Pub Date : 2026-02-01Epub Date: 2025-11-05DOI: 10.1016/j.micres.2025.128393
Cihua Zheng , Jian Xie , Furui Tang , Zhuoya Wang , Li Liu , Yimin Pi , Yuchun Zhong , Zhidong He , Tian Liu , Jiacheng Zheng , Jun Luo
Obesity disrupts bone formation-resorption balance. Despite the established role of Bacteroides acidifaciens (B. acidifaciens) in modulating metabolic homeostasis, reducing inflammation, and improving lipid metabolism, its impact on obesity-associated osteoporosis is still not well understood. In this study, we delved into the potential protective influence of B. acidifaciens on high-fat diet (HFD) induced bone loss. The results showed that B. acidifaciens sharply improved weight gain, glucose and lipid metabolism in 16 weeks HFD mice. Both In vitro and in vivo experiments have conclusively demonstrated that the introduction of B. acidifaciens notably ameliorated the imbalance of HFD induced osteogenesis and osteoclastogenesis. B. acidifaciens also regulated HFD induced gut microbiota and bile acid metabolism, and strengthened intestinal mucosal barrier function. Additionally, B. acidifaciens significantly activated the AMPK-PPARα signaling pathway in bone tissue. Thus, our study indicated that B. acidifaciens regulated metabolism, restored gut microbiota balance, and activated AMPK-PPARα pathway to prevent HFD-induced bone loss, potentially aiding in preventing and treating obesity-related osteoporosis.
{"title":"Bacteroides acidifaciens alleviates high-fat diet-induced obesity-related osteoporosis by regulating gut microbiota and bile acid metabolism via the gut-bone axis","authors":"Cihua Zheng , Jian Xie , Furui Tang , Zhuoya Wang , Li Liu , Yimin Pi , Yuchun Zhong , Zhidong He , Tian Liu , Jiacheng Zheng , Jun Luo","doi":"10.1016/j.micres.2025.128393","DOIUrl":"10.1016/j.micres.2025.128393","url":null,"abstract":"<div><div>Obesity disrupts bone formation-resorption balance. Despite the established role of <em>Bacteroides acidifaciens</em> (<em>B. acidifaciens</em>) in modulating metabolic homeostasis, reducing inflammation, and improving lipid metabolism, its impact on obesity-associated osteoporosis is still not well understood. In this study, we delved into the potential protective influence of <em>B. acidifaciens</em> on high-fat diet (HFD) induced bone loss. The results showed that <em>B. acidifaciens</em> sharply improved weight gain, glucose and lipid metabolism in 16 weeks HFD mice. Both <em>In vitro</em> and <em>in vivo</em> experiments have conclusively demonstrated that the introduction of <em>B. acidifaciens</em> notably ameliorated the imbalance of HFD induced osteogenesis and osteoclastogenesis. <em>B. acidifaciens</em> also regulated HFD induced gut microbiota and bile acid metabolism, and strengthened intestinal mucosal barrier function. Additionally, <em>B. acidifaciens</em> significantly activated the AMPK-PPARα signaling pathway in bone tissue. Thus, our study indicated that <em>B. acidifaciens</em> regulated metabolism, restored gut microbiota balance, and activated AMPK-PPARα pathway to prevent HFD-induced bone loss, potentially aiding in preventing and treating obesity-related osteoporosis.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"303 ","pages":"Article 128393"},"PeriodicalIF":6.9,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145466792","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: 2025-10-28DOI: 10.1016/j.micres.2025.128382
Elina Kadriu, Sophie Qin, Stephanie M. Prezioso, Dinesh Christendat
Carbon utilization strategies are fundamental to microbial proliferation within complex ecosystems like the soil microbiome. These strategies dictate how microbes prioritize, and metabolize available carbon compounds, shaping community dynamics and ecological outcomes. Pseudomonas putida KT2440, a soil bacterium renowned for its metabolic versatility, exemplifies this adaptive capacity. However, the regulatory mechanism it employs to prioritize sugars vs aromatic compounds for their energy requirement remains poorly understood. Here, we investigated two IclR-type transcriptional regulators, LigR1 and LigR2, which control expression of the lig1 and lig2 operons. Functional analyses reveal that LigR1 and LigR2 activate lig1 but repress the lig2 operon. 4-hydroxybenzoate binding to LigR1 represses gene expression, whereas quinate, protocatechuate, and 4-hydroxybenzoate bind to LigR2 to induce lig2 operon expression. Additionally, ligR1 deletion causes growth defects on glucose and 4-hydroxybenzoate, accompanied by cell elongation and aggregation. We propose that the lig1 operon mediates dual influx of glucose and aromatics via its major facilitator superfamily transporter, while the lig2 operon catalyzes aromatic breakdown through a protocatechuate intermediate and meta-cleavage pathway, supplying oxaloacetate to the TCA cycle. Importantly, P. putida prioritizes shikimate pathway intermediates as energy sources under specific metabolic conditions, such as their accumulation. Overall, these findings redefine the metabolic flexibility of soil pseudomonads and reveal a novel mechanism for thriving in chemically diverse environments. By illuminating a dual regulatory system, our study offers new insight into microbial carbon flux and on the traditional biosynthetic paradigm of the shikimate pathway, revealing its unexpected role in supplying the organism with energy generating compounds.
