Pub Date : 2025-04-23DOI: 10.1016/j.micres.2025.128192
Hassan Etesami , Gustavo Santoyo
Legumes are vital for sustainable agriculture due to their unique ability to fix atmospheric nitrogen through symbiosis with rhizobia. Recent research has highlighted the significant role of non-rhizobial bacteria (NRB) within root nodules in enhancing this symbiotic relationship, particularly under stress conditions. These NRB exhibit plant growth-promoting (PGP) metabolites by modulating phytohormones and enhancing nutrient availability, thereby improving nodule development and function. Bacteria produce essential hormones, such as auxin (indole-3-acetic acid), cytokinins, gibberellic acids abscisic acid, jasmonic acid, and salicylic acid, and enzymes like 1-aminocyclopropane-1-carboxylate deaminase, which mitigate ethylene's inhibitory effects on nodulation. Furthermore, NRB contribute to nutrient cycling by solubilizing minerals like phosphate, potassium, silicate, zinc, and iron, essential for effective nitrogen fixation. The co-inoculation of legumes with both rhizobia and NRB with multiple PGP metabolites has shown synergistic effects on plant growth, yield, and resilience against environmental stresses. This review emphasizes the need to further explore the diversity and functional roles of nodule-associated non-rhizobial endophytes, aiming to optimize legume productivity through improved nutrient and hormonal management. Understanding these interactions is crucial for developing sustainable agricultural practices that enhance the efficiency of legume-rhizobia symbiosis, ultimately contributing to food security and ecosystem health.
{"title":"Boosting Rhizobium-legume symbiosis: The role of nodule non-rhizobial bacteria in hormonal and nutritional regulation under stress","authors":"Hassan Etesami , Gustavo Santoyo","doi":"10.1016/j.micres.2025.128192","DOIUrl":"10.1016/j.micres.2025.128192","url":null,"abstract":"<div><div>Legumes are vital for sustainable agriculture due to their unique ability to fix atmospheric nitrogen through symbiosis with rhizobia. Recent research has highlighted the significant role of non-rhizobial bacteria (NRB) within root nodules in enhancing this symbiotic relationship, particularly under stress conditions. These NRB exhibit plant growth-promoting (PGP) metabolites by modulating phytohormones and enhancing nutrient availability, thereby improving nodule development and function. Bacteria produce essential hormones, such as auxin (indole-3-acetic acid), cytokinins, gibberellic acids abscisic acid, jasmonic acid, and salicylic acid, and enzymes like 1-aminocyclopropane-1-carboxylate deaminase, which mitigate ethylene's inhibitory effects on nodulation. Furthermore, NRB contribute to nutrient cycling by solubilizing minerals like phosphate, potassium, silicate, zinc, and iron, essential for effective nitrogen fixation. The co-inoculation of legumes with both rhizobia and NRB with multiple PGP metabolites has shown synergistic effects on plant growth, yield, and resilience against environmental stresses. This review emphasizes the need to further explore the diversity and functional roles of nodule-associated non-rhizobial endophytes, aiming to optimize legume productivity through improved nutrient and hormonal management. Understanding these interactions is crucial for developing sustainable agricultural practices that enhance the efficiency of legume-rhizobia symbiosis, ultimately contributing to food security and ecosystem health.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"297 ","pages":"Article 128192"},"PeriodicalIF":6.1,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143869702","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 : 2025-04-17DOI: 10.1016/j.micres.2025.128188
Haolong Li , Tianmeng Guo , Ziyi Luo , Jingying Chen , Xuewen Xie , Golam Jalal Ahammed , Airong Liu , Shuangchen Chen
Biocontrol fungi may exert antagonistic effects by emitting volatile organic compounds (VOCs), thus identifying fungal VOCs is crucial for understanding biocontrol mechanisms and developing novel biofungicides. In this study, we examined the antagonistic effect of Irpex lacteus LL210 against three major fungal pathogens: Botrytis cinerea (tomato gray mold), Fusarium oxysporum (cucumber wilt), and Alternaria alternata (pepper leaf spots) using in vitro assays. The results of both the dual-culture and dual-petri-dish methods showed that I. lacteus LL210 strongly inhibited the growth of B. cinerea, likely through the release of volatile compounds. SPME-GC-MS analysis of I. lacteus LL210 identified 770 volatile compounds, of which 26 key volatiles were screened on the basis of their relative odor activity values, peak areas and concentrations. Further evaluation using the dual-petri-dish method showed that compounds such as 2-Octen-1-ol, (E)-; Benzeneacetaldehyde; (E)-2-Octenal; Hexanal; (E)-2-Butenal; 5-Heptenal, 2,6-dimethyl-; 1-Octanol; 2,3-dihydro-Benzofuran; Diallyl Sulfur compounds exhibited significant inhibition of B. cinerea, suggesting their potential utility in the development of novel fungicides. We also tested their effects on plant growth and physiology and found that 1-octanol had minimal deleterious effects on tomato plants, as evidenced by growth and oxidative stress markers. This study systematically deciphered the VOCs profile of I. lacteus LL210, revealing critical mechanisms of pathogen inhibition through both direct inhibitory effects of VOCs and plant-mediated enhanced defense. These findings have driven the development of potential biocontrol agents based on VOCs, thereby providing sustainable solutions for crop disease management.
