Microbiological research最新文献

{"title":"From probiotic chassis to modification strategies, control and improvement of genetically engineered probiotics for inflammatory bowel disease","authors":"","doi":"10.1016/j.micres.2024.127928","DOIUrl":"10.1016/j.micres.2024.127928","url":null,"abstract":"<div><div>With the rising morbidity of inflammatory bowel disease (IBD) year by year, conventional therapeutic drugs with systemic side effects are no longer able to meet the requirements of patients. Probiotics can improve gut microbiota, enhance intestinal barrier function, and regulate mucosal immunity, making them a potential complementary or alternative therapy for IBD. To compensate for the low potency of probiotics, genetic engineering technology has been widely used to improve their therapeutic function. In this review, we systematically summarize the genetically engineered probiotics used for IBD treatment, including probiotic chassis, genetic modification strategies, methods for controlling probiotics, and means of improving efficacy. Finally, we provide prospects on how genetically engineered probiotics can be extended to clinical applications.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142433205","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomics reveals the regulation of the immune system of the mushroom-forming fungus Schizophyllum commune during interaction with four competitors","authors":"","doi":"10.1016/j.micres.2024.127929","DOIUrl":"10.1016/j.micres.2024.127929","url":null,"abstract":"<div><div>Mushroom-forming fungi frequently encounter competitors during their lifecycle, but their defense mechanisms remain largely unexplored. We studied the response of the mushroom-forming fungus <em>Schizophyllum commune</em> during interaction with the fungal competitors <em>Trichoderma harzianum</em>, <em>Trichoderma aggressivum</em> and <em>Purpureocillium lilacinum</em> and the bacterial competitor <em>Serratia quinivorans.</em> Transcriptomics revealed 632 up-regulated genes in the direct interaction zone, which were enriched in small secreted proteins and transporters. A set of 26 genes were up-regulated during all interactions, indicating a core transcriptomic defense response. In the non-interacting edge of the mycelium of <em>S. commune</em>, there were 154 up-regulated genes, suggesting that there is a systemic response due to a signal that reaches unaffected areas. The GATA zinc finger transcription factor gene <em>gat1</em> was up-regulated during interaction and a Δ<em>gat1</em> strain displayed increased colonization by <em>T. harzianum</em>. Previously linked to mushroom development, this transcription factor apparently has a dual role. Moreover, 138 genes were up-regulated during both interaction and mushroom development, indicating priming of the defense response during development to prepare the fruiting body for future interactions. Overall, we unveiled a defensive response of <em>S. commune</em> during interaction with fungal and bacterial competitors and identified a regulator of this response.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142441778","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Christensenellaceae minuta modulates epithelial healing via PI3K-AKT pathway and macrophage differentiation in the colitis","authors":"","doi":"10.1016/j.micres.2024.127927","DOIUrl":"10.1016/j.micres.2024.127927","url":null,"abstract":"<div><div>Ulcerative colitis (UC) is a chronic inflammatory disorder with an unsatisfactory cure rate and mucosal healing is a key treatment objective. <em>Christensenellaceae minuta</em> (<em>C. minuta</em>) has emerged as a next-generation of probiotic for maintaining intestinal health. We investigated the therapeutic efficacy of <em>C. minuta</em> in dextran sulfate sodium (DSS)-induced colitis, focusing on mucosal healing and the underlying mechanisms. <em>C. minuta</em> effectively alleviated colitis and promoted the regeneration of intestinal epithelial cells (IECs). Using 16S rRNA sequencing and metabolomics, we found that <em>C. minuta</em> administration increased beneficial bacteria, decreased pathogenic bacteria, and significantly elevated propionic acid levels. Additionally<em>, C. minuta</em> activated the PI3K-AKT pathway by upregulating systemic and local IGF-1 expression. Inhibiting the PI3K-AKT pathway reduced the therapeutic effects of <em>C. minuta</em> and impaired IEC regeneration. Furthermore, <em>C. minuta</em> promoted macrophage differentiation into the M2 phenotype and decreased proinflammatory factors. We propose that <em>C. minuta</em> alleviates colitis by regulating the gut microbiota, modulating macrophage differentiation, and enhancing mucosal healing by activating the PI3K-AKT pathway via IGF-1 secretion induced by short-chain fatty acids. Our findings provide evidence from animal experiments to support future clinical trials and the therapeutic translation of <em>C. minuta</em>.