{"title":"The interplay between glucose and aromatic compound regulation by two IclR-type transcription factors, LigR1 and LigR2, in Pseudomonas putida KT2440","authors":"Elina Kadriu, Sophie Qin, Stephanie M. Prezioso, Dinesh Christendat","doi":"10.1016/j.micres.2025.128382","DOIUrl":"10.1016/j.micres.2025.128382","url":null,"abstract":"<div><div>Carbon utilization strategies are fundamental to microbial proliferation within complex ecosystems like the soil microbiome. These strategies dictate how microbes prioritize, and metabolize available carbon compounds, shaping community dynamics and ecological outcomes. <em>Pseudomonas putida</em> KT2440, a soil bacterium renowned for its metabolic versatility, exemplifies this adaptive capacity. However, the regulatory mechanism it employs to prioritize sugars vs aromatic compounds for their energy requirement remains poorly understood. Here, we investigated two IclR-type transcriptional regulators, LigR1 and LigR2, which control expression of the <em>lig1</em> and <em>lig2</em> operons. Functional analyses reveal that LigR1 and LigR2 activate <em>lig1</em> but repress the <em>lig2</em> operon. 4-hydroxybenzoate binding to LigR1 represses gene expression, whereas quinate, protocatechuate, and 4-hydroxybenzoate bind to LigR2 to induce <em>lig2</em> operon expression. Additionally, <em>ligR1</em> deletion causes growth defects on glucose and 4-hydroxybenzoate, accompanied by cell elongation and aggregation. We propose that the <em>lig1</em> operon mediates dual influx of glucose and aromatics via its major facilitator superfamily transporter, while the <em>lig2</em> operon catalyzes aromatic breakdown through a protocatechuate intermediate and meta-cleavage pathway, supplying oxaloacetate to the TCA cycle. Importantly, <em>P. putida</em> prioritizes shikimate pathway intermediates as energy sources under specific metabolic conditions, such as their accumulation. Overall, these findings redefine the metabolic flexibility of soil pseudomonads and reveal a novel mechanism for thriving in chemically diverse environments. By illuminating a dual regulatory system, our study offers new insight into microbial carbon flux and on the traditional biosynthetic paradigm of the shikimate pathway, revealing its unexpected role in supplying the organism with energy generating compounds.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"303 ","pages":"Article 128382"},"PeriodicalIF":6.9,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145418811","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}
Post-stroke depression (PSD), a frequent and debilitating complication after stroke, severely hinders rehabilitation. Emerging evidence underscores the role of neuroinflammation and the gut microbiota in PSD pathogenesis. This review systematically elaborates the mechanisms by which gut dysbiosis contributes to PSD-related neuroinflammation via immune cell regulation (e.g., Treg/Th17 balance), microbial metabolites (e.g., SCFAs, tryptophan derivatives), and neural pathways (vagus nerve, HPA axis). A key focus is the comparative analysis of the gut microbiota in PSD against major depressive disorder (MDD) and Alzheimer's disease (AD), revealing a unique, stroke-induced microbial signature characterized by a loss of protective symbionts and a bloom of pro-inflammatory taxa. We further discuss the translational potential of microbiota-targeted interventions (e.g., probiotics, prebiotics) for PSD. By integrating clinical microbial ecology with mechanistic insights, this review synthesizes evidence suggesting that the gut microbiome may represent a promising diagnostic and therapeutic target for PSD, offering a distinct perspective from previous literature.
