Microbiome最新文献

{"title":"Longitudinal host-microbiome dynamics of metatranscription identify hallmarks of progression in periodontitis.","authors":"Ana Duran-Pinedo, Jose O Solbiati, Flavia Teles, Zhang Yanping, Jorge Frias-Lopez","doi":"10.1186/s40168-025-02108-8","DOIUrl":"10.1186/s40168-025-02108-8","url":null,"abstract":"<p><strong>Background: </strong>In periodontitis, the interplay between the host and microbiome generates a self-perpetuating cycle of inflammation of tooth-supporting tissues, potentially leading to tooth loss. Despite increasing knowledge of the phylogenetic compositional changes of the periodontal microbiome, the current understanding of in situ activities of the oral microbiome and the interactions among community members and with the host is still limited. Prior studies on the subgingival plaque metatranscriptome have been cross-sectional, allowing for only a snapshot of a highly variable microbiome, and do not include the transcriptome profiles from the host, a critical element in the progression of the disease.</p><p><strong>Results: </strong>To identify the host-microbiome interactions in the subgingival milieu that lead to periodontitis progression, we conducted a longitudinal analysis of the host-microbiome metatranscriptome from clinically stable and progressing sites in 15 participants over 1 year. Our research uncovered a distinct timeline of activities of microbial and host responses linked to disease progression, revealing a significant clinical and metabolic change point (the moment in time when the statistical properties of a time series change) at the 6-month mark of the study, with 1722 genes differentially expressed (DE) in the host and 111,705 in the subgingival microbiome. Genes associated with immune response, especially antigen presentation genes, were highly up-regulated in stable sites before the 6-month change point but not in the progressing sites. Activation of cobalamin, porphyrin, and motility in the microbiome contribute to the progression of the disease. Conversely, inhibition of lipopolysaccharide and glycosphingolipid biosynthesis in stable sites coincided with increased immune response. Correlation delay analysis revealed that the positive feedback loop of activities leading to progression consists of immune regulation and response activation in the host that leads to an increase in potassium ion transport and cobalamin biosynthesis in the microbiome, which in turn induces the immune response. Causality analysis identified two clusters of microbiome genes whose progression can accurately predict the outcomes at specific sites with high confidence (AUC = 0.98095 and 0.97619).</p><p><strong>Conclusions: </strong>A specific timeline of host-microbiome activities characterizes the progression of the disease. The metabolic activities of the dysbiotic microbiome and the host are responsible for the positive feedback loop of reciprocally reinforced interactions leading to progression and tissue destruction. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"119"},"PeriodicalIF":13.8,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12077055/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144078675","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic insights into novel extremotolerant bacteria isolated from the NASA Phoenix mission spacecraft assembly cleanrooms.","authors":"Júnia Schultz, Tahira Jamil, Pratyay Sengupta, Shobhan Karthick Muthamilselvi Sivabalan, Anamika Rawat, Niketan Patel, Srinivasan Krishnamurthi, Intikhab Alam, Nitin K Singh, Karthik Raman, Alexandre Soares Rosado, Kasthuri Venkateswaran","doi":"10.1186/s40168-025-02082-1","DOIUrl":"https://doi.org/10.1186/s40168-025-02082-1","url":null,"abstract":"<p><strong>Background: </strong>Human-designed oligotrophic environments, such as cleanrooms, harbor unique microbial communities shaped by selective pressures like temperature, humidity, nutrient availability, cleaning reagents, and radiation. Maintaining the biological cleanliness of NASA's mission-associated cleanrooms, where spacecraft are assembled and tested, is critical for planetary protection. Even with stringent controls such as regulated airflow, temperature management, and rigorous cleaning, resilient microorganisms can persist in these environments, posing potential risks for space missions.