AMB Express最新文献

The secondary metabolite A40926, a precursor to the glycopeptide antibiotic dalbavancin, is synthesized by the rare actinomycete Nonomuraea gerenzanensis (N. gerenzanensis) within the pharmaceutical industry. The biosynthesis of A40926 is accompanied by the production of an orange pigment, which poses significant challenges and incurs high costs in the purification process of A40926. To identify this orange pigment, a comprehensive analysis was conducted, including the examination of the biosynthetic gene cluster, potential biosynthetic pathways, purification processes, and structural identification. Additionally, the ispF gene, which encodes the enzyme 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase and is implicated in the biosynthesis of orange pigment, was deleted using the CRISPR/Cas9 system. To enhance A40926 production in the ΔIspF mutant, the overexpression of the cyclic AMP receptor protein (Crp) was implemented to assess its regulatory impact on A40926 biosynthesis. Consequently, the orange pigment produced by N. gerenzanensis was identified as lycopene, synthesized via the methylerythritol phosphate (MEP) pathway. Although the ΔIspF mutant was unable to biosynthesize the orange pigment, its production of A40926 was adversely affected and was lower than that of the original strain. Consequently, the overexpression of the global regulator Crp significantly enhanced A40926 production, achieving a yield of 841.1 mg/L. The investigation of pigment-free mutants presented in this study offers valuable insights for effectively reducing production costs within the microbial pharmaceutical industry.

The diamine oxidase from Glutamicibacter halophytocola (DAO-GH) was recombinantly produced in K. phaffii using the constitutive glyceraldehyde-3-phosphate dehydrogenase promoter for methanol-free production. Firstly, K. phaffii clones were generated for intracellular and secretory DAO-GH production that still possessed antibiotic resistance due to the cloning procedure. For intracellular production, a maximum intracellular DAO activity of 15,404 nkat/L_culture was achieved in fed-batch bioreactor cultivations, while for secretory production, the highest extracellular DAO activity of 6,078 nkat/L_culture was achieved using the αMF signal peptide without its EAEA sequence. The intracellularly produced DAO-GH was partially purified in several purification steps with a yield of 80%, a purification factor of about 10 and specific DAO activity of 16.7 nkat/mg_protein. The secretory DAO-GH production resulted in a specific DAO activity of 15.4 nkat/mg_protein already in the cell-free culture supernatant at the end of cultivation without further purification steps. The food industry aims to avoid the use of antimicrobial resistance in enzyme production, therefore, a new cassette plasmid with self-excisable antibiotic resistance markers was constructed for secretory DAO-GH production. The antibiotic-resistance-free K. phaffii clone generated with this plasmid achieved a maximum extracellular DAO activity of 4,770 nkat/L_culture in a fed-batch bioreactor cultivation. The DAO-GH obtained in this cultivation was spray-dried, resulting in a storable powder with 23 nkat/g_powder DAO activity and a water activity value of 0.12. This study demonstrated the secretion of recombinant DAO in a microbial host such as K. phaffii for the first time and provides a strategy for generating antibiotic-resistance-free K. phaffii clones.

