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Correction: Parabacteroides distasonis regulates the infectivity and pathogenicity of SVCV at different water temperatures. 更正:在不同水温条件下,副嗜水杆菌(Parabacteroides distasonis)可调节 SVCV 的感染性和致病性。
IF 13.8 1区 生物学
Microbiome Pub Date : 2024-11-18 DOI: 10.1186/s40168-024-01968-w
Yujun Zhang, Yan Gao, Chen Li, Yong-An Zhang, Yuanan Lu, Jing Ye, Xueqin Liu
{"title":"Correction: Parabacteroides distasonis regulates the infectivity and pathogenicity of SVCV at different water temperatures.","authors":"Yujun Zhang, Yan Gao, Chen Li, Yong-An Zhang, Yuanan Lu, Jing Ye, Xueqin Liu","doi":"10.1186/s40168-024-01968-w","DOIUrl":"10.1186/s40168-024-01968-w","url":null,"abstract":"","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"243"},"PeriodicalIF":13.8,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142668083","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}
引用次数: 0
The intestinal microbiome and Cetobacterium somerae inhibit viral infection through TLR2-type I IFN signaling axis in zebrafish. 斑马鱼肠道微生物群和单细胞鲸鱼杆菌通过 TLR2 I 型 IFN 信号轴抑制病毒感染
IF 13.8 1区 生物学
Microbiome Pub Date : 2024-11-18 DOI: 10.1186/s40168-024-01958-y
Hui Liang, Ming Li, Jie Chen, Wenhao Zhou, Dongmei Xia, Qianwen Ding, Yalin Yang, Zhen Zhang, Chao Ran, Zhigang Zhou
{"title":"The intestinal microbiome and Cetobacterium somerae inhibit viral infection through TLR2-type I IFN signaling axis in zebrafish.","authors":"Hui Liang, Ming Li, Jie Chen, Wenhao Zhou, Dongmei Xia, Qianwen Ding, Yalin Yang, Zhen Zhang, Chao Ran, Zhigang Zhou","doi":"10.1186/s40168-024-01958-y","DOIUrl":"10.1186/s40168-024-01958-y","url":null,"abstract":"<p><strong>Background: </strong>Evidence has accumulated to demonstrate that intestinal microbiome can inhibit viral infection. However, our knowledge of the signaling pathways and identity of specific commensal microbes that mediate the antiviral response is limited. Zebrafish have emerged as a powerful animal model for study of vertebrate-microbiota interactions. Here, a rhabdoviral infection model in zebrafish allows us to investigate the modes of action of microbiome-mediated antiviral effect.</p><p><strong>Results: </strong>We observed that oral antibiotics-treated and germ-free zebrafish exhibited greater spring viremia of carp virus (SVCV) infection. Mechanistically, depletion of the intestinal microbiome alters TLR2-Myd88 signaling and blunts neutrophil response and type I interferon (IFN) antiviral innate immunity. Through 16S rRNA sequencing of the intestinal contents from control and antibiotic(s)-treated fish, we identified a single commensal bacterial species, Cetobacterium somerae, that can restore the TLR2- and neutrophil-dependent type I IFN response to restrict SVCV infection in gnotobiotic zebrafish. Furthermore, we found that C. somerae exopolysaccharides (CsEPS) was the effector molecule that engaged TLR2 to mediate the type I IFN-dependent antiviral function.</p><p><strong>Conclusions: </strong>Together, our results suggest a conserved role of intestinal microbiome in regulating type I IFN antiviral response among vertebrates and reveal that the intestinal microbiome inhibits viral infection through a CsEPS-TLR2-type I IFN signaling axis in zebrafish. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"244"},"PeriodicalIF":13.8,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142668085","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}
引用次数: 0
The fall armyworm converts maize endophytes into its own probiotics to detoxify benzoxazinoids and promote caterpillar growth. 秋季军虫将玉米内生菌转化为自身的益生菌,以解毒苯并恶嗪类化合物并促进毛虫生长。
IF 13.8 1区 生物学
Microbiome Pub Date : 2024-11-16 DOI: 10.1186/s40168-024-01957-z
Jinfeng Qi, Fangjie Xiao, Xingxing Liu, Jing Li, Haocai Wang, Shu Li, Hongwei Yu, Yuxing Xu, Hang Wang
