Pub Date : 2026-02-01Epub Date: 2025-11-07DOI: 10.1016/j.micres.2025.128387
Hokuto Ohtsuka, Takafumi Shimasaki, Hirofumi Aiba
In nature, nutrient-poor environments are more common than exposure to nutrient-rich environments, and living organisms have developed countermeasures to survive nutrient starvation. Increasing research has revealed beneficial aspects of starvation for an individual’s life, including lifespan extension. The fission yeast Schizosaccharomyces pombe is a model unicellular eukaryotic organism and has greatly contributed to the understanding of various cellular processes, including the cell cycle, cell morphology, sexual development, cell lifespan, and nutritional responses. Traditionally, research on starvation in fission yeast has focused on glucose starvation and nitrogen starvation. Recently, studies on cellular responses to the starvation of various nutrients, such as phosphorus, sulfur, iron, zinc, copper, and amino acids have been reported, revealing similarities and differences among the various types of nutrient starvation. In fission yeast, Ecl proteins, which are conserved among fungi, can sense the starvation of multiple nutrients. These proteins also repress the target of rapamycin complex 1 (TORC1), which is conserved across eukaryotes. They channel a variety of starvation signals into common cellular responses, such as growth arrest, sexual differentiation, autophagy, and lifespan extension. This review summarizes and discusses the signaling mechanisms involved in the initial cellular responses of fission yeast to the starvation of various nutrients.
{"title":"Responses to nutrient starvation in the fission yeast Schizosaccharomyces pombe","authors":"Hokuto Ohtsuka, Takafumi Shimasaki, Hirofumi Aiba","doi":"10.1016/j.micres.2025.128387","DOIUrl":"10.1016/j.micres.2025.128387","url":null,"abstract":"<div><div>In nature, nutrient-poor environments are more common than exposure to nutrient-rich environments, and living organisms have developed countermeasures to survive nutrient starvation. Increasing research has revealed beneficial aspects of starvation for an individual’s life, including lifespan extension. The fission yeast <em>Schizosaccharomyces pombe</em> is a model unicellular eukaryotic organism and has greatly contributed to the understanding of various cellular processes, including the cell cycle, cell morphology, sexual development, cell lifespan, and nutritional responses. Traditionally, research on starvation in fission yeast has focused on glucose starvation and nitrogen starvation. Recently, studies on cellular responses to the starvation of various nutrients, such as phosphorus, sulfur, iron, zinc, copper, and amino acids have been reported, revealing similarities and differences among the various types of nutrient starvation. In fission yeast, Ecl proteins, which are conserved among fungi, can sense the starvation of multiple nutrients. These proteins also repress the target of rapamycin complex 1 (TORC1), which is conserved across eukaryotes. They channel a variety of starvation signals into common cellular responses, such as growth arrest, sexual differentiation, autophagy, and lifespan extension. This review summarizes and discusses the signaling mechanisms involved in the initial cellular responses of fission yeast to the starvation of various nutrients.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"303 ","pages":"Article 128387"},"PeriodicalIF":6.9,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145495840","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}
Pub Date : 2026-02-01Epub Date: 2025-10-26DOI: 10.1016/j.micres.2025.128378
Wilfred Mabeche Anjago , Siqiao Chen , Yishen Zhao , Jiaqi Lu , Yajuan Chen , Dongmei Zhou , Irina S. Druzhinina , Lihui Wei , Paul Daly
The breakdown of oomycete necromass is an important source of organic matter for composting. How Trichoderma harzianum, an important composting fungus, regulates gene expression and produces exo-proteins for degradation of oomycete necromass is poorly understood, especially related to cellulose, an important component of oomycete necromass. Complementary techniques of chemical compositional analysis, transcriptomics, exo-proteomics, enzymatic assays, and fungal genetics were used to analyze the degradation of inactivated oomycete mycelial powder – a surrogate for oomycete necromass. In total, 1556 genes were upregulated and 212 exo-proteins were produced in T. harzianum oomycete mycelial powder cultures, and about 25 % of the produced proteins showed corresponding gene upregulation. The enzymes detected, such as β-1,3-glucanases, and β-1,4-glucanases (cellulases), matched well with the composition of oomycete mycelial powder. Linkage compositional analysis showed that the mycelial powder contained ∼ 60 % 1,3 linkages and ∼19 % 1,4 linkages. The enzyme cocktail from the submerged cultures converted approximately one-third of the mycelial powder to glucose by in vitro assays. The conversion of the mycelial powder to glucose was not substantially reduced by deletion of the cellulolytic transcriptional activator XYR1. Deletion of XYR1 did decrease cellulase activity but only ∼1 % of mycelial powder-induced genes appeared to be XYR1-regulated. In conclusion, T. harzianum produces suitable enzyme cocktails for oomycete mycelial powder degradation, with β-1,3-glucanases likely playing a more important role than cellulases. T. harzianum cellulases may either be relatively unimportant for the degradation, or may not be co-activated alongside CAZymes degrading less recalcitrant parts of the mycelial powder.