{"title":"Volatile organic compounds from Irpex lacteus inhibit pathogenic fungi and enhance plant resistance to Botrytis cinerea in tomato","authors":"Haolong Li , Tianmeng Guo , Ziyi Luo , Jingying Chen , Xuewen Xie , Golam Jalal Ahammed , Airong Liu , Shuangchen Chen","doi":"10.1016/j.micres.2025.128188","DOIUrl":"10.1016/j.micres.2025.128188","url":null,"abstract":"<div><div>Biocontrol fungi may exert antagonistic effects by emitting volatile organic compounds (VOCs), thus identifying fungal VOCs is crucial for understanding biocontrol mechanisms and developing novel biofungicides. In this study, we examined the antagonistic effect of <em>Irpex lacteus</em> LL210 against three major fungal pathogens: <em>Botrytis cinerea</em> (tomato gray mold), <em>Fusarium oxysporum</em> (cucumber wilt), and <em>Alternaria alternata</em> (pepper leaf spots) using <em>in vitro</em> assays. The results of both the dual-culture and dual-petri-dish methods showed that <em>I. lacteus</em> LL210 strongly inhibited the growth of <em>B. cinerea</em>, likely through the release of volatile compounds. SPME-GC-MS analysis of <em>I. lacteus</em> LL210 identified 770 volatile compounds, of which 26 key volatiles were screened on the basis of their relative odor activity values, peak areas and concentrations. Further evaluation using the dual-petri-dish method showed that compounds such as 2-Octen-1-ol, (E)-; Benzeneacetaldehyde; (E)-2-Octenal; Hexanal; (E)-2-Butenal; 5-Heptenal, 2,6-dimethyl-; 1-Octanol; 2,3-dihydro-Benzofuran; Diallyl Sulfur compounds exhibited significant inhibition of <em>B. cinerea</em>, suggesting their potential utility in the development of novel fungicides. We also tested their effects on plant growth and physiology and found that 1-octanol had minimal deleterious effects on tomato plants, as evidenced by growth and oxidative stress markers. This study systematically deciphered the VOCs profile of <em>I. lacteus</em> LL210, revealing critical mechanisms of pathogen inhibition through both direct inhibitory effects of VOCs and plant-mediated enhanced defense. These findings have driven the development of potential biocontrol agents based on VOCs, thereby providing sustainable solutions for crop disease management.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"297 ","pages":"Article 128188"},"PeriodicalIF":6.1,"publicationDate":"2025-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143854774","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 : 2025-04-17DOI: 10.1016/j.micres.2025.128187
M. Oliveira, J. Barbosa, P. Teixeira
Following ingestion via contaminated food, Listeria monocytogenes faces multiple hurdles through the human digestive system, thereby influencing its capacity to cause infection. This review provides a comprehensive overview of the multifaceted mechanisms employed by L. monocytogenes to overcome gastrointestinal hurdles and interact with the host's microbiota, facing chemical and physical barriers such as saliva, stomach acidity, bile salts and mechanical clearance. Proposed evasion strategies will be highlighted, exploring the bacteriocins produced by L. monocytogenes, such as the well-described bacteriocin Listeriolysin S (LLS), a bacteriocin that inhibits inflammogenic species – Lmo2776, and a phage tail-like bacteriocin, monocin. The competitive dynamic interactions within the gut microbiota, as well as the modulation of microbiota composition and immune responses, will also be explored. Finally, the adhesion and invasion of the intestinal epithelium by L. monocytogenes is described, exploring the mechanism of pathogenesis, biofilm and aggregation capacities and other virulence factors. Unlike previous reviews that may focus on individual aspects of L. monocytogenes pathogenicity, this review offers a holistic perspective on the bacterium's ability to persist and cause infection, integrating information about survival strategies, including bacteriocin production, immune modulation, and virulence factors. By connecting recent findings on microbial interactions and infection dynamics, this review incorporates recent developments in the field and connects various lines of research that explore both host and microbial factors influencing infection outcomes.
