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Li R, Li Z, Zhang K, Zhang C, Sun Y, Zhang J, Zheng Y, Yao Y, Qin X. The responses of root exudates and microbiome in the rhizosphere of main plant and aromatic intercrops to soil Cr stress. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2025; 366:125528. [PMID: 39672367 DOI: 10.1016/j.envpol.2024.125528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2024] [Revised: 11/30/2024] [Accepted: 12/11/2024] [Indexed: 12/15/2024]
Abstract
Soil chromium (Cr) stress has a well-recognized negative impact on plant growth, and intercropping is a commonly used method to mitigate heavy metal toxicity to main plants. However, the responses of root exudates-microbial and their interactions among soil zones to soil Cr stress are always in need of clarification in intercropping system. In this study, three intercropping patterns (CT, Malus only; TM, Malus × Mentha and TA, Malus × Ageratum) with different soil Cr addition levels (NCR, LCR, HCR) were applied, and the rhizosphere ecological traits in the main plant (FRS) and intercrop (ARS) were investigated. The results indicate that intercropping with either Mentha or Ageratum has a positive effect on main plants response to soil Cr stress, and intercropping with Ageratum showing a more significant effect. Importantly, we found that the rhizosphere of main plant tends to alleviate stress by accumulating organic acids and amino acids, while aromatic plants exhibit a broader accumulation of metabolites. Additionally, we identified five core differential microbial genera. Our findings provide novel insights into intercrop Cr detoxification in the main plant.
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Affiliation(s)
- Rui Li
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, China
| | - Zhenglin Li
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, China
| | - Kui Zhang
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, China
| | - Cong Zhang
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, China
| | - Yue Sun
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Jie Zhang
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, China
| | - Yi Zheng
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, China
| | - Yuncong Yao
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, China
| | - Xiaoxiao Qin
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, China.
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Su FZ, Zhu EL, Bai CX, Zhang WS, Liu M, Li B, Jia CC, Zhang P, Zhang BW, Zou R, Li QX, Yang BY, Kuang HX, Wang QH. A comparative study on the antipyretic effect and underlying mechanisms of different bile-fermented Arisaemas. JOURNAL OF ETHNOPHARMACOLOGY 2025; 337:118951. [PMID: 39423945 DOI: 10.1016/j.jep.2024.118951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Revised: 10/11/2024] [Accepted: 10/14/2024] [Indexed: 10/21/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Cattle bile Arisaema (CBA) and Pig bile Arisaema (PBA) are both processed products fermented from Arisaema erubescens (Wall.) Schott and animal bile, which are recorded in China Pharmacopoeia. Traditionally, bile Arisaema was often used for clearing heat and eliminating phlegm, calming wind and calming panic. Modern pharmacological researches suggest that both two drugs exert an antipyretic effect, while there is lack of the systematical and comparative evidence on underlying mechanism. AIM OF THE STUDY To comprehensively clarify the differences and underlying mechanisms of antipyretic effect of the two drugs. METHODS In this study, an accurate and reliable detection method based on ultra-performance liquid chromatography coupled with triple quadrupole mass spectrometry (UPLC-TQ MS) for comparing the content difference of bile acids from the two drugs was successfully established and applied. Besides, a dry yeast-induced fever rat model was established, and rectal temperature and content of pyrogenic cytokines were conducted to evaluate the antipyretic effect of CBA and PBA. Serum and hypothalamus untargeted metabolomics analysis based on ultra-performance liquid chromatography coupled with quadrupole-time of flight-mass spectrometry (UPLC-Q-TOF-MS/MS) technology were performed for elucidating the changes of metabolic profile. RESULTS The results indicated that CBA and PBA both exerted a significantly antipyretic effect, but CBA showed the characteristic of quicker onset and longer duration than that of PBA. The ELISA and western blotting analysis exhibited that the underlying antipyretic mechanism of the two drugs was closely associated with inhibiting inflammation through regulating TLR4/NF-κB signaling pathway. Moreover, the metabolism pathway analysis revealed that lipid metabolism and amino acid metabolism were greatly disturbed, which showed a certain correlation with antipyretic effect of two drugs. CONCLUSION Collectively, our results delineate a potential mechanism of two different bile Arisaemas against febrile via regulating metabolic disorders and targeting inhibition of inflammation for the improvement of fever symptom of the body. Notably, our current study suggested that CBA might be a better choice for suppressing fever clinically.
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Affiliation(s)
- Fa-Zhi Su
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, 24 Heping Road, Xiangfang District, Harbin, 150040, China.
| | - En-Lin Zhu
- Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Chen-Xi Bai
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, 24 Heping Road, Xiangfang District, Harbin, 150040, China
| | - Wen-Sen Zhang
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, 24 Heping Road, Xiangfang District, Harbin, 150040, China
| | - Meng Liu
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, 24 Heping Road, Xiangfang District, Harbin, 150040, China
| | - Biao Li
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, 24 Heping Road, Xiangfang District, Harbin, 150040, China
| | - Chen-Chen Jia
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, 24 Heping Road, Xiangfang District, Harbin, 150040, China
| | - Peng Zhang
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, 24 Heping Road, Xiangfang District, Harbin, 150040, China
| | - Bao-Wu Zhang
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, 24 Heping Road, Xiangfang District, Harbin, 150040, China
| | - Run Zou
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, 24 Heping Road, Xiangfang District, Harbin, 150040, China
| | - Qing-Xia Li
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, 24 Heping Road, Xiangfang District, Harbin, 150040, China
| | - Bing-You Yang
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, 24 Heping Road, Xiangfang District, Harbin, 150040, China
| | - Hai-Xue Kuang
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, 24 Heping Road, Xiangfang District, Harbin, 150040, China.
| | - Qiu-Hong Wang
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, 24 Heping Road, Xiangfang District, Harbin, 150040, China; School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, 510006, China.
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Zhao X, Liang X, Zhu Z, Yuan Z, Yu S, Liu Y, Wang J, Mason-Jones K, Kuzyakov Y, Chen J, Ge T, Wang S. Phages Affect Soil Dissolved Organic Matter Mineralization by Shaping Bacterial Communities. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2025. [PMID: 39836728 DOI: 10.1021/acs.est.4c08274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2025]
Abstract
Viruses are considered to regulate bacterial communities and terrestrial nutrient cycling, yet their effects on bacterial metabolism and the mechanisms of carbon (C) dynamics during dissolved organic matter (DOM) mineralization remain unknown. Here, we added active and inactive bacteriophages (phages) to soil DOM with original bacterial communities and incubated them at 18 or 23 °C for 35 days. Phages initially (1-4 days) reduced CO2 efflux rate by 13-21% at 18 °C and 3-30% at 23 °C but significantly (p < 0.05) increased by 4-29% at 18 °C and 9-41% at 23 °C after 6 days, raising cumulative CO2 emissions by 14% at 18 °C and 21% at 23 °C. Phages decreased dominant bacterial taxa and increased bacterial community diversity (consistent with a "cull-the-winner" dynamic), thus altering the predicted microbiome functions. Specifically, phages enriched some taxa (such as Pseudomonas, Anaerocolumna, and Caulobacter) involved in degrading complex compounds and consequently promoted functions related to C cycling. Higher temperature facilitated phage-bacteria interactions, increased bacterial diversity, and enzyme activities, boosting DOM mineralization by 16%. Collectively, phages impact soil DOM mineralization by shifting microbial communities and functions, with moderate temperature changes modulating the magnitude of these processes but not qualitatively altering their behavior.
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Affiliation(s)
- Xiaolei Zhao
- College of Land and Environment, Shenyang Agricultural University, Shenyang 110866, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA, Key Laboratory of Green Plant Protection of Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Xiaolong Liang
- CAS Key Laboratory of Forest Ecology and Silviculture, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Zhenke Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA, Key Laboratory of Green Plant Protection of Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Zhaofeng Yuan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA, Key Laboratory of Green Plant Protection of Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Senxiang Yu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA, Key Laboratory of Green Plant Protection of Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Yalong Liu
- College of Land and Environment, Shenyang Agricultural University, Shenyang 110866, China
| | - Jingkuan Wang
- College of Land and Environment, Shenyang Agricultural University, Shenyang 110866, China
| | - Kyle Mason-Jones
- Department of Geoscience, University of Tübingen, 72074 Tübingen, Germany
| | - Yakov Kuzyakov
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA, Key Laboratory of Green Plant Protection of Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Department of Soil Science of Temperate Ecosystems, Department of Agricultural Soil Science, University of Goettingen, 37077 Goettingen, Germany
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA, Key Laboratory of Green Plant Protection of Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Tida Ge
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA, Key Laboratory of Green Plant Protection of Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Shuang Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA, Key Laboratory of Green Plant Protection of Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
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Yang QE, Lin Z, Gan D, Li M, Liu X, Zhou S, Walsh TR. Microplastics mediates the spread of antimicrobial resistance plasmids via modulating conjugal gene expression. ENVIRONMENT INTERNATIONAL 2025; 195:109261. [PMID: 39813956 DOI: 10.1016/j.envint.2025.109261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2024] [Revised: 01/06/2025] [Accepted: 01/07/2025] [Indexed: 01/18/2025]
Abstract
Antimicrobial resistance (AMR) and environmental degradation are existential global public health threats. Linking microplastics (MPs) and AMR is particularly concerning as MPs pollution would have significant ramifications on controlling of AMR; however, the effects of MPs on the spread and genetic mechanisms of AMR bacteria remain unclear. Herein, we performed Simonsen end-point conjugation to investigate the impact of four commonly used MPs on transfer of clinically relevant plasmids. The transfer breadth of a representative pA/C_MCR-8 plasmid across bacterial communities was confirmed by the cell sorting and 16S rRNA gene amplicon sequencing. Our study shows that exposure to four commonly found MPs promotes the conjugation rates of four clinically relevant AMR plasmids by up to 200-fold, when compared to the non-exposed group and that the transfer rates are MP concentrations demonstrate a positive correlation with higher transfer rates. Furthermore, we show that MPs induce the expression of plasmid-borne conjugal genes and SOS-linked genes such as recA, lexA, dinB and dinD. High-throughput sequencing of the broad transmission of plasmid pA/C_MCR-8, shows distribution over two main phyla, Pseudomonadota (50.0 %-95.0 %) and Bacillota (0.4 %-2.0 %). These findings definitively link two global health emergencies - AMR and environmental degradation via MPs, and to tackle global AMR, we must also now consider plastic utilisation and waste management.