{"title":"The gut microbiota in post-stroke depression: A systematic review of microbial mechanisms and therapeutic targeting of neuroinflammation","authors":"Qianwen Zhang , Shiqing Zhang , Xingqin Cao , Yinghao Zhi , Ying Guo","doi":"10.1016/j.micres.2025.128391","DOIUrl":"10.1016/j.micres.2025.128391","url":null,"abstract":"<div><div>Post-stroke depression (PSD), a frequent and debilitating complication after stroke, severely hinders rehabilitation. Emerging evidence underscores the role of neuroinflammation and the gut microbiota in PSD pathogenesis. This review systematically elaborates the mechanisms by which gut dysbiosis contributes to PSD-related neuroinflammation via immune cell regulation (e.g., Treg/Th17 balance), microbial metabolites (e.g., SCFAs, tryptophan derivatives), and neural pathways (vagus nerve, HPA axis). A key focus is the comparative analysis of the gut microbiota in PSD against major depressive disorder (MDD) and Alzheimer's disease (AD), revealing a unique, stroke-induced microbial signature characterized by a loss of protective symbionts and a bloom of pro-inflammatory taxa. We further discuss the translational potential of microbiota-targeted interventions (e.g., probiotics, prebiotics) for PSD. By integrating clinical microbial ecology with mechanistic insights, this review synthesizes evidence suggesting that the gut microbiome may represent a promising diagnostic and therapeutic target for PSD, offering a distinct perspective from previous literature.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"303 ","pages":"Article 128391"},"PeriodicalIF":6.9,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145557409","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: 2025-11-03DOI: 10.1016/j.micres.2025.128384
Abhishek Kumar , Caiming Xu , Tikam Chand Dakal
Gut microbiome (GME) is a dynamic ecosystem composed of diverse microorganisms with extensive functional potential that influence host physiology, endocrinology, and neurology. This review explores how multiomics (mOMICS) and machine learning (ML) enhance understanding of the GME and its implications for human disease and therapy. Integrating metagenomics, metatranscriptomics, metaproteomics, and metabolomics with ML enables the linkage of microbial composition and function to clinical outcomes. Combined mOMICS approaches elucidate species and strain dynamics, metabolic pathways, and metabolite production within the gut environment. Techniques such as shotgun metagenomics, metagenome-assembled genomes, and pathway mapping reveal associations between dysbiosis and diseases including inflammatory bowel disease, colorectal cancer, cardiometabolic, and neurological disorders. Mechanistic insights highlight short-chain fatty acids in immune regulation, bile acid transformations in metabolic signaling, and trimethylamine N-oxide in cardiovascular risk. ML models trained on heterogeneous datasets identify disease-related microbial modules, improve patient stratification, and predict therapeutic responses, such as differentiating IBD subtypes and detecting cancer-linked microbial signatures. Network analyses uncover gut microbial interaction patterns influencing host physiology. Emerging integrative tools like MOFA+ , DIABLO, and MintTea strengthen cross-modal analysis and biomarker discovery. Standardized workflows addressing quality control, assembly, binning, annotation, and visualization ensure reproducibility. Together, mOMICS and ML establish a robust framework for translating GME ecology into clinically relevant biomarkers and precision interventions. To enhance reliability, GME studies should adopt uniform sampling protocols, correct compositional biases, employ interpretable models, and validate findings across multi-site cohorts to advance microbiome-based diagnostics and therapeutics in precision medicine.