{"title":"The fall armyworm converts maize endophytes into its own probiotics to detoxify benzoxazinoids and promote caterpillar growth.","authors":"Jinfeng Qi, Fangjie Xiao, Xingxing Liu, Jing Li, Haocai Wang, Shu Li, Hongwei Yu, Yuxing Xu, Hang Wang","doi":"10.1186/s40168-024-01957-z","DOIUrl":"10.1186/s40168-024-01957-z","url":null,"abstract":"<p><strong>Background: </strong>The fall armyworm (FAW, Spodoptera frugiperda) threatens maize production worldwide, and benzoxazinoids (Bxs) are known as the main secondary metabolites produced by maize to defend against FAW. However, we do not yet know whether and in what ways certain endophytes in the digestive system of FAW can metabolize Bxs, thus enhancing the fitness of FAW when feeding on maize.</p><p><strong>Results: </strong>Using Bxs as the sole carbon and nitrogen source, we isolated Pantoea dispersa from the guts of FAW. P. dispersa can colonize maize roots and leaves as indicated by GFP-labeling and further successfully established itself as an endophyte in the Malpighian tubules and the gut of FAW after FAW feeding activities. Once established, it can be vertically transmitted through FAW eggs, suggesting the potential that FAW can convert maize-derived endophytes into symbiotic bacteria for intergenerational transmission. The prevalence of P. dispersa in FAW guts and maize leaves was also confirmed over large geographic regions, indicating its evolutionary adaptation in fields. Bxs determination in the gut and frass of FAW combined with bioassays performance on maize bx2 mutants revealed that the colonization of P. dispersa can promote FAW growth by metabolizing Bxs rather than other metabolites. Additionally, genome and transcriptome analyses identified plasmid-borne genes, rather than chromosomes of this species, were crucial for Bxs metabolism. This was further validated through in vitro prokaryotic expression assays by expressing two candidate genes form the plasmid.</p><p><strong>Conclusions: </strong>FAW can convert maize endophytes into its own probiotics to detoxify Bxs and thus enhance caterpillar growth. This represents a novel strategy for lepidopteran pests-transforming allies of the host into its own-thereby shedding light on the rapid spread of FAW and enhancing our understanding of ecological and evolutionary mechanisms underlying the pest-microbe-plant interactions. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"240"},"PeriodicalIF":13.8,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11568528/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142643987","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}
引用次数: 0
Integrated multi-approaches reveal unique metabolic mechanisms of Vestimentifera to adapt to deep sea. 综合多种方法揭示了维斯提夫拉(Vestimentifera)适应深海的独特新陈代谢机制。
IF 13.8 1区 生物学
Microbiome Pub Date : 2024-11-16 DOI: 10.1186/s40168-024-01960-4
Qinglei Sun, Zihao Yuan, Yuanyuan Sun, Li Sun
{"title":"Integrated multi-approaches reveal unique metabolic mechanisms of Vestimentifera to adapt to deep sea.","authors":"Qinglei Sun, Zihao Yuan, Yuanyuan Sun, Li Sun","doi":"10.1186/s40168-024-01960-4","DOIUrl":"10.1186/s40168-024-01960-4","url":null,"abstract":"<p><strong>Background: </strong>Vestimentiferan tubeworms are deep-sea colonizers, in which chemoautotrophic symbiosis was first observed. These animals are gutless and depend on endosymbiotic bacteria for organic compound synthesis and nutrition supply. Taxonomically, vestimentiferans belong to Siboglinidae and Annelida. Compared with other siboglinids, vestimentiferans are distinguished by high tolerance of the prevailing hydrogen sulfide in hydrothermal vents, rapid growth in local habitats, and a physical structure consisting of a thick chitinous tube. The metabolic mechanisms contributing to these features remain elusive.</p><p><strong>Results: </strong>Comparative genomics revealed that unlike other annelids, vestimentiferans possessed trehaloneogenesis and lacked gluconeogenesis. Transcriptome and metabolome analyses detected the expression of trehalose-6-phosphate synthase/phosphatase (TPSP), the key enzyme of trehaloneogenesis, and trehalose production in vestimentiferan tissues. In addition to trehaloneogenesis, glycogen biosynthesis evidenced by packed glycogen granules was also found in vestimentiferan symbionts, but not in other Siboglinidae symbionts. Data mining and analyses of invertebrate TPSP revealed that the TPSP in Vestimentifera, as well as Cnidaria, Rotifera, Urochordata, and Cephalochordata, likely originated from Arthropoda, possibly as a result of transposon-mediated inter-phyla gene transfer.</p><p><strong>Conclusion: </strong>This study indicates a critical role of bacterial glycogen biosynthesis in the highly efficient symbiont - vestimentiferan cooperation. This study provides a new perspective for understanding the environmental adaptation strategies of vestimentiferans and adds new insights into the mechanism of metabolic evolution in Metazoa. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"241"},"PeriodicalIF":13.8,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11568676/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142644477","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}