{"title":"Listeria monocytogenes gut interactions and listeriosis: Gut modulation and pathogenicity","authors":"M. Oliveira, J. Barbosa, P. Teixeira","doi":"10.1016/j.micres.2025.128187","DOIUrl":"10.1016/j.micres.2025.128187","url":null,"abstract":"<div><div>Following ingestion via contaminated food, <em>Listeria monocytogenes</em> faces multiple hurdles through the human digestive system, thereby influencing its capacity to cause infection. This review provides a comprehensive overview of the multifaceted mechanisms employed by <em>L. monocytogenes</em> to overcome gastrointestinal hurdles and interact with the host's microbiota, facing chemical and physical barriers such as saliva, stomach acidity, bile salts and mechanical clearance. Proposed evasion strategies will be highlighted, exploring the bacteriocins produced by <em>L. monocytogenes</em>, such as the well-described bacteriocin Listeriolysin S (LLS), a bacteriocin that inhibits inflammogenic species – Lmo2776, and a phage tail-like bacteriocin, monocin. The competitive dynamic interactions within the gut microbiota, as well as the modulation of microbiota composition and immune responses, will also be explored. Finally, the adhesion and invasion of the intestinal epithelium by <em>L. monocytogenes</em> is described, exploring the mechanism of pathogenesis, biofilm and aggregation capacities and other virulence factors. Unlike previous reviews that may focus on individual aspects of <em>L. monocytogenes</em> pathogenicity, this review offers a holistic perspective on the bacterium's ability to persist and cause infection, integrating information about survival strategies, including bacteriocin production, immune modulation, and virulence factors. By connecting recent findings on microbial interactions and infection dynamics, this review incorporates recent developments in the field and connects various lines of research that explore both host and microbial factors influencing infection outcomes.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"297 ","pages":"Article 128187"},"PeriodicalIF":6.1,"publicationDate":"2025-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143863633","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 : 2025-04-16DOI: 10.1016/j.micres.2025.128181
Belén Llobregat, Antonio Abad-Fuentes, Josep V. Mercader, Luis González-Candelas, Ana-Rosa Ballester
Histone modifications are key epigenetic mechanisms for gene regulation in response to environmental stimuli. Histone acetylation is crucial for regulating chromatin accessibility and is controlled by histone-modifying enzymes: histone acetyltransferases (HATs) and histone deacetylases (HDACs). This study examined the roles of two HDACs, HosA and HosB, in the fungus Penicillium expansum. While the deletion of hosB did not affect the phenotype, HosA was found to play a crucial role in growth, development, and conidiation. The ΔhosA strain exhibited a characteristic fluffy phenotype and a significant reduction in conidiation. Expression analysis indicated that these differences were related to lower expression of the core regulatory gene wetA, and, to a lesser extent, brlA and abaA. Additionally, the growth of ΔhosA was negatively affected by the addition of calcofluor white and sodium chloride, while the deletion of hosA increased tolerance to sodium dodecyl sulfate and hydrogen peroxide on solid media. Furthermore, the ΔhosA strain showed an abnormal pattern of patulin production during in vitro growth, and reduced virulence likely due to growth retardation and impaired conidiation. These findings suggest that HosA is an epigenetic regulator of conidiation and plays an indirect role in secondary metabolite production and virulence in P. expansum.
{"title":"The role of Penicillium expansum histone deacetylases HosA and HosB in growth, development, and patulin production","authors":"Belén Llobregat, Antonio Abad-Fuentes, Josep V. Mercader, Luis González-Candelas, Ana-Rosa Ballester","doi":"10.1016/j.micres.2025.128181","DOIUrl":"10.1016/j.micres.2025.128181","url":null,"abstract":"<div><div>Histone modifications are key epigenetic mechanisms for gene regulation in response to environmental stimuli. Histone acetylation is crucial for regulating chromatin accessibility and is controlled by histone-modifying enzymes: histone acetyltransferases (HATs) and histone deacetylases (HDACs). This study examined the roles of two HDACs, HosA and HosB, in the fungus <em>Penicillium expansum</em>. While the deletion of <em>hosB</em> did not affect the phenotype, HosA was found to play a crucial role in growth, development, and conidiation. The Δ<em>hosA</em> strain exhibited a characteristic fluffy phenotype and a significant reduction in conidiation. Expression analysis indicated that these differences were related to lower expression of the core regulatory gene <em>wetA</em>, and, to a lesser extent, <em>brlA</em> and <em>abaA</em>. Additionally, the growth of Δ<em>hosA</em> was negatively affected by the addition of calcofluor white and sodium chloride, while the deletion of <em>hosA</em> increased tolerance to sodium dodecyl sulfate and hydrogen peroxide on solid media. Furthermore, the Δ<em>hosA</em> strain showed an abnormal pattern of patulin production during <em>in vitro</em> growth, and reduced virulence likely due to growth retardation and impaired conidiation. These findings suggest that HosA is an epigenetic regulator of conidiation and plays an indirect role in secondary metabolite production and virulence in <em>P. expansum</em>.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"297 ","pages":"Article 128181"},"PeriodicalIF":6.1,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143854771","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 : 2025-04-15DOI: 10.1016/j.micres.2025.128173
Yumin Kim , Min Seo Ki , Mi Hwa Shin , Ji Soo Choi , Moo Suk Park , Yeongmin Kim , Chang-Myung Oh , Sang Hoon Lee
Summary
Our study shows that Bifidobacterium spp. supplementation reduces lung damage in acute lung injury by enhancing immune cell activity and restoring thrombospondin-1 levels, offering a promising therapeutic approach for the treatment of ALI/ARDS.