The maize rhizobacterium Enterobacter cloacae Mz49 exhibits diverse plant growth-promoting and stress-adaptive traits, indicating strong potential for bioinoculant development. Mz49 was isolated from the Egyptian rhizosphere, and demonstrated in vitro production of indole-3-acetic acid (64.89 µg/mL), antioxidant activity (IC₅₀ = 11.71 µg/mL), and anti-inflammatory properties (IC₅₀ = 63.1 µg/mL). Whole-genome sequencing revealed a 5.34 Mb genome with 5,158 protein-coding genes linked to nutrient acquisition, abiotic stress tolerance, and secondary metabolite biosynthesis. Genes associated with nitrogen fixation (nirBD, ureABCDEFGJ, amtB), phosphate solubilization (pqqIFL, phoA, pstIPN), and phytohormone synthesis (iaaT, ysnE, ipdC, ppdC, amiE) were identified. Genome analysis also revealed phytase-related genes (agp, suhB), which contribute to the release of bioavailable phosphorus, an essential nutrient for maize growth. This genetic potential highlights the strain's contribution to enhanced plant growth and nutrient-use efficiency, particularly under phosphorus-limited conditions. Additionally, stress-response genes (sodABC, katE, betB, proABCY, dnaJK, cspA) were identified, conferring resistance to oxidative, osmotic, thermal, and cold stresses. The presence of heavy metal resistance genes (arsenic, copper, zinc, nickel) suggests suitability for use in contaminated soils. AntiSMASH analysis identified biosynthetic gene clusters for siderophores, arylpolyenes, and non-ribosomal peptides. GC-MS profiling further detected bioactive compounds, including 2, 3-butanediol, D-pinitol, succinic acid, tyrosol, and azelaic acid, which are associated with plant growth promotion and defense responses. Collectively, these findings highlight Mz49's potential for sustainable maize cultivation, particularly in phosphorus-limited or stress-prone soils. Future research should prioritize field trials to validate its efficacy and assess potential risks associated with its application.

Microbial biosurfactants are versatile biomolecules with potential to support sustainable chemistry and bio-based solutions for climate action. However, their use remains limited primarily owing to the complexities in their bioprocess. This review aims to evaluate current trends in biosurfactant research, with a special focus on artificial intelligence (AI)-based optimization techniques to clearly bring forth the qualitative research directions, the quantitative tools adopted, and most promising AI driven strategies for enhanced biosurfactant bioprocess. Systematic review revealed Artificial neural network, coupled to Response surface methodology, as the most extensively explored techniques till date, consistently delivering near accurate predictions in process optimization for biosurfactant production. Qualitative analysis suggested the potential of hybrid AI techniques with optimization algorithms to be most promising as they leverage the strength of both approaches. For the first time, this study integrates bibliometric analysis with AI-based review to provide a dual perspective on both research progression and technological innovations, with clear future research directions. Despite notable advancements, challenges such as limited datasets, model transferability, and microbial metabolic diversity persist. The study suggests that open-access, multi-dimensional datasets and hybrid AI models could significantly advance biosurfactant research and industrial scalability.

Breast cancer remains the leading cause of cancer morbidity and mortality worldwide, with limited efficacy in advanced breast cancer patients due to tumor heterogeneity and drug resistance. Emerging evidence suggests that the gut microbiota is associated with breast cancer progression through metabolites and immunomodulatory effects. However, mechanistic insights and therapeutic targets combining the gut microbiota and host genetics remain underexplored. In this study, we performed Mendelian randomization (MR) analysis via cis-eQTLs from breast cancer GWASs and druggable gene datasets to identify genes causally associated with breast cancer risk. Differential gene expression analysis was conducted using TCGA data. Gut microbiota-target-metabolite networks were constructed from the gutMGene database, and immunophenotyping was assessed via CIBERSORT. Molecular docking and molecular dynamics simulations were used to evaluate the interactions between gut microbiota metabolites and key targets. Magnetic resonance and transcriptome analyses revealed 14 candidate genes associated with breast cancer risk, of which CXCL10 was positively associated with disease progression (OR = 1.124, P = 0.007). CXCL10 expression was strongly correlated with the infiltration of CD4 + memory-activated T cells, CD4 + follicular helper T cells, CD8 + T cells, and gamma delta T cells. Network analysis revealed that Enterococcus faecalis was associated with the activation of CXCL10. Stable molecular dynamics simulations indicated that Lariciresinol was a high-affinity ligand for CXCL10. This comprehensive study highlights the role of the gut microbiota-metabolite-gene axis in breast cancer progression, particularly in Enterococcus faecalis-mediated CXCL10 activation. By modulating CXCL10, Lariciresinol has emerged as a promising candidate for targeted therapy. These findings suggest that the gut microbiota-metabolite-gene axis may play a regulatory role in breast cancer progression and propose Lariciresinol as a potential therapeutic candidate. However, given the computational foundation and in vitro validation, this study should be considered hypothesis-generating, and further in vivo and clinical investigations are warranted to confirm the proposed mechanisms.