{"title":"Microbiome based precision medicine through integrated multiomics and machine learning","authors":"Abhishek Kumar , Caiming Xu , Tikam Chand Dakal","doi":"10.1016/j.micres.2025.128384","DOIUrl":"10.1016/j.micres.2025.128384","url":null,"abstract":"<div><div>Gut microbiome (GME) is a dynamic ecosystem composed of diverse microorganisms with extensive functional potential that influence host physiology, endocrinology, and neurology. This review explores how multiomics (m<sup>OMICS</sup>) and machine learning (ML) enhance understanding of the GME and its implications for human disease and therapy. Integrating metagenomics, metatranscriptomics, metaproteomics, and metabolomics with ML enables the linkage of microbial composition and function to clinical outcomes. Combined m<sup>OMICS</sup> approaches elucidate species and strain dynamics, metabolic pathways, and metabolite production within the gut environment. Techniques such as shotgun metagenomics, metagenome-assembled genomes, and pathway mapping reveal associations between dysbiosis and diseases including inflammatory bowel disease, colorectal cancer, cardiometabolic, and neurological disorders. Mechanistic insights highlight short-chain fatty acids in immune regulation, bile acid transformations in metabolic signaling, and trimethylamine N-oxide in cardiovascular risk. ML models trained on heterogeneous datasets identify disease-related microbial modules, improve patient stratification, and predict therapeutic responses, such as differentiating IBD subtypes and detecting cancer-linked microbial signatures. Network analyses uncover gut microbial interaction patterns influencing host physiology. Emerging integrative tools like MOFA+ , DIABLO, and MintTea strengthen cross-modal analysis and biomarker discovery. Standardized workflows addressing quality control, assembly, binning, annotation, and visualization ensure reproducibility. Together, m<sup>OMICS</sup> and ML establish a robust framework for translating GME ecology into clinically relevant biomarkers and precision interventions. To enhance reliability, GME studies should adopt uniform sampling protocols, correct compositional biases, employ interpretable models, and validate findings across multi-site cohorts to advance microbiome-based diagnostics and therapeutics in precision medicine.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"303 ","pages":"Article 128384"},"PeriodicalIF":6.9,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145452364","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 : 2026-01-01Epub Date: 2025-09-02DOI: 10.1016/j.micres.2025.128326
Wensi Zhang , Qian Liu , Bharat Manna , Naresh Singhal , Jian Wang , Boyu Lyu , Xueyang Zhou , Yurong Qian
Cadmium (Cd) contamination in coastal regions poses severe environmental risks, yet bacterial defense mechanisms against Cd remain poorly understood. This study unveils distinct tolerant strategies of two highly Cd-tolerant bacteria isolated from the Yangtze River estuary: Comamonas sp. Y49 and Aeromonas sp. Y23. We exposed two bacterial strains to Cd2 + concentrations ranging from sub-lethal to near-lethal levels, based on their minimum inhibitory concentrations, to investigate their stress response mechanisms. The cellular adaptations were comprehensively analyzed through transcriptomic profiling and scanning electron microscopy coupled with energy dispersive X-ray spectroscopy (SEM-EDS). Transcriptomic analyses revealed that both strains significantly stimulated carbon, nitrogen and sulfur metabolism under Cd stress for maintaining essential substance and energy resources. They both enhanced reactive oxygen scavenger and polyamine biosynthesis gene regulation, suggesting a shared strategy for mitigating oxidative stress. Strain Comamonas sp. Y49 showed a 2.97-fold increase in metal efflux gene regulation and secreted extracellular polysaccharide-like substances with SEM-EDS detecting 0.50 % Cd on cell surfaces, while Aeromonas sp. Y23 potentially reduced Cd uptake by forming long-chain cellular structures. Besides, Comamonas sp. Y49 downregulated motility genes by 2.07-fold, while Aeromonas sp. Y23 upregulated them by 1.12-fold, indicating divergent biofilm formation strategies. This study provides novel insights into bacterial Cd resistance, revealing strain-specific adaptive mechanisms that combine metabolic rewiring, morphological changes, and molecular defense strategies. Our findings provide valuable insights on bacterial adaptations to metal stress and establish a molecular foundation for developing microbial-based strategies to address metal contamination in estuarine environments.