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Affiliation(s)
- Qiu E Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhenyan Lin
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dehao Gan
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Fujian Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Minchun Li
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xuedan Liu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Timothy R Walsh
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford OX1 3RE, United Kingdom.
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Weng R, Xu Y, Gao X, Cao L, Su J, Yang H, Li H, Ding C, Pu J, Zhang M, Hao J, Xu W, Ni W, Qian K, Gu Y. Non-Invasive Diagnosis of Moyamoya Disease Using Serum Metabolic Fingerprints and Machine Learning. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2405580. [PMID: 39737836 DOI: 10.1002/advs.202405580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 11/03/2024] [Indexed: 01/01/2025]
Abstract
Moyamoya disease (MMD) is a progressive cerebrovascular disorder that increases the risk of intracranial ischemia and hemorrhage. Timely diagnosis and intervention can significantly reduce the risk of new-onset stroke in patients with MMD. However, the current diagnostic methods are invasive and expensive, and non-invasive diagnosis using biomarkers of MMD is rarely reported. To address this issue, nanoparticle-enhanced laser desorption/ionization mass spectrometry (LDI MS) was employed to record serum metabolic fingerprints (SMFs) with the aim of establishing a non-invasive diagnosis method for MMD. Subsequently, a diagnostic model was developed based on deep learning algorithms, which exhibited high accuracy in differentiating the MMD group from the HC group (AUC = 0.958, 95% CI of 0.911 to 1.000). Additionally, hierarchical clustering analysis revealed a significant association between SMFs across different groups and vascular cognitive impairment in MMD. This approach holds promise as a novel and intuitive diagnostic method for MMD. Furthermore, the study may have broader implications for the diagnosis of other neurological disorders.
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Affiliation(s)
- Ruiyuan Weng
- Department of Neurosurgery, Huashan Hospital of Fudan University, Shanghai, 200040, P. R. China
- Neurosurgical Institute of Fudan University, Shanghai, 201107, P. R. China
| | - Yudian Xu
- Department of Traditional Chinese Medicine, RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
- School of Biomedical Engineering, Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Xinjie Gao
- Department of Neurosurgery, Huashan Hospital of Fudan University, Shanghai, 200040, P. R. China
- Neurosurgical Institute of Fudan University, Shanghai, 201107, P. R. China
| | - Linlin Cao
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, P. R. China
| | - Jiabin Su
- Department of Neurosurgery, Huashan Hospital of Fudan University, Shanghai, 200040, P. R. China
- Neurosurgical Institute of Fudan University, Shanghai, 201107, P. R. China
| | - Heng Yang
- Department of Neurosurgery, Huashan Hospital of Fudan University, Shanghai, 200040, P. R. China
- Neurosurgical Institute of Fudan University, Shanghai, 201107, P. R. China
| | - He Li
- Department of Traditional Chinese Medicine, RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Chenhuan Ding
- Department of Traditional Chinese Medicine, RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Jun Pu
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, P. R. China
| | - Meng Zhang
- Department of Neurosurgery, Liaocheng People's Hospital, Shandong, 252000, China
- Department of Neurosurgery, The First Affiliated Hospital of Fujian Medical University, Fujian, 350000, China
| | - Jiheng Hao
- Department of Neurosurgery, Liaocheng People's Hospital, Shandong, 252000, China
| | - Wei Xu
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, P. R. China
| | - Wei Ni
- Department of Neurosurgery, Huashan Hospital of Fudan University, Shanghai, 200040, P. R. China
- Neurosurgical Institute of Fudan University, Shanghai, 201107, P. R. China
| | - Kun Qian
- School of Biomedical Engineering, Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Yuxiang Gu
- Department of Neurosurgery, Huashan Hospital of Fudan University, Shanghai, 200040, P. R. China
- Neurosurgical Institute of Fudan University, Shanghai, 201107, P. R. China
- Department of Neurosurgery, The First Affiliated Hospital of Fujian Medical University, Fujian, 350000, China
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Wang M, Lin M, Liu Q, Zhang Y, Luo R, Pang X. Altitudinal decline of vegetation restoration effects on soil microbial communities on high-altitude roadside slops: Environmental drivers and management implications. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 957:177424. [PMID: 39522786 DOI: 10.1016/j.scitotenv.2024.177424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2024] [Revised: 11/03/2024] [Accepted: 11/04/2024] [Indexed: 11/16/2024]
Abstract
Construction activities in high-altitude regions have left many bare roadside slopes vulnerable to degradation, complicating restoration efforts. Soil microorganisms are vital for plant growth and nutrient cycling, yet their responses to restoration efforts at various altitudes remains uncertain. This study investigates soil microbial composition, network properties, ecological functions, keystone taxa, and environmental drivers across three restored vegetation types: herbaceous plants (H), shrubs + herbaceous plants (SH), and trees + shrubs + herbaceous plants (TSH) at elevations from 3100 to 3800 m. Our structural equation model identifies elevation and vegetation type as key factors influencing microbial communities, directly or indirectly, through their effects on plant and soil properties. We also found that bacterial α-diversity decreased with elevation, while fungal α-diversity increased, resulting in more complex but less stable microbial networks. R-strategists predominated in the herbaceous type (H) and at lower altitudes, whereas K-strategists dominated in the SH and TSH types, and at higher altitudes. Keystone species of type H, associated with pathotrophs and plant pathogens, showed a negative correlation with plant properties, which weakened at higher altitudes. Both bacterial and fungal communities were driven more by abiotic factors, especially ammonium (NH4+-N) and dissolved organic nitrogen (DON) for bacteria and soil water content (SWC) for fungi. This study proposes managing restoration-sensitive microbes and keystone taxa associated with specific vegetation types for effective restoration at appropriate altitudes, especially those shared by SH and TSH. Furthermore, integrating suitable legume or nitrogen-fixing woody vegetation into restoration efforts at lower altitudes and herbaceous vegetation into higher altitudes has the potential to significantly enhance plant growth and health at high altitudes. This study offers valuable guidance for optimizing restoration strategies by effectively addressing key environmental factors and nurturing essential microbial species crucial for successful restoration efforts and global warming mitigation.
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Affiliation(s)
- Min Wang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Maoxian Mountain Ecosystem Research Station, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu 610041, China; University of Chinese Academy of Sciences, China; Restoration Ecology, Technical University of Munich, Germany
| | - Mao Lin
- College of Geography and Resources, Sichuan Normal University, Chengdu 610101, China
| | - Qinghua Liu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Maoxian Mountain Ecosystem Research Station, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu 610041, China
| | - Yan Zhang
- J.F. Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Göttingen, Germany
| | - Ruyi Luo
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Maoxian Mountain Ecosystem Research Station, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu 610041, China
| | - Xueyong Pang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Maoxian Mountain Ecosystem Research Station, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu 610041, China.