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142406615","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Brassinosteroids mediate arbuscular mycorrhizal symbiosis through multiple potential pathways and partial identification in tomato","authors":"","doi":"10.1016/j.micres.2024.127924","DOIUrl":"10.1016/j.micres.2024.127924","url":null,"abstract":"<div><div>Currently, little is known regarding the specific processes through which brassinosteroids (BR) affect arbuscular mycorrhizal (AM) symbiosis. Understanding this relationship is vital for advancing plant physiology and agricultural applications. In this study, we aimed to elucidate the regulatory mechanisms of BR in AM symbiosis. According to the log2 fold change-value and adjP-value, we integrated the common differentially expressed genes (DEGs) in maize (<em>Zea mays</em> L.) treated with BR and AM, Arabidopsis (<em>Arabidopsis thaliana</em>) mutants deficient in BR receptors, and tomato (<em>Solanum lycopersicum</em>) plants inoculated with AM fungi. In addition, we characterized the symbiotic performance of tomato plants with BR receptor defects and overexpression. The results indicated that the common differential genes induced by BR and AM were involved in metabolic processes, such as cell wall modification, cytoskeleton remodeling, auxin and ethylene signaling, photosynthesis, mineral nutrient transport, and stress defense. Specifically, these include the <em>BR1</em> gene, which modifies the cell wall. However, the fungal colonization rate of BR receptor-deficient tomato plants was significantly reduced, and the total phosphorus concentration was increased. Conversely, the performance of the overexpressing tomato transformation plants demonstrated a significant contrast. Additionally, the mild rescue of mycorrhizal attenuation in mutants treated with exogenous BR suggests the possibility of direct feedback from BR synthesis to AM. Notably, the cell wall modification gene (<em>SlBR1</em>) and calcium spike gene (<em>SlIPD3</em>) were induced by both BR and AM, suggesting that BR may influence cell penetration during the early stages of AM colonization. Synthesis: Our results demonstrated that BR positively regulates AM symbiosis through multiple pathways. These findings pave the way for future research, including isolation of the individual contributions of each pathway to this complex process and exploration of possible agricultural applications.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142417751","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chemoreceptor MCP4580 of Vibrio splendidus mediates chemotaxis toward L-glutamic acid contributing to bacterial virulence","authors":"","doi":"10.1016/j.micres.2024.127917","DOIUrl":"10.1016/j.micres.2024.127917","url":null,"abstract":"<div><div>Chemotaxis has an essential function in flagellar bacteria that allows them to sense and respond to specific environmental signals, enabling their survival and colonization. <em>Vibrio splendidus</em> is an important opportunistic pathogen that infects a wide range of hosts including fish, bivalve, and sea cucumber<em>.</em> Our study demonstrated that <em>V. splendidus</em> AJ01 exhibited chemotaxis toward L-glutamic acid (L-Glu), an abundant amino acid in the intestinal and respiratory tree tissues of the sea cucumber. Bacterial samples collected from two locations in soft agar swimming plates were subjected to RNA-sequencing (RNA-Seq) analysis to identify the methyl-accepting chemotaxis protein (MCP) respond to L-Glu. Among the 40 annotated chemoreceptors, MCP4580 was identified as the MCP that mediates L-Glu-response. Molecular docking and site-directed mutagenesis revealed that L-arginine at residue 81 (R81) and L-glutamine at residue 88 (Q88) in the ligand-binding domain (LBD) are crucial for L-Glu recognition. Bacterial two-hybrid assay (BTH) showed that MCP4580 forms dimers and interacts with the histidine kinase CheA via the coupling protein CheW1 and CheW2. Phosphorylation analysis showed that the binding of L-Glu to MCP4580 results in the inhibition of CheA phosphorylation mainly via CheW1. Notably, sea cucumbers stimulated with each mutant strain of chemotaxis protein exhibited reduced mortality, highlighting the importance of chemotaxis in <em>V. splendidus</em> virulence. The present study provides valuable insights into the molecular components and signal transduction involved in the chemotaxis of <em>V. splendidus</em> toward L-Glu, and highlights the importance of chemotaxis in its virulence.