Staphylococcus aureus is a common foodborne pathogen and a frequent cause of clinical infections. It forms dense biofilms by adhering to surfaces of objects or the human body, thereby reducing the bactericidal efficacy of antibiotics and disinfectants. This study aimed to investigate the inhibitory effect of Turkish gall extract on S. aureus biofilm formation and its potential molecular mechanisms. The minimum inhibitory concentration (MIC) of the extract was 56.25 µg/mL, and the minimum bactericidal concentration (MBC) was 112.5 µg/mL. Following treatment with the extract, extracellular AKP and nucleic acid content significantly increased, indicating disruption of bacterial cell wall membrane integrity. qRT-PCR analysis revealed that sarA gene expression was significantly downregulated during the initial biofilm adhesion stage; and during the biofilm aggregation and maturation phase, the icaADB gene cluster expression was significantly downregulated, while the expression of the negative regulator icaR was upregulated. The Turkish gall extract exhibits significant antibacterial activity against S. aureus and effectively suppresses its biofilm formation. This extract may directly cause bacterial death by disrupting cell wall membrane integrity. Simultaneously, it may interfere with initial bacterial adhesion and intercellular aggregation by affecting the transcriptional levels of sarA and ica operon-related genes, thereby inhibiting biofilm development at multiple stages. This study provides new strategies and theoretical basis for developing plant-derived anti-biofilm agents.
Kraft lignin (KL) generated from the pulp and paper industry is brown in color, and it causes damage to the aquatic environment and contributes to the toxicity of the effluent. However, through biodegradation, the KL structure can be modified, leading to more sustainable usage. Complex degradation techniques pose economic and environmental challenges. Hence, microbial systems are used as they are cost-effective and leave low residues. Previous studies have demonstrated that Serratia liquefaciens could be used for lignin biodegradation, but its complex structure posed challenges. To tackle this issue, process optimization was undertaken in the present study to enhance the conditions and increase degradation efficiency. In this study, the biodegradation potential of the ligninolytic bacteria Serratia liquefaciens was evaluated. Kraft lignin was characterized before and after bacterial treatment by instrumental analysis. Its biodegradation was optimized by Response Surface Methodology using Box-Behnken design. Toxicity evaluation was assessed in terms of phytotoxicity using Vigna radiata L. S. liquefaciens, with lignin peroxidase enzyme activity (22 IU ml− 1), degraded kraft lignin by 53
Plant growth-promoting rhizobacteria (PGPR) widely improve plant growth. Siderophore-producing bacteria (SPB) are a valuable PGPR type worthy of in-depth exploration. In this study, five SPB strains were selected as the research subjects. Pot experiments were conducted to evaluate their impact on maize growth in Alfisol. It was observed that the five SPB strains improved maize growth and nutrient uptake to varying degrees. Among them, CNRSB01 had the most significant effect. Compared with the control, CNRSB01 raised maize P, K, Ca, Mg, Fe, Mn, Cu and Zn content by 27.33
After Gastrodia elata was established as a source of both food and medicine, large-scale cultivation and extensive production and processing have led to an increase in substandard products. In order to explore the high utilization value of these unqualified products and their potential applications in livestock and poultry breeding, this study examined the effects of low-, medium-, and high-dose Gastrodia elata powder supplementation on serum biochemistry, gut bacterial and fungal diversity in broilers. Sixty 21-day-old broilers were randomly divided into control (CON), low- (LDG, 250 mg/kg), medium- (MDG, 500 mg/kg), and high-dose (HDG, 750 mg/kg) groups, with 5 replicates of 3 birds each. After 56 days, serum parameters were measured, and cecal bacterial and fungi were analyzed via 16S rRNA (V3–V4) and ITS gene amplicon sequencing. The results showed that dietary supplementation with Gastrodia elata powder had no significant effect on serum biochemical parameters. Dietary supplementation with Gastrodia elata powder modulated the intestinal bacterial structure. Specifically, the relative abundances of Oscillospira, Parasutterella, and Negativibacillus significantly decreased, while those of Ruminiclostridium, Erysipelatoclostridium, and Enterorhabdus significantly increased. Fungal diversity and relative abundance also responded to the supplementation: the Chao index of the HDG group was significantly higher than that of the CON group. Under the present experimental conditions, Gastrodia elata altered specific bacterial taxa and tended to modulate serum alkaline phosphatase (ALP) and high-density lipoprotein (HDL) levels.