{"title":"Metabolic rewiring and morphological adaptations drive bacterial strain-specific cadmium defense in the Yangtze River estuary","authors":"Wensi Zhang , Qian Liu , Bharat Manna , Naresh Singhal , Jian Wang , Boyu Lyu , Xueyang Zhou , Yurong Qian","doi":"10.1016/j.micres.2025.128326","DOIUrl":"10.1016/j.micres.2025.128326","url":null,"abstract":"<div><div>Cadmium (Cd) contamination in coastal regions poses severe environmental risks, yet bacterial defense mechanisms against Cd remain poorly understood. This study unveils distinct tolerant strategies of two highly Cd-tolerant bacteria isolated from the Yangtze River estuary: <em>Comamonas</em> sp. Y49 and <em>Aeromonas</em> sp. Y23. We exposed two bacterial strains to Cd<sup>2 +</sup> concentrations ranging from sub-lethal to near-lethal levels, based on their minimum inhibitory concentrations, to investigate their stress response mechanisms. The cellular adaptations were comprehensively analyzed through transcriptomic profiling and scanning electron microscopy coupled with energy dispersive X-ray spectroscopy (SEM-EDS). Transcriptomic analyses revealed that both strains significantly stimulated carbon, nitrogen and sulfur metabolism under Cd stress for maintaining essential substance and energy resources. They both enhanced reactive oxygen scavenger and polyamine biosynthesis gene regulation, suggesting a shared strategy for mitigating oxidative stress. Strain <em>Comamonas</em> sp. Y49 showed a 2.97-fold increase in metal efflux gene regulation and secreted extracellular polysaccharide-like substances with SEM-EDS detecting 0.50 % Cd on cell surfaces, while <em>Aeromonas</em> sp. Y23 potentially reduced Cd uptake by forming long-chain cellular structures. Besides, <em>Comamonas</em> sp. Y49 downregulated motility genes by 2.07-fold, while <em>Aeromonas</em> sp. Y23 upregulated them by 1.12-fold, indicating divergent biofilm formation strategies. This study provides novel insights into bacterial Cd resistance, revealing strain-specific adaptive mechanisms that combine metabolic rewiring, morphological changes, and molecular defense strategies. Our findings provide valuable insights on bacterial adaptations to metal stress and establish a molecular foundation for developing microbial-based strategies to address metal contamination in estuarine environments.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"302 ","pages":"Article 128326"},"PeriodicalIF":6.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145004977","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 : 2026-01-01Epub Date: 2025-09-16DOI: 10.1016/j.micres.2025.128343
Md. Mizanur Rahaman , Karma Yeshi , Mehedi Hasan Bappi , Md. Zohorul Islam , Phurpa Wangchuk , Subir Sarker
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 Acutalibacter muris, Monoglobus pectinilyticus, Streptococcus pneumoniae, Parabacteroides merdae, and Haemophilus influenzae, while decreasing Staphylococcus ureilyticus and Mailhella massiliensis. 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. In silico 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.
炎症性肠病（IBD）是一种慢性、多因素的胃肠道疾病，通常与肠道微生物群的生态失调有关。虽然IBD的确切病因尚不清楚，但肠道微生物组组成和功能的改变被认为是IBD发病的关键因素。具有抗炎特性的天然化合物越来越多地被探索作为IBD的潜在治疗选择。本研究在2,4,6 -三硝基苯磺酸（TNBS）诱导的小鼠结肠炎模型中，评估了两种新分离的没食子酰葡萄糖苷——没食子酰lawsoniside A （comp-4）和尿myrtoside （comp-6）与地塞米松（DEX）一起对微生物组的调节作用。我们对小鼠结肠组织采用PacBio HiFi全长度16S rRNA基因测序来评估肠道微生物组及其相关功能通路的变化。tnbs诱导的结肠炎显著改变了微生物组成，增加了死亡针状杆菌、果胶单胞杆菌、肺炎链球菌、merdae副杆菌和流感嗜血杆菌的丰度，同时减少了尿毒葡萄球菌和马塞勒麦氏杆菌的丰度。对照4和对照6有效地恢复了不平衡的菌群。功能通路分析显示，结肠炎减少了微生物通路，包括肽聚糖生物合成和双歧杆菌分流。用我们的植物源性化合物处理后，这些破坏得以恢复。功能改善可能与减少IL-6产生和恢复肠屏障完整性有关。值得注意的是，comp-4在微生物和宿主相关参数中都表现出最显著的治疗效果。硅对接进一步支持了这些化合物的抗炎和免疫调节潜力。总之，我们的研究结果强调了IBD中微生物功能和宿主免疫之间的相互作用，并确定了植物来源的没食子酰糖苷是微生物组靶向IBD治疗的有希望的候选者。
{"title":"Novel plant-derived compounds modulate gut microbiome dysbiosis in colitis mice: A potential therapeutic avenue for inflammatory bowel disease","authors":"Md. Mizanur Rahaman , Karma Yeshi , Mehedi Hasan Bappi , Md. Zohorul Islam , Phurpa Wangchuk , 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}
Pub Date : 2026-01-01Epub Date: 2025-09-30DOI: 10.1016/j.micres.2025.128355
Jun Zhang , Xiaobing Zhou , Xiaoying Rong , Benfeng Yin , Lei Zhang , Yuanming Zhang
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 > plant functional traits > abiotic environment > 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.