{"title":"Regulation of Trichoderma harzianum gene expression and protein production in submerged cultures with inactivated oomycete mycelium","authors":"Wilfred Mabeche Anjago , Siqiao Chen , Yishen Zhao , Jiaqi Lu , Yajuan Chen , Dongmei Zhou , Irina S. Druzhinina , Lihui Wei , Paul Daly","doi":"10.1016/j.micres.2025.128378","DOIUrl":"10.1016/j.micres.2025.128378","url":null,"abstract":"<div><div>The breakdown of oomycete necromass is an important source of organic matter for composting. How <em>Trichoderma harzianum</em>, an important composting fungus, regulates gene expression and produces exo-proteins for degradation of oomycete necromass is poorly understood, especially related to cellulose, an important component of oomycete necromass. Complementary techniques of chemical compositional analysis, transcriptomics, exo-proteomics, enzymatic assays, and fungal genetics were used to analyze the degradation of inactivated oomycete mycelial powder – a surrogate for oomycete necromass. In total, 1556 genes were upregulated and 212 exo-proteins were produced in <em>T. harzianum</em> oomycete mycelial powder cultures, and about 25 % of the produced proteins showed corresponding gene upregulation. The enzymes detected, such as β-1,3-glucanases, and β-1,4-glucanases (cellulases), matched well with the composition of oomycete mycelial powder. Linkage compositional analysis showed that the mycelial powder contained ∼ 60 % 1,3 linkages and ∼19 % 1,4 linkages. The enzyme cocktail from the submerged cultures converted approximately one-third of the mycelial powder to glucose by <em>in vitro</em> assays. The conversion of the mycelial powder to glucose was not substantially reduced by deletion of the cellulolytic transcriptional activator XYR1. Deletion of XYR1 did decrease cellulase activity but only ∼1 % of mycelial powder-induced genes appeared to be XYR1-regulated. In conclusion, <em>T. harzianum</em> produces suitable enzyme cocktails for oomycete mycelial powder degradation, with β-1,3-glucanases likely playing a more important role than cellulases. <em>T. harzianum</em> cellulases may either be relatively unimportant for the degradation, or may not be co-activated alongside CAZymes degrading less recalcitrant parts of the mycelial powder.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"303 ","pages":"Article 128378"},"PeriodicalIF":6.9,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145505595","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}
Pub Date : 2026-02-01Epub Date: 2025-11-01DOI: 10.1016/j.micres.2025.128386
Zhuoren Ling , Ruicheng Zheng , Yanjun Dong , Wenjuan Yin , Lu Qiao , Rong Zhang , Pramod K. Jangir , Qiaoling Sun , Gerald Larrouy-Maumus , Craig MacLean , Yang Wang , Jianzhong Shen , Timothy R. Walsh
Colistin is one of the last treatment options against human infections caused by multi-drug resistant Klebsiella pneumoniae. Colistin resistant K. pneumoniae arises through modifying bacterial lipopolysaccharide (LPS) via two mechanisms: the mgrB inactivation on chromosome and mcr-1 expression - usually plasmid-mediated. Notably, chromosomal-mediated resistance is more common in naturally-occurring clinical K. pneumoniae than plasmid-borne resistance. Herein we demonstrated that K. pneumoniae strain with a mutant mgrB (ΔmgrB) gene exhibited increased pathogenicity compared to those carrying mcr-1, as evidenced in Galleria mellonella and murine bacteraemia model. Strain possessing ΔmgrB showed higher mortality rate, greater bacterial accumulation, and increased damage to host tissue. Although both ΔmgrB and mcr-1 impose fitness cost on K. pneumoniae and enhance bacterial evasion from phagocytosis, ΔmgrB mediated greater bacterial resistance to host defence peptides than mcr-1, providing an evolutionary advantage. These findings indicated distinct features of mgrB-inactivated K. pneumoniae and mcr-1-positive K. pneumoniae in host immunity responses, and promote understanding of how antibiotic-resistant determinants influence host-pathogens interactions.