Background
Acute lung injury (ALI) and acute respiratory distress syndrome (ARDS) are critical conditions characterized by severe lung inflammation and damage, often exacerbated by mechanical ventilation. Probiotics, particularly those containing Bifidobacterium spp. (Bifidus) have shown promise in modulating immune responses and reducing inflammation.
Methods
In this study, we investigated the effects of Bifidus supplementation in a mouse model of lipopolysaccharide induced ALI and ventilator-induced lung injury.
Results
Our results demonstrate that Bifidus significantly ameliorates lung injury by enhancing efferocytosis and reducing pro-inflammatory cytokine levels. Single-cell RNA sequencing revealed significant changes in lung immune cell populations, particularly macrophages and monocytes, which showed increased efferocytosis activity and modulation of key signaling pathways such as TNF, MAPK and TLR. Notably, Bifidus feeding restored thrombospondin-1 levels in lung tissue, facilitating clearance of apoptotic cells and promoting resolution of inflammation.
Conclusions
Overall, our study highlights the potential of Bifidus as a therapeutic strategy to mitigate lung injury in ALI/ARDS.
{"title":"Thrombospondin-1 modulation by Bifidobacterium spp. mitigates lung damage in an acute lung injury mouse model","authors":"Yumin Kim , Min Seo Ki , Mi Hwa Shin , Ji Soo Choi , Moo Suk Park , Yeongmin Kim , Chang-Myung Oh , Sang Hoon Lee","doi":"10.1016/j.micres.2025.128173","DOIUrl":"10.1016/j.micres.2025.128173","url":null,"abstract":"<div><h3>Summary</h3><div>Our study shows that Bifidobacterium spp. supplementation reduces lung damage in acute lung injury by enhancing immune cell activity and restoring thrombospondin-1 levels, offering a promising therapeutic approach for the treatment of ALI/ARDS.</div></div><div><h3>Background</h3><div>Acute lung injury (ALI) and acute respiratory distress syndrome (ARDS) are critical conditions characterized by severe lung inflammation and damage, often exacerbated by mechanical ventilation. Probiotics, particularly those containing <em>Bifidobacterium</em> spp. (Bifidus) have shown promise in modulating immune responses and reducing inflammation.</div></div><div><h3>Methods</h3><div>In this study, we investigated the effects of Bifidus supplementation in a mouse model of lipopolysaccharide induced ALI and ventilator-induced lung injury.</div></div><div><h3>Results</h3><div>Our results demonstrate that Bifidus significantly ameliorates lung injury by enhancing efferocytosis and reducing pro-inflammatory cytokine levels. Single-cell RNA sequencing revealed significant changes in lung immune cell populations, particularly macrophages and monocytes, which showed increased efferocytosis activity and modulation of key signaling pathways such as TNF, MAPK and TLR. Notably, Bifidus feeding restored thrombospondin-1 levels in lung tissue, facilitating clearance of apoptotic cells and promoting resolution of inflammation.</div></div><div><h3>Conclusions</h3><div>Overall, our study highlights the potential of Bifidus as a therapeutic strategy to mitigate lung injury in ALI/ARDS.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"297 ","pages":"Article 128173"},"PeriodicalIF":6.1,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143859922","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}
Xenophagy is an important antibacterial defense mechanism that many organisms use to engulf intracellular pathogens. However, the mechanisms of xenophagy triggered by insect-borne plant bacteria are not well understood. Candidatus Liberibacter asiaticus (CLas) causes Huanglongbing, which poses a serious threat to citrus production. CLas is a phloem-limited unculturable bacterium that is transmitted by the Asian citrus psyllid in a persistent and propagative manner in nature. Here, we found that CLas infection in the gut of psyllids triggered a mild and anti-bacterial xenophagy. Xenophagy limited excessive propagation of CLas to maintain psyllid survival, because overload of CLas was detrimental to psyllid life. Furthermore, the outer membrane β-barrel protein (OMBB) of CLas is the key secreted protein that induces xenophagy in psyllids by interacting with ATG8 and ATG14. OMBB can independently induce autophagy in psyllid and non-host cells. Together, these results revealed that an insect-borne plant bacterium activates mild xenophagy to control its propagation, thereby achieving persistent infection in insect vectors.
