Microbiological research最新文献

{"title":"Novel plant-derived compounds modulate gut microbiome dysbiosis in colitis mice: A potential therapeutic avenue for inflammatory bowel disease","authors":"Md. Mizanur Rahaman ,&nbsp;Karma Yeshi ,&nbsp;Mehedi Hasan Bappi ,&nbsp;Md. Zohorul Islam ,&nbsp;Phurpa Wangchuk ,&nbsp;Subir Sarker","doi":"10.1016/j.micres.2025.128343","DOIUrl":"10.1016/j.micres.2025.128343","url":null,"abstract":"<div><div>Inflammatory bowel disease (IBD) is a chronic, multifactorial disorder of the gastrointestinal tract, often associated with dysbiosis in gut microbiota. While the exact cause of IBD remains unclear, alterations in gut microbiome composition and function are recognised as key contributors to IBD pathogenesis. Natural compounds with anti-inflammatory properties are increasingly explored as potential therapeutic options for IBD. This study evaluated the therapeutic effects of two newly isolated galloyl glucosides—galloyl-lawsoniaside A (comp-4) and uromyrtoside (comp-6)—alongside dexamethasone (DEX) on microbiome regulation in a 2, 4, 6-Trinitrobenzene sulfonic acid (TNBS)-induced colitis mouse model. We employed PacBio HiFi full-length 16S rRNA gene sequencing on mouse colon tissue to assess changes in the intestinal microbiome and its associated functional pathways. TNBS-induced colitis significantly altered microbial composition, increasing the abundance of <em>Acutalibacter muris</em>, <em>Monoglobus pectinilyticus</em>, <em>Streptococcus pneumoniae</em>, <em>Parabacteroides merdae</em>, and <em>Haemophilus influenzae</em>, while decreasing <em>Staphylococcus ureilyticus</em> and <em>Mailhella massiliensis</em>. Treatment with comps 4 and 6 effectively restored the imbalanced microbiota. Functional pathway analysis revealed that colitis reduced microbial pathways, including peptidoglycan biosynthesis and the Bifidobacterium shunt. These disruptions were restored following treatment with our plant-derived compounds. Functional improvements were likely associated with reduced IL-6 production and restoring intestinal barrier integrity. Notably, comp-4 exhibited the most pronounced therapeutic efficacy across both microbial and host-associated parameters. <em>In silico</em> docking further supported the anti-inflammatory and immunomodulatory potential of these compounds. Together, our findings highlight the interplay between microbial function and host immunity in IBD and identify plant-derived galloyl glucosides as promising candidates for microbiome-targeted IBD therapeutics.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"302 ","pages":"Article 128343"},"PeriodicalIF":6.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145099372","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":"Host phylogeny and traits shape the composition and network structure of the phyllosphere microbial communities in temperate desert plants","authors":"Jun Zhang ,&nbsp;Xiaobing Zhou ,&nbsp;Xiaoying Rong ,&nbsp;Benfeng Yin ,&nbsp;Lei Zhang ,&nbsp;Yuanming Zhang","doi":"10.1016/j.micres.2025.128355","DOIUrl":"10.1016/j.micres.2025.128355","url":null,"abstract":"<div><div>Phyllosphere microorganisms play a vital role in enhancing the adaptability and functionality of their host plants. Although the effects of phyllosphere microbial communities on host functional traits and their association with host phylogeny has been widely investigated, it remains unclear whether host selection consistently drives the assembly of these communities. In this study, bacterial and fungal communities on the surfaces of 734 leaf samples were characterized using bacterial and fungal amplicon sequencing. These microbial communities were associated with 42 plant species native to the Gurbantunggut Desert, a representative temperate desert located in Central Asia. The research assessed the relative contributions of plant-related factors, abiotic environmental variables (such as climate and soil), and spatial components to the observed variation in phyllosphere microbial communities, and further inferred the topological structure of plant-microbe interaction networks. The results indicate that plant phylogeny, plant functional traits, abiotic environment conditions, and spatial factors account for variations in the bacterial community composition (36.4 %, 4.6 %, 1.0 %, and 0.1 %, respectively) and the fungal community composition (28.6 %, 3.0 %, 1.5 %, and 1.2 %, respectively), following a hierarchical trend of plant phylogeny &gt; plant functional traits &gt; abiotic environment &gt; space. Plant phylogeny and functional traits play a central role in shaping the assembly of phyllosphere microbial communities, indicating that plant filtering effects significantly influence microbial composition. Analysis of plant-microbe interactions reveals distinct preferences of microbial taxa for plant hosts across different taxonomic levels and geographic regions. Bipartite network analysis further illustrates that plant-microbe networks are highly specialized and modular, with plant-fungal networks exhibiting greater host specificity compared to plant-bacterial networks. Collectively, these findings underscore plant filtering as the primary determinant of microbial community assembly in the desert phyllosphere and provide valuable insights into the macroecological patterns shaping plant-microbe interactions in arid ecosystems.