{"title":"mgrB inactivation confers enhanced pathogenicity and immune evasion over mcr-1 expression in colistin-resistant Klebsiella pneumoniae","authors":"Zhuoren Ling , Ruicheng Zheng , Yanjun Dong , Wenjuan Yin , Lu Qiao , Rong Zhang , Pramod K. Jangir , Qiaoling Sun , Gerald Larrouy-Maumus , Craig MacLean , Yang Wang , Jianzhong Shen , Timothy R. Walsh","doi":"10.1016/j.micres.2025.128386","DOIUrl":"10.1016/j.micres.2025.128386","url":null,"abstract":"<div><div>Colistin is one of the last treatment options against human infections caused by multi-drug resistant <em>Klebsiella pneumoniae</em>. Colistin resistant <em>K. pneumoniae</em> arises through modifying bacterial lipopolysaccharide (LPS) via two mechanisms: the <em>mgrB</em> inactivation on chromosome and <em>mcr-1</em> expression - usually plasmid-mediated. Notably, chromosomal-mediated resistance is more common in naturally-occurring clinical <em>K. pneumoniae</em> than plasmid-borne resistance. Herein we demonstrated that <em>K. pneumoniae</em> strain with a mutant <em>mgrB</em> (Δ<em>mgrB</em>) gene exhibited increased pathogenicity compared to those carrying <em>mcr-1</em>, as evidenced in <em>Galleria mellonella</em> and murine bacteraemia model. Strain possessing Δ<em>mgrB</em> showed higher mortality rate, greater bacterial accumulation, and increased damage to host tissue. Although both Δ<em>mgrB</em> and <em>mcr-1</em> impose fitness cost on <em>K. pneumoniae</em> and enhance bacterial evasion from phagocytosis, Δ<em>mgrB</em> mediated greater bacterial resistance to host defence peptides than <em>mcr-1</em>, providing an evolutionary advantage. These findings indicated distinct features of <em>mgrB</em>-inactivated <em>K. pneumoniae</em> and <em>mcr-1</em>-positive <em>K. pneumoniae</em> in host immunity responses, and promote understanding of how antibiotic-resistant determinants influence host-pathogens interactions.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"303 ","pages":"Article 128386"},"PeriodicalIF":6.9,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145445262","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}
Pub Date : 2026-02-01Epub Date: 2025-11-07DOI: 10.1016/j.micres.2025.128394
Lizhen Li , Shaocong Huang , Zhiyi Bai , Hao Xu , Qun Ji , Wei Song
The development of the digestive system and its interaction with microbiota are critical for fish growth and health. Transcriptomic and 16S rRNA sequencing analyses were conducted to investigate the gene expression profiles of the digestive system and microbial community dynamics in Larimichthys crocea from the embryonic stage to day 28 to elucidate their potential roles in larval and juvenile development and their associations with immune and metabolic functions. The results revealed stage-specific changes in gene expression and microbial composition during development, and two critical transitional phases were identified: day 1 vs embryonic stage (C1 vs CE) and day 15 vs day 9 (C15 vs C9). Microbial succession demonstrated clear temporal characteristics: Pseudoalteromonas were dominant during the embryonic stage (CE), which was succeeded by Stenotrophomonas after hatching (C1, C3, C4, and C9), by Cohaesibacter on day 15 (C15), and by Psychrobacter as the core genus after formulated feed introduction on day 19. Functional enrichment analyses revealed predominant enrichment of differentially expressed genes in immune- and metabolic-related pathways, such as calcium signaling, steroid biosynthesis, and amino acid metabolism. Weighted gene co-expression network and correlation analyses revealed significant associations between specific genera (e.g., Rhodococcus and Psychrobacter) and immune- and metabolism-related genes. This study analyzed the developmental patterns of the digestive system of L. crocea and revealed significant correlations between shifts in the microbiota and host metabolism and immunity, highlighting the close association between the microbiota and metabolic and immune responses.
消化系统的发育及其与微生物群的相互作用对鱼类的生长和健康至关重要。通过转录组学和16S rRNA测序分析，研究了胭脂鱼（Larimichthys crocea）从胚胎期到第28天消化系统和微生物群落动态的基因表达谱，以阐明其在幼虫和幼鱼发育中的潜在作用及其与免疫和代谢功能的关联。结果揭示了发育过程中基因表达和微生物组成的阶段性变化，并确定了两个关键过渡阶段：第1天与胚胎期（C1 vs CE）和第15天与第9天（C15 vs C9）。微生物演替表现出明显的时间特征：假互变单胞菌在胚胎期（CE）占主导地位，孵化后为窄养单胞菌（C1、C3、C4和C9），第15天为Cohaesibacter (C15)，第19天引入配方饲料后为Psychrobacter成为核心属。功能富集分析显示，差异表达基因主要富集于免疫和代谢相关途径，如钙信号、类固醇生物合成和氨基酸代谢。加权基因共表达网络和相关分析显示，特定属（如红球菌和冷杆菌）与免疫和代谢相关基因之间存在显著关联。本研究分析了羊草消化系统的发育模式，揭示了微生物群的变化与宿主代谢和免疫之间的显著相关性，强调了微生物群与代谢和免疫应答之间的密切联系。