</p><p><strong>Results: </strong>During the Phoenix spacecraft mission, genomes of 215 bacterial isolates were sequenced and based on overall genome-related indices, 53 strains belonging to 26 novel species were recognized. Metagenome mapping indicated less than 0.1% of the reads associated with novel species, suggesting their rarity. Genes responsible for biofilm formation, such as BolA (COG0271) and CvpA (COG1286), were predominantly found in proteobacterial members but were absent in other non-spore-forming and spore-forming species. YqgA (COG1811) was detected in most spore-forming members but was absent in Paenibacillus and non-spore-forming species. Cell fate regulators, COG1774 (YaaT), COG3679 (YlbF, YheA/YmcA), and COG4550 (YmcA, YheA/YmcA), controlling sporulation, competence, and biofilm development processes, were observed in all spore-formers but were missing in non-spore-forming species. COG analyses further revealed resistance-conferring proteins in all spore-formers (n = 13 species) and eight actinobacterial species, responsible for enhanced membrane transport and signaling under radiation (COG3253), transcription regulation under radiation stress (COG1108), and DNA repair and stress responses (COG2318). Additional functional analysis revealed that Agrococcus phoenicis, Microbacterium canaveralium, and Microbacterium jpeli contained biosynthetic gene clusters (BGCs) for ε-poly-L-lysine, beneficial in food preservation and biomedical applications. Two novel Sphingomonas species exhibited for zeaxanthin, an antioxidant beneficial for eye health. Paenibacillus canaveralius harbored genes for bacillibactin, crucial for iron acquisition. Georgenia phoenicis had BGCs for alkylresorcinols, compounds with antimicrobial and anticancer properties used in food preservation and pharmaceuticals.</p><p><strong>Conclusion: </strong>Despite stringent decontamination and controlled environmental conditions, cleanrooms harbor unique bacterial species that form biofilms, resist various stressors, and produce valuable biotechnological compounds. The reduced microbial competition in these environments enhances the discovery of novel microbial diversity, contributing to the mitigation of microbial contamination and fostering biotechnological innovation. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"117"},"PeriodicalIF":13.8,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12067966/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144001999","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dietary selection of distinct gastrointestinal microorganisms drives fiber utilization dynamics in goats.","authors":"Xiaoli Zhang, Rongzhen Zhong, Jian Wu, Zhiliang Tan, Jinzhen Jiao","doi":"10.1186/s40168-025-02112-y","DOIUrl":"https://doi.org/10.1186/s40168-025-02112-y","url":null,"abstract":"<p><strong>Background: </strong>Dietary fiber is crucial to animal productivity and health, and its dynamic utilization process is shaped by the gastrointestinal microorganisms in ruminants. However, we lack a holistic understanding of the metabolic interactions and mediators of intestinal microbes under different fiber component interventions compared with that of their rumen counterparts. Here, we applied nutritional, amplicon, metagenomic, and metabolomic approaches to compare characteristic microbiome and metabolic strategies using goat models with fast-fermentation fiber (FF) and slow-fermentation fiber (SF) dietary interventions from a whole gastrointestinal perspective.</p><p><strong>Results: </strong>The SF diet selected fibrolytic bacteria Fibrobacter and Ruminococcus spp. and enriched for genes encoding for xylosidase, endoglucanase, and galactosidase in the rumen and cecum to enhance cellulose and hemicellulose utilization, which might be mediated by the enhanced microbial ATP production and cobalamin biosynthesis potentials in the rumen. The FF diet favors pectin-degrading bacteria Prevotella spp. and enriched for genes encoding for pectases (PL1, GH28, and CE8) to improve animal growth. Subsequent SCFA patterns and metabolic pathways unveiled the favor of acetate production in the rumen and butyrate production in the cecum for SF goats. Metagenomic binning verified this distinct selection of gastrointestinal microorganisms and metabolic pathways of different fiber types (fiber content and polysaccharide chemistry).</p><p><strong>Conclusions: </strong>These findings provide novel insights into the key metabolic pathways and distinctive mechanisms through which dietary fiber types benefit the host animals from the whole gastrointestinal perspective. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"118"},"PeriodicalIF":13.8,"publicationDate":"2025-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12067950/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144024650","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial metabolism in laboratory reared marine snow as revealed by a multi-omics approach.","authors":"Lei Hou, Zihao Zhao, Barbara Steger-Mähnert, Nianzhi Jiao, Gerhard J Herndl, Yao Zhang","doi":"10.1186/s40168-025-02097-8","DOIUrl":"https://doi.org/10.1186/s40168-025-02097-8","url":null,"abstract":"<p><strong>Background: </strong>Marine snow represents an organic matter-rich habitat and provides substrates for diverse microbial populations in the marine ecosystem. However, the functional diversity and metabolic interactions within the microbial community inhabiting marine snow remain largely underexplored, particularly for specific metabolic pathways involved in marine snow degradation. Here, we used a multi-omics approach to explore the microbial response to laboratory-reared phytoplankton-derived marine snow.