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"302 ","pages":"Article 128355"},"PeriodicalIF":6.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145244386","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":"Corrigendum to “Gut microbiota-driven BCAA biosynthesis via Staphylococcus aureus -expressed acetolactate synthase impairs glycemic control in type 2 diabetes in South China” [Microbiol. Res. 296 (2025) 128145]","authors":"Tingting Liang ,&nbsp;Tong Jiang ,&nbsp;Zhuang Liang ,&nbsp;Longyan Li ,&nbsp;Ya Chen ,&nbsp;Tong Chen ,&nbsp;Lingshuang Yang ,&nbsp;Ni Zhang ,&nbsp;Bo Dong ,&nbsp;Xinqiang Xie ,&nbsp;Bing Gu ,&nbsp;Qingping Wu","doi":"10.1016/j.micres.2025.128344","DOIUrl":"10.1016/j.micres.2025.128344","url":null,"abstract":"","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"302 ","pages":"Article 128344"},"PeriodicalIF":6.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145113720","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":"Crosstalk between the m6A modification and the gut microbiota in lipid metabolism","authors":"Haiyan Chen,&nbsp;Yaolin Ren,&nbsp;Jie Yu,&nbsp;Jing Ren,&nbsp;Yuan Zeng,&nbsp;Yifan Wu,&nbsp;Qian Zhang,&nbsp;Xinhua Xiao","doi":"10.1016/j.micres.2025.128356","DOIUrl":"10.1016/j.micres.2025.128356","url":null,"abstract":"<div><div>Lipid metabolism is essential for maintaining cellular homeostasis and human health, and its dysregulation can contribute to metabolic disorders such as obesity and diabetes. As one of the most prevalent RNA modifications, the N6-methyladenosine (m6A) modification plays a pivotal role in regulating gene expression and metabolic pathways. The gut microbiota influences lipid metabolism by modulating the host's m6A modification patterns. Research has shown that the gut microbiota can regulate the levels of the m6A modification in host tissues, while the m6A modification also impacts the composition and functionality of the gut microbiota. This review comprehensively examines the interaction between the m6A modification and the gut microbiota, elucidating its underlying mechanisms in lipid metabolism and highlighting the potential applications of this crosstalk in addressing metabolic diseases. Future investigations should aim to further elucidate the precise molecular mechanisms governing the interplay between the m6A modification and the gut microbiota, thereby providing novel therapeutic targets and strategies for metabolic disease management.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"302 ","pages":"Article 128356"},"PeriodicalIF":6.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145220713","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":"Biochar amendment improves Morchella sextelata yield by enhancing soil NO3--N availability and increasing the diversity while decreasing the absolute abundance of fungal community","authors":"Xia Kang ,&nbsp;Yang Yu ,&nbsp;Shengyin Zhang ,&nbsp;Xiang Wu ,&nbsp;Jing Li ,&nbsp;Tianhai Liu ,&nbsp;Francis M. Martin ,&nbsp;Hao Tan","doi":"10.1016/j.micres.2025.128325","DOIUrl":"10.1016/j.micres.2025.128325","url":null,"abstract":"<div><div>Black morel (<em>Morchella sextelata</em>) is widely regarded as a post-fire mushroom because of its prolific fruiting in post-fire forest soils enriched with charcoal. Intriguingly, artificial cultivation of <em>M. sextelata</em> often incorporates biochar as a soil amendment to enhance yield, although the underlying physicochemical and ecological mechanisms remain unclear. This study evaluates the effects of biochar amendment (0, 7.5, 15, and 30 t ha⁻¹) in a sandy loam soil on the yield of morel fruiting and the composition of soil bacterial and fungal communities. Our findings reveal that higher biochar levels significantly increased fungal α-diversity, promoted saprotrophic, symbiotrophic and ectomycorrhizal guilds, suppressed fungal pathogens, and lowered the absolute abundance of competing fungi. Fungal ecological networks were more cohesive and resilient than bacterial networks, with a moderate biochar level (15 t ha⁻¹) promoting optimal stability. Machine-learning based correlation analysis reveal that the concentration of soil NO₃^--N upon fructification played a key role (<em>R</em>^<em>2</em> = 0.928, RMSE = 0.084, <em>P</em> &lt; 0.001) in microbial community dynamics and morel yield. Structural equation model further show that soil nitrogen contents (total N, NO₃^--N and NH₄⁺-N) served as the direct driver of fungal diversity (path coefficient = 1.062, <em>P</em> &lt; 0.05), which in turn exerted a strong indirect influence on morel yield. These findings not only highlight the potential of biochar amendments to boost mushroom productivity but also provide insights into why morels fruit abundantly in post-fire environments, where altered N availability and reduced fungal competition likely play key roles.