{"title":"Combined transcriptome and microbiome characterization highlights digestive system development involved in the metabolism and immunity of the large yellow croaker (Larimichthys crocea)","authors":"Lizhen Li , Shaocong Huang , Zhiyi Bai , Hao Xu , Qun Ji , Wei Song","doi":"10.1016/j.micres.2025.128394","DOIUrl":"10.1016/j.micres.2025.128394","url":null,"abstract":"<div><div>The development of the digestive system and its interaction with microbiota are critical for fish growth and health. Transcriptomic and 16S rRNA sequencing analyses were conducted to investigate the gene expression profiles of the digestive system and microbial community dynamics in <em>Larimichthys crocea</em> from the embryonic stage to day 28 to elucidate their potential roles in larval and juvenile development and their associations with immune and metabolic functions. The results revealed stage-specific changes in gene expression and microbial composition during development, and two critical transitional phases were identified: day 1 vs embryonic stage (C1 vs CE) and day 15 vs day 9 (C15 vs C9). Microbial succession demonstrated clear temporal characteristics: <em>Pseudoalteromonas</em> were dominant during the embryonic stage (CE), which was succeeded by <em>Stenotrophomonas</em> after hatching (C1, C3, C4, and C9), by <em>Cohaesibacter</em> on day 15 (C15), and by <em>Psychrobacter</em> as the core genus after formulated feed introduction on day 19. Functional enrichment analyses revealed predominant enrichment of differentially expressed genes in immune- and metabolic-related pathways, such as calcium signaling, steroid biosynthesis, and amino acid metabolism. Weighted gene co-expression network and correlation analyses revealed significant associations between specific genera (e.g., <em>Rhodococcus</em> and <em>Psychrobacter</em>) and immune- and metabolism-related genes. This study analyzed the developmental patterns of the digestive system of <em>L. crocea</em> and revealed significant correlations between shifts in the microbiota and host metabolism and immunity, highlighting the close association between the microbiota and metabolic and immune responses.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"303 ","pages":"Article 128394"},"PeriodicalIF":6.9,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145568959","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}
Pub Date : 2026-02-01Epub Date: 2025-11-11DOI: 10.1016/j.micres.2025.128395
María Emilia Cuervo , Diego Del Balzo , María Natalia Zanetti , Mariela Beatriz Nolly , Hugo Lachuer , Rostislav Petkov , Nour Ismail , John Manzi , Rubén Walter Caron , Christophe Le Clainche , Maria Teresa Damiani , Julien Pernier , Kristine Schauer , Anahi Capmany
Chlamydia trachomatis (Ct), a Gram-negative obligate intracellular pathogen, manipulates host actin dynamics to facilitate its entry, development, and exit. It assembles a dynamic actin cage around its intracellular niche, known as the ‘inclusion’, which provides structural stability for bacterial growth, and is crucial for exit via the non-cell-lytic extrusion process. We found that Ct recruits Myosin 1 C (MYO1C), a ubiquitous actin dependent motor protein, to the inclusion throughout its life cycle. Consequently, loss of MYO1C activity reduced Ct infection and the production of bacterial progenies. Mechanistically, MYO1C functions as a dynamic tether that assembles an actin cage around the inclusion membrane, as depletion of MYO1C or its inhibition by pentachloropseudilin (PClP) leads to the loss of the actin network surrounding the inclusion. In vitro reconstitution assays revealed that the presence of purified MYO1C was necessary and sufficient to build an actin cage around giant membranous vesicles. In summary, our findings identified MYO1C as a novel host target of Ct and provided mechanistic evidence for its role as a dynamic tether to recruit the essential actin cage around the bacterial inclusion.
沙眼衣原体（Ct）是一种革兰氏阴性专性细胞内病原体，操纵宿主肌动蛋白动力学以促进其进入、发展和退出。它在其细胞内生态位周围组装了一个动态肌动蛋白笼，称为“内含物”，它为细菌生长提供了结构稳定性，并且对于通过非细胞裂解挤出过程退出至关重要。我们发现Ct在其整个生命周期中招募肌动蛋白1 C (MYO1C)，这是一种普遍存在的肌动蛋白依赖的运动蛋白。因此，MYO1C活性的丧失减少了Ct感染和细菌后代的产生。在机制上，MYO1C作为一个动态系绳，在包涵膜周围组装一个肌动蛋白笼，因为MYO1C的耗尽或其被五氯代戊二醇（PClP）抑制导致包涵周围的肌动蛋白网络的丢失。体外重建分析显示，纯化的MYO1C的存在是必要的，足以在巨大的膜囊泡周围建立肌动蛋白笼。总之，我们的研究结果确定了MYO1C是Ct的一个新的宿主靶点，并为其作为一种动态系绳在细菌包涵体周围招募必需肌动蛋白笼的作用提供了机制证据。
{"title":"Chlamydia trachomatis highjacks host MYO1C for actin cage recruitment at the bacterial inclusion","authors":"María Emilia Cuervo , Diego Del Balzo , María Natalia Zanetti , Mariela Beatriz Nolly , Hugo Lachuer , Rostislav Petkov , Nour Ismail , John Manzi , Rubén Walter Caron , Christophe Le Clainche , Maria Teresa Damiani , Julien Pernier , Kristine Schauer , Anahi Capmany","doi":"10.1016/j.micres.2025.128395","DOIUrl":"10.1016/j.micres.2025.128395","url":null,"abstract":"<div><div><em>Chlamydia trachomatis</em> (Ct), a Gram-negative obligate intracellular pathogen, manipulates host actin dynamics to facilitate its entry, development, and exit. It assembles a dynamic actin cage around its intracellular niche, known as the ‘inclusion’, which provides structural stability for bacterial growth, and is crucial for exit via the non-cell-lytic extrusion process. We found that Ct recruits Myosin 1 C (MYO1C), a ubiquitous actin dependent motor protein, to the inclusion throughout its life cycle. Consequently, loss of MYO1C activity reduced Ct infection and the production of bacterial progenies. Mechanistically, MYO1C functions as a dynamic tether that assembles an actin cage around the inclusion membrane, as depletion of MYO1C or its inhibition by pentachloropseudilin (PClP) leads to the loss of the actin network surrounding the inclusion. In vitro reconstitution assays revealed that the presence of purified MYO1C was necessary and sufficient to build an actin cage around giant membranous vesicles. In summary, our findings identified MYO1C as a novel host target of Ct and provided mechanistic evidence for its role as a dynamic tether to recruit the essential actin cage around the bacterial inclusion.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"303 ","pages":"Article 128395"},"PeriodicalIF":6.9,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145517483","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}
