Pseudomonas species clades and the genera Azomonas and Azotobacter which branch in between them. The identified CSIs provide strong independent evidence of the genetic cohesiveness of these…

While significant progress has been made in understanding and applying gene silencing mechanisms and the treatment of human diseases, there have been still several obstacles in therapeutic use. For the first time, ONPATTRO, as the first small interfering RNA (siRNA) based drug was invented in 2018 for treatment of hTTR with polyneuropathy. Additionally, four other siRNA based drugs naming Givosiran, Inclisiran, Lumasiran, and Vutrisiran have been approved by the US Food and Drug Administration and the European Medicines Agency for clinical use by hitherto. In this review, we have discussed the key and promising advances in the development of siRNA-based drugs in preclinical and clinical stages, the impact of these molecules in bacterial and viral infection diseases, delivery system issues, the impact of administration methods, limitations of siRNA application and how to overcome them and a glimpse into future developments.

Biofilms account for a great deal of infectious diseases and contribute significantly to antimicrobial resistance. Efflux pumps confer antimicrobial resistance to microorganisms and involve multiple processes of biofilm formation. Efflux pump inhibitors (EPIs) are attracting considerable attention as a biofilm inhibition strategy. The regulatory functions of efflux pumps in biofilm formation such as mediating adherence, quorum sensing (QS) systems, and the expression of biofilm-associated genes have been increasingly identified. The versatile properties confer efflux pumps both positive and negative effects on biofilm formation. Furthermore, the expression and function of efflux pumps in biofilm formation are species-specific. Therefore, this review aims to detail the double-edged sword role of efflux pumps in biofilm formation to provide potential inhibition targets and give an overview of the effects of EPIs on biofilm formation.