Allergic rhinitis (AR) is a common immune-related disorder recently associated with gut microbiota (GM), though the underlying mechanisms remain unclear. This study employed Mendelian randomization (MR) to investigate causal relationships between GM and AR, combined with transcriptomic analyses, including both bulk and single-cell RNA sequencing (scRNA-seq), to explore molecular mechanisms at tissue and cellular resolutions. Data for AR and GM were sourced from public databases. MR identified causal microbial taxa, whose associated SNPs were mapped to genes. These were intersected with differentially expressed genes (DEGs) from transcriptomic data to identify candidate genes. Key genes were validated through expression analysis, immune infiltration, functional enrichment, regulatory network prediction, drug screening, and molecular docking. Single-cell RNA sequencing was used to identify key cell types and pseudotime trajectories. MR analysis identified 29 GM taxa causally linked to AR. For instance, family.Porphyromonadaceae.id.943 was protective, while genus.unknowngenus.id.1000006162 was a risk factor. SNP-based gene mapping yielded 246 genes, which overlapped with 1329 DEGs to identify INPP5D and KIF16B as key genes. These were enriched in pathways such as ribosome, peroxisome, and systemic lupus erythematosus. Immune infiltration revealed altered abundances of natural killer T cells and activated CD4 + T cells. Single-cell analysis highlighted Th1 cells as central to AR pathogenesis, with stable expression of INPP5D and KIF16B during Th1 differentiation. This study establishes a causal link between GM and AR and identifies INPP5D and KIF16B as potential key genes, with Th1 cells as a critical immune subset, providing new insights into AR's molecular mechanisms.

Despite the widespread practice of using probiotics in aquaculture for their potential benefits, the consistency of their impact on disease resistance in fish is still being scrutinized. This study aimed to address this gap by investigating the influence of the probiotic Pediococcus acidilactici (PCA) on hematological indices, body composition, serum metabolites, water quality, growth metrics, the transcriptomic profile of genes related to immune function, and the ability of red tilapia (Oreochromis niloticus × O. mossambicus) to resist challenge with the bacterial pathogen Aeromonas hydrophila. A total of 180 tilapia fingerlings (average weight 17.10 ± 0.46 g) were distributed into four groups and fed a basal diet supplemented with 0 (PCA0), 1 (PCA1), 2 (PCA2), and 3 (PCA3) g of PCA per kg of diet for 63 days. Water quality analysis indicated a significant decrease in both salinity and dissolved oxygen concentrations in all PCA-supplemented groups compared to a PCA-free diet (P < 0.05). Fish fed diets having 2 or 3 PCA had superior FBW, SGR, and ADG, while these levels significantly improved the FCR compared to the untreated diet (P < 0.001). In fish supplemented with PCA, body composition analysis showed a statistically significant increase in protein and ash content, accompanied by a statistically significant decrease in lipid content (P < 0.05). Furthermore, dietary PCA significantly enhanced phagocytic index, and serum IgG and IgM levels in a dose-dependent response. Notable improvements in hematological variables and blood protein fractions were observed in the PCA2 and PCA3 groups compared to other groups (P < 0.05). Dietary PCA administration sustained liver enzymes and kidney functions (P < 0.05). Dietary supplementation with PCA resulted in a significant upregulation (P < 0.05) of growth-related genes (GH, IGF-1, and IGF1-R) and immunity-associated genes (CXC chemokine, IL8, and IL1β) in a dose-dependent manner. Furthermore, dietary PCA improved the histological structure of the liver and enhanced intestinal integrity in Tilapia. Following pathogen challenge, the survival rate was significantly higher in all PCA-supplemented groups compared to the control group, with the highest survival observed in the PCA3 group. In summary, this research highlights the significant benefits of dietary Pediococcus acidilactici supplementation at 2 and 3 g/kg for improving growth, blood physiology, immunity, and disease resistance in red tilapia. These findings underscore the potential of Pediococcus acidilactici as a practical and effective strategy for enhancing productivity and sustainability in red tilapia aquaculture.