Pub Date : 2026-02-01Epub Date: 2025-10-29DOI: 10.1016/j.micres.2025.128375
Li Cheng , Xinyuan Wang , Qianqian Wang , Kehan Yin, Bo Wang, Biyu Wu, Ping Xu, Hongyi Qiu, Wenjing Ge, Jiali Sun, Qing Shi, Xiujuan Yan , Shengliang Chen
Circadian rhythm disturbance caused by shift work has become increasingly prevalent, emerging as a risk factor for digestive diseases. Both the host’s and the microbial metabolic pathways and functions might be markedly altered by circadian disruption. However, metabolic changes in the gut during shift work are poorly reported. Here, we demonstrated intestinal metabolome signatures in individuals with shift work disorder and identified sebacic acid as a symptoms-related metabolite. Shift work-related circadian rhythm disturbance leads to enhanced hepatic fatty acid ω-oxidation and a significant increase in dicarboxylic fatty acids in feces. Among these, the increased sebacic acid impaired the intestinal mucus barrier by regulating composition of mucus-related gut bacteria, characterized by an increase in Muribaculaceae and a decrease in Akkermansia abundance, along with activated immune system characterized by increased B cell responses, thereby driving the occurrence of intestinal inflammation. The application of the inhibitor for CYP4A, a key ω-hydroxylase in fatty acid oxidation, effectively improved intestinal dysfunction caused by circadian rhythm disturbance. Our findings provide a deep insight into understanding the role of circadian rhythm in maintaining intestinal homeostasis.
{"title":"Circadian rhythm disturbance impairs intestinal mucus barrier and immune microenvironment via sebacic acid-mediated gut dysbiosis","authors":"Li Cheng , Xinyuan Wang , Qianqian Wang , Kehan Yin, Bo Wang, Biyu Wu, Ping Xu, Hongyi Qiu, Wenjing Ge, Jiali Sun, Qing Shi, Xiujuan Yan , Shengliang Chen","doi":"10.1016/j.micres.2025.128375","DOIUrl":"10.1016/j.micres.2025.128375","url":null,"abstract":"<div><div>Circadian rhythm disturbance caused by shift work has become increasingly prevalent, emerging as a risk factor for digestive diseases. Both the host’s and the microbial metabolic pathways and functions might be markedly altered by circadian disruption. However, metabolic changes in the gut during shift work are poorly reported. Here, we demonstrated intestinal metabolome signatures in individuals with shift work disorder and identified sebacic acid as a symptoms-related metabolite. Shift work-related circadian rhythm disturbance leads to enhanced hepatic fatty acid ω-oxidation and a significant increase in dicarboxylic fatty acids in feces. Among these, the increased sebacic acid impaired the intestinal mucus barrier by regulating composition of mucus-related gut bacteria, characterized by an increase in <em>Muribaculaceae</em> and a decrease in <em>Akkermansia</em> abundance, along with activated immune system characterized by increased B cell responses, thereby driving the occurrence of intestinal inflammation. The application of the inhibitor for CYP4A, a key ω-hydroxylase in fatty acid oxidation, effectively improved intestinal dysfunction caused by circadian rhythm disturbance. Our findings provide a deep insight into understanding the role of circadian rhythm in maintaining intestinal homeostasis.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"303 ","pages":"Article 128375"},"PeriodicalIF":6.9,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145418897","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}
Pub Date : 2026-02-01Epub Date: 2025-10-24DOI: 10.1016/j.micres.2025.128377
Xueqiang Xin , Kai Peng , Qiaojun Wang , Mashkoor Mohsin , Antonio Ruzzini , Zhiqiang Wang , Ruichao Li
The escalating prevalence of antimicrobial resistance (AMR) constitutes a global public health crisis. This is exacerbated by the continuous emergence of new variants and the discovery of previously unrecognized antibiotic resistance genes (ARGs). While advanced AMR surveillance efforts include time-consuming epidemiological investigations and retrospective analyses, critical gaps often remain towards our understanding of the sources of newly identified ARGs. Here, we established a framework integrating omics-based epidemiological investigations, genomic feature analysis of ARGs-carrying bacteria and evolution analysis of novel ARGs. We took the novel resistance gene estT as an example and analyzed it following this framework. Our study revealed that the estT gene was widely prevalent, capable of cross-phyla transmission, and predominantly present in human- and animal-derived bacteria. We explored the genomic characteristics of estT-positive Escherichia coli, Bacillus spp., Mannheimia haemolytica, and Riemerella anatipestifer, uncovering their public health risks. Evolution analysis of estT homologs found historical connections between estTs and tet(X)s. This study provides a systematic strategy for the proactive surveillance of emerging ARGs, enabling omics-data-driven monitoring of ARG evolution and dissemination to mitigate the escalating crisis of AMR.