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142378082","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The global transcription factor Clp exerts positive regulatory effects in the walnut bacterial black spot pathogen, Xanthomonas arboricola pv. juglandis","authors":"","doi":"10.1016/j.micres.2024.127921","DOIUrl":"10.1016/j.micres.2024.127921","url":null,"abstract":"<div><div>Walnut blight caused by the bacterium <em>Xanthomonas arboricola</em> pv. <em>juglandis</em> (<em>Xaj</em>) is one of the most common diseases of walnut (<em>Juglans</em> spp.), resulting in serious yield decline and significant economic losses. Crp-like protein (Clp) is an important global regulatory transcription factor in bacteria. In this study, we sought to elucidate the role of Clp in the pathogenicity of <em>Xaj</em> strain DW3F3 and the associated regulatory mechanism. The results indicated that <em>clp</em> gene deficiency significantly reduced the pathogenicity of <em>Xaj</em> DW3F3 in walnut without affecting the growth of the bacterium. We found that Clp positively regulates biofilm formation, extracellular polysaccharide production, exoenzyme secretion, and motility of <em>Xaj</em>, which was consistent with the transcript levels of virulence factor-encoding genes. However, overexpression of <em>clp</em> does not enhance the expression of all virulence genes, it may inhibit the expression of a part of virulence factor-related genes. EMSA assay further showed that Clp specifically binds to the promoters of these genes and regulates their expression, and CD spectra test certified that the ligand of Clp was c-di-GMP. Our findings contribute to the in-depth understanding of the pathogenic mechanism of <em>Xaj</em> and highlight the potential of Clp as a drug target for the development of agents to prevent and control walnut diseases.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142372309","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sterol regulatory element-binding proteins mediate intrinsic fungicide tolerance and antagonism in the fungal biocontrol agent Clonostachys rosea IK726","authors":"","doi":"10.1016/j.micres.2024.127922","DOIUrl":"10.1016/j.micres.2024.127922","url":null,"abstract":"<div><div>Sterol regulatory element-binding proteins (SREBPs) are transcription factors governing various biological processes in fungi, including virulence and fungicide tolerance, by regulating ergosterol biosynthesis and homeostasis. While studied in model fungal species, their role in fungal species used for biocontrol remains elusive. This study delves into the biological and regulatory function of SREBPs in the fungal biocontrol agent (BCA) <em>Clonostachys rosea</em> IK726, with a specific focus on fungicide tolerance and antagonism<em>. Clonostachys rosea</em> genome contains two SREBP coding genes (<em>sre1</em> and <em>sre2</em>) with distinct characteristics. Deletion of <em>sre1</em> resulted in mutant strains with pleiotropic phenotypes, including reduced <em>C. rosea</em> growth on medium supplemented with prothioconazole and boscalid fungicides, hypoxia mimicking agent CoCl₂ and cell wall stressor SDS, and altered antagonistic abilities against <em>Botrytis cinerea</em> and <em>Rhizoctonia solani</em>. However, Δ<em>sre2</em> strains showed no significant effect. Consistent with the gene deletion results, overexpression of <em>sre1</em> in <em>Saccharomyces cerevisiae</em> enhanced tolerance to prothioconazole. The functional differentiation between SRE1 and SRE2 was elucidated by the yeast-two-hybridization assay, which showed an interaction between SREBP cleavage-activating protein (SCAP) and SRE1 but not between SRE2 and SCAP. Transcriptome analysis of the Δ<em>sre1</em> strain unveiled SRE1-mediated expression regulation of genes involved in lipid metabolism, respiration, and xenobiotic tolerance. Notably, genes coding for antimicrobial compounds chitinases and polyketide synthases were downregulated, aligning with the altered antagonism phenotype. This study uncovers the role of SREBPs in fungal BCAs, providing insights for <em>C. rosea</em> IK726 application into integrated pest management strategies.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142378083","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Inhibition of calpain reduces oxidative stress and attenuates pyroptosis and ferroptosis in Clostridium perfringens Beta-1 toxin-induced macrophages","authors":"","doi":"10.1016/j.micres.2024.127916","DOIUrl":"10.1016/j.micres.2024.127916","url":null,"abstract":"<div><div><em>Clostridium perfringens</em> Beta-1 toxin (CPB1) is a lethal toxin, which can lead to necrotic enteritis, but the pathological mechanism has not been elucidated. We investigated whether reactive oxygen species (ROS) participated in CPB1-induced pyroptosis and ferroptosis, and investigated the effects of calpain on CPB1-induced oxidative stress and inflammation. Scavenging ROS by N-Acetyl-L cysteine (NAC) led to the reduction of ROS, inhibited the death of macrophages, cytoplasmic swelling and membrane rupture, the expression of pyroptosis-related proteins and proinflammatory factor, while increased the expression of anti-inflammatory factors in cells treated with rCPB1. Adenosine triphosphate (ATP) synthase, H⁺ transporting, mitochondrial F1 complex, alpha subunit 1 (ATP5A1) was identified specifically interact with rCPB1. Silencing ATP5A1 inhibited accumulation of ATP and ROS, leaded to less cytoplasmic swelling and membrane rupture, attenuated pyroptosis and inflammation in rCPB1-treated cells. We also found that rCPB1 induces ferroptosis in macrophages, and the level of ferroptosis was