{"title":"A phloem-limited unculturable bacterium induces mild xenophagy in insect vectors for persistent infection","authors":"Zhongkai Yu , Yuxin Guo , Hongyan Chen , Wenqiang Wan, Mengting Hu, You Li, Taiyun Wei, Qian Chen","doi":"10.1016/j.micres.2025.128186","DOIUrl":"10.1016/j.micres.2025.128186","url":null,"abstract":"<div><div>Xenophagy is an important antibacterial defense mechanism that many organisms use to engulf intracellular pathogens. However, the mechanisms of xenophagy triggered by insect-borne plant bacteria are not well understood. <em>Candidatus</em> Liberibacter asiaticus (<em>C</em>Las) causes Huanglongbing, which poses a serious threat to citrus production. <em>C</em>Las is a phloem-limited unculturable bacterium that is transmitted by the Asian citrus psyllid in a persistent and propagative manner in nature. Here, we found that <em>C</em>Las infection in the gut of psyllids triggered a mild and anti-bacterial xenophagy. Xenophagy limited excessive propagation of <em>C</em>Las to maintain psyllid survival, because overload of <em>C</em>Las was detrimental to psyllid life. Furthermore, the outer membrane β-barrel protein (OMBB) of <em>C</em>Las is the key secreted protein that induces xenophagy in psyllids by interacting with ATG8 and ATG14. OMBB can independently induce autophagy in psyllid and non-host cells. Together, these results revealed that an insect-borne plant bacterium activates mild xenophagy to control its propagation, thereby achieving persistent infection in insect vectors.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"297 ","pages":"Article 128186"},"PeriodicalIF":6.1,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143851827","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 : 2025-04-15DOI: 10.1016/j.micres.2025.128182
Bin Li , Chengbo Liang , Bo Xu , Pengfei Song , Daoxin Liu , Jingjie Zhang , Haifeng Gu , Feng Jiang , Hongmei Gao , Zhenyuan Cai , Tongzuo Zhang
Qinghai-Tibet Plateau (QTP) is marked by harsh environments that drive the evolution of unique nutrient metabolism mechanism in indigenous animal gut microbiotas. Yet, responses of these microbiotas to different extreme environments remain poorly understood. White-lipped deer (Przewalskium albirostris), a native endangered species in the QTP, serves as an ideal model to study how gut microbiotas adapt to season and human disturbances. Here, a multi-omics integrated analysis of 16S rRNA, metagenomics, and untargeted metabolomics was performed to investigate the composition, function, and metabolic characteristics of gut microbiota in White-lipped deer across different seasons and living environments. Our results revealed that extreme winter environment dominated the composition, function, and metabolism of gut microbiota in white-lipped deer. The white-lipped deer exhibited an enriched gut microbiota associated with producing short-chain fatty acids in winter, with core feature genera including norank_o_Rhodospirillales, Rikenellaceae_RC9_gut_group, and unclassified_c_Clostridia. However, potential pathogenic bacteria and few short-chain fatty acid producers, with core feature genera including norank_f_p-2534–18B5_gut_group, Cellulosilyticum, and Paeniclostridium, showed enrichment in captivity. Pathways associated with carbohydrate metabolism, amino acid metabolism, and immune regulation showed enrichment in winter group as an adaptation to the cold and food scarcity. Among these, Rikenellaceae_RC9_gut_group and unclassified_c_Clostridia contributed significantly to these metabolic pathways. The gut microbiota of white-lipped deer exhibited enrichment in pathways related to intestinal inflammation and enhanced immune regulation to alleviate the stress of captivity. Among these, norank_f_p-2534–18B5_gut_group contributed the most to these pathways. Butyric, valeric, and valproic acids were significantly more abundant in the winter group, while 3-hydroxybutyric and (S)-beta-aminoisobutyric acids were higher in the captive group. Furthermore, enriched metabolites and associated pathways in both groups further supported the inferences on metagenomic functions. This study confirms the key role of specific gut microbiota in adapting to high-altitude winters and anthropogenic disturbances, emphasizing its importance for environmental resilience in wild, high-altitude mammals.