{"title":"An omics-based framework for investigating the emerging antibiotic resistance gene: The case of estT","authors":"Xueqiang Xin , Kai Peng , Qiaojun Wang , Mashkoor Mohsin , Antonio Ruzzini , Zhiqiang Wang , Ruichao Li","doi":"10.1016/j.micres.2025.128377","DOIUrl":"10.1016/j.micres.2025.128377","url":null,"abstract":"<div><div>The escalating prevalence of antimicrobial resistance (AMR) constitutes a global public health crisis. This is exacerbated by the continuous emergence of new variants and the discovery of previously unrecognized antibiotic resistance genes (ARGs). While advanced AMR surveillance efforts include time-consuming epidemiological investigations and retrospective analyses, critical gaps often remain towards our understanding of the sources of newly identified ARGs. Here, we established a framework integrating omics-based epidemiological investigations, genomic feature analysis of ARGs-carrying bacteria and evolution analysis of novel ARGs. We took the novel resistance gene <em>estT</em> as an example and analyzed it following this framework. Our study revealed that the <em>estT</em> gene was widely prevalent, capable of cross-phyla transmission, and predominantly present in human- and animal-derived bacteria. We explored the genomic characteristics of <em>estT</em>-positive <em>Escherichia coli</em>, <em>Bacillus</em> spp., <em>Mannheimia haemolytica</em>, and <em>Riemerella anatipestifer</em>, uncovering their public health risks. Evolution analysis of <em>estT</em> homologs found historical connections between <em>estT</em>s and <em>tet</em>(X)s. This study provides a systematic strategy for the proactive surveillance of emerging ARGs, enabling omics-data-driven monitoring of ARG evolution and dissemination to mitigate the escalating crisis of AMR.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"303 ","pages":"Article 128377"},"PeriodicalIF":6.9,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145401201","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}
Pub Date : 2026-02-01Epub Date: 2025-11-01DOI: 10.1016/j.micres.2025.128385
Ganghua Han , Lei Zhao , Ruixin Li , Ruihua Liu , Yingying Wang , Mark Bartlam
Temperate and virulent phages coexist in natural environments and can collaboratively contribute to the lysis of bacterial biofilms. However, their therapeutic potential and the dynamics of phage-biofilm interactions, particularly in clinical contexts, remain poorly understood. In this study, we demonstrated the strong biofilm-lysing capabilities of the temperate phage PaoP1 and virulent phage PaoP5 against Pseudomonas aeruginosa biofilms, highlighting their potential for phage therapy. RNA-seq analysis revealed a shared host resistance mechanism involving the downregulation of flagellar biosynthesis and enhanced biofilm formation. Despite this common host response, the two phages exhibited distinct infection strategies: PaoP1 integrated quiescently into the host genome, while PaoP5 rapidly and abundantly expressed its genes, potentially hijacking the host transcriptional machinery through an as-yet-unknown mechanism. These findings deepen our understanding of phage-biofilm interactions and support the development of phage-based approaches to treat biofilm-associated infections.
{"title":"Coordinated host resistance and distinct phage strategies shape biofilm-phage dynamics in Pseudomonas aeruginosa","authors":"Ganghua Han , Lei Zhao , Ruixin Li , Ruihua Liu , Yingying Wang , Mark Bartlam","doi":"10.1016/j.micres.2025.128385","DOIUrl":"10.1016/j.micres.2025.128385","url":null,"abstract":"<div><div>Temperate and virulent phages coexist in natural environments and can collaboratively contribute to the lysis of bacterial biofilms. However, their therapeutic potential and the dynamics of phage-biofilm interactions, particularly in clinical contexts, remain poorly understood. In this study, we demonstrated the strong biofilm-lysing capabilities of the temperate phage PaoP1 and virulent phage PaoP5 against <em>Pseudomonas aeruginosa</em> biofilms, highlighting their potential for phage therapy. RNA-seq analysis revealed a shared host resistance mechanism involving the downregulation of flagellar biosynthesis and enhanced biofilm formation. Despite this common host response, the two phages exhibited distinct infection strategies: PaoP1 integrated quiescently into the host genome, while PaoP5 rapidly and abundantly expressed its genes, potentially hijacking the host transcriptional machinery through an as-yet-unknown mechanism. These findings deepen our understanding of phage-biofilm interactions and support the development of phage-based approaches to treat biofilm-associated infections.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"303 ","pages":"Article 128385"},"PeriodicalIF":6.9,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145459196","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}
Pub Date : 2026-02-01Epub Date: 2025-10-27DOI: 10.1016/j.micres.2025.128379
Alberto Bombelli , Natalia Crespo Tapia , Marcel H. Tempelaars , Sjef Boeren , Heidy M.W. den Besten , Tjakko Abee , Yue Liu
Biofilm formation is key in Listeria monocytogenes’ transmission and persistence in food processing environments. To further understand the mechanisms contributing to biofilm formation, an experimental evolution system was used to isolate strong biofilm producing strains of L. monocytogenes EGDe (reference strain) and FBR16 (hypermutator food isolate). After cycles of plastic surface colonisation, biofilm formation, dispersal and attachment to new surfaces, evolved variants (EV) strains were isolated and found to produce up to seven-fold more biofilm than their respective ancestral (AN) strains. Phenotypic assays revealed an increase in cell surface hydrophobicity as a shared dominant feature of EGDe and FBR16 EV isolates. Proteomic analysis showed proteins Lmo1798, a predicted glucosyltransferase, and Lmo1799, a putative peptidoglycan binding protein with 226 Ala-Asp tandem repeats, to be the most upregulated proteins in both EV strains compared to the AN strains. Genomic analysis of the EGDe EV strain identified a single-nucleotide insertion in the upstream region of lmo1799 and an in-frame deletion of 42 nucleotides in lmo1799, conceivably resulting in high-level expression of a functional protein with 219 Ala-Asp repeats. To evaluate the impact of Lmo1799 on the EV phenotypes and the overall biofilm capacity of L. monocytogenes, EGDe EV mutants lacking lmo1799 and/or the upstream insertion were constructed. Notably, both constructed mutants showed reduced biofilm formation and lower surface hydrophobicity compared to the EV strain, indicating the importance of these mutations for the strong biofilm capacity. Overall, these observations indicate a critical role of Lmo1799 in L. monocytogenes cell surface characteristics and biofilm formation.