similar with H₂O₂. Of note, H₂O₂ is a major ROS source, indicated that ROS production may play a major role in the regulation of ferroptosis in macrophages treated with rCPB1. This finding was further corroborated in rCPB1- induced human acute monocytic leukemia cells, which were treated with NAC. In addition, the inhibition of ferroptosis using liproxstatin-1 inhibited the shriveled mitochondrial morphology, increased the expression of glutathione peroxidase 4, nicotinamide adenine dinucleotide (phosphate) hydrogen: quinone oxidoreductase 1 and cysteine/glutamic acid reverse transport solute carrier family 7 members 11, decreased the expression of heme oxygenase 1, nuclear receptor coactivator 4 and transferrin receptor proteins, reduced malondialdehyde and lipid peroxidation levels, and increased intracellular L-glutathione levels in cells treated with rCPB1. Furthermore, calpain inhibitor PD151746 was used to investigate how pyroptosis and ferroptosis were involved simultaneously in rCPB1-treated macrophages. We showed that PD151746 inhibited ATP and ROS production, reversed the representative pyroptosis/ferroptosis indicators and subsequently reduced inflammation. The above findings indicate that rCPB1 might lead to macrophage pyroptosis and ferroptosis through the large and sustained increase in intracellular calpain and oxidative stress, further lead to inflammation.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142349959","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deletion of PMP3 increases ketoconazole resistance by affecting plasma membrane potential in Candida albicans","authors":"","doi":"10.1016/j.micres.2024.127918","DOIUrl":"10.1016/j.micres.2024.127918","url":null,"abstract":"<div><div>Ketoconazole is a classical antifungal drug commonly used in the clinic. With the increased use of ketoconazole in recent years, an increasing number of drug-resistant strains have emerged during clinical treatment. It is well known that fungi acquire drug resistance in multiple ways, while the molecular mechanisms underlying ketoconazole resistance remain for comprehensive exploration. In this study, we found that the expression of the small plasma membrane protein-encoding gene <em>PMP3</em> was significantly down-regulated in several clinically isolated ketoconazole-resistant strains, indicating the relationship between <em>PMP3</em> expression and ketoconazole resistance. By knocking out the <em>PMP3</em>, we found that the absence of the Pmp3 resulted in a significant increase in resistance of <em>Candida albicans</em> to ketoconazole, which was also confirmed in a systemic infection model in mice. We further demonstrated that various physiological properties, such as cell membrane fluidity, plasma membrane potential, permeability and ergosterol distribution were altered in the <em>pmp3</em>Δ/Δ mutant, which is associated with the enhanced cellular resistance to ketoconazole. In addition, overexpression rather than deletion of <em>PMP3</em> alters the hyphal development and biofilm formation capacity in <em>C. albicans</em>. This study reveals the contribution of Pmp3 to alteration of drug resistance in fungal pathogens, which may guide the development of novel antifungal strategies.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142349958","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The expanding antimicrobial diversity of the genus Pantoea","authors":"","doi":"10.1016/j.micres.2024.127923","DOIUrl":"10.1016/j.micres.2024.127923","url":null,"abstract":"<div><div>With the rise of antimicrobial resistance, there is high demand for novel antimicrobials to combat multi-drug resistant pathogens. The bacterial genus <em>Pantoea</em> produces a diversity of antimicrobial natural products effective against a wide range of bacterial and fungal targets. These antimicrobials are synthesized by specialized biosynthetic gene clusters that have unique distributions across <em>Pantoea</em> as well as several other genera outside of the <em>Erwiniaceae</em>. Phylogenetic and genomic evidence shows that these clusters can mobilize within and between species and potentially between genera. <em>Pantoea</em> antimicrobials belong to unique structural classes with diverse mechanisms of action, but despite their potential in antagonizing a wide variety of plant, human, and animal pathogens, little is known about many of these metabolites and how they function. This review will explore the known antimicrobials produced by <em>Pantoea</em>: agglomerins, andrimid, D-alanylgriseoluteic acid, dapdiamide, herbicolins, pantocins, and the various <em>Pantoea</em> Natural Products (PNPs). It will include information on the structure of each compound, their genetic basis, biosynthesis, mechanism of action, spectrum of activity, and distribution, highlighting the significance of <em>Pantoea</em> antimicrobials as potential therapeutics and for applications in biocontrol.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142378084","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}