{"title":"Extreme winter environment dominates gut microbiota and metabolome of white-lipped deer","authors":"Bin Li , Chengbo Liang , Bo Xu , Pengfei Song , Daoxin Liu , Jingjie Zhang , Haifeng Gu , Feng Jiang , Hongmei Gao , Zhenyuan Cai , Tongzuo Zhang","doi":"10.1016/j.micres.2025.128182","DOIUrl":"10.1016/j.micres.2025.128182","url":null,"abstract":"<div><div>Qinghai-Tibet Plateau (QTP) is marked by harsh environments that drive the evolution of unique nutrient metabolism mechanism in indigenous animal gut microbiotas. Yet, responses of these microbiotas to different extreme environments remain poorly understood. White-lipped deer (<em>Przewalskium albirostris</em>), a native endangered species in the QTP, serves as an ideal model to study how gut microbiotas adapt to season and human disturbances. Here, a multi-omics integrated analysis of 16S rRNA, metagenomics, and untargeted metabolomics was performed to investigate the composition, function, and metabolic characteristics of gut microbiota in White-lipped deer across different seasons and living environments. Our results revealed that extreme winter environment dominated the composition, function, and metabolism of gut microbiota in white-lipped deer. The white-lipped deer exhibited an enriched gut microbiota associated with producing short-chain fatty acids in winter, with core feature genera including norank_o_Rhodospirillales, <em>Rikenellaceae_RC9_gut_group</em>, and unclassified_c_Clostridia. However, potential pathogenic bacteria and few short-chain fatty acid producers, with core feature genera including <em>norank_f_p-2534–18B5_gut_group</em>, <em>Cellulosilyticum</em>, and <em>Paeniclostridium</em>, showed enrichment in captivity. Pathways associated with carbohydrate metabolism, amino acid metabolism, and immune regulation showed enrichment in winter group as an adaptation to the cold and food scarcity. Among these, <em>Rikenellaceae_RC9_gut_group</em> and unclassified_c_Clostridia contributed significantly to these metabolic pathways. The gut microbiota of white-lipped deer exhibited enrichment in pathways related to intestinal inflammation and enhanced immune regulation to alleviate the stress of captivity. Among these, <em>norank_f_p-2534–18B5_gut_group</em> contributed the most to these pathways. Butyric, valeric, and valproic acids were significantly more abundant in the winter group, while 3-hydroxybutyric and (S)-beta-aminoisobutyric acids were higher in the captive group. Furthermore, enriched metabolites and associated pathways in both groups further supported the inferences on metagenomic functions. This study confirms the key role of specific gut microbiota in adapting to high-altitude winters and anthropogenic disturbances, emphasizing its importance for environmental resilience in wild, high-altitude mammals.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"297 ","pages":"Article 128182"},"PeriodicalIF":6.1,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143847733","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 : 2025-04-14DOI: 10.1016/j.micres.2025.128184
Meiqi Mu , Muzhapaer Tuluhong , Jingwen Jiang , Minghao Yang , Xi Long , Zicheng Wang , Wanting Nie , Siwen Zhao , Yuchen Wu , Jun Hong , Fang Liu , Guowen Cui , Xiujie Yin
Red clover (Trifolium pratense), a high-quality forage plant, faces significant threats from anthracnose in northeastern China, but the pathogen responsible remains unidentified. The phyllosphere microbiota is crucial in plantpathogen interactions, yet its role in the resistance of red clover to anthracnose is poorly understood. Using morphological, molecular, and multigene phylogenetic analyses, we identified Colletotrichum americae-borealis (Cab) as the pathogen that causes anthracnose in red clover in China. We also investigated changes in the phyllosphere microbiomes of highly resistant (XJ) and susceptible (SC) red clover materials after Cab infection, via 16S rRNA gene sequencing. The results revealed significant differences in bacterial α- and β-diversity, with novel microbial taxa and a complex microbial network emerging postinfection. Notably, after Cab inoculation, the Shannon diversity index in XJ exhibited more pronounced changes, manifested as an increase in the abundance of beneficial microorganisms such as Bacillus, Pantoea, and Pseudomonas. Network analysis revealed that the XJ microbiome was more complex and stable than the SC microbiome was, regardless of infection status. Bacillus J2, the dominant bacterium, significantly inhibited Cab growth in vitro and reduced the disease index by 33.4–47.7 % when it was reapplied to the leaf surface, suggesting its role in enhancing disease resistance. This study is the first to report that C. americae-borealis causes anthracnose in red clover in China, and demonstrates the potential of the beneficial bacterium J2 in enhancing disease resistance, providing insights into disease resistance mechanisms and the role of the phyllosphere microbiome in pathogen challenge.
