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Wang R, Li X, Lv F, He J, Lv R, Wei L. Sesame bacterial wilt significantly alters rhizosphere soil bacterial community structure, function, and metabolites in continuous cropping systems. Microbiol Res 2024; 282:127649. [PMID: 38402727 DOI: 10.1016/j.micres.2024.127649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 02/07/2024] [Accepted: 02/12/2024] [Indexed: 02/27/2024]
Abstract
Bacterial wilt is the leading disease of sesame and alters the bacterial community composition, function, and metabolism of sesame rhizosphere soil. However, its pattern of change is unclear. Here, the purpose of this study was to investigate how these communities respond to three differing severities of bacterial wilt in mature continuously cropped sesame plants by metagenomic and metabolomic techniques, namely, absence (WH), moderate (WD5), and severe (WD9) wilt. The results indicated that bacterial wilt could significantly change the bacterial community structure in the rhizosphere soil of continuously cropped sesame plants. The biomarker species with significant differences will also change with increasing disease severity. In particular, the gene expression levels of Ralstonia solanacearum in the WD9 and WD5 treatments increased by 25.29% and 33.61%, respectively, compared to those in the WH treatment (4.35 log10 copies g-1). The occurrence of bacterial wilt significantly altered the functions of the bacterial community in rhizosphere soil. KEEG and CAZy functional annotations revealed that the number of significantly different functions in WH was greater than that in WD5 and WD9. Bacterial wilt significantly affected the relative content of metabolites, especially acids, in the rhizosphere soil, and compared with those in the rhizosphere soil from WH, 10 acids (including S-adenosylmethionine, N-acetylleucine, and desaminotyrosine, etc.) in the rhizosphere soil from WD5 or WD9 significantly increased. In comparison, the changes in the other 10 acids (including hypotaurine, erucic acid, and 6-hydroxynicotinic acid, etc.) were reversed. The occurrence of bacterial wilt also significantly inhibited metabolic pathways such as ABC transporter and amino acid biosynthesis pathways in rhizosphere soil and had a significant impact on two key enzymes (1.1.1.11 and 2.6.1.44). In conclusion, sesame bacterial wilt significantly alters the rhizosphere soil bacterial community structure, function, and metabolites. This study enhances the understanding of sesame bacterial wilt mechanisms and lays the groundwork for future prevention and control strategies against this disease.
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Affiliation(s)
- Ruiqing Wang
- Soil Fertilizer and Resource Environment Institute, Jiangxi Academy of Agricultural Sciences, No. 602, Nanlian Road, Nanchang, Jiangxi Province 330200, PR China; Key Laboratory of Crop Ecophysiology and Farming System for the Middle and Lower Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, PR China; National Engineering Technology Research Center for Red Soil Improvement, PR China; National Agricultural Experimental Station for Agricultural Environment Yichun, PR China.
| | - Xinsheng Li
- Institute of Plant Protection, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi Province 330200, PR China
| | - Fengjuan Lv
- Soil Fertilizer and Resource Environment Institute, Jiangxi Academy of Agricultural Sciences, No. 602, Nanlian Road, Nanchang, Jiangxi Province 330200, PR China; Key Laboratory of Crop Ecophysiology and Farming System for the Middle and Lower Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, PR China; National Engineering Technology Research Center for Red Soil Improvement, PR China; National Agricultural Experimental Station for Agricultural Environment Yichun, PR China
| | - Junhai He
- Soil Fertilizer and Resource Environment Institute, Jiangxi Academy of Agricultural Sciences, No. 602, Nanlian Road, Nanchang, Jiangxi Province 330200, PR China; Key Laboratory of Crop Ecophysiology and Farming System for the Middle and Lower Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, PR China; National Engineering Technology Research Center for Red Soil Improvement, PR China; National Agricultural Experimental Station for Agricultural Environment Yichun, PR China
| | - Rujie Lv
- Soil Fertilizer and Resource Environment Institute, Jiangxi Academy of Agricultural Sciences, No. 602, Nanlian Road, Nanchang, Jiangxi Province 330200, PR China; Key Laboratory of Crop Ecophysiology and Farming System for the Middle and Lower Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, PR China; National Engineering Technology Research Center for Red Soil Improvement, PR China; National Agricultural Experimental Station for Agricultural Environment Yichun, PR China
| | - Lingen Wei
- Soil Fertilizer and Resource Environment Institute, Jiangxi Academy of Agricultural Sciences, No. 602, Nanlian Road, Nanchang, Jiangxi Province 330200, PR China; Key Laboratory of Crop Ecophysiology and Farming System for the Middle and Lower Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, PR China; National Engineering Technology Research Center for Red Soil Improvement, PR China; National Agricultural Experimental Station for Agricultural Environment Yichun, PR China.