</p><p><strong>Results: </strong>Our results demonstrated a dramatic shift in both taxonomic and functional profiles of the microbial community after the formation of phytoplankton-derived marine snow using a rolling tank system. The changes in microbial metabolic processes were more pronounced in the metaproteome than in the metagenome in response to marine snow. Fast-growing taxa within the Gammaproteobacteria were the most dominant group at both the metagenomic and metaproteomic level. These Gammaproteobacteria possessed a variety of carbohydrate-active enzymes (CAZymes) and transporters facilitating substrate cleavage and uptake, respectively. Analysis of metagenome-assembled genomes (MAGs) revealed that the response to marine snow amendment was primarily mediated by Alteromonas, Vibrio, and Thalassotalea. Among these, Alteromonas exclusively expressing auxiliary activities 2 (AA2) of the CAZyme subfamily were abundant in both the free-living (FL) and marine snow-attached (MA) microbial communities. Thus, Alteromonas likely played a pivotal role in the degradation of marine snow. The enzymes of AA2 produced by these Alteromonas MAGs are capable of detoxifying peroxide intermediates generated during the breakdown of marine snow into smaller poly- and oligomers, providing available substrates for other microorganisms within the system. In addition, Vibrio and Thalassotalea MAGs exhibited distinct responses to these hydrolysis products of marine snow in different size fractions, suggesting a distinct niche separation. Although chemotaxis proteins were found to be enriched in the proteome of all three MAGs, differences in transporter proteins were identified as the primary factor contributing to the niche separation between these two groups. Vibrio in the FL fraction predominantly utilized ATP-binding cassette transporters (ABCTs), while Thalassotalea MAGs in the MA fraction primarily employed TonB-dependent outer membrane transporters (TBDTs).</p><p><strong>Conclusions: </strong>Our findings shed light on the essential metabolic interactions within marine snow-degrading microbial consortia, which employ complementary physiological mechanisms and survival strategies to effectively scavenge marine snow. This work advances our understanding of the fate of marine snow and the role of microbes in carbon sequestration in the ocean. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"114"},"PeriodicalIF":13.8,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12054258/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144017619","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transmission of the human respiratory microbiome and antibiotic resistance genes in healthy populations.","authors":"Lili Ren, Jing Yang, Yan Xiao, Li Guo, Jian Rao, Chao Wu, Xinming Wang, Ying Wang, Linfeng Zhang, Li Zhang, Xiaoqing Jiang, Jiaxin Zhong, Jingchuan Zhong, Weizhong Yang, Chen Wang, Jianwei Wang, Mingkun Li","doi":"10.1186/s40168-025-02107-9","DOIUrl":"https://doi.org/10.1186/s40168-025-02107-9","url":null,"abstract":"<p><strong>Background: </strong>The human microbiome is transmissible between individuals, including pathogens and commensals with metabolic and immune-modulating effects, which could influence susceptibility, severity, and outcomes of both infection and non-infection diseases. However, limited studies of respiratory microbiome transmission within populations have been conducted. Herein, we performed species- and strain-level metagenomic analyses on oropharyngeal (OP) swabs from 1046 healthy urban dwellers across 13 districts, including 111 households with at least two cohabitants, to elucidate the transmission dynamics of the respiratory microbiome within households and communities.</p><p><strong>Results: </strong>We found that geographic districts accounted for the greatest variation in the OP microbiome, with unrelated individuals from the same district showing greater microbiome similarity and higher strain-sharing rates than those from different districts. Cohabitants, especially spouses and siblings, exhibited similar microbial abundances and shared more strains, with 16.7% (IQR 0.0-33.3%) of strains shared among cohabitants, compared to 0.0% (IQR 0.0-11.1%) in non-cohabiting pairs (p < 0.05). Both respiratory commensals and opportunistic pathogens were shared among cohabitants. In contrast, no evidence of vertical transmission was detected between mother-offspring pairs. Additionally, the OP microbiome contained diverse antibiotic resistance genes (ARGs), with 15.0% linked to mobile genetic elements (MGEs) or plasmids; the flanking sequences of these ARGs were more conserved across species than those of non-MGE-associated ARGs, suggesting horizontal transfer of ARGs among respiratory microorganisms.