{"title":"Role of the beneficial phyllosphere microbiome in the defense against red clover anthracnose caused by Colletotrichum americae-borealis","authors":"Meiqi Mu , Muzhapaer Tuluhong , Jingwen Jiang , Minghao Yang , Xi Long , Zicheng Wang , Wanting Nie , Siwen Zhao , Yuchen Wu , Jun Hong , Fang Liu , Guowen Cui , Xiujie Yin","doi":"10.1016/j.micres.2025.128184","DOIUrl":"10.1016/j.micres.2025.128184","url":null,"abstract":"<div><div>Red clover (<em>Trifolium pratense</em>), a high-quality forage plant, faces significant threats from anthracnose in northeastern China, but the pathogen responsible remains unidentified. The phyllosphere microbiota is crucial in plant<img>pathogen interactions, yet its role in the resistance of red clover to anthracnose is poorly understood. Using morphological, molecular, and multigene phylogenetic analyses, we identified <em>Colletotrichum americae-borealis</em> (Cab) as the pathogen that causes anthracnose in red clover in China. We also investigated changes in the phyllosphere microbiomes of highly resistant (XJ) and susceptible (SC) red clover materials after Cab infection, via 16S rRNA gene sequencing. The results revealed significant differences in bacterial α- and β-diversity, with novel microbial taxa and a complex microbial network emerging postinfection. Notably, after Cab inoculation, the Shannon diversity index in XJ exhibited more pronounced changes, manifested as an increase in the abundance of beneficial microorganisms such as <em>Bacillus</em>, <em>Pantoea</em>, and <em>Pseudomonas</em>. Network analysis revealed that the XJ microbiome was more complex and stable than the SC microbiome was, regardless of infection status. <em>Bacillus</em> J2, the dominant bacterium, significantly inhibited Cab growth in vitro and reduced the disease index by 33.4–47.7 % when it was reapplied to the leaf surface, suggesting its role in enhancing disease resistance. This study is the first to report that <em>C. americae-borealis</em> causes anthracnose in red clover in China, and demonstrates the potential of the beneficial bacterium J2 in enhancing disease resistance, providing insights into disease resistance mechanisms and the role of the phyllosphere microbiome in pathogen challenge.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"297 ","pages":"Article 128184"},"PeriodicalIF":6.1,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143828572","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 : 2025-04-14DOI: 10.1016/j.micres.2025.128185
Jian Xiao , Yu Zhu , Liyuan Liao , Baoling Chen , Wenjun Liu , Shangdong Yang
The fruit set in the Cucurbitaceae family is a critical determinant of fruit production and development. However, limited information is available regarding the regulatory mechanisms relating to pumpkin fruit sets. To elucidate the interplay between pumpkin fruit setting and endophytic microorganisms, we conducted a comparative analysis of the endophytic microbiota and metabolite profiles in the stems of naturally pollinated and non-pollinated pumpkin using microbiome and untargeted metabolomics approaches. The results showed that both the alpha- (reduced by 18.33∼21.88 % and 16.63∼24.08 %) and beta-diversities (reduced by 12.40 % and 40.00 %) of endophytic microorganisms (bacteria and fungi) in stems of pollinated pumpkins were significantly reduced which were significantly reduced compared to those in non-pollinated pumpkins. Meanwhile, in comparison with pollinated pumpkins, the deficiency of endophytic bacterial genera that regulate endogenous hormones and metabolites, such as Pantoea, Staphylococcus, Brevundimonas, Tatumella, and Gluconobacter, and the weak metabolic pathways, viz, the relatively stable homeostasis, such as flavone and flavonol biosynthesis, alanine, aspartate, and glutamate metabolism, and phenylpropanoid biosynthesis in stems of non-pollinated pumpkin were important reasons why fruits could not bear fruits without pollination. All above results reveal that endophytic microorganisms are closely related to the growth and development of pumpkins, also, the endophytic microbial community structures in stems of pumpkins can be reshaped by man-made measures, such as pollination.
{"title":"Integrated microbiome and metabolome approaches reveal the regulatory mechanism of pumpkin pollination","authors":"Jian Xiao , Yu Zhu , Liyuan Liao , Baoling Chen , Wenjun Liu , Shangdong Yang","doi":"10.1016/j.micres.2025.128185","DOIUrl":"10.1016/j.micres.2025.128185","url":null,"abstract":"<div><div>The fruit set in the <em>Cucurbitaceae</em> family is a critical determinant of fruit production and development. However, limited information is available regarding the regulatory mechanisms relating to pumpkin fruit sets. To elucidate the interplay between pumpkin fruit setting and endophytic microorganisms, we conducted a comparative analysis of the endophytic microbiota and metabolite profiles in the stems of naturally pollinated and non-pollinated pumpkin using microbiome and untargeted metabolomics approaches. The results showed that both the <em>alpha</em>- (reduced by 18.33∼21.88 % and 16.63∼24.08 %) and <em>beta</em>-diversities (reduced by 12.40 % and 40.00 %) of endophytic microorganisms (bacteria and fungi) in stems of pollinated pumpkins were significantly reduced which were significantly reduced compared to those in non-pollinated pumpkins. Meanwhile, in comparison with pollinated pumpkins, the deficiency of endophytic bacterial genera that regulate endogenous hormones and metabolites, such as <em>Pantoea</em>, <em>Staphylococcus</em>, <em>Brevundimonas</em>, <em>Tatumella</em>, and <em>Gluconobacter</em>, and the weak metabolic pathways, viz, the relatively stable homeostasis, such as flavone and flavonol biosynthesis, alanine, aspartate, and glutamate metabolism, and phenylpropanoid biosynthesis in stems of non-pollinated pumpkin were important reasons why fruits could not bear fruits without pollination. All above results reveal that endophytic microorganisms are closely related to the growth and development of pumpkins, also, the endophytic microbial community structures in stems of pumpkins can be reshaped by man-made measures, such as pollination.