Members of the phylum Actinomycetota are widely distributed across diverse environments and are well known for their metabolic versatility and capacity to produce bioactive compounds. In this study, strain ZE1316R2Aᵀ was isolated from the saline water collected from Lake Zima (Morocco) and subjected to comprehensive polyphasic taxonomic characterisation. Phylogenetic analysis based on the 16 S rRNA gene placed strain ZE1316R2Aᵀ within the genus Streptomyces, showing highest sequence similarity with S. albidoflavus DSM 40,455T (99.71
Microbial diversity during coffee fermentation has been suggested to be specific to each geographical region. However, more studies are required to understand yeast preference for a particular coffee variety, niche, their response to fermentation methods or to climate change. The aim of this study was to isolate and identify yeasts participating in fermentation of Coffea arabica L. cv. Catuaí from Boquete in the Republic of Panama using molecular data. We selectively targeted thermotolerant yeasts that may be further evaluated for their capacity to become starter cultures. The diversity of yeasts was surprisingly high: 32 OTUs out of 80 isolates. BLAST analyses of nuclear ribosomal internal transcribed spacers and 5.8S (i.e., ITS rDNA) sequences of all isolated strains, cultured during the fermentation process, showed they belong to five different clades corresponding to genera Clavispora, Nakaseomyces, Meyerozyma, Candida and Pichia. The major representative genera found at the beginning of the fermentation process were Clavispora and Meyerozyma. Pichia was cultured only after 8 hours of fermentation and persisted as the main isolated genus until the end of the process. With this method, two strains belonging to Pichia and one to Clavispora were selected as starter cultures producing coffee that ranked over 81 points in the Specialty Coffee Associations scale. An unexpectedly high species diversity was found, suggesting that previous studies using lower isolation temperatures may have missed several thermotolerant or thermophilic taxa. Thus, a method used to specifically isolate thermotolerant microorganisms was successfully applied to target potentially useful strains to create starter cultures in a fast and efficient manner.
Antimicrobial resistance (AMR) is increasingly recognized as an environmental and One Health problem driven by interconnected ecological, infrastructural, and anthropogenic processes. However, hyper-arid ecosystems remain underrepresented in most AMR research globally, despite rapid urbanization, widespread use of reclaimed water, and large-scale seawater desalination in the Arabian Gulf. This review examines the roles of ecological reservoirs and engineered water systems in the emergence and spread of AMR within hyper-arid Gulf ecosystems. Studies published from 2005 to 2025 in PubMed, Web of Science, Scopus, and Google Scholar were reviewed using a structured narrative process. The search terms encompassed concepts related to antimicrobial resistance, resistomes, dryland ecosystem(s), wastewater reuse and desalination, aerosols, livestock, wildlife, and One Health in the Arabian Gulf. Eligible studies included environmental surveillance studies, metagenomic analyses, and reports on AMR reservoirs or transmission routes relevant to arid environments. Evidence suggests that hyper-arid Gulf environments harbor interconnected AMR reservoirs in desert soils, wastewater treatment plants, reclaimed irrigation systems, wildlife-livestock interfaces, atmospheric dust, and coastal waters. Engineered water infrastructure, especially wastewater reuse and desalination, is a focal point for multispecies microbial interactions and horizontal gene transfer. Climatic stressors such as extreme aridity, high salinity, and dust storms, further promote the persistence and dissemination of antibiotic resistance genes (ARGs) and resistant microorganisms. AMR transmission in hyper-arid Gulf ecosystems is driven by the interplay between climatic stress, engineered water infrastructure and human–animal–environment interfaces. We propose a Gulf-specific One Health Transmission framework to guide environmental surveillance and mitigation efforts. Monitoring of soils, wastewater reuse systems, aerosols, wildlife, and coastal ecosystems should be strengthened and integrated into regional AMR control strategies.