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"302 ","pages":"Article 128325"},"PeriodicalIF":6.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144997487","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":"Citrus fruit microbiome changes under copper-based and biological alternative treatments and its biocontrol potential","authors":"M.F. Lombardo ,&nbsp;A. Abdelfattah ,&nbsp;V. Catara ,&nbsp;N. Wang ,&nbsp;G. Cirvilleri","doi":"10.1016/j.micres.2025.128346","DOIUrl":"10.1016/j.micres.2025.128346","url":null,"abstract":"<div><div>Citrus, a globally significant fruit crop, harbours a distinctive microbial community crucial for maintaining citrus health and enhancing disease resistance. While the structure and shaping factors, including phytosanitary treatments, of citrus root and leaf microbiomes are well documented, the carposphere (fruit surface) microbiome and its response to phytosanitary inputs remain poorly understood. In the present study, we combined culture independent (amplicon sequencing) and culture dependent techniques to analyse the citrus carposphere microbiome across three citrus hosts and its response to field-applied phytosanitary treatments (biologicals and copper-antimicrobials). Despite host-specific variation in the relative abundance of dominant taxa such as Proteobacteria, Firmicutes, and Basidiomycota, all three citrus hosts shared a core microbiome, consistently present across fruit samples. Bacterial diversity and composition were negatively influenced by copper treatments, whereas biological products (chitosan, sweet orange essential oils and their mixtures) had minimal or no negative impacts. Fungal communities, including potential pathogens, appeared less sensitive to treatments. Network analysis confirmed that copper altered microbial interactions, increasing mutual exclusion relationships between bacterial taxa compared to untreated or biologically treated samples, which were dominated by positive interactions. A parallel survey of cultivable microbiota from the same samples identified potential biocontrol agents (BCAs) against <em>Colletotrichum gloeosporioides</em> and <em>Alternaria alternata</em>. Notably, cross-referencing cultivable BCAs with core Amplicon Sequence Variants (ASVs) showed that 81.7 % of bacterial core members represent potential biocontrol agents. This study highlights the importance of management practices for sustaining beneficial microbiomes. Furthermore, it establishes a valuable resource of core-associated BCAs, offering promising avenues for the biological control of fungal pathogens.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"302 ","pages":"Article 128346"},"PeriodicalIF":6.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145186302","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":"c-di-GMP regulates the resistance of Pseudomonas aeruginosa to heat shock and aminoglycoside antibiotics by targeting the σ factor RpoH","authors":"Xinyi Huo ,&nbsp;Lianying Mao ,&nbsp;Chenyu Dong,&nbsp;Wenguang Yang,&nbsp;Heng Zhang,&nbsp;Lei Zhang","doi":"10.1016/j.micres.2025.128347","DOIUrl":"10.1016/j.micres.2025.128347","url":null,"abstract":"<div><div>Cyclic di-GMP (c-di-GMP) is a second messenger molecule that is widely distributed in bacteria and plays various physiologically important regulatory roles through interactions with a variety of effector molecules. Sigma (σ) factors are the predominant transcription factors involved in transcription regulation in bacteria. While c-di-GMP has been shown to bind to a range of transcription factors, c-di-GMP-binding σ factors have never been reported before. In a c-di-GMP/σ factors binding screen, we identified the σ factor RpoH as a c-di-GMP-responsive transcription factor in <em>Pseudomonas aeruginosa</em> PAO1. We further show that the binding of c-di-GMP to RpoH inhibits binding of RpoH to the promoters of its target genes such as <em>asrA</em> and <em>dnaK</em>, thereby downregulating the expression of these genes and reducing the resistance of <em>P. aeruginosa</em> to heat shock and aminoglycoside antibiotics. RpoH from <em>Escherichia coli, Burkholderia thailandensis</em> and <em>Agrobacterium tumefaciens</em> are also capable of binding c-di-GMP, suggesting that c-di-GMP-mediated control of the activity of RpoH is conserved in members of Proteobacteria.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"302 ","pages":"Article 128347"},"PeriodicalIF":6.