</p><p><strong>Conclusions: </strong>In summary, we characterized the transmissible nature of the OP microbiome and the risk of ARG dissemination among respiratory microorganisms. These findings underscore the role of respiratory microbes and ARGs exchange in shaping the microbiome of healthy populations and emphasize their relevance to public health strategies for respiratory health management. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"115"},"PeriodicalIF":13.8,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12054256/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144018008","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nitrogen cycle induced by plant growth-promoting rhizobacteria drives \"microbial partners\" to enhance cadmium phytoremediation.","authors":"Yaowei Chi, Xianzhong Ma, Shaohua Chu, Yimin You, Xunfeng Chen, Juncai Wang, Renyuan Wang, Xia Zhang, Dongwei Zhang, Ting Zhao, Dan Zhang, Pei Zhou","doi":"10.1186/s40168-025-02113-x","DOIUrl":"https://doi.org/10.1186/s40168-025-02113-x","url":null,"abstract":"<p><strong>Background: </strong>Using plant growth-promoting rhizobacteria (PGPR) combined with hyperaccumulator is an ecologically viable way to remediate cadmium (Cd) pollution in agricultural soil. Despite recent advances in elucidating PGPR-enhanced phytoremediation, the response of plant-associated microbiota to PGPR remains unclear.</p><p><strong>Results: </strong>Here, we found that the effective colonization of PGPR reshaped the rhizosphere nutrient microenvironment, especially driving the nitrogen cycle, primarily mediated by soil nitrate reductase (S-NR). Elevated S-NR activity mobilized amino acid metabolism and synthesis pathways in the rhizosphere, subsequently driving a shift in life history strategies of the rhizosphere microbiota, and enriching specific rare taxa. The reconstructed synthetic community (SynCom3) confirmed that the inclusion of two crucial collaborators (Lysobacter and Microbacterium) could efficiently foster the colonization of PGPR and aid PGPR in executing phytoremediation enhancement. Finally, the multi-omics analysis highlighted the critical roles of phenylpropanoid biosynthesis and tryptophan metabolism pathways in inducing SynCom3 reorganization and PGPR-enhanced phytoremediation.</p><p><strong>Conclusions: </strong>Our results underscore the significance of the rhizosphere microenvironment modification by PGPR for its colonization and efficacy, and highlight the collaborative role of rare microbiota in the context of PGPR-enhanced phytoremediation. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"113"},"PeriodicalIF":13.8,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12054286/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144011955","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In utero human intestine contains maternally derived bacterial metabolites.","authors":"Wenjia Wang, Weihong Gu, Ron Schweitzer, Omry Koren, Soliman Khatib, George Tseng, Liza Konnikova","doi":"10.1186/s40168-025-02110-0","DOIUrl":"https://doi.org/10.1186/s40168-025-02110-0","url":null,"abstract":"<p><strong>Background: </strong>Understanding when host-microbiome interactions are first established is crucial for comprehending normal development and identifying disease prevention strategies. Furthermore, bacterially derived metabolites play critical roles in shaping the intestinal immune system. Recent studies have demonstrated that memory T cells infiltrate human intestinal tissue early in the second trimester, suggesting that microbial components such as peptides that can prime adaptive immunity and metabolites that can influence the development and function of the immune system are also present in utero. Our previous study reported a unique fetal intestinal metabolomic profile with an abundance of several bacterially derived metabolites and aryl hydrocarbon receptor (AHR) ligands implicated in mucosal immune regulation.</p><p><strong>Results: </strong>In the current study, we demonstrate that a number of microbiome-associated metabolites present in the fetal intestines are also present in the placental tissue, and their abundance is different across the fetal intestine, fetal meconium, fetal placental villi, and the maternal decidua. The fetal gastrointestinal samples and maternal decidua samples show substantially higher positive correlation on the abundance of these microbial metabolites than the correlation between the fetal gastrointestinal samples and meconium samples. The expression of genes associated with the transport and signaling of some microbial metabolites is also detectable in utero.