{"title":"Evolution of Listeria monocytogenes to a strong biofilm producer via the overexpression of Lmo1799","authors":"Alberto Bombelli , Natalia Crespo Tapia , Marcel H. Tempelaars , Sjef Boeren , Heidy M.W. den Besten , Tjakko Abee , Yue Liu","doi":"10.1016/j.micres.2025.128379","DOIUrl":"10.1016/j.micres.2025.128379","url":null,"abstract":"<div><div>Biofilm formation is key in <em>Listeria monocytogenes</em>’ transmission and persistence in food processing environments. To further understand the mechanisms contributing to biofilm formation, an experimental evolution system was used to isolate strong biofilm producing strains of <em>L. monocytogenes</em> EGDe (reference strain) and FBR16 (hypermutator food isolate). After cycles of plastic surface colonisation, biofilm formation, dispersal and attachment to new surfaces, evolved variants (EV) strains were isolated and found to produce up to seven-fold more biofilm than their respective ancestral (AN) strains. Phenotypic assays revealed an increase in cell surface hydrophobicity as a shared dominant feature of EGDe and FBR16 EV isolates. Proteomic analysis showed proteins Lmo1798, a predicted glucosyltransferase, and Lmo1799, a putative peptidoglycan binding protein with 226 Ala-Asp tandem repeats, to be the most upregulated proteins in both EV strains compared to the AN strains. Genomic analysis of the EGDe EV strain identified a single-nucleotide insertion in the upstream region of <em>lmo1799</em> and an in-frame deletion of 42 nucleotides in <em>lmo1799</em>, conceivably resulting in high-level expression of a functional protein with 219 Ala-Asp repeats. To evaluate the impact of Lmo1799 on the EV phenotypes and the overall biofilm capacity of <em>L. monocytogenes</em>, EGDe EV mutants lacking <em>lmo1799</em> and/or the upstream insertion were constructed. Notably, both constructed mutants showed reduced biofilm formation and lower surface hydrophobicity compared to the EV strain, indicating the importance of these mutations for the strong biofilm capacity. Overall, these observations indicate a critical role of Lmo1799 in <em>L. monocytogenes</em> cell surface characteristics and biofilm formation.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"303 ","pages":"Article 128379"},"PeriodicalIF":6.9,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145445186","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}
Pub Date : 2026-02-01Epub Date: 2025-10-22DOI: 10.1016/j.micres.2025.128376
Francesco Tini , Giovanni Beccari , Lorenzo Covarelli , Nora A. Foroud , Claudia Camplone , Aurelie H. Benfield , Donald M. Gardiner , Linda J. Harris , Michael Sulyok , Roberto Romani , Ilaria Bellezza , Luisa Ederli
Fusarium graminearum and Fusarium avenaceum, causal agents of Fusarium head blight (FHB), are known to produce secondary metabolites such as deoxynivalenol (DON) and enniatins (ENNs), respectively. These species, along with other FHB pathogens, Fusarium culmorum and Fusarium poae, often co-exist in a single host-plant head, potentially resulting in the accumulation of different secondary metabolites. This study aimed to investigate the in vitro role of ENNs and DON in Fusarium development, metabolism and competition. The effects of three concentrations of enniatin B (ENB) and DON, alone or in combination, were assessed on the growth of F. avenaceum, F. graminearum, F. poae, and F. culmorum on potato dextrose agar (PDA). The expression of F. graminearum genes potentially related to stress response, growth and involved in trichothecene biosynthesis, was analyzed to elucidate the secondary metabolite action. The role of ENNs and DON in interspecific competition was explored through dual-culture experiments on PDA and rice flour agar (RFA) using mutant strains of F. avenaceum and F. graminearum. A combination of ENB and DON at the highest concentration (100 mg L⁻¹) had the most significant inhibitory effect on the growth of all tested species. Even at the lowest concentration (10 mg L⁻¹), ENB+DON significantly inhibited the growth of F. graminearum (5 %) and F. avenaceum (14 %). Gene expression analysis in F. graminearum revealed that exposure to 100 mg L⁻¹ of ENB, DON, or their combination induced a stress response. However, dual-culture experiments demonstrated that ENNs and DON did not play a role in the in vitro interactions between F. graminearum and F. avenaceum. The results obtained may prove useful in shedding light on the competitive dynamics among the various Fusarium species involved in causing FHB, and on how their secondary metabolites may play a role, either alone or in combination, in the development of the disease.