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145155921","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":"Metabolic control of cytokinesis by glucose cAMP–PKA signaling in fission yeast","authors":"Antonio Marín-Castillo,&nbsp;Sergio León-Zaragoza,&nbsp;Alejandro Franco,&nbsp;Jero Vicente-Soler,&nbsp;Andrés Núñez,&nbsp;Teresa Soto,&nbsp;Marisa Madrid,&nbsp;José Cansado","doi":"10.1016/j.micres.2025.128345","DOIUrl":"10.1016/j.micres.2025.128345","url":null,"abstract":"<div><div>Cytokinesis, the final step of cell division, must be precisely coordinated with the cellular metabolic status, yet the underlying regulatory mechanisms remain poorly understood. Here we show that in <em>Schizosaccharomyces pombe</em>, glucose signaling promotes cytokinesis via the evolutionarily conserved cAMP–PKA signaling pathway. Loss of the Pka1 catalytic subunit delays assembly and constriction of the contractile actomyosin ring (CAR), whereas constitutive PKA activation enhances CAR integrity and accelerates cytokinesis. Mechanistically, Pka1 downregulates the basal activity of the stress-activated MAPK Sty1 under glucose-rich conditions, thereby stabilizing the formin For3 and its nucleated actin cables, which collaborate to regulate CAR dynamics. Remarkably, cAMP–PKA signaling also facilitates cytokinesis through a parallel, actin cable–independent mechanism. Additionally, mitochondrial respiration contributes to cytokinesis in the presence of glucose through a PKA-independent pathway. These findings reveal a multilayered network that links carbon source metabolism to cytoskeletal organization and underscore the importance of tight PKA activity control for robust cell division.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"302 ","pages":"Article 128345"},"PeriodicalIF":6.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145118922","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":"Corrigendum to “A molecular overview of the polymyxin-LPS interaction in the context of its mode of action and resistance development” [Microbiol. Res. 283 (2024) 127679]","authors":"Indira Padhy,&nbsp;Sambit K. Dwibedy,&nbsp;Saswat S. Mohapatra","doi":"10.1016/j.micres.2025.128335","DOIUrl":"10.1016/j.micres.2025.128335","url":null,"abstract":"","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"302 ","pages":"Article 128335"},"PeriodicalIF":6.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145030155","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 oxidative stress-related peroxiredoxin Tsa1b of Candidozyma (Candida) auris contributes to virulence and infection","authors":"Maialen Areitio ,&nbsp;Oier Rodriguez-Erenaga ,&nbsp;Leire Aparicio-Fernandez ,&nbsp;Lucía Abio-Dorronsoro ,&nbsp;Leire Martin-Souto ,&nbsp;Uxue Perez-Cuesta ,&nbsp;Idoia Buldain ,&nbsp;Beñat Zaldibar ,&nbsp;Alba Ruiz-Gaitan ,&nbsp;Javier Pemán ,&nbsp;Salomé LeibundGut-Landmann ,&nbsp;Aitor Rementeria ,&nbsp;Aitziber Antoran ,&nbsp;Andoni Ramirez-Garcia","doi":"10.1016/j.micres.2025.128353","DOIUrl":"10.1016/j.micres.2025.128353","url":null,"abstract":"<div><div>The difficulty of accurately identifying <em>Candidozyma auris</em> (formerly <em>Candida auris</em>) and the high resistance rates presented have increased the concern in the healthcare setting. Due to this, the aim of this study was to analyse the fungal response to oxidative stress. To achieve this goal, gene and protein expression were examined using qPCR and two-dimensional electrophoresis, respectively, peroxiredoxin Tsa1b being found to be upregulated under oxidative stress. Subsequently, the significance of Tsa1b was next investigated by characterizing the <em>C. auris</em> Δ<em>tsa1b</em> and <em>C. auris</em> Δ<em>tsa1b::TSA1B</em> strains generated by CRISPR-Cas9. The findings demonstrated that the Δ<em>tsa1b</em> strain was more susceptible to oxidative and cell wall stressors than the wild-type strain, which was consistent with an increase in the cell wall β-glucan amounts when grown in the presence of oxidative stress. Importantly, Tsa1b has also been detected as an antigen by patient sera. Furthermore, the Δ<em>tsa1b</em> strain was also more vulnerable to the presence of dendritic cells and bone marrow-derived macrophages. Finally, <em>in vivo</em> infections performed in <em>Galleria mellonella</em> and mice showed a slower progression of the disease in animals infected with the mutant strain. In conclusion, the peroxiredoxin Tsa1b has been identified as a potential candidate to be studied as a virulence factor implicated in the oxidative stress response of <em>C. auris</em>. These findings advance the knowledge of the pathobiology of <em>C. auris</em> and point out the potential of Tsa1b for the development of new diagnostic and therapeutic approaches.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"302 ","pages":"Article 128353"},"PeriodicalIF":6.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145206891","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}