</p><p><strong>Conclusions: </strong>We suggest that the microbiome-associated metabolites are maternally derived and vertically transmitted to the fetus. Notably, these bacterially derived metabolites, particularly short-chain fatty acids and secondary bile acids, are likely biologically active and functional in regulating the fetal immune system and preparing the gastrointestinal tract for postnatal microbial encounters, as the transcripts for their various receptors and carrier proteins are present in second trimester intestinal tissue through single-cell transcriptomic data. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"116"},"PeriodicalIF":13.8,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12054239/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144016064","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gut microbiota dysbiosis orchestrates vitiligo-related oxidative stress through the metabolite hippuric acid.","authors":"Qingrong Ni, Lin Xia, Ye Huang, Xiaoying Yuan, Weijie Gu, Yueqi Chen, Yijin Wang, Meng Nian, Shengxi Wu, Hong Cai, Jing Huang","doi":"10.1186/s40168-025-02102-0","DOIUrl":"https://doi.org/10.1186/s40168-025-02102-0","url":null,"abstract":"<p><strong>Background: </strong>Vitiligo, a depigmenting autoimmune skin disease characterized by melanocyte dysfunction or death, is known to be associated with an imbalance in gut microbiota. Oxidative stress plays a critical role in the pathogenesis of vitiligo. However, the complex promising interaction between abnormal accumulation of reactive oxygen species (ROS) in the skin and gut microbiota has remained unclear.</p><p><strong>Results: </strong>Here, we compared transcriptome data of vitiligo lesions and normal skin and identified a high expression of oxidative stress-related genes in vitiligo lesions. We also established a vitiligo mouse model and found that the presence of gut microbiota influenced the expression of ROS-related genes. Depletion of gut microbiota reduced abnormal ROS accumulation and mitochondrial abnormalities in melanocytes, significantly improving depigmentation. Our findings from manipulating gut microbiota through cohousing, fecal microbiota transplantation (FMT), and probiotic supplementation showed that transferring gut microbiota from mice with severe vitiligo-like phenotypes exacerbated skin depigmentation while probiotics inhibited its progression. Targeted metabolomics of fecal, serum, and skin tissues revealed gut microbiota-dependent accumulation of hippuric acid, mediating excessive ROS in the skin. Elevated serum hippuric acid levels were also confirmed in vitiligo patients. Additionally, a microbiota-dependent increase in intestinal permeability in vitiligo mice mediated elevated hippuric acid levels, and we found that hippuric acid could directly bind to ROS-related proteins (NOS2 and MAPK14).</p><p><strong>Conclusions: </strong>Our results suggested the important role of gut microbiota in regulating vitiligo phenotypes and oxidative stress. We identified hippuric acid, a gut microbiota-host co-metabolite, as a critical mediator of oxidative stress in vitiligo skin and its binding targets (NOS2 and MAPK14), resulting in oxidative stress. Validation in a small human cohort suggested that hippuric acid could serve as a novel diagnostic biomarker and therapeutic target for vitiligo. These findings provided new insights into how gut microbiota regulates skin oxidative stress in vitiligo and suggested potential treatment strategies for the disease. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"112"},"PeriodicalIF":13.8,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12054231/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144016100","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbe-mediated stress resistance in plants: the roles played by core and stress-specific microbiota.","authors":"Sijia Liu, Jiadong Wu, Zhen Cheng, Haofei Wang, Zhelun Jin, Xiang Zhang, Deqiang Zhang, Jianbo Xie","doi":"10.1186/s40168-025-02103-z","DOIUrl":"https://doi.org/10.1186/s40168-025-02103-z","url":null,"abstract":"<p><strong>Background: </strong>Plants in natural surroundings frequently encounter diverse forms of stress, and microbes are known to play a crucial role in assisting plants to withstand these challenges. However, the mining and utilization of plant-associated stress-resistant microbial sub-communities from the complex microbiome remains largely elusive.