引用次数: 0
Multi-omics investigation into long-distance road transportation effects on respiratory health and immunometabolic responses in calves. 多组学研究长途公路运输对小牛呼吸健康和免疫代谢反应的影响
IF 13.8 1区 生物学
Microbiome Pub Date : 2024-11-16 DOI: 10.1186/s40168-024-01962-2
Jiancheng Qi, Fangyuan Huang, Linli Gan, Xueke Zhou, Liping Gou, Yue Xie, Hongrui Guo, Jing Fang, Zhicai Zuo
{"title":"Multi-omics investigation into long-distance road transportation effects on respiratory health and immunometabolic responses in calves.","authors":"Jiancheng Qi, Fangyuan Huang, Linli Gan, Xueke Zhou, Liping Gou, Yue Xie, Hongrui Guo, Jing Fang, Zhicai Zuo","doi":"10.1186/s40168-024-01962-2","DOIUrl":"10.1186/s40168-024-01962-2","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Long-distance road transportation is a common practice in the beef industry, frequently resulting in bovine respiratory disease (BRD) and compromised growth performance. However, a comprehensive investigation integrating clinical performance, physiological conditions, and nasopharyngeal microflora remains lacking.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Methods: &lt;/strong&gt;This study aimed to evaluate the respiratory health and immunometabolic status of 54 beef calves subjected to a 3000-km journey. The respiratory health of calves was monitored over 60 days post-arrival using a modified clinical scoring system. Nasopharyngeal microflora and venous blood samples were collected at 3 time points: before transportation (A), 30 days post-arrival (B), and 60 days post-arrival (C), for 16S rRNA microbiomics, whole-blood transcriptomics, serum metabolomics, and laboratory assays.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Result: &lt;/strong&gt;Within the first week post-arrival, the appetite and mental scores of calves dropped to zero, while other respiratory-related scores progressively declined over the 60 days. The α-diversity of nasopharyngeal microflora in calves was similar at time points A and B, both significantly higher than at time point C. The structure of these microbial communities varied significantly across different time points, with a notably higher relative abundance of BRD-related genera, such as Pasteurella and Mannheimia, detected at time point A compared to B and C. The composition and gene expression profiles of circulating blood cells at time point A were significantly different from those at B and C. Specifically, higher expression levels of oxidative- and inflammatory-related genes, cytokines, and enzymes were observed at time point A compared to B and C. Higher levels of catabolism-related metabolites and enzymes were detected at time point A, while higher levels of anabolism-related metabolites and enzymes were observed at time points B and C. Additionally, significant correlations were found among microorganisms, genes, and metabolites with differing abundances, expression levels, and concentrations across time points. Stronger correlations were observed between calves' performance and nasopharyngeal microflora and immunometabolic status at time point A compared to B or C.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusions: &lt;/strong&gt;Collectively, these results confirm that 3000 km of road transportation significantly alters the composition and gene expression profiles of circulating white blood cells in calves, affects their metabolic processes, disrupts the balance of the respiratory microbial community, and leads to pronounced respiratory symptoms that persist for at least 60 days. During this period, the influenced composition and gene expression of circulating blood cells, metabolic processes, and nasopharyngeal microbial community gradually return to equilibrium, and the respiratory symptoms gradually diminish. This observational research indicates that transportation induc","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"242"},"PeriodicalIF":13.8,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11568561/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142643494","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}