{"title":"Host phylogeny and traits shape the composition and network structure of the phyllosphere microbial communities in temperate desert plants","authors":"Jun Zhang , Xiaobing Zhou , Xiaoying Rong , Benfeng Yin , Lei Zhang , 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 > plant functional traits > abiotic environment > 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}
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.
{"title":"Crosstalk between the m6A modification and the gut microbiota in lipid metabolism","authors":"Haiyan Chen, Yaolin Ren, Jie Yu, Jing Ren, Yuan Zeng, Yifan Wu, Qian Zhang, 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}
Pub Date : 2026-01-01Epub Date: 2025-08-30DOI: 10.1016/j.micres.2025.128325
Xia Kang , Yang Yu , Shengyin Zhang , Xiang Wu , Jing Li , Tianhai Liu , Francis M. Martin , Hao Tan
Black morel (Morchella sextelata) 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 M. sextelata 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 (R2 = 0.928, RMSE = 0.084, P < 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, P < 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.
黑羊肚菌（Morchella sextelata）被广泛认为是一种火后蘑菇，因为它在火后富含木炭的森林土壤中多产。有趣的是，人工种植的六棱草经常加入生物炭作为土壤改良剂来提高产量，尽管潜在的物理化学和生态机制尚不清楚。本研究评价了生物炭（0、7.5、15和30 t ha⁻¹）对沙质壤土羊粪结实产量和土壤细菌和真菌群落组成的影响。结果表明，较高的生物炭水平显著增加了真菌α-多样性，促进腐养、共生和外生菌根行会，抑制真菌病原体，降低竞争真菌的绝对丰度。真菌生态网络比细菌网络更具凝聚力和弹性，适度的生物炭水平（15 / ha - 1）促进了最佳稳定性。基于机器学习的相关分析表明，结实期土壤NO3—N浓度对微生物群落动态和羊粪产量起关键作用（R2 = 0.928, RMSE = 0.084, P <； 0.001）。结构方程模型进一步表明，土壤氮含量（全N、NO3—N和NH4+-N）是真菌多样性的直接驱动因子（通径系数= 1.062,P <； 0.05），进而对油菜产量产生强烈的间接影响。这些发现不仅突出了生物炭改性提高蘑菇产量的潜力，而且还提供了为什么羊绒菌在火灾后环境中大量结果的见解，在火灾后环境中，氮可用性的改变和真菌竞争的减少可能起着关键作用。
{"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 , Yang Yu , Shengyin Zhang , Xiang Wu , Jing Li , Tianhai Liu , Francis M. Martin , 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<sup>−1</sup>) promoting optimal stability. Machine-learning based correlation analysis reveal that the concentration of soil NO<sub>3</sub><sup>-</sup>-N upon fructification played a key role (<em>R</em><sup><em>2</em></sup> = 0.928, RMSE = 0.084, <em>P</em> < 0.001) in microbial community dynamics and morel yield. Structural equation model further show that soil nitrogen contents (total N, NO<sub>3</sub><sup>-</sup>-N and NH<sub>4</sub><sup>+</sup>-N) served as the direct driver of fungal diversity (path coefficient = 1.062, <em>P</em> < 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}
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