Vermicomposting is a sustainable biotechnology application that encompasses conversion of organic waste into nutrientrich components through the combined activity of earthworms and their associated gut microbiota. In recent years, the role of earthworm gut microbes as key drivers of organic matter decomposition, nutrient cycling, and microbial community restructuring during vermicomposting have gained increased attention. The earthworm gut acts as a transient but highly active microenvironment characterized by enhanced enzymatic activity, selective microbial enrichment, and accelerated mineralization of organic substrates. Passage through the gut promotes the proliferation of functional microbial groups involved in carbon degradation, nitrogen transformation, and phosphorus solubilization, while simultaneously reducing wasteassociated and pathogenic microorganisms. Following excretion, castassociated processes further stabilize organic matter and support the development of beneficial microbial consortia in vermicompost. The resulting product is enriched in humic substances, plantavailable nutrients, and biologically active microbes that enrich soil structure, fertility, and plant growth, while contributing to pathogen suppression and sustainable waste management. Despite progress in our current knowledge, in this domain, our understanding remains largely incomplete on the earthworm-microbe interactions, microbes driven processes, shifts in microbial community during vermicomposting at the molecular level and the agronomic and environmental benefits of microbially enriched vermicompost. Therefore this review highlights mechanistic insights on the, (i) Gut associated processes (ii) Cast associated processes and (iii) Microbial dynamics in vermicomposting (iv) Community shifts, (iv) diversity, functions, and ecological significance of earthworm gutassociated microorganisms, microbe-earthworm interactions with roles in vermicomposting, (iv) and their contributions to vermicompost quality and soil–plant health, pathogen suppression. This review also highlights the need for metatranscriptomic and metabolomics based approaches to link microbial function with process performance and the road ahead with future research directions, towards microbial inoculation strategies, functional microbiome engineering, and integration of omics-based tools to optimize vermicomposting systems at industrial scales, towards advances in optimization and wider application of vermicomposting systems.
Fresh vegetables are essential human dietary components but are increasingly implicated in foodborne infections caused by Escherichia coli. Contamination may occur during cultivation, irrigation, handling, and retail display, and the presence of pathogenic or antimicrobial-resistant E. coli poses significant public health risks. Despite widespread vegetable consumption in Ogun State, Nigeria, limited data exist on the resistance and virulence characteristics of E. coli in these foods. This study therefore assessed antimicrobial resistance profiles and virulence genes in E. coli isolated from tomatoes, carrots, and cucumbers sold across three senatorial districts of Ogun State. A cross-sectional survey was conducted between March and October 2023, yielding 509 vegetable samples collected aseptically during three visits. Samples were enriched, cultured on MacConkey agar, and identified using standard microbiological methods. Thereafter, antimicrobial susceptibility testing was performed using the Kirby–Bauer disc diffusion method. Genomic DNA was extracted from the microbe, followed by Polymerase Chain Reaction (PCR) to detect key virulence (stx1, stx2, eae) and resistance (blaSHV, blaTEM, blaCTX, NDM, IMP, KPC, OXA-48) genes. Of the 509 vegetables analysed, 73 (14.4
Abstract Purpose The diversity of eukaryote communities formed in brackish waters along the southern coast of the Korean Peninsula was analyzed. Physico-chemical factors (temperature, pH, electrical conductivity, salinity, dissolved oxygen, and turbidity) were measured in the field. Methods eDNA metabarcoding was performed targeting the V4 region of 18 S rRNA using the Illumina MiSeq sequencing platform. The revealed eukaryotic communities abundantly included Arthropoda, Bacillariophyta, Basidiomycota, Ciliophora, Mollusca, and Nematoda at the phylum level. At the species level, Halicyclops sp., Leptocaris brevicornis , Spinileberis quadriaculeata , Melosira sp., Lentinula edodes , and Strombidinopsis sp. were included as dominant species with a relative abundance of > 10%. Results Depending on the dominance of eukaryote communities, the species composition and dominance of each species varied; this tendency could suggest a potential predation influence. Phytoplankton was dominant in the community with weak potential trophic influence, whereas Navicula was the dominant taxa with strong potential trophic influence. Furthermore, the community species diversity increased as the zooplankton species, which was responsible for the potential trophic influence. The plankton community is expected to be affected by environmental factors and the potential trophic influence of eukaryotes on each species. Particularly, salinity is a highly variable factor in estuaries. The abundance of Bacillariophyta increased under high salinity, whereas the abundance of Ciliophora and Nematoda increased under low salinity. Furthermore, the only terrestrially derived fungal plankton was detected in Songpo, which was expected to have lower salinity due to the strong influence of freshwater. These results suggest that despite the plankton communities forming at the estuaries sharing the same shore region, they can have different characteristics and a consistent tendency to be affected by biological and environmental factors. Conclusions Research raises the importance of information on biological and environmental factors for understanding eukaryote communities. Furthermore, it provides insight into the differences that exist between eukaryote communities in closely related environments.