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7
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Xiong X, Yu C, Qiu M, Zhang Z, Hu C, Zhu S, Yang L, Peng H, Song X, Chen J, Xia B, Wang J, Qing Y, Yang C. Genomic and Gut Microbiome Evaluations of Growth and Feed Efficiency Traits in Broilers. Animals (Basel) 2024; 14:3615. [PMID: 39765519 PMCID: PMC11672845 DOI: 10.3390/ani14243615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2024] [Revised: 12/10/2024] [Accepted: 12/13/2024] [Indexed: 01/11/2025] Open
Abstract
In this study, we combined genomic and gut microbiome data to evaluate 13 economically important growth and feed efficiency traits in 407 Dahen broilers, including body weight (BW) at four, six, nine, and ten weeks of age (BW4, BW6, BW9, and BW10), as well as the average daily gain (ADG6, ADG9, and ADG10), feed conversion ratio (FCR6, FCR9, and FCR10), and residual feed intake (RFI6, RFI9, and RFI10) for the three growing ages. The highest ADG and lowest FCR were observed at nine and six weeks of age, respectively. We obtained 47,872 high-quality genomic single-nucleotide polymorphisms (SNPs) by sequencing the genomes and 702 amplicon sequence variants (ASVs) of the gut microbiome by sequencing the 16S rRNA gene, both of which were used for analyses of linear mixed models. The heritability estimates (± standard error, SE) ranged from 0.103 ± 0.072 to 0.156 ± 0.079 for BW, 0.154 ± 0.074 to 0.276 ± 0.079 for the ADG, 0.311 ± 0.076 to 0.454 ± 0.076 for the FCR, and 0.413 ± 0.077 to 0.609 ± 0.076 for the RFI traits. We consistently observed moderate and low negative genetic correlations between the BW traits and the FCR and RFI traits (r = -0.562 to -0.038), whereas strong positive correlations were observed between the FCR and RFI traits (r = 0.564 to 0.979). For the FCR and RFI traits, strong positive correlations were found between the measures at the three ages. In contrast to the genomic contribution, we did not detect a gut microbial contribution to all of these traits, as the estimated microbiabilities did not confidently deviate from zero. We systematically evaluated the contributions of host genetics and gut microbes to several growth and feed efficiency traits in Dahen broilers, and the results show that only the host genetics had significant effects on the phenotypic variations in a flock. The parameters obtained in this study, based on the combined use of genomic and gut microbiota data, may facilitate the implementation of efficient breeding schemes in Dahen broilers.
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Affiliation(s)
- Xia Xiong
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China; (X.X.); (C.Y.); (M.Q.); (Z.Z.); (C.H.); (S.Z.); (L.Y.); (H.P.); (X.S.); (J.C.); (B.X.); (J.W.)
| | - Chunlin Yu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China; (X.X.); (C.Y.); (M.Q.); (Z.Z.); (C.H.); (S.Z.); (L.Y.); (H.P.); (X.S.); (J.C.); (B.X.); (J.W.)
| | - Mohan Qiu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China; (X.X.); (C.Y.); (M.Q.); (Z.Z.); (C.H.); (S.Z.); (L.Y.); (H.P.); (X.S.); (J.C.); (B.X.); (J.W.)
| | - Zengrong Zhang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China; (X.X.); (C.Y.); (M.Q.); (Z.Z.); (C.H.); (S.Z.); (L.Y.); (H.P.); (X.S.); (J.C.); (B.X.); (J.W.)
| | - Chenming Hu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China; (X.X.); (C.Y.); (M.Q.); (Z.Z.); (C.H.); (S.Z.); (L.Y.); (H.P.); (X.S.); (J.C.); (B.X.); (J.W.)
| | - Shiliang Zhu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China; (X.X.); (C.Y.); (M.Q.); (Z.Z.); (C.H.); (S.Z.); (L.Y.); (H.P.); (X.S.); (J.C.); (B.X.); (J.W.)
| | - Li Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China; (X.X.); (C.Y.); (M.Q.); (Z.Z.); (C.H.); (S.Z.); (L.Y.); (H.P.); (X.S.); (J.C.); (B.X.); (J.W.)
| | - Han Peng
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China; (X.X.); (C.Y.); (M.Q.); (Z.Z.); (C.H.); (S.Z.); (L.Y.); (H.P.); (X.S.); (J.C.); (B.X.); (J.W.)
| | - Xiaoyan Song
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China; (X.X.); (C.Y.); (M.Q.); (Z.Z.); (C.H.); (S.Z.); (L.Y.); (H.P.); (X.S.); (J.C.); (B.X.); (J.W.)
| | - Jialei Chen
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China; (X.X.); (C.Y.); (M.Q.); (Z.Z.); (C.H.); (S.Z.); (L.Y.); (H.P.); (X.S.); (J.C.); (B.X.); (J.W.)
| | - Bo Xia
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China; (X.X.); (C.Y.); (M.Q.); (Z.Z.); (C.H.); (S.Z.); (L.Y.); (H.P.); (X.S.); (J.C.); (B.X.); (J.W.)
| | - Jiangxian Wang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China; (X.X.); (C.Y.); (M.Q.); (Z.Z.); (C.H.); (S.Z.); (L.Y.); (H.P.); (X.S.); (J.C.); (B.X.); (J.W.)
| | - Yi Qing
- Chengdu Livestock and Poultry Genetic Resources Protection Center, Chengdu 610081, China
| | - Chaowu Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China; (X.X.); (C.Y.); (M.Q.); (Z.Z.); (C.H.); (S.Z.); (L.Y.); (H.P.); (X.S.); (J.C.); (B.X.); (J.W.)
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8
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Ma Y, Zhu X, Ni L, Du C, Sang W, Xu C, Shi J, Li Y, Li S, Pang Y, Zhang L. Effects of artemisinin sustained-release algaecides on in-situ cyanobacterial inhibition and microbes-floating plants dominated ecosystem functions in artificial landscape lake. JOURNAL OF HAZARDOUS MATERIALS 2024; 480:136182. [PMID: 39427356 DOI: 10.1016/j.jhazmat.2024.136182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 10/09/2024] [Accepted: 10/14/2024] [Indexed: 10/22/2024]
Abstract
The artemisinin sustained-release algaecides (ASAs) have been proven to be a safe and effective mean of inhibiting cyanobacteria in laboratory experiments. However, their effectiveness and impacts on ecosystem functions (EF) in natural waters are still unclear. In this study, the in-situ inhibitory effect of ASAs on cyanobacteria in natural waters was investigated over a period of 110 days to assess EF impacts dominated by microbes and floating plants. The results indicated that ASAs had a long-term inhibitory effect on cyanobacteria. ASAs did not affect sediment but increased TOC and TP in the water column in 2-10 days. Microbial diversity and network analyses indicated that ASAs enhanced bacterial diversity, network complexity, and hub-bacteria in networks. Metabolic pathway predictions and CCA analysis showed that ASAs maintained the stability of EF by enhancing the metabolic capacities of bacteria, and the relationships between metabolic microorganisms and environmental factors. PLS-PM revealed that ASAs primarily drove bacterial resistance to cyanobacteria, which was the key mechanism for its long-term inhibition of cyanobacteria. However, the early outbreak of floating plants was not conducive to the long-term inhibition of cyanobacteria by ASAs. This study provides new insights into the mechanisms and ecological impacts of cyanobacterial inhibition by ASAs in complex aquatic environments.
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Affiliation(s)
- Yushen Ma
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Xiaoming Zhu
- CCCC Shanghai Waterway Engineering Design and Consulting Co. Ltd., Shanghai 200120, China
| | - Lixiao Ni
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China.
| | - Cunhao Du
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Wenlu Sang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Chu Xu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Jiahui Shi
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Yiping Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Shiyin Li
- College of Environment, Nanjing Normal University, Nanjing 210024, China
| | - Yalun Pang
- College of Engineering, China Pharmaceutical University, Nanjing 211198, China
| | - Linyun Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
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9
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Mogna-Peláez P, Riezu-Boj JI, Milagro FI, Clemente-Larramendi I, Esteban Echeverría S, Herrero JI, Elorz M, Benito-Boillos A, Tobaruela-Resola AL, González-Muniesa P, Tur JA, Martínez JA, Abete I, Zulet MA. Sex-Dependent Gut Microbiota Features and Functional Signatures in Metabolic Disfunction-Associated Steatotic Liver Disease. Nutrients 2024; 16:4198. [PMID: 39683591 DOI: 10.3390/nu16234198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2024] [Revised: 11/30/2024] [Accepted: 12/02/2024] [Indexed: 12/18/2024] Open
Abstract
Background/Objectives: This study investigates the gut microbiota's role in metabolic dysfunction-associated steatotic liver disease (MASLD), focusing on microbial and functional signatures and sex-based differences. Methods: Using baseline data from 98 MASLD patients and 45 controls from the Fatty Liver in Obesity (FLiO) study, the gut microbiota was profiled with 16S gene sequencing, followed by statistical and machine learning analyses to identify disease-associated microbial signatures. Results: Notable alpha and beta diversity differences were observed between MASLD patients and the controls, varying by sex. Machine learning models highlighted specific microbial signatures for each sex, achieving high accuracy (area under the receiver operating characteristic curves of 0.91 for women and 0.72 for men). The key microbial taxa linked to MASLD included Christensenella and Limosilactobacillus in women and Beduinibacterium and Anaerotruncus in men. Functional profiling showed that MASLD patients had increased pathways for amine biosynthesis and amino acid degradation, while the controls exhibited enhanced fermentation pathways. These microbial features were associated with systemic inflammation, insulin resistance, and metabolite production linked to gut dysbiosis. Conclusions: The findings support the potential of gut microbiota signatures to be used as non-invasive indicators of MASLD and highlight sex-specific variations that could inform personalized diagnostic and therapeutic approaches.