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Tan YR, Lu Y. Molecular mechanism of Rhubarb in the treatment of non-small cell lung cancer based on network pharmacology and molecular docking technology. Mol Divers 2022:10.1007/s11030-022-10501-w. [PMID: 35933455 DOI: 10.1007/s11030-022-10501-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/15/2022] [Indexed: 12/24/2022]
Abstract
Non-small cell lung cancer (NSCLC) is one of the leading causes of death in the world. Rhubarb, a traditional Chinese medicine, has been widely used in the treatment of inflammatory and autoimmune diseases. This study aimed to investigate the possible mechanism of the rhubarb herb in the treatment of NSCLC by means of network pharmacology and molecular docking and to provide a theoretical basis for experiments and clinical application of traditional Chinese medicine for treating lung cancer. The main active chemical components and targets of rhubarb were screened through Swiss Target Prediction, TargetNet, and Traditional Chinese Medicine Systems Pharmacology (TCMSP) database. The protein-protein interaction (PPI) network was built via an in-depth exploration of the relationships between the proteins. The enrichment analyses of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were applied to predict the potential roles in the pathogenesis of NSCLC via the R package cluster Profiler. Potential targets and active ingredients associated with anti-tumor effects of rhubarb were screened by reverse molecular docking. By searching databases and literature, a total of 295 targets were found for the 21 active ingredients in rhubarb. There were 68 common target genes associated with NSCLC, of which 9 are derived from FDA-approved drugs. GO Gene Set Enrichment Analysis (GSEA) explored up to 1103 biological processes, 62 molecular functions, and 18 cellular components. KEGG GSEA explored 65 basic pathways, and 71 disease pathways. Four key targets (JUN, EGFR, BCL2, and JAK2) were screened through the protein-protein interaction network, target-pathway network, and FDA drug-target network. Molecular docking results showed that these key targets had relatively strong binding activities with rhubarb's active ingredients. The present study explored the potential pharmacological mechanisms of rhubarb on NSCLC, promoting the clinical application of rhubarb in treating NSCLC, and providing references for advanced research.
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Affiliation(s)
- Ye-Ru Tan
- The First Affiliated Hospital, Department of Medical Oncology, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Yu Lu
- The First Affiliated Hospital, Department of General Practice, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China.
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Li F, Yang S, Zhang L, Qiao L, Wang L, He S, Li J, Yang N, Yue B, Zhou C. Comparative metagenomics analysis reveals how the diet shapes the gut microbiota in several small mammals. Ecol Evol 2022; 12:e8470. [PMID: 35136548 PMCID: PMC8809447 DOI: 10.1002/ece3.8470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/29/2021] [Accepted: 12/01/2021] [Indexed: 11/19/2022] Open
Abstract
The gut microbiomes of the host are large and complex communities, which helps to maintain homeostasis, improves digestive efficiency, and promotes the development of the immune system. The small mammals distributed in Sichuan Province are the most popular species for biodiversity research in Southwest China. However, the effects of different diets on the structure and function of the gut microbial community of these small mammals are poorly understood. In this study, whole-metagenome shotgun sequencing has been used to analyze the composition and functional structures of the gut microbiota of seven small mammals in Laojunshan National Nature Reserve, Sichuan Province, China. Taxonomic classification revealed that the most abundant phyla in the gut of seven small mammals were Bacteroides, Proteobacteria, and Firmicutes. Moreover, Hafnia, Lactobacillus, and Yersinia were the most abundant genus in the gut microbiomes of these seven species. At the functional level, we annotated a series of KEGG functional pathways, six Cazy categories, and 46,163 AROs in the gut microbiomes of the seven species. Comparative analysis found that the difference in the gut microbiomes between the Soricidea and Muridae concentrated on the increase in the F/B (Firmicutes/Bacteroides) ratio in the Soricidea group, probably driven by the high-fat and -calorie digestive requirements due to their insectivorous diet. The comparative functional profiling revealed that functions related to metabolism and carbohydrates were significantly more abundant in Muridae group, which may be attributed to their high carbohydrate digestion requirements caused by their herbivorous diet. These data suggested that different diets in the host may play an important role in shaping the gut microbiota, and lay the foundation for teasing apart the influences of heritable and environmental factors on the evolution of gut microbial communities.