Abstract Background Bacteriocins are peptides that demonstrate antimicrobial activity and are produced by bacteria. Bacillus velezensis is considered a reliable producer of bacteriocins, with a strong antimicrobial spectrum and antimicrobial activity. In this study, B. velezensis G7 isolated from mangrove plant roots was used as the experimental strain. Whole-genome sequencing (WGS) analysis was performed to annotate functional genes. Results The results demonstrated that B. velezensis G7 has a genome size of 3,894,836 bp, a GC content of 46.67%, and predicts 3,715 CDSs, 10 rRNA genes, and 83 tRNA genes. Gene annotation revealed pathways related to bacteriocin synthesis and immunity. Identified 8 bacteriocin and secondary metabolite biosynthetic gene clusters in B. velezensis G7, including Sactipeptides, LCI, Amylocyclicin, ComX4, Mersacidin, Lanthipeptide, Bacilysin, and NRPS. The crude protein from B. velezensis G7 shows broad-spectrum antibacterial activity, with the strongest inhibition against Listeria monocytogenes and the weakest against Staphylococcus aureus . Conclusions The genome of B. velezensis G7 was analyzed, and bacteriocin-related genes were identified. The results suggest that B. velezensis G7 has the potential to produce bacteriocins, thereby providing a theoretical basis for future studies on bacteriocin production in B. velezensis . In addition, these findings may facilitate further advances in bacteriocin research and bioinformatics analysis.
Abstract Objectives This study aimed to characterize drug-resistant Streptococcus spp. isolated from food and human sources in Upper Egypt, focusing on their virulence and antimicrobial resistance profiles, and to evaluate the in vitro antibacterial activity of an oregano essential oil nanoemulsion. Materials and methods A total of 440 food and human samples were collected in Aswan, Upper Egypt, and screened using conventional microbiological methods. Molecular confirmation was performed by detecting the tuf gene, followed by species identification using the 16 S rRNA and spn9802 genes. Selected virulence (scpB, Rib, Lmb, and cylE) and resistance (aac6-aph2, pbp1A, and tetO) genes were detected by PCR. Antimicrobial susceptibility testing and the multiple antibiotic resistance (MAR) index were determined. The antibacterial activity of the oregano nanoemulsion was assessed using inhibition zone assays at varying concentrations. Results Streptococcus spp. were detected in 22% of samples, with higher prevalence in throat swabs (34%) and raw milk (21.9%). Predominant species included S. agalactiae, S. pyogenes, S. dysgalactiae, S. pneumoniae, and S. uberis. Virulence genes were variably distributed, with scpB (33%) and cylE (31.8%) most frequent. Resistance genes were moderately detected, particularly tetO (21.2%). Most isolates were resistant to β-lactams but fully susceptible to ceftaroline and fosfomycin; the mean MAR index was 0.477. The oregano nanoemulsion showed concentration-dependent antibacterial activity. Conclusion Drug-resistant Streptococcus spp. from food and human sources in Upper Egypt carry important virulence and resistance determinants. The oregano essential oil nanoemulsion demonstrated promising in vitro antibacterial activity, suggesting potential as a natural antimicrobial; however, further in vivo and safety studies are required.