High-fat diet (HFD) consumption poses a significant public health threat due to its strong association with obesity, hyperlipidemia, cardiovascular diseases, and metabolic syndrome. While Akkermansia muciniphila has emerged as a promising probiotic for ameliorating metabolic disorders, the underlying mechanisms-specifically its interplay with intestinal tryptophan metabolism-remain poorly understood. Here, we demonstrate that A. muciniphila supplementation mitigates HFD-induced metabolic dysfunction in zebrafish by orchestrating a gut microbiota-tryptophan metabolite-AhR signaling axis. Firstly, A. muciniphila treatment effectively reduced the final weight of zebrafish, partially mitigated weight gain caused by HFD, and improved survival rate. In addition, A. muciniphila treatment reduced zebrafish adiposity, hepatic steatosis, and endotoxemia while enhancing the antioxidant capacity of the liver. We further found that A. muciniphila exerted anti-apoptotic effects, improved chronic low-grade inflammatory responses, enhanced antioxidant capacity, and repaired intestinal barriers induced by HFD. These effects were partially abolished by antibiotic pretreatment, confirming microbiota dependency. Subsequent 16S rRNA sequencing analysis revealed that A. muciniphila supplementation reshaped gut microbiota, enriching Staphylococcus and Vibrionaceae, while depleting Acinetobacter, Perlucidica, and Massilia. In addition to reducing lipid synthesis, metabolomic profiled the substantial changes in microbiota-regulated tryptophan metabolism, including increased levels of indole-3-lactic acid, indole-3-acetaldehyde, and 5-hydroxyindole acetic acid in Amuc group. These metabolites activated aryl hydrocarbon receptor (AhR), upregulating downstream IL-22 and improving intestinal integrity and chronic inflammatory response. Pathway analysis and enzyme gene expression detection indicated that A. muciniphila may inhibit the KP pathway while promoting the microbiota-dependent tryptophan metabolic pathway. This study establishes a novel link by which A. muciniphila exerts protective effects against HFD-induced metabolic syndrome through microbiota-mediated enhancement of tryptophan metabolism.

Bacillus subtilis is one of the most important production organisms in industrial biotechnology. However, there is still limited knowledge about the kinetics of fed-batch processes in bioreactors, as well as a lack of biological performance indicators, such as production yields, particularly regarding their variation over time. Understanding these kinetics and changes is crucial for optimizing the productivity in fed-batch processes. Fed-batch bioreactor cultures of Bacillus subtilis BMV9 in high cell density processes for surfactin production have been characterized with a kinetic model composed of first-order ordinary differential equations, describing the time course of biomass, substrate, surfactin and acetate. This model contributes to understanding critical restrictions and the knowledge gained was used to design and implement a model-based process. The model integrates biomass growth based on Monod kinetics, substrate consumption, surfactin synthesis and formation of the by-product acetate. After the model was parameterized for B. subtilis BMV9 using 12 different fed-batch bioreactor experiments, the kinetic model was able to accurately describe biomass accumulation, substrate consumption, product formation rates and, to some extent, the overflow metabolism involving acetate. Based on this, the kinetic model was used for a process design, in which the batch was omitted, which led to a product titre of 46.33 g/L and a space-time-yield of 2.11 g/(L*h) was achieved. The kinetic model developed in this study enables the description of the time course of biomass growth, substrate consumption and product formation and thus significantly improves process understanding. The computation of process parameters, which are not analytically accessible at any time, could be realized. A sensitivity analysis identified the maximum specific growth rate, substrate-related maintenance and the maximum acetate formation rate as key parameters influencing model outputs.