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Affiliation(s)
- Paola Mogna-Peláez
- Department of Nutrition, Food Sciences and Physiology and Centre for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, 31008 Pamplona, Spain
| | - José I Riezu-Boj
- Department of Nutrition, Food Sciences and Physiology and Centre for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, 31008 Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
| | - Fermin I Milagro
- Department of Nutrition, Food Sciences and Physiology and Centre for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, 31008 Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
- Biomedical Research Centre Network in Physiopathology of Obesity and Nutrition (CIBERobn), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Iñigo Clemente-Larramendi
- Department of Nutrition, Food Sciences and Physiology and Centre for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, 31008 Pamplona, Spain
| | - Sergio Esteban Echeverría
- Department of Nutrition, Food Sciences and Physiology and Centre for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, 31008 Pamplona, Spain
| | - José I Herrero
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
- Liver Unit, Clínica Universidad de Navarra, 31008 Pamplona, Spain
- Biomedical Research Centre Network in Hepatic and Digestive Diseases (CIBERehd), 28029 Madrid, Spain
| | - Mariana Elorz
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
- Department of Radiology, Clínica Universidad de Navarra, 31008 Pamplona, Spain
| | - Alberto Benito-Boillos
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
- Department of Radiology, Clínica Universidad de Navarra, 31008 Pamplona, Spain
| | - Ana Luz Tobaruela-Resola
- Department of Nutrition, Food Sciences and Physiology and Centre for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, 31008 Pamplona, Spain
| | - Pedro González-Muniesa
- Department of Nutrition, Food Sciences and Physiology and Centre for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, 31008 Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
- Biomedical Research Centre Network in Physiopathology of Obesity and Nutrition (CIBERobn), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Josep A Tur
- Biomedical Research Centre Network in Physiopathology of Obesity and Nutrition (CIBERobn), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Research Group on Community Nutrition and Oxidative Stress, University of Balearic Islands-IUNICS & IDISBA, 07122 Palma, Spain
| | - J Alfredo Martínez
- Biomedical Research Centre Network in Physiopathology of Obesity and Nutrition (CIBERobn), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Precision Nutrition and Cardiovascular Health Program, IMDEA Food, CEI UAM + CSIC, 28049 Madrid, Spain
| | - Itziar Abete
- Department of Nutrition, Food Sciences and Physiology and Centre for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, 31008 Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
- Biomedical Research Centre Network in Physiopathology of Obesity and Nutrition (CIBERobn), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - M Angeles Zulet
- Department of Nutrition, Food Sciences and Physiology and Centre for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, 31008 Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
- Biomedical Research Centre Network in Physiopathology of Obesity and Nutrition (CIBERobn), Instituto de Salud Carlos III, 28029 Madrid, Spain
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10
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Zhang T, Li H, Jiang M, Hou H, Gao Y, Li Y, Wang F, Wang J, Peng K, Liu YX. Nanopore sequencing: flourishing in its teenage years. J Genet Genomics 2024; 51:1361-1374. [PMID: 39293510 DOI: 10.1016/j.jgg.2024.09.007] [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: 07/18/2024] [Revised: 09/09/2024] [Accepted: 09/10/2024] [Indexed: 09/20/2024]
Abstract
Over the past decade, nanopore sequencing has experienced significant advancements and changes, transitioning from an initially emerging technology to a significant instrument in the field of genomic sequencing. However, as advancements in next-generation sequencing technology persist, nanopore sequencing also improves. This paper reviews the developments, applications, and outlook on nanopore sequencing technology. Currently, nanopore sequencing supports both DNA and RNA sequencing, making it widely applicable in areas such as telomere-to-telomere (T2T) genome assembly, direct RNA sequencing (DRS), and metagenomics. The openness and versatility of nanopore sequencing have established it as a preferred option for an increasing number of research teams, signaling a transformative influence on life science research. As the nanopore sequencing technology advances, it provides a faster, more cost-effective approach with extended read lengths, demonstrating the significant potential for complex genome assembly, pathogen detection, environmental monitoring, and human disease research, offering a fresh perspective in sequencing technologies.
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Affiliation(s)
- Tianyuan Zhang
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; Wuhan Benagen Technology Co., Ltd, Wuhan, Hubei 430000, China
| | - Hanzhou Li
- Wuhan Benagen Technology Co., Ltd, Wuhan, Hubei 430000, China
| | - Mian Jiang
- Wuhan Benagen Technology Co., Ltd, Wuhan, Hubei 430000, China
| | - Huiyu Hou
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Yunyun Gao
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Yali Li
- Wuhan Benagen Technology Co., Ltd, Wuhan, Hubei 430000, China
| | - Fuhao Wang
- Wuhan Benagen Technology Co., Ltd, Wuhan, Hubei 430000, China
| | - Jun Wang
- Wuhan Benagen Technology Co., Ltd, Wuhan, Hubei 430000, China
| | - Kai Peng
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225000, China
| | - Yong-Xin Liu
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China.
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11
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Kostka A, Gruszecka‐Kosowska A, Ruiz‐Rodríguez A, Aguilera M. Multi-omics approach in gut and environmental microbiota research under the One Health concept. EFSA J 2024; 22:e221104. [PMID: 39712914 PMCID: PMC11659745 DOI: 10.2903/j.efsa.2024.e221104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2024] Open
Abstract
The One Health concept, although formulated two decades ago, remains challenging to implement. It necessitates the integration of numerous scientific disciplines, diverse techniques and various professional expertise. Furthermore, it often requires the collaboration of different institutions, encompassing both scientific and administrative entities. This concept posits that human health is intrinsically linked to and dependent on the well-being of animals, plants and the broader environment, while the environment not only sustains life but can also serve as a source of xenobiotics that affect the health-disease balance. In this context, all components of the potential exposome, encompassing the entirety of factors of various natures that influence health throughout life, must be considered comprehensively. Achieving this holistic understanding typically demands the application of multiple research techniques, known as the multi-omics approach and the adoption of an integrated method for data analysis. This project endeavoured to utilise such an integrated approach, examining data from diverse origins: human (children stool for gut microbiota analysis) and environmental (groundwater for hyporheic zone microbial analysis), as well as implementing comprehensive informatic tools for data processing. Analysis of stool samples revealed significant differences in gut microbiota composition across various taxonomic levels between normal weight, overweight and obese children. Additionally, a potential link between certain xenobiotics and gut microbiota composition, body weight and overall health status was identified. Analysis of groundwater samples revealed significant differences in hyporheic zone microbial composition at various taxonomic levels based on the sampling location and depth. Key geochemical factors influencing sample diversity were also identified. The promising results obtained not only demonstrate the viability of this methodology but also pave the way for future research initiatives.
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Affiliation(s)
- Anna Kostka
- Department of Environmental Protection, Faculty of Geology, Geophysics and Environmental ProtectionAGH University of KrakowKrakowPoland
- Institute of Nutrition and Food Technology ‘José Mataix Verdú’University of Granada (INYTA‐UGR)GranadaSpain
| | - Agnieszka Gruszecka‐Kosowska
- Department of Environmental Protection, Faculty of Geology, Geophysics and Environmental ProtectionAGH University of KrakowKrakowPoland
| | - Alicia Ruiz‐Rodríguez
- Institute of Nutrition and Food Technology ‘José Mataix Verdú’University of Granada (INYTA‐UGR)GranadaSpain
- Microbiology Department, Faculty of PharmacyUniversity of GranadaGranadaSpain
| | - Margarita Aguilera
- Institute of Nutrition and Food Technology ‘José Mataix Verdú’University of Granada (INYTA‐UGR)GranadaSpain
- Microbiology Department, Faculty of PharmacyUniversity of GranadaGranadaSpain
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12
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Tang G, Song Q, Dou J, Chen Z, Hu X, Li Z, Li X, Wang T, Dong S, Zhang H. Neutrophil-centric analysis of gastric cancer: prognostic modeling and molecular insights. Cell Mol Life Sci 2024; 81:452. [PMID: 39540948 PMCID: PMC11564594 DOI: 10.1007/s00018-024-05484-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2024] [Revised: 10/05/2024] [Accepted: 10/18/2024] [Indexed: 11/16/2024]
Abstract
Gastric cancer remains a significant global health concern with poor prognosis. This study investigates the role of neutrophils in gastric cancer progression and their potential as prognostic indicators. Using multi-omics approaches, including Weighted Gene Co-expression Network Analysis (WGCNA), machine learning, and single-cell analysis, we identified neutrophil-associated gene signatures and developed a robust prognostic model. Our findings reveal distinct gastric cancer subtypes based on neutrophil-associated genes, with one subtype showing increased neutrophil infiltration and poorer prognosis. Single-cell analysis uncovered neutrophil-associated alterations in cell composition, gene expression profiles, and intercellular communication within the tumor microenvironment. Additionally, we explored the relationship between neutrophil-associated genes, microbiota composition, and alternative splicing events in gastric cancer. Furthermore, we identified QKI as a key regulator of alternative splicing and demonstrated its role in promoting malignant phenotypes and enhancing TGF-beta signaling and epithelial-mesenchymal transition in gastric cancer cells by wet experiment. Lastly, the role of QKI in the association with drug resistance and the identification of specific agents for treating QKI-associated drug resistance were also explored. This comprehensive study provides novel insights into the complex interplay between neutrophils, the tumor microenvironment, microbiota, alternative splicing and gastric cancer progression, offering potential new targets for therapeutic intervention.