引用次数: 0
Wild again: recovery of a beneficial Cannabis seed endophyte from low domestication genotypes. 野性再现:从低驯化基因型中恢复有益的大麻种子内生菌。
IF 13.8 1区 生物学
Microbiome Pub Date : 2024-11-15 DOI: 10.1186/s40168-024-01951-5
Carolina Lobato, João Machado de Freitas, Daniel Habich, Isabella Kögl, Gabriele Berg, Tomislav Cernava
{"title":"Wild again: recovery of a beneficial Cannabis seed endophyte from low domestication genotypes.","authors":"Carolina Lobato, João Machado de Freitas, Daniel Habich, Isabella Kögl, Gabriele Berg, Tomislav Cernava","doi":"10.1186/s40168-024-01951-5","DOIUrl":"10.1186/s40168-024-01951-5","url":null,"abstract":"<p><strong>Background: </strong>Beyond carrying the plant embryo, seeds harbour intricate microbial communities whose transmission across successive plant generations can significantly influence the ecological and evolutionary dynamics of plant-microbe symbioses. The process of plant domestication has potential repercussions in genes involved in plant-microbiome interactions. However, the extent to which breeding can impact the seed microbiome is sparsely explored. Cannabis is a high-value crop but sparsely subjected to agricultural innovations established in other crop species during the last century. Here, we conduct a large-scale analysis of the bacterial seed microbiome of Cannabis across different domestication grades and investigate the potential of seed-associated endophytes as plant growth-promoting agents under both controlled and field conditions.</p><p><strong>Results: </strong>Analysis of Cannabis seed endophyte composition and diversity across 46 plant genotypes revealed 813 different bacterial genera with a predominance of Gammaproteobacteria, Bacilli, Actinobacteria and Alphaproteobacteria but a genotype-specific microbiome. The assessment of domestication and breeding on microbial assembly revealed a higher bacterial diversity in low domestication genotypes (Shannon index, H': 1.21 vs. 1.05) and a higher homogeneity in bacterial composition caused by line development. Further, a seed bacterial isolate (Bacillus frigoritolerans C1141) associated with low domestication genotypes, and with genes associated with bio-fertilization, bioremediation and phytohormone production, increased plant growth by 42.3% at the time of harvest, under field conditions.</p><p><strong>Conclusion: </strong>This study addresses critical knowledge gaps related to the assembly of the Cannabis seed-endophytic microbiome. It reveals that Cannabis breeding is linked to alterations of seed microbial communities, which potentially led to the loss of bacteria with functional significance. These results highlight the importance of preserving seed microbiomes in plant breeding to support sustainable plant health and growth enhancement in Cannabis. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"239"},"PeriodicalIF":13.8,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11568533/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142643997","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}
引用次数: 0
Effect of plant-derived microbial soil legacy in a grafting system-a turn for the better. 嫁接系统中植物源微生物土壤遗产的影响--好转。
IF 13.8 1区 生物学
Microbiome Pub Date : 2024-11-14 DOI: 10.1186/s40168-024-01938-2
Tingting Wang, Yang Ruan, Qicheng Xu, Qirong Shen, Ning Ling, Philippe Vandenkoornhuyse