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Affiliation(s)
- Fengjun Li
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education)College of Life SciencesSichuan UniversityChengduChina
| | - Shengzhi Yang
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education)College of Life SciencesSichuan UniversityChengduChina
| | - Linwan Zhang
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education)College of Life SciencesSichuan UniversityChengduChina
| | - Lu Qiao
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education)College of Life SciencesSichuan UniversityChengduChina
| | - Lei Wang
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education)College of Life SciencesSichuan UniversityChengduChina
| | - Song He
- Laojunshan National Nature ReserveSichuan ProvincePingshanChina
| | - Jian Li
- Laojunshan National Nature ReserveSichuan ProvincePingshanChina
| | - Nan Yang
- Institute of Qinghai‐Tibetan PlateauSouthwest Minzu UniversityChengduChina
| | - Bisong Yue
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education)College of Life SciencesSichuan UniversityChengduChina
| | - Chuang Zhou
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education)College of Life SciencesSichuan UniversityChengduChina
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Guo L, He J, Zhang J, Zhang X, Zhang D, Zhou L, Yuan Y, Fu S, Qiu Y, Ye C, Liu Y, Wu Z, Hu CAA. Baicalin-Aluminum Modulates the Broiler Gut Microbiome. DNA Cell Biol 2021; 40:881-894. [PMID: 33945308 DOI: 10.1089/dna.2021.0080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Baicalin-aluminum regulates the gut microbiome of piglets with diarrhea. However, whether it affects poultry gut microbiome composition and function remains unknown. In this study, we used metagenomic sequencing to explore the effects of baicalin-aluminum on gut microbiome changes in poultry when compared with animals administered colistin sulfate. Our data showed that important gut microbiome components consisted of Ruminococcaceae, Subdoligranulum, Bifidobacterium, Bifidobacterium pseudolongum, and Pseudoflavonifractor when broilers were administered baicalin-aluminum compared with colistin. At the species level, Lactobacillus salivarius, Bacteroides uniformis, Oscillibacter unclassified, Bacteroides fragilis, Ruminococcus torques, and Subdoligranulum unclassified abundance were significantly upregulated upon baicalin-aluminum treatment when compared with colistin administration. In addition, Gene Ontology (GO) enrichment analysis indicated that functional differentially expressed genes, which were in the top 30 GO enrichment terms, were associated with metabolic processes, catalytic activity, and cellular processes. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated that ABC transporters, oxidative phosphorylation, and phosphotransferase systems were the dominant signaling pathways in the baicalin-aluminum group when compared with the colistin group. Taken together, our data indicated that baicalin-aluminum modified broiler gut microbiome composition. These observations enhance our physiological insights of baicalin-aluminum-mediated functions in the broiler microbiome and potentially provide a novel therapy to manage both animal and human health.
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Affiliation(s)
- Ling Guo
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, P.R. China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, P.R. China
| | - Jing He
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, P.R. China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, P.R. China
| | - Jiacheng Zhang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, P.R. China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, P.R. China
| | - Xiaofang Zhang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, P.R. China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, P.R. China
| | - Dan Zhang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, P.R. China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, P.R. China
| | - Linglu Zhou
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, P.R. China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, P.R. China
| | - Yuzhen Yuan
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, P.R. China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, P.R. China
| | - Shulin Fu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, P.R. China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, P.R. China
| | - Yinsheng Qiu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, P.R. China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, P.R. China
| | - Chun Ye
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, P.R. China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, P.R. China
| | - Yu Liu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, P.R. China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, P.R. China
| | - Zhongyuan Wu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, P.R. China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, P.R. China
| | - Chien-An Andy Hu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, P.R. China.,Biochemistry and Molecular Biology, University of New Mexico School of Medicine, Albuquerque, New Mexico, USA
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