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Affiliation(s)
- Guangbo Tang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, Shaanxi Province, People's Republic of China
| | - Qiong Song
- Department of Nephrology, Shaanxi Second People's Hospital, Xi'an, 710004, Shaanxi Province, People's Republic of China
| | - Jianhua Dou
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases, Xi'an, 710032, Shaanxi Province, People's Republic of China
| | - Zhangqian Chen
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, 710049, Shaanxi Province, People's Republic of China
| | - Xi Hu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, Shaanxi Province, People's Republic of China
| | - Zihang Li
- Department of Hematology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi Province, People's Republic of China
- Genome Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, Shaanxi Province, People's Republic of China
| | - Xiujuan Li
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710032, Shaanxi Province, People's Republic of China
| | - Tingjie Wang
- Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, 450003, Henan Province, People's Republic of China.
| | - Shanshan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, Shaanxi Province, People's Republic of China.
| | - Huqin Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, Shaanxi Province, People's Republic of China.
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13
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Wu X, Yang X, Dai Y, Zhao Z, Zhu J, Guo H, Yang R. Single-cell sequencing to multi-omics: technologies and applications. Biomark Res 2024; 12:110. [PMID: 39334490 PMCID: PMC11438019 DOI: 10.1186/s40364-024-00643-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 08/17/2024] [Indexed: 09/30/2024] Open
Abstract
Cells, as the fundamental units of life, contain multidimensional spatiotemporal information. Single-cell RNA sequencing (scRNA-seq) is revolutionizing biomedical science by analyzing cellular state and intercellular heterogeneity. Undoubtedly, single-cell transcriptomics has emerged as one of the most vibrant research fields today. With the optimization and innovation of single-cell sequencing technologies, the intricate multidimensional details concealed within cells are gradually unveiled. The combination of scRNA-seq and other multi-omics is at the forefront of the single-cell field. This involves simultaneously measuring various omics data within individual cells, expanding our understanding across a broader spectrum of dimensions. Single-cell multi-omics precisely captures the multidimensional aspects of single-cell transcriptomes, immune repertoire, spatial information, temporal information, epitopes, and other omics in diverse spatiotemporal contexts. In addition to depicting the cell atlas of normal or diseased tissues, it also provides a cornerstone for studying cell differentiation and development patterns, disease heterogeneity, drug resistance mechanisms, and treatment strategies. Herein, we review traditional single-cell sequencing technologies and outline the latest advancements in single-cell multi-omics. We summarize the current status and challenges of applying single-cell multi-omics technologies to biological research and clinical applications. Finally, we discuss the limitations and challenges of single-cell multi-omics and potential strategies to address them.
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Affiliation(s)
- Xiangyu Wu
- Department of Urology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, 321 Zhongshan Road, Nanjing, 210008, Jiangsu, China
| | - Xin Yang
- Department of Urology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, 321 Zhongshan Road, Nanjing, 210008, Jiangsu, China
| | - Yunhan Dai
- Medical School, Nanjing University, Nanjing, China
| | - Zihan Zhao
- Department of Urology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, 321 Zhongshan Road, Nanjing, 210008, Jiangsu, China
| | - Junmeng Zhu
- Department of Oncology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Hongqian Guo
- Department of Urology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, 321 Zhongshan Road, Nanjing, 210008, Jiangsu, China.
| | - Rong Yang
- Department of Urology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, 321 Zhongshan Road, Nanjing, 210008, Jiangsu, China.
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14
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Fitzjerrells RL, Ollberding NJ, Mangalam AK. Looking at the full picture, using topic modeling to observe microbiome communities associated with disease. GUT MICROBES REPORTS 2024; 1:1-11. [PMID: 39183943 PMCID: PMC11340690 DOI: 10.1080/29933935.2024.2378067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/24/2024] [Accepted: 07/01/2024] [Indexed: 08/27/2024]
Abstract
The microbiome, a complex micro-ecosystem, helps the host with various vital physiological processes. Alterations of the microbiome (dysbiosis) have been linked with several diseases, and generally, differential abundance testing between the healthy and patient groups is performed to identify important bacteria. However, providing a singular species of bacteria to an individual as treatment has not been as successful as fecal microbiota transplant therapy, where the entire microbiome of a healthy individual is transferred. These observations suggest that a combination of bacteria might be crucial for the beneficial effects. Here we provide the framework to utilize topic modeling, an unsupervised machine learning approach, to identify a community of bacteria related to health or disease. Specifically, we used our previously published gut microbiome data of patients with multiple sclerosis (MS), a neurodegenerative disease linked to a dysbiotic gut microbiome. We identified communities of bacteria associated with MS, including genera previously discovered, but also others that would have been overlooked by differential abundance testing. This method can be a useful tool for analyzing the microbiome, and it should be considered along with the commonly utilized differential abundance tests to better understand the role of the gut microbiome in health and disease.
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Affiliation(s)
- Rachel L. Fitzjerrells
- Interdisciplinary Graduate Program in Informatics, University of Iowa, Iowa City, IA, 52242, USA
- College of Dentistry, University of Iowa, Iowa City, IA, 52242, USA
| | - Nicholas J. Ollberding
- Division of Biostatistics and Epidemiology; Cincinnati Children’s Hospital Medical Center; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45267, USA
| | - Ashutosh K. Mangalam
- Interdisciplinary Graduate Program in Informatics, University of Iowa, Iowa City, IA, 52242, USA
- College of Dentistry, University of Iowa, Iowa City, IA, 52242, USA
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
- Iowa City VA Health Care System, 601 US-6 W, Iowa City, IA 52246, USA
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15
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Piłsyk S, Perlińska-Lenart U, Janik A, Skalmowska P, Znój A, Gawor J, Grzesiak J, Kruszewska JS. Native and Alien Antarctic Grasses as a Habitat for Fungi. Int J Mol Sci 2024; 25:8475. [PMID: 39126044 PMCID: PMC11313430 DOI: 10.3390/ijms25158475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 07/31/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024] Open
Abstract
Biological invasions are now seen as one of the main threats to the Antarctic ecosystem. An example of such an invasion is the recent colonization of the H. Arctowski Polish Antarctic Station area by the non-native grass Poa annua. This site was previously occupied only by native plants like the Antarctic hair grass Deschampsia antarctica. To adapt successfully to new conditions, plants interact with soil microorganisms, including fungi. The aim of this study was to determine how the newly introduced grass P. annua established an interaction with fungi compared to resident grass D. antarctica. We found that fungal diversity in D. antarctica roots was significantly higher compared with P. annua roots. D. antarctica managed a biodiverse microbiome because of its ability to recruit fungal biocontrol agents from the soil, thus maintaining a beneficial nature of the endophyte community. P. annua relied on a set of specific fungal taxa, which likely modulated its cold response, increasing its competitiveness in Antarctic conditions. Cultivated endophytic fungi displayed strong chitinolysis, pointing towards their role as phytopathogenic fungi, nematode, and insect antagonists. This is the first study to compare the root mycobiomes of both grass species by direct culture-independent techniques as well as culture-based methods.
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Affiliation(s)
- Sebastian Piłsyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw, Poland; (S.P.); (U.P.-L.); (A.J.); (P.S.); (A.Z.); (J.G.)
| | - Urszula Perlińska-Lenart
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw, Poland; (S.P.); (U.P.-L.); (A.J.); (P.S.); (A.Z.); (J.G.)
| | - Anna Janik
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw, Poland; (S.P.); (U.P.-L.); (A.J.); (P.S.); (A.Z.); (J.G.)
| | - Patrycja Skalmowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw, Poland; (S.P.); (U.P.-L.); (A.J.); (P.S.); (A.Z.); (J.G.)
| | - Anna Znój
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw, Poland; (S.P.); (U.P.-L.); (A.J.); (P.S.); (A.Z.); (J.G.)
- Botanical Garden—Center for Biological Diversity Conservation, Polish Academy of Sciences, Prawdziwka 2, 02-973 Warsaw, Poland
| | - Jan Gawor
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw, Poland; (S.P.); (U.P.-L.); (A.J.); (P.S.); (A.Z.); (J.G.)
| | - Jakub Grzesiak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw, Poland; (S.P.); (U.P.-L.); (A.J.); (P.S.); (A.Z.); (J.G.)
| | - Joanna S. Kruszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw, Poland; (S.P.); (U.P.-L.); (A.J.); (P.S.); (A.Z.); (J.G.)
