Integrated metagenomics and metabolomics analysis reveals changes in the microbiome and metabolites in the rhizosphere soil of Fritillaria unibracteata

Liu, Chengcheng; Yu, Jiahui; Ying, Jie‐Zheng; Zhang, Kai; Hu, Zhigang; Liu, Zhixiang; Chen, Shilin

doi:10.3389/fpls.2023.1223720

Cited by 5 publications

(2 citation statements)

References 57 publications

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“…To illustrate, the bacterial community diversity within the rhizosphere soil of diseased Fritillaria ussuriensis plants was significantly reduced, accompanied by an increase in pathogen abundance when compared to the state of normal Fritillaria ussuriensis plants [32]. The α-diversity of its rhizosphere soil microbial community changed slightly but not significantly during FC cultivation, which was inconsistent with the results of our rhizosphere soil microstudy in Fritillaria unibracteata, suggesting that the rhizosphere microbial community of FC was more stable during cultivation, compared to Fritillaria unibracteata [33]. This discovery may indicate that FC may be more tolerant to continuous cropping obstacles than Fritillaria unibracteata.…”

Section: Discussioncontrasting

confidence: 97%

Changes in Rhizosphere Soil Microorganisms and Metabolites during the Cultivation of Fritillaria cirrhosa

Liu,

Ying,

Liu

2024

Biology

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Fritillaria cirrhosa is an important cash crop, and its industrial development is being hampered by continuous cropping obstacles, but the composition and changes of rhizosphere soil microorganisms and metabolites in the cultivation process of Fritillaria cirrhosa have not been revealed. We used metagenomics sequencing to analyze the changes of the microbiome in rhizosphere soil during a three-year cultivation process, and combined it with LC-MS/MS to detect the changes of metabolites. Results indicate that during the cultivation of Fritillaria cirrhosa, the composition and structure of the rhizosphere soil microbial community changed significantly, especially regarding the relative abundance of some beneficial bacteria. The abundance of Bradyrhizobium decreased from 7.04% in the first year to about 5% in the second and third years; the relative abundance of Pseudomonas also decreased from 6.20% in the first year to 2.22% in the third year; and the relative abundance of Lysobacter decreased significantly from more than 4% in the first two years of cultivation to 1.01% in the third year of cultivation. However, the relative abundance of some harmful fungi has significantly increased, such as Botrytis, which increased significantly from less than 3% in the first two years to 7.93% in the third year, and Talaromyces fungi, which were almost non-existent in the first two years of cultivation, significantly increased to 3.43% in the third year of cultivation. The composition and structure of Fritillaria cirrhosa rhizosphere metabolites also changed significantly, the most important of which were carbohydrates represented by sucrose (48.00–9.36–10.07%) and some amino acid compounds related to continuous cropping obstacles. Co-occurrence analysis showed that there was a significant correlation between differential microorganisms and differential metabolites, but Procrustes analysis showed that the relationship between bacteria and metabolites was closer than that between fungi and metabolites. In general, in the process of Fritillaria cirrhosa cultivation, the beneficial bacteria in the rhizosphere decreased, the harmful bacteria increased, and the relative abundance of carbohydrate and amino acid compounds related to continuous cropping obstacles changed significantly. There is a significant correlation between microorganisms and metabolites, and the shaping of the Fritillaria cirrhosa rhizosphere’s microecology by bacteria is more relevant.

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Section: Discussioncontrasting

confidence: 97%

Changes in Rhizosphere Soil Microorganisms and Metabolites during the Cultivation of Fritillaria cirrhosa

Liu,

Ying,

Liu

2024

Biology

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“…[ 12 , 13 ]. The disruptions of gut microbiome and their impact on metabolic and physiological functions exert an indispensable role as well [ 14 ]. Research indicates that gut dysbiosis can disrupt both host immune responses and gut barrier function [ 15 ].…”

Section: Introductionmentioning

confidence: 99%

Protective Mechanism of Eurotium amstelodami from Fuzhuan Brick Tea against Colitis and Gut-Derived Liver Injury Induced by Dextran Sulfate Sodium in C57BL/6 Mice

Wang,

Liu,

Wei

et al. 2024

Nutrients

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The study explored the potential protective impact of the probiotic fungus Eurotium amstelodami in Fuzhuan brick tea on ulcerative colitis, along with the underlying mechanism. A spore suspension of E. amstelodami was administered to C57BL/6 mice to alleviate DSS-induced colitis. The findings indicated that administering E. amstelodami evidently enhanced the ultrastructure of colonic epithelium, showing characteristics such as enhanced TJ length, reduced microvilli damage, and enlarged intercellular space. After HLL supplementation, the activation of the liver inflammation pathway, including TLR4/NF-kB and NLRP3 inflammasome caused by DSS, was significantly suppressed, and bile acid metabolism, linking liver and gut, was enhanced, manifested by restoration of bile acid receptor (FXR, TGR5) level. The dysbiosis of the gut microbes in colitis mice was also restored by HLL intervention, characterized by the enrichment of beneficial bacteria (Lactobacillus, Bifidobacterium, Akkermansia, and Faecalibaculum) and fungi (Aspergillus, Trichoderma, Wallemia, Eurotium, and Cladosporium), which was closely associated with lipid metabolism and amino acid metabolism, and was negatively correlated with inflammatory gene expression. Hence, the recovery of gut microbial community structure, implicated deeply in the inflammatory index and metabolites profile, might play a crucial role in the therapeutic mechanism of HLL on colitis.

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Exploring microbial dynamics, metabolic functions and microbes–metabolites correlation in a millennium paddy soil chronosequence using metabolome and microbiome

Li,

Gao,

Chen

et al. 2024

Chem. Biol. Technol. Agric.

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Integrated metagenomics and metabolomics analysis reveals changes in the microbiome and metabolites in the rhizosphere soil of Fritillaria unibracteata

Cited by 5 publications

References 57 publications

Changes in Rhizosphere Soil Microorganisms and Metabolites during the Cultivation of Fritillaria cirrhosa

Changes in Rhizosphere Soil Microorganisms and Metabolites during the Cultivation of Fritillaria cirrhosa

Protective Mechanism of Eurotium amstelodami from Fuzhuan Brick Tea against Colitis and Gut-Derived Liver Injury Induced by Dextran Sulfate Sodium in C57BL/6 Mice

Exploring microbial dynamics, metabolic functions and microbes–metabolites correlation in a millennium paddy soil chronosequence using metabolome and microbiome

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