</p><p><strong>Results: </strong>This study was based on the microbial communities over 13 weeks under four treatments (control, drought, salt, and disease) to define the shared core microbiota and stress-specific microbiota. Through co-occurrence network analysis, the dynamic change networks of microbial communities under the four treatments were constructed, revealing distinct change trajectories corresponding to different treatments. Moreover, by simulating species extinction, the impact of the selective removal of microbes on network robustness was quantitatively assessed. It was found that under varying environmental conditions, core microbiota made significant potential contributions to the maintenance of network stability. Our assessment utilizing null and neutral models indicated that the assembly of stress-specific microbiota was predominantly driven by deterministic processes, whereas the assembly of core microbiota was governed by stochastic processes. We also identified the microbiome features from functional perspectives: the shared microbiota tended to enhance the ability of organisms to withstand multiple types of environmental stresses and stress-specific microbial communities were associated with the diverse mechanisms of mitigating specific stresses. Using a culturomic approach, 781 bacterial strains were isolated, and nine strains were selected to construct different SynComs. These experiments confirmed that communities containing stress-specific microbes effectively assist plants in coping with environmental stresses.</p><p><strong>Conclusions: </strong>Collectively, we not only systematically revealed the dynamics variation patterns of rhizosphere microbiome under various stresses, but also sought constancy from the changes, identified the potential contributions of core microbiota and stress-specific microbiota to plant stress tolerance, and ultimately aimed at the beneficial microbial inoculation strategies for plants. Our research provides novel insights into understanding the microbe-mediated stress resistance process in plants. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"111"},"PeriodicalIF":13.8,"publicationDate":"2025-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12051278/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143989789","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Plant nickel-exclusion versus hyperaccumulation: a microbial perspective.","authors":"Julie Dijoux, Sarah Gigante, Gael Lecellier, Linda Guentas, Valérie Burtet-Sarramegna","doi":"10.1186/s40168-025-02098-7","DOIUrl":"https://doi.org/10.1186/s40168-025-02098-7","url":null,"abstract":"<p><strong>Background: </strong>In New Caledonia, nearly 2000 plant species grow on ultramafic substrates, which contain prominent levels of heavy metals and are deficient in essential plant nutrients. To colonize these habitats, such plants, known as metallophytes, have developed various adaptive behaviors towards metals (exclusion, tolerance, or hyperaccumulation). Ultramafic substrates also host many unique microorganisms, which are adapted to metallic environments and capable of boosting plant growth while assisting plants in acquiring essential micronutrients. Hence, plant-microbiota interactions play a key role in adapting to environmental stress. Here, we hypothesised that microbial associations in the different aboveground and underground compartments of metallophytes could be associated to their metal hyperaccumulation or exclusion phenotypes. This hypothesis was tested using a systematic comparative metabarcoding approach on the different compartments of two New Caledonian metallophytes belonging to the same genus and living in sympatry on ultramafic substrates: Psychotria gabriellae, a nickel-hyperaccumulator (Ni-HA), and Psychotria semperflorens, the related non-accumulator (nA) species.</p><p><strong>Results: </strong>The study of the diversity and specificity of fungal amplicon sequence variants (ASVs) reveals a structuring of fungal communities at both the plant phenotype and compartment levels. In contrast, the structure of bacterial communities was primarily shaped by the belowground compartments. Additionally, we observed a lower diversity in the bacterial communities of the aboveground compartments of each species. For each plant species, we highlighted a distinct global microbial signature (biomarkers), as well as compartment-specific microbial associations.</p><p><strong>Conclusion: </strong>To our knowledge, this study is the first to systematically compare the microbiomes associated with different compartments of New Caledonian metallophyte species growing on the same substrate and under identical environmental conditions but exhibiting different adaptive phenotypes. Our results reveal distinct microbial biomarkers between the Ni-hyperaccumulator and non-accumulator Psychotria species. Most of the highlighted biomarkers are abundant in various plants under metal stress and may contribute to improving the phytoextraction or phytostabilization processes. They are also known to tolerate heavy metals and enhance metal stress tolerance in plants. The present findings highlight that the microbial perspective is essential for better understanding the mechanisms of hyperaccumulation and exclusion at the whole-plant level. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"110"},"PeriodicalIF":13.8,"publicationDate":"2025-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12051281/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144025379","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}