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16
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Park CE, Jo YJ, Jung DR, Park HC, Shin JH. Comparative Analysis of Gut Microbiota between Captive and Wild Long-Tailed Gorals for Ex Situ Conservation. Microorganisms 2024; 12:1419. [PMID: 39065187 PMCID: PMC11278867 DOI: 10.3390/microorganisms12071419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 07/10/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
The long-tailed goral is close to extinction, and ex situ conservation is essential to prevent this phenomenon. Studies on the gut microbiome of the long-tailed goral are important for understanding the ecology of this species. We amplified DNA from the 16S rRNA regions and compared the microbiomes of wild long-tailed gorals and two types of captive long-tailed gorals. Our findings revealed that the gut microbiome diversity of wild long-tailed gorals is greatly reduced when they are reared in captivity. A comparison of the two types of captive long-tailed gorals confirmed that animals with a more diverse diet exhibit greater gut microbiome diversity. Redundancy analysis confirmed that wild long-tailed gorals are distributed throughout the highlands, midlands, and lowlands. For the first time, it was revealed that the long-tailed goral are divided into three groups depending on the height of their habitat, and that the gut bacterial community changes significantly when long-tailed gorals are raised through ex situ conservation. This provides for the first time a perspective on the diversity of food plants associated with mountain height that will be available to long-tailed goral in the future.
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Affiliation(s)
- Chang-Eon Park
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea; (C.-E.P.); (Y.-J.J.); (D.-R.J.)
- Institute of Ornithology, Ex Situ Conservation Institution Designated by the Ministry of Environment, Gumi 39105, Republic of Korea;
| | - Young-Jae Jo
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea; (C.-E.P.); (Y.-J.J.); (D.-R.J.)
| | - Da-Ryung Jung
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea; (C.-E.P.); (Y.-J.J.); (D.-R.J.)
| | - Hee-Cheon Park
- Institute of Ornithology, Ex Situ Conservation Institution Designated by the Ministry of Environment, Gumi 39105, Republic of Korea;
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea; (C.-E.P.); (Y.-J.J.); (D.-R.J.)
- NGS Core Facility, Kyungpook National University, Daegu 41566, Republic of Korea
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17
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Li C, Liu C, Li H, Liao H, Xu L, Yao M, Li X. The microgeo: an R package rapidly displays the biogeography of soil microbial community traits on maps. FEMS Microbiol Ecol 2024; 100:fiae087. [PMID: 38866720 PMCID: PMC11212663 DOI: 10.1093/femsec/fiae087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 04/26/2024] [Accepted: 06/11/2024] [Indexed: 06/14/2024] Open
Abstract
Many R packages provide statistical approaches for elucidating the diversity of soil microbes, yet they still struggle to visualize microbial traits on a geographical map. This creates challenges in interpreting microbial biogeography on a regional scale, especially when the spatial scale is large or the distribution of sampling sites is uneven. Here, we developed a lightweight, flexible, and user-friendly R package called microgeo. This package integrates many functions involved in reading, manipulating, and visualizing geographical boundary data; downloading spatial datasets; and calculating microbial traits and rendering them onto a geographical map using grid-based visualization, spatial interpolation, or machine learning. Using this R package, users can visualize any trait calculated by microgeo or other tools on a map and can analyze microbiome data in conjunction with metadata derived from a geographical map. In contrast to other R packages that statistically analyze microbiome data, microgeo provides more-intuitive approaches in illustrating the biogeography of soil microbes on a large geographical scale, serving as an important supplement to statistically driven comparisons and facilitating the biogeographic analysis of publicly accessible microbiome data at a large spatial scale in a more convenient and efficient manner. The microgeo R package can be installed from the Gitee (https://gitee.com/bioape/microgeo) and GitHub (https://github.com/ChaonanLi/microgeo) repositories. Detailed tutorials for the microgeo R package are available at https://chaonanli.github.io/microgeo.
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Affiliation(s)
- Chaonan Li
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang 621000, China
| | - Chi Liu
- Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hankang Li
- Department of Electrical Engineering and Computer Science, University of California, Irvine, CA 92697, United States
| | - Haijun Liao
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang 621000, China
- Engineering Research Center of Chuanxibei RHS Construction at Mianyang Normal University of Sichuan Province, Mianyang Normal University, Mianyang 621000, China
| | - Lin Xu
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River & Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Minjie Yao
- Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiangzhen Li
- Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Huang W, Ma T, Liu X, Xu Y, Gu J, Gu Y, Yuan J, Wen T, Xue C, Shen Q. Degradation of Complex Carbon Sources in Organic Fertilizers Facilitates Nitrogen Fixation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:12988-13000. [PMID: 38820247 DOI: 10.1021/acs.jafc.4c01727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2024]
Abstract
Biological nitrogen fixation is crucial for agriculture and improving fertilizer efficiency, but organic fertilizers in enhancing this process remain debated. Here, we investigate the impact of organic fertilizers on biological nitrogen fixation through experiments and propose a new model where bacterial interactions with complex carbon sources enhance nitrogen fixation. Field experiments showed that adding organic fertilizers increased the nitrogenase activity by 57.85%. Subculture experiments revealed that organic fertilizer addition enriched genes corresponding to complex carbon and energy metabolism, as well as nifJ involved in electron transfer for nitrogenase. It also enhanced bacterial interactions and enhanced connectors associated with complex carbon degradation. Validation experiments demonstrated that combinations increased nitrogenase activity by 2.98 times compared to the single. Our findings suggest that organic fertilizers promoted nitrogen fixation by enhancing microbial cooperation, improved the degradation of complex carbon sources, and thereby provided utilizable carbon sources, energy, and electrons to N-fixers, thus increasing nitrogenase activity and nitrogen fixation.
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Affiliation(s)
- Weijie Huang
- The key lab of organic-based fertilizers of China and Jiangsu provincial key lab for solid organic waste utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Tengfei Ma
- State Key Laboratory of Grassland Agro-ecosystems, Centre for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, Gansu, China
| | - Xingyan Liu
- The key lab of organic-based fertilizers of China and Jiangsu provincial key lab for solid organic waste utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Yihan Xu
- The key lab of organic-based fertilizers of China and Jiangsu provincial key lab for solid organic waste utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Jingting Gu
- The key lab of organic-based fertilizers of China and Jiangsu provincial key lab for solid organic waste utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Yifan Gu
- The key lab of organic-based fertilizers of China and Jiangsu provincial key lab for solid organic waste utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Jun Yuan
- The key lab of organic-based fertilizers of China and Jiangsu provincial key lab for solid organic waste utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Tao Wen
- The key lab of organic-based fertilizers of China and Jiangsu provincial key lab for solid organic waste utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Chao Xue
- The key lab of organic-based fertilizers of China and Jiangsu provincial key lab for solid organic waste utilization, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Green Intelligent Fertilizer Innovation, MARD, Sinong Bio-organic Fertilizer Institute, Nanjing 210000, China
| | - Qirong Shen
- The key lab of organic-based fertilizers of China and Jiangsu provincial key lab for solid organic waste utilization, Nanjing Agricultural University, Nanjing 210095, China
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Yang M, Chen T, Liu Y, Huang L. Visualizing set relationships: EVenn's comprehensive approach to Venn diagrams. IMETA 2024; 3:e184. [PMID: 38898979 PMCID: PMC11183158 DOI: 10.1002/imt2.184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 02/24/2024] [Accepted: 03/01/2024] [Indexed: 06/21/2024]
Abstract
Venn diagrams serve as invaluable tools for visualizing set relationships due to their ease of interpretation. Widely applied across diverse disciplines such as metabolomics, genomics, transcriptomics, and proteomics, their utility is undeniable. However, the operational complexity has been compounded by the absence of standardized data formats and the need to switch between various platforms for generating different Venn diagrams. To address these challenges, we introduce the EVenn platform, a versatile tool offering a unified interface for efficient data exploration and visualization of diverse Venn diagrams. EVenn (http://www.ehbio.com/test/venn) streamlines the data upload process with a standardized format, enhancing the capabilities for multimodule analysis. This comprehensive protocol outlines various applications of EVenn, featuring representative results of multiple Venn diagrams, data uploads in the centralized data center, and step-by-step case demonstrations. Through these functionalities, EVenn emerges as a valuable and user-friendly tool for the in-depth exploration of multiomics data.
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Affiliation(s)
- Mei Yang
- Institute of Traditional Chinese MedicineTianjin University of Traditional Chinese MedicineTianjinChina
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao‐di Herbs, National Resource Center for Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina
| | - Tong Chen
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao‐di Herbs, National Resource Center for Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina
| | - Yong‐Xin Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Luqi Huang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao‐di Herbs, National Resource Center for Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina
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20
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Wang T, Li P, Bai X, Tian S, Yang M, Leng D, Kui H, Zhang S, Yan X, Zheng Q, Luo P, He C, Jia Y, Wu Z, Qiu H, Li J, Wan F, Ali MA, Mao R, Liu Y, Li D. Vaginal microbiota are associated with in vitro fertilization during female infertility. IMETA 2024; 3:e185. [PMID: 38898981 PMCID: PMC11183179 DOI: 10.1002/imt2.185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/02/2024] [Accepted: 03/02/2024] [Indexed: 06/21/2024]
Abstract
The vaginal microbiome plays an essential role in the reproductive health of human females. As infertility increases worldwide, understanding the roles that the vaginal microbiome may have in infertility and in vitro fertilization (IVF) treatment outcomes is critical. To determine the vaginal microbiome composition of 1411 individuals (1255 undergoing embryo transplantation) and their associations with reproductive outcomes, clinical and biochemical features are measured, and vaginal samples are 16S rRNA sequenced. Our results suggest that both too high and too low abundance of Lactobacillus is not beneficial for pregnancy; a moderate abundance is more beneficial. A moderate abundance of Lactobacillus crispatus and Lactobacillus iners (~80%) (with a pregnancy rate of I-B: 54.35% and III-B: 57.73%) is found beneficial for pregnancy outcomes compared with a higher abundance (>90%) of Lactobacillus (I-A: 44.81% and III-A: 51.06%, respectively). The community state type (CST) IV-B (contains a high to moderate relative abundance of Gardnerella vaginalis) shows a similar pregnant ratio (48.09%) with I-A and III-A, and the pregnant women in this CST have a higher abundance of Lactobacillus species. Metagenome analysis of 71 samples shows that nonpregnant women are detected with more antibiotic-resistance genes, and Proteobacteria and Firmicutes are the main hosts. The inherent differences within and between women in different infertility groups suggest that vaginal microbes might be used to detect infertility and potentially improve IVF outcomes.