{"title":"Effect of plant-derived microbial soil legacy in a grafting system-a turn for the better.","authors":"Tingting Wang, Yang Ruan, Qicheng Xu, Qirong Shen, Ning Ling, Philippe Vandenkoornhuyse","doi":"10.1186/s40168-024-01938-2","DOIUrl":"10.1186/s40168-024-01938-2","url":null,"abstract":"<p><strong>Background: </strong>Plant-soil feedback arises from microbial legacies left by plants in the soil. Grafting is a common technique used to prevent yield declines in monocultures. Yet, our understanding of how grafting alters the composition of soil microbiota and how these changes affect subsequent crop performance remains limited. Our experiment involved monoculturing ungrafted and grafted watermelons to obtain conditioned soils, followed by growing the watermelons on the conditioned soils to investigate plant-soil feedback effects.</p><p><strong>Results: </strong>Ungrafted plants grew better in soil previously conditioned by a different plant (heterospecific soil) while grafted plants grew better in soil conditioned by the same plant (conspecific soil). We demonstrated experimentally that these differences in growth were linked to changes in microorganisms. Using a supervised machine learning algorithm, we showed that differences in the relative abundance of certain genera, such as Rhizobium, Chryseobacterium, Fusarium, and Aspergillus, significantly influenced the conspecific plant-soil feedback. Metabolomic analyses revealed that ungrafted plants in heterospecific soil enriched arginine biosynthesis, whereas grafted plants in conspecific soil increased sphingolipid metabolism. Elsewhere, the metagenome-assembled genomes (MAGs) of ungrafted plants identified in heterospecific soil include Chryseobacterium and Lysobacter, microorganisms having been prominently identified in earlier research as contributors to plant growth. Metabolic reconstruction revealed the putative ability of Chryseobacterium to convert D-glucono-1,5-lactone to gluconic acid, pointing to distinct disease-suppressive mechanisms and hence distinct microbial functional legacies between grafted and ungrafted plants.</p><p><strong>Conclusions: </strong>Our findings show a deep impact of the soil microbial reservoir on plant growth and suggest the necessity to protect and improve this microbial community in agricultural soils. The work also suggests possibilities of optimizing microbiota-mediated benefits through grafting herein, a way that \"engineered\" soil microbial communities for better plant growth. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"234"},"PeriodicalIF":13.8,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11566652/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142623780","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}
引用次数: 0
F. prausnitzii potentially modulates the association between citrus intake and depression. F. prausnitzii有可能调节柑橘摄入量与抑郁症之间的关系。
IF 13.8 1区 生物学
Microbiome Pub Date : 2024-11-14 DOI: 10.1186/s40168-024-01961-3
Chatpol Samuthpongtorn, Allison A Chan, Wenjie Ma, Fenglei Wang, Long H Nguyen, Dong D Wang, Olivia I Okereke, Curtis Huttenhower, Andrew T Chan, Raaj S Mehta
{"title":"F. prausnitzii potentially modulates the association between citrus intake and depression.","authors":"Chatpol Samuthpongtorn, Allison A Chan, Wenjie Ma, Fenglei Wang, Long H Nguyen, Dong D Wang, Olivia I Okereke, Curtis Huttenhower, Andrew T Chan, Raaj S Mehta","doi":"10.1186/s40168-024-01961-3","DOIUrl":"10.1186/s40168-024-01961-3","url":null,"abstract":"<p><strong>Background: </strong>The gut microbiome modulates the effects of diet on host health, but it remains unclear which specific foods and microbial features interact to influence risk of depression. To understand this interplay, we leveraged decades of dietary and depression data from a longitudinal cohort of women (n = 32,427), along with fecal metagenomics and plasma metabolomics from a substudy (n = 207) nested in this cohort, as well as an independent validation cohort of men (n = 307).</p><p><strong>Results: </strong>We report that citrus intake and its components are prospectively associated with a lower risk of depression and altered abundance of 15 gut microbial species, including enriched Faecalibacterium prausnitzii. In turn, we found a lower abundance of F. prausnitzii and its metabolic pathway, S-adenosyl-L-methionine (SAM) cycle I in participants with depression. To explore causality, we found that lower SAM production by F. prausnitzii may decrease intestinal monoamine oxidase A gene expression implicated in serotonin and dopamine synthesis.</p><p><strong>Conclusions: </strong>These data underscore the role of diet in the prevention of depression and offer a plausible explanation for how the intestinal microbiome modulates the influence of citrus on mental health. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"237"},"PeriodicalIF":13.8,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11566247/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142623783","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}