Abstract Purpose Staphylococcal contamination of smoked fish represents a public health concern, particularly in informal food markets. This study investigated the microbial risk associated with Staphylococcus-contaminated smoked fish, processing practices, and potential public health implications in Benin City, Nigeria. Structured questionnaires were administered to smoked fish vendors to document processing, handling, and storage practices. Materials and methods Smoked fish samples (Scomber, Meluza, Sese, catfish, and herring) were collected and analyzed using standard culture-based and molecular techniques. Questionnaire data were analyzed using chi-square and correlation analyses. Quantitative Microbial Risk Assessment (QMRA) was conducted to estimate the probability of adverse health outcomes following consumption of contaminated fish, using the exponential dose–response model. Results The results showed that 98% of the smoked fish samples were contaminated with Staphylococcus species, including coagulase-positive strains. Methicillin-resistant Staphylococcus aureus (MRSA) was detected in 37.78% of the samples. Fish stored for more than two days post-smoking exhibited significantly higher bacterial counts (p < 0.05), with marked logarithmic increases observed within 24–48 h after smoking. Scomber and Meluza samples had significantly higher staphylococcal loads than those of other fish species. The use of preservatives, vendors’ awareness of bacterial contamination, and the type of smoking material (wood or sawdust) did not significantly (p > 0.05) influence bacterial loads. QMRA outcomes indicated a high predicted probability (> 90%) of adverse health effects under ambient storage conditions over 2–4 d. Conclusion These findings underscore the need for improved hygiene practices, enhanced consumer and vendor education, better preservation strategies, and stricter regulatory oversight to reduce the risk of staphylococcal foodborne illnesses associated with smoked fish consumption.
Abstract Background The fluctuations in the growth of the thermophilic cyanobacterium Oscillatoria terebriformis population dynamics, environmental drivers, seasonal abundance, and the fluctuations in the expression of cellular proteins were recorded from sulfur water hot springs during high temperature environmental conditions. This study aimed to determine the effect of temperature on the growth of O. terebriformis. Methods The growth curve of O. terebriformis was investigated on BG11 at the two different optimum temperatures (± 30 °C and ± 40 °C) to dissect the impact of the temperature change on growth. Furthermore, high temperature-induced cellular proteins were characterized and identified using SDS-PAGE technique and mass spectrometry analysis, respectively. Results At the eighth day of cultivation, O. terebriformis recorded high optical density in case of both studied temperatures. Concerning the expression of the cellular proteins, several polypeptides running at approximately 120, 85, 70, 50, 35, 30, and 20 kDa were significantly upregulated downstream of the high temperature stress conditions specifically at 70 °C. Induction of protein overexpression was detected in O. terebriformis samples incubated at 70 °C (as high temperature stress). Three unique polypeptides, running at approximately 35, 30, and 20 kDa were analyzed by nano HPLC–ESI–MS/MS mass spectrometry. The first and third polypeptides were identified as biopolymer transport inner membrane (Energy transduction protein D:ExbD) protein. The second polypeptide was identified as orotate phosphoribosyl transferase (OPRT) protein. The identified proteins are involved in iron transport/heat stress response and pyrimidine biosynthesis, respectively. The High temperature-induced proteins most likely contributed to thermotolerance cascades regulating the fluctuations in O. terebriformis during temperature changes, specifically at high temperature conditions. The impact of temperature stress on the expression pattern of some O. terebriformis proteins was studied to delineate the thermotolerance underpinning seasonal temperature changes. Conclusions The results of this study may provide a better understanding of the cellular defense mechanisms against temperature stress in cyanobacteria, specifically thermophilic O. terebriformis.