稻谷镰刀菌（Fusarium graminearum）和avenaceum是导致枯萎病（Fusarium head blight， FHB）的病原体，已知它们分别产生脱氧雪腐镰刀菌醇（脱氧雪腐镰刀菌醇，DON）和腐腐镰刀菌素（enniatins, ENNs）等次生代谢物。这些物种，连同其他FHB病原体，镰刀菌和poae镰刀菌，经常共存于一个单一的寄主植株头部，可能导致不同次生代谢物的积累。本研究旨在探讨ENNs和DON在体外镰刀菌发育、代谢和竞争中的作用。研究了三种不同浓度的enniatin B （ENB）和DON单独或联合施用对马铃薯葡萄糖琼脂（PDA）上avenaceum、F. graminearum、F. poae和F. culmorum生长的影响。分析了禾粒霉在胁迫反应、生长和毛霉合成等方面的基因表达，以阐明其次生代谢作用。利用突变菌株avavaceum和F. graminearum在PDA和米粉琼脂（RFA）上的双重培养实验，探讨了ENNs和DON在种间竞争中的作用。最高浓度（100 mg L - 1）的ENB和DON的组合对所有被试物种的生长都有最显著的抑制作用。即使在最低浓度（10 mg L⁻¹）下，ENB+DON也能显著抑制F. graminearum（5 %）和F. avenaceum（14 %）的生长。对F. graminearum的基因表达分析显示，暴露于100 mg L⁻¹ 的ENB、DON或它们的组合会引起应激反应。然而，双培养实验表明，在F. graminearum和F. avenaceum的体外相互作用中，ENNs和DON没有发挥作用。所获得的结果可能有助于阐明引起FHB的各种镰刀菌物种之间的竞争动态，以及它们的次级代谢物如何单独或联合在疾病的发展中发挥作用。
{"title":"Role of enniatins and deoxynivalenol in interspecific growth and competition in vitro among the principal causal agents of Fusarium head blight","authors":"Francesco Tini , Giovanni Beccari , Lorenzo Covarelli , Nora A. Foroud , Claudia Camplone , Aurelie H. Benfield , Donald M. Gardiner , Linda J. Harris , Michael Sulyok , Roberto Romani , Ilaria Bellezza , Luisa Ederli","doi":"10.1016/j.micres.2025.128376","DOIUrl":"10.1016/j.micres.2025.128376","url":null,"abstract":"<div><div><em>Fusarium graminearum</em> and <em>Fusarium avenaceum</em>, causal agents of Fusarium head blight (FHB), are known to produce secondary metabolites such as deoxynivalenol (DON) and enniatins (ENNs), respectively. These species, along with other FHB pathogens, <em>Fusarium culmorum</em> and <em>Fusarium poae</em>, often co-exist in a single host-plant head, potentially resulting in the accumulation of different secondary metabolites. This study aimed to investigate the <em>in vitro</em> role of ENNs and DON in <em>Fusarium</em> development, metabolism and competition. The effects of three concentrations of enniatin B (ENB) and DON, alone or in combination, were assessed on the growth of <em>F. avenaceum</em>, <em>F. graminearum</em>, <em>F. poae</em>, and <em>F. culmorum</em> on potato dextrose agar (PDA). The expression of <em>F. graminearum</em> genes potentially related to stress response, growth and involved in trichothecene biosynthesis, was analyzed to elucidate the secondary metabolite action. The role of ENNs and DON in interspecific competition was explored through dual-culture experiments on PDA and rice flour agar (RFA) using mutant strains of <em>F. avenaceum</em> and <em>F. graminearum</em>. A combination of ENB and DON at the highest concentration (100 mg L⁻¹) had the most significant inhibitory effect on the growth of all tested species. Even at the lowest concentration (10 mg L⁻¹), ENB+DON significantly inhibited the growth of <em>F. graminearum</em> (5 %) and <em>F. avenaceum</em> (14 %). Gene expression analysis in <em>F. graminearum</em> revealed that exposure to 100 mg L⁻¹ of ENB, DON, or their combination induced a stress response. However, dual-culture experiments demonstrated that ENNs and DON did not play a role in the <em>in vitro</em> interactions between <em>F. graminearum</em> and <em>F. avenaceum</em>. The results obtained may prove useful in shedding light on the competitive dynamics among the various <em>Fusarium</em> species involved in causing FHB, and on how their secondary metabolites may play a role, either alone or in combination, in the development of the disease.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"303 ","pages":"Article 128376"},"PeriodicalIF":6.9,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145364921","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}
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