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Affiliation(s)
- Tao Wang
- Antibiotics Research and Re‐evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of PharmacyChengdu UniversityChengduChina
| | - Penghao Li
- Jinxin Research Institute for Reproductive Medicine and Genetics, Sichuan Jinxin Xi'nan Women's and Children's HospitalChengduChina
| | - Xue Bai
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
- College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Shilin Tian
- College of Life SciencesWuhan UniversityWuhanChina
| | - Maosen Yang
- Antibiotics Research and Re‐evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of PharmacyChengdu UniversityChengduChina
| | - Dong Leng
- College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Hua Kui
- College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Sujuan Zhang
- Jinxin Research Institute for Reproductive Medicine and Genetics, Sichuan Jinxin Xi'nan Women's and Children's HospitalChengduChina
| | - Xiaomiao Yan
- Jinxin Research Institute for Reproductive Medicine and Genetics, Sichuan Jinxin Xi'nan Women's and Children's HospitalChengduChina
| | - Qu Zheng
- Jinxin Research Institute for Reproductive Medicine and Genetics, Sichuan Jinxin Xi'nan Women's and Children's HospitalChengduChina
| | - Pulin Luo
- Jinxin Research Institute for Reproductive Medicine and Genetics, Sichuan Jinxin Xi'nan Women's and Children's HospitalChengduChina
| | - Changming He
- Jinxin Research Institute for Reproductive Medicine and Genetics, Sichuan Jinxin Xi'nan Women's and Children's HospitalChengduChina
| | - Yan Jia
- Jinxin Research Institute for Reproductive Medicine and Genetics, Sichuan Jinxin Xi'nan Women's and Children's HospitalChengduChina
| | - Zhoulin Wu
- College of Food and Biological EngineeringChengdu UniversityChengduChina
| | - Huimin Qiu
- College of AgricultureKunming UniversityKunmingChina
| | - Jing Li
- College of AgricultureKunming UniversityKunmingChina
| | - Feng Wan
- State Key Laboratory of Southwestern Chinese Medicine ResourcesChengdu University of Traditional Chinese MedicineChengduChina
| | - Muhammad A. Ali
- School of Biological SciencesUniversity of the PunjabLahorePakistan
| | - Rurong Mao
- Jinxin Research Institute for Reproductive Medicine and Genetics, Sichuan Jinxin Xi'nan Women's and Children's HospitalChengduChina
| | - Yong‐Xin Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Diyan Li
- Antibiotics Research and Re‐evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of PharmacyChengdu UniversityChengduChina
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21
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Dantas CWD, Martins DT, Nogueira WG, Alegria OVC, Ramos RTJ. Tools and methodology to in silico phage discovery in freshwater environments. Front Microbiol 2024; 15:1390726. [PMID: 38881659 PMCID: PMC11176557 DOI: 10.3389/fmicb.2024.1390726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 05/16/2024] [Indexed: 06/18/2024] Open
Abstract
Freshwater availability is essential, and its maintenance has become an enormous challenge. Due to population growth and climate changes, freshwater sources are becoming scarce, imposing the need for strategies for its reuse. Currently, the constant discharge of waste into water bodies from human activities leads to the dissemination of pathogenic bacteria, negatively impacting water quality from the source to the infrastructure required for treatment, such as the accumulation of biofilms. Current water treatment methods cannot keep pace with bacterial evolution, which increasingly exhibits a profile of multidrug resistance to antibiotics. Furthermore, using more powerful disinfectants may affect the balance of aquatic ecosystems. Therefore, there is a need to explore sustainable ways to control the spreading of pathogenic bacteria. Bacteriophages can infect bacteria and archaea, hijacking their host machinery to favor their replication. They are widely abundant globally and provide a biological alternative to bacterial treatment with antibiotics. In contrast to common disinfectants and antibiotics, bacteriophages are highly specific, minimizing adverse effects on aquatic microbial communities and offering a lower cost-benefit ratio in production compared to antibiotics. However, due to the difficulty involving cultivating and identifying environmental bacteriophages, alternative approaches using NGS metagenomics in combination with some bioinformatic tools can help identify new bacteriophages that can be useful as an alternative treatment against resistant bacteria. In this review, we discuss advances in exploring the virome of freshwater, as well as current applications of bacteriophages in freshwater treatment, along with current challenges and future perspectives.
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Affiliation(s)
- Carlos Willian Dias Dantas
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Laboratory of Simulation and Computational Biology - SIMBIC, High Performance Computing Center - CCAD, Federal University of Pará, Belém, Pará, Brazil
- Laboratory of Bioinformatics and Genomics of Microorganisms, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - David Tavares Martins
- Laboratory of Simulation and Computational Biology - SIMBIC, High Performance Computing Center - CCAD, Federal University of Pará, Belém, Pará, Brazil
- Laboratory of Bioinformatics and Genomics of Microorganisms, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Wylerson Guimarães Nogueira
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Oscar Victor Cardenas Alegria
- Laboratory of Simulation and Computational Biology - SIMBIC, High Performance Computing Center - CCAD, Federal University of Pará, Belém, Pará, Brazil
- Laboratory of Bioinformatics and Genomics of Microorganisms, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Rommel Thiago Jucá Ramos
- Laboratory of Simulation and Computational Biology - SIMBIC, High Performance Computing Center - CCAD, Federal University of Pará, Belém, Pará, Brazil
- Laboratory of Bioinformatics and Genomics of Microorganisms, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
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22
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Parente E, Ricciardi A. A Comprehensive View of Food Microbiota: Introducing FoodMicrobionet v5. Foods 2024; 13:1689. [PMID: 38890917 PMCID: PMC11171936 DOI: 10.3390/foods13111689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 05/21/2024] [Accepted: 05/24/2024] [Indexed: 06/20/2024] Open
Abstract
Amplicon-targeted metagenomics is now the standard approach for the study of the composition and dynamics of food microbial communities. Hundreds of papers on this subject have been published in scientific journals and the information is dispersed in a variety of sources, while raw sequences and their metadata are available in public repositories for some, but not all, of the published studies. A limited number of web resources and databases allow scientists to access this wealth of information but their level of annotation on studies and samples varies. Here, we report on the release of FoodMicrobionet v5, a comprehensive database of metataxonomic studies on bacterial and fungal communities of foods. The current version of the database includes 251 published studies (11 focusing on fungal microbiota, 230 on bacterial microbiota, and 10 providing data for both bacterial and fungal microbiota) and 14,035 samples with data on bacteria and 1114 samples with data on fungi. The new structure of the database is compatible with interactive apps and scripts developed for previous versions and allows scientists, R&D personnel in industries and regulators to access a wealth of information on food microbial communities.
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Affiliation(s)
- Eugenio Parente
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, 85100 Potenza, Italy;
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23
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Zhu L, Li J, Yang J, Li X, Lin D, Wang M. Fermentation broth from fruit and vegetable waste works: Reducing the risk of human bacterial pathogens in soil by inhibiting quorum sensing. ENVIRONMENT INTERNATIONAL 2024; 188:108753. [PMID: 38761431 DOI: 10.1016/j.envint.2024.108753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/06/2024] [Accepted: 05/13/2024] [Indexed: 05/20/2024]
Abstract
Fermentation broth from fruit and vegetable waste (FFVW) has demonstrated remarkable ability as a soil amendment and in reducing antibiotic resistance genes (ARGs) pollution. However, the potential of FFVW to mitigate other microbial contamination such as human bacterial pathogens (HBPs) and virulence factor genes (VFGs), which are closely associated with human health, remains unknown. In this study, metagenomic analysis revealed that FFVW reduced the HBPs with high-risk of ARGs and VFGs including Klebsiella pneumoniae (reduced by 40.4 %), Mycobacterium tuberculosis (reduced by 21.4 %) and Streptococcus pneumoniae (reduced by 38.7 %). Correspondingly, VFG abundance in soil decreased from 3.40 copies/cell to 2.99 copies/cell. Further analysis illustrated that these was mainly attributed to the inhibition of quorum sensing (QS). FFVW reduced the abundance of QS signals, QS synthesis genes such as rpaI and luxS, as well as receptor genes such as rpfC and fusK, resulting in a decreased in risk of ARGs and VFGs. The pure culture experiment revealed that the expression of genes related to QS, VFGs, ARGs and mobile genetic elements (MGEs) were downregulated in Pseudomonas aeruginosa, Staphylococcus aureus, Escherichia coli and K. pneumoniae treated by FFVW, consistent with the result of metagenomic analysis. This study suggested an environmentally friendly approach for controlling soil VFGs/ARGs-carrying HBPs, which is crucial for both soil and human health under the framework of "One Health".