Abstract Background Soil fungi play important roles in organic matter decomposition, nutrient cycling, and plant-soil interactions. However, their responses to contrasting farming systems, input intensity, crop phenology, and climatic variability in tropical agroecosystems remain insufficiently documented particularly in Sub-Saharan Africa where long-term datasets are scarce. Methods This study assessed soil fungal diversity and community composition after more than 15 years of continuous management in the Farming Systems Comparison in the Tropics (SysCom) trial at two Kenyan sites representing contrasting agroecological conditions: a humid highland site (Chuka) and semi-arid site (Thika). Four farming systems were evaluated: conventional high input (Conv-High), conventional low input (Conv-Low), organic high input (Org-High), and organic low input (Org-Low). Soil samples were collected across key crop growth stages in cereal- and potato-based rotations. Fungal communities were characterized using ITS-based Illumina MiSeq sequencing and analyzed using DADA2 and phyloseq. Prior to diversity analyses, sequence data were rarefied to an equal sequencing depth to account for uneven sequencing effort (17,500 reads per sample for Chuka and 32,300 reads per sample for Thika). Alpha and beta diversity, ordination, and exploratory differential abundance analyses were conducted in relation to soil chemical properties and site conditions. Results Fungal community composition varied across farming systems, input intensity, crop growth stages, seasons, and sites. Differences in alpha diversity were generally modest and context-dependent across sites and seasons, whereas clearer patterns were observed in community composition. Organic systems were frequently associated with higher relative abundances of taxa such as Mortierella, Purpureocillium, Beauveria, Serendipita, and Flammulina, while conventional systems were more often associated with taxa including Fusidium, Cladosporium, Alternaria, and Wallemia. Associations between fungal community composition and soil chemical variables particularly ammonium-N, available phosphorus, and pH were detected at the semi-arid Thika site but not at the humid Chuka site, highlighting strong site-specific responses. Crop growth stage and season were also associated with shifts in the relative abundance of fungal taxa, as indicated by exploratory differential abundance analyses. Conclusions This long-term study shows that soil fungal community composition in Kenyan tropical agroecosystems varies with management intensity, crop development, and site conditions. The findings underscore the importance of long-term, context-aware research for understanding how diversified nutrient management and cropping practices are associated with soil fungal community patterns in tropical farming systems.
Abstract Background The global market for dietary supplements and probiotic products has expanded rapidly in recent years, raising concerns regarding product quality, regulatory compliance and consumer safety. As probiotic benefits depend on maintaining adequate viable microbial counts throughout shelf life, this study aimed to evaluate the accuracy of product labelling with respect to labelled viable counts and strain composition. Therefore, a total of 28 commercially available probiotic products in various formulations, including capsules, suspensions, powders, drops, chocolate bars, and chewable tablets, were analysed. Colony-forming units (CFU) counts were determined by standard plate counting, while microbial composition was assessed using DNA-based 16S rRNA and ITS sequencing. Results 46.43% of the commercial probiotics tested exhibited CFU counts lower than the labelled values, including two chocolate bars, two powders, one suspension, one drop formulation, and seven freeze-dried capsule products. However, the greatest discrepancy was observed in both chocolate products (#3, #4), where the reduction exceeded 1.5 log(CFU) compared to the labelled counts. DNA analysis confirmed the presence of most labelled species; however, products containing more than three strains showed discrepancies from the label. Furthermore, outdated strain names were used on the labels of several products, highlighting the need to align them with current taxonomic standards. Conclusion The findings reveal considerable inconsistencies between labelled and actual microbial content in a substantial proportion of commercial probiotic products. These discrepancies, underscore the need for improved quality control, accurate labelling practices and stronger regulatory oversight to ensure consumer safety and compliance with current scientific and regulatory standards.