引用次数: 0
Synthetic communities derived from the core endophytic microbiome of hyperaccumulators and their role in cadmium phytoremediation. 源自高积累植物核心内生微生物群的合成群落及其在镉植物修复中的作用。
IF 13.8 1区 生物学
Microbiome Pub Date : 2024-11-14 DOI: 10.1186/s40168-024-01959-x
Lukuan Huang, Ziyan Fan, Zhipeng Hu, Zhesi Li, Yingyi Fu, Qiong Wang, Xianyong Lin, Ying Feng
{"title":"Synthetic communities derived from the core endophytic microbiome of hyperaccumulators and their role in cadmium phytoremediation.","authors":"Lukuan Huang, Ziyan Fan, Zhipeng Hu, Zhesi Li, Yingyi Fu, Qiong Wang, Xianyong Lin, Ying Feng","doi":"10.1186/s40168-024-01959-x","DOIUrl":"10.1186/s40168-024-01959-x","url":null,"abstract":"<p><strong>Background: </strong>Although numerous endophytic bacteria have been isolated and characterized from cadmium (Cd) hyperaccumulators, the contribution and potential application of the core endophytic microbiomes on facilitating phytoremediation were still lack of intensive recognition. Therefore, a 2-year field sampling in different location were firstly conducted to identify the unique core microbiome in Cd hyperaccumulators, among which the representative cultivable bacteria of different genera were then selected to construct synthetic communities (SynComs). Finally, the effects and mechanisms of the optimized SynCom in regulating Cd accumulation in different ecotypes of Sedum alfredii were studied to declare the potential application of the bacterial agents based on core microbiome.</p><p><strong>Results: </strong>Through an innovative network analysis workflow, 97 core bacterial taxa unique to hyperaccumulator Sedum was identified based on a 2-year field 16S rRNA sequencing data. A SynCom comprising 13 selected strains belonging to 6 different genera was then constructed. Under the combined selection pressure of the plant and Cd contamination, Alcaligenes sp. exhibited antagonistic relationships with other genera and plant Cd concentration. Five representative strains of the other five genera were further conducted genome resequencing and developed six SynComs, whose effects on Cd phytoremediation were compared with single strains by hydroponic experiments. The results showed that SynCom-NS comprising four strains (including Leifsonia shinshuensis, Novosphingobium lindaniclasticum, Ochrobactrum anthropi, and Pseudomonas izuensis) had the greatest potential to enhance Cd phytoremediation. After inoculation with SynCom-NS, genes related to Cd transport, antioxidative defense, and phytohormone signaling pathways were significantly upregulated in both ecotypes of S. alfredii, so as to promote plant growth, Cd uptake, and translocation.</p><p><strong>Conclusion: </strong>In this study, we designed an innovative network analysis workflow to identify the core endophytic microbiome in hyperaccumulator. Based on the cultivable core bacteria, an optimized SynCom-NS was constructed and verified to have great potential in enhancing phytoremediation. This work not only provided a framework for identifying core microbiomes associated with specific features but also paved the way for the construction of functional synthetic communities derived from core microbiomes to develop high efficient agricultural agents. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"236"},"PeriodicalIF":13.8,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11566637/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142623791","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}
引用次数: 0
Unveiling bat-borne viruses: a comprehensive classification and analysis of virome evolution. 揭开蝙蝠传播病毒的神秘面纱:病毒组进化的全面分类和分析。
IF 13.8 1区 生物学
Microbiome Pub Date : 2024-11-14 DOI: 10.1186/s40168-024-01955-1
Yuyang Wang, Panpan Xu, Yelin Han, Wenliang Zhao, Lamei Zhao, Rui Li, Junpeng Zhang, Shuyi Zhang, Jian Lu, Peter Daszak, Qi Jin, Zhiqiang Wu
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