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"297 ","pages":"Article 128185"},"PeriodicalIF":6.1,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143847734","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 : 2025-04-12DOI: 10.1016/j.micres.2025.128175
Rodrigo Monteiro , Beatriz Santamarina Alcantud , Sjouke Piersma , Antoni P.A. Hendrickx , Sandra Maaß , Dörte Becher , Joana Azeredo , Erik Bathoorn , Jan Maarten van Dijl
Infections caused by carbapenem-resistant Acinetobacter baumannii (A. baumannii; CRAb) are associated with high patient morbidity and mortality. The serious threat for human health imposed by CRAb was recently underscored by identification of close-to-untouchable carbapenem- and tetracycline-resistant isolates. Since outer membrane vesicles (OMVs) of Gram-negative bacteria may contribute to antimicrobial resistance, our present study was aimed at investigating OMVs produced by the first two carbapenem- and tetracycline-resistant A. baumannii isolates in Europe. These isolates, denoted CRAb1 and CRAb2, contain large, nearly identical plasmids that specify multiple resistances. Both isolates produce OMVs that were analyzed by differential light scattering, transmission electron microscopy and proteomics. By comparison with OMVs from the plasmid-free non-carbapenem-resistant A. baumannii isolate Ab1, which is an isogenic ancestor of the CRAb1 isolate, we show that plasmid carriage by the CRAb1 and CRAb2 isolates leads to an increased OMV size that is accompanied by increased diversity of the OMV proteome. Our analyses show that OMVs from CRAb1 and CRAb2 are major reservoirs of proteins involved in antimicrobial resistance, including the plasmid-encoded carbapenemases New Delhi metallo-β-lactamase-1 (NDM-1), and carbapenem-hydrolyzing oxacillinase OXA-97 (OXA-97). Here we report that these OMV-borne carbapenemases hydrolyze imipenem and protect otherwise carbapenem-sensitive A. baumannii and Escherichia coli (E. coli) isolates against this antibiotic. In conclusion, our findings demonstrate that OMVs from highly drug-resistant CRAb confer protection against last-resort antibiotics to non-resistant bacterial pathogens.
{"title":"Outer membrane vesicles of carbapenem-resistant clinical Acinetobacter baumannii isolates protect both the vesicle-producing bacteria and non-resistant bacteria against carbapenems","authors":"Rodrigo Monteiro , Beatriz Santamarina Alcantud , Sjouke Piersma , Antoni P.A. Hendrickx , Sandra Maaß , Dörte Becher , Joana Azeredo , Erik Bathoorn , Jan Maarten van Dijl","doi":"10.1016/j.micres.2025.128175","DOIUrl":"10.1016/j.micres.2025.128175","url":null,"abstract":"<div><div>Infections caused by carbapenem-resistant <em>Acinetobacter baumannii</em> (<em>A. baumannii</em>; CRAb) are associated with high patient morbidity and mortality. The serious threat for human health imposed by CRAb was recently underscored by identification of close-to-untouchable carbapenem- and tetracycline-resistant isolates. Since outer membrane vesicles (OMVs) of Gram-negative bacteria may contribute to antimicrobial resistance, our present study was aimed at investigating OMVs produced by the first two carbapenem- and tetracycline-resistant <em>A. baumannii</em> isolates in Europe. These isolates, denoted CRAb1 and CRAb2, contain large, nearly identical plasmids that specify multiple resistances. Both isolates produce OMVs that were analyzed by differential light scattering, transmission electron microscopy and proteomics. By comparison with OMVs from the plasmid-free non-carbapenem-resistant <em>A. baumannii</em> isolate Ab1, which is an isogenic ancestor of the CRAb1 isolate, we show that plasmid carriage by the CRAb1 and CRAb2 isolates leads to an increased OMV size that is accompanied by increased diversity of the OMV proteome. Our analyses show that OMVs from CRAb1 and CRAb2 are major reservoirs of proteins involved in antimicrobial resistance, including the plasmid-encoded carbapenemases New Delhi metallo-β-lactamase-1 (NDM-1), and carbapenem-hydrolyzing oxacillinase OXA-97 (OXA-97). Here we report that these OMV-borne carbapenemases hydrolyze imipenem and protect otherwise carbapenem-sensitive <em>A. baumannii</em> and <em>Escherichia coli</em> (<em>E. coli</em>) isolates against this antibiotic. In conclusion, our findings demonstrate that OMVs from highly drug-resistant CRAb confer protection against last-resort antibiotics to non-resistant bacterial pathogens.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"297 ","pages":"Article 128175"},"PeriodicalIF":6.1,"publicationDate":"2025-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143833824","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}