Two Gram-positive, facultatively anaerobic, motile, rod-shaped Bacillus isolates—designated FPIN1 and FPIN2—were obtained from Ngari, a traditional fermented fish product of Manipur, India, during the exploration of indigenous functional probiotic microorganisms. The isolates were subjected to comprehensive safety and probiotic evaluations, including assessments of hemolytic and DNase activities, antibiotic susceptibility, acid and bile salt tolerance, phenol and NaCl tolerance, temperature adaptability, auto-aggregation, and adhesion to epithelial cells. Molecular identification was performed through 16S rRNA gene sequencing and phylogenetic analysis. Both isolates exhibited non-hemolytic and DNase-negative phenotypes, confirming their non-pathogenic nature. Antibiotic susceptibility profiling revealed sensitivity to a wide spectrum of clinically important antibiotics, minimizing potential risks of antibiotic resistance transfer. Strains FPIN1 and FPIN2 demonstrated exceptional physiological resilience, showing optimal growth at 37 °C, strong acid tolerance (47–52
Abstract Objective To investigate the effects of Bacillus subtilis GYH20240327-1, isolated from traditional fermented yogurt, on the rhizosphere microbiomics and metabolomics of Platycodon grandiflorus and Scutellaria baicalensis Georgi. Methods The Bacillus subtilis strain was isolated from yogurt, applied to fertilizer, and used in the planting field. By measuring four apparent plant growth indicators, high-throughput sequencing (16S rRNA and ITS), and LC-MS-based metabolomics analysis of related rhizosphere soil samples, we preliminarily explored and compared the effects of Bacillus subtilis-containing fertilizer on the growth and development, microbial communities, and metabolite profiles of two medicinal plants. Results The results show that fertilization treatment has a certain growth-promoting effect on Platycodon grandiflorus and Scutellaria baicalensis during the critical three-month period from flowering to harvest, and it also reshapes their rhizosphere microbial communities. In Platycodon grandiflorus soil, the abundances of Acidobacteriota and Gemmatimonadota increased, while Proteobacteria decreased. In Scutellaria baicalensis soil, Basidiomycota increased, whereas Ascomycota and Mortierellomycota decreased. Metabolomics revealed significant enrichment in pathways for plant hormone biosynthesis, linoleic acid metabolism, biosynthesis of plant secondary metabolites, and vitamin B6 metabolism. Conclusion Bacillus subtilis GYH20240327-1 can effectively promote the growth and development of the rhizosphere of medicinal plants, alter the soil microbial community structure, and affect the composition of plant metabolites, showing its potential as a biofertilizer to improve cultivation efficiency.
Milk-borne lactic acid bacteria (LAB) and Gram-negative co-colonizers, such as Limnobacter and Burkholderia, often coexist in early life. However, the mechanisms underlying the dominance of LAB in these niches remain unclear. This study aimed to elucidate potential factors contributing to LAB predominance by integrating physiological, molecular, and computational analyses of Gram-negative isolates alongside LAB antagonism assays. From previously surveyed human milk and infant stool samples, nine Gram-negative isolates (Limnobacter spp., L. thiooxidans, Burkholderia glathei) were obtained and identified using 16 S rRNA maximum-likelihood phylogeny. All isolates were Gram-negative, motile, catalase-positive, non-sporulating mesophilic rods exhibiting oxidative metabolism utilizing tricarboxylic acid intermediates and glutamate. The isolates survived but did not proliferate at pH 3.0 and exhibited 0.3–0.6 log growth penalties in 0.5
GacA is a regulatory protein that facilitates various metabolic processes in Pseudomonas species, including the two-component system, denitrification, carbon metabolism, and biofilm formation. This protein is crucial for converting short-term infections into chronic ones and for facilitating symbiotic relationships. It regulates the development of biofilms and the maturation of carbon. The GacA mutant showed a significant reduction in growth rate relative to the wild-type A1501. In the study, we examined alterations in gene expression throughout the entire genome of P. stutzeri A1501 at 6 and 8-h time points to provide a comprehensive overview of the growing transcriptome. The proliferation of the strain under investigation was monitored using minimal media. The analysis of the transcriptome demonstrated varied expression across several genes. We detected significant changes in the expression levels of narH, narJ, narI, algA, and eda1. Additionally, a confirmation investigation utilizing quantitative polymerase chain reaction (RT-qPCR) was conducted on nine genes in total. The analytical results exhibited comparable expression patterns consistent with the transcriptome analysis findings. The analysis was conducted on both the wild-type and gacA mutant strains, which were cultured in K-medium. Transcriptome data analysis indicates that the GacA response regulator is implicated in denitrification, carbon metabolism, biofilm formation. Transcriptional data shows how gacA gene loss affects downstream genes necessary for extreme survival. Thus, a gacA deficiency disturbs this complex post-transcriptional regulatory cascade, altering gene expression and affecting physiological activities essential for adaptation and survival. It was not reported earlier that a gacA mutation leads to impairment in growth, which has significant implications for carbon metabolism and biofilm formation.