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Affiliation(s)
- Lin Zhu
- Science and Technology Cooperation Platform for Low-Carbon Recycling of Waste and Green Development, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, Zhejiang, China; Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Jingpeng Li
- Science and Technology Cooperation Platform for Low-Carbon Recycling of Waste and Green Development, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, Zhejiang, China; Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Jian Yang
- Science and Technology Cooperation Platform for Low-Carbon Recycling of Waste and Green Development, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, Zhejiang, China; Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Xiaodi Li
- Science and Technology Cooperation Platform for Low-Carbon Recycling of Waste and Green Development, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, Zhejiang, China; Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Da Lin
- Science and Technology Cooperation Platform for Low-Carbon Recycling of Waste and Green Development, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, Zhejiang, China; Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Meizhen Wang
- Science and Technology Cooperation Platform for Low-Carbon Recycling of Waste and Green Development, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, Zhejiang, China; Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China.
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24
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Zaparte A, Dore E, White S, Paliarin F, Gabriel C, Copenhaver K, Basavanhalli S, Garcia E, Vaddavalli R, Luo M, Taylor CM, Welsh DA, Maiya R. Standard rodent diets differentially impact alcohol consumption, preference, and gut microbiome diversity. Front Neurosci 2024; 18:1383181. [PMID: 38803684 PMCID: PMC11129685 DOI: 10.3389/fnins.2024.1383181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 04/12/2024] [Indexed: 05/29/2024] Open
Abstract
Alcohol use disorder (AUD) is a complex and widespread disease with limited pharmacotherapies. Preclinical animal models of AUD use a variety of voluntary alcohol consumption procedures to recapitulate different phases of AUD, including binge alcohol consumption and dependence. However, voluntary alcohol consumption in mice is widely variable, making it difficult to reproduce results across labs. Accumulating evidence indicates that different brands of commercially available rodent chow can profoundly influence alcohol intake. In this study, we investigated the effects of three commercially available and widely used rodent diet formulations on alcohol consumption and preference in C57BL/6 J mice using the 24 h intermittent access procedure. The three brands of chow tested were LabDiet 5,001 (LD5001), LabDiet 5,053 (LD5053), and Teklad 2019S (TL2019S) from two companies (Research Diets and Envigo, respectively). Mice fed LD5001 and LD5053 displayed higher levels of alcohol consumption and preference compared to mice fed TL2019S. We also found that alcohol consumption and preference could be rapidly switched by changing the diet 48 h prior to alcohol administration. Sucrose, saccharin, and quinine preferences were not altered, suggesting that the diets did not alter sweet and bitter taste perception. We also found that mice fed LD5001 displayed increased quinine-resistant alcohol intake compared to mice fed TL2019S, suggesting that diets could influence the development of compulsive behaviors such as alcohol consumption. We profiled the gut microbiome of water- and alcohol-drinking mice that were maintained on different diets and found significant differences in bacterial alpha- and beta-diversities, which could impact the gut-brain axis signaling and alcohol consumption.
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Affiliation(s)
- Aline Zaparte
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center New Orleans, New Orleans, LA, United States
| | - Evan Dore
- Department of Physiology, Louisiana State University Health Sciences Center New Orleans, New Orleans, LA, United States
| | - Selby White
- Department of Physiology, Louisiana State University Health Sciences Center New Orleans, New Orleans, LA, United States
| | - Franciely Paliarin
- Department of Physiology, Louisiana State University Health Sciences Center New Orleans, New Orleans, LA, United States
| | - Cameron Gabriel
- Department of Physiology, Louisiana State University Health Sciences Center New Orleans, New Orleans, LA, United States
| | - Katherine Copenhaver
- Department of Physiology, Louisiana State University Health Sciences Center New Orleans, New Orleans, LA, United States
| | - Samhita Basavanhalli
- Department of Physiology, Louisiana State University Health Sciences Center New Orleans, New Orleans, LA, United States
| | - Emily Garcia
- Department of Physiology, Louisiana State University Health Sciences Center New Orleans, New Orleans, LA, United States
| | - Rishith Vaddavalli
- Department of Physiology, Louisiana State University Health Sciences Center New Orleans, New Orleans, LA, United States
| | - Meng Luo
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center New Orleans, New Orleans, LA, United States
| | - Christopher M. Taylor
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center New Orleans, New Orleans, LA, United States
| | - David Allen Welsh
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center New Orleans, New Orleans, LA, United States
| | - Rajani Maiya
- Department of Physiology, Louisiana State University Health Sciences Center New Orleans, New Orleans, LA, United States
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25
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Wang M, Lin M, Liu Q, Li C, Pang X. Fungal, but not bacterial, diversity and network complexity promote network stability during roadside slope restoration. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 922:171007. [PMID: 38401731 DOI: 10.1016/j.scitotenv.2024.171007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 02/10/2024] [Accepted: 02/13/2024] [Indexed: 02/26/2024]
Abstract
To restore degraded roadside ecosystems, conventional methods such as revegetation and soil amendment are frequently employed. However, our understanding of the long-term effects of these restoration approaches on soil microbial diversity and network complexity across different vegetation types remains poor, which contributes to poor restoration outcomes. In this study, we explored the effects of roadside slope restoration on microbial communities across different vegetation types at varying stages of restoration. We found that restoration time had a more pronounced impact on microbial diversity than specific vegetation type. As restoration progressed, microbial network complexity and fungal diversity increased, but bacterial diversity declined, suggesting that keystone taxa may contribute to network complexity. Interestingly, bacterial network complexity increased concomitant with decreasing network modularity and robustness, which may compromise system stability. Distinct vegetation types were associated with restoration-sensitive microbial communities at different restoration stages. Leguminouse and nitrogen-fixing plants, such as Albiziak alkora, Ginkgo biloba, Rhus chinensis, Rhapis excels, and Rubia cordifolia exhibited such associations after five years of restoration. These keystone taxa included Proteobacteria, Actinobacteria, Chloroflexi, Gemmatimonadota, and Myxococcota. We also found that bacterial alpha diversity was significantly correlated with restoration time, soil pH, moisture, available phosphate, nitrate nitrogen, and plant height, while fungal diversity was primarily shaped by restoration time. Together, our findings suggest that soil properties, environmental factors, vegetation type, and dominant species can be manipulated to guide the trajectory of ecological recovery by regulating the abundance of certain microbial taxa.
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Affiliation(s)
- Min Wang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu 610041, China; School of Ecology and Environment, Hainan University, China
| | - Mao Lin
- College of Geography and Resources, Sichuan Normal University, Chengdu 610101, China
| | - Qinghua Liu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu 610041, China
| | - Cheng Li
- School of Ecology and Environment, Hainan University, China
| | - Xueyong Pang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu 610041, China.
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26
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Ranauda MA, Zuzolo D, Maisto M, Tartaglia M, Scarano P, Prigioniero A, Sciarrillo R, Guarino C. Microplastics affect soil-plant system: Implications for rhizosphere biology and fitness of sage (Salvia officinalis L.). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 346:123656. [PMID: 38408506 DOI: 10.1016/j.envpol.2024.123656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/23/2024] [Accepted: 02/24/2024] [Indexed: 02/28/2024]
Abstract
A mesocosm experiment was set-up to investigate the effects of low-density polyethylene (LDPE) fragments deriving from plastic film on soil ecology, rhizosphere and plant (Salvia officinalis L.) fitness. The internal transcribed spacer (ITS) and 16S metagenomic analysis was adopted to evaluate taxonomic and functional shifts of both soil and rhizosphere under the influence of microplastics (MPs). Photosynthetic parameters and enzymes involved in oxidative stress were assessed to unveil the plant physiological state. MP fragments were analysed by scanning electron microscope (SEM) and metagenomics to investigate the plastisphere. Microbial biomarkers of MPs pollution were identified in soil and rhizosphere, reinforcing the concept of molecular biomonitoring. Overall, Bacillus, Nocardioides and Streptomyces genera are bacterial biomarkers of MPs pollution in soil whereas Aspergillus, Fusarium and Trichoderma genera, and Nectriaceae family are fungal biomarkers of MPs polluted soil. The data show that the presence of MPs promotes the abundance of taxa involved in the soil N cycle, but simultaneously reduces the endophytic interaction capability and enhances pathogen related functions at the rhizosphere level. A significant decrease in chlorophyll levels and increase of oxidative stress enzymes was observed in plants grown in MPs-polluted soil. The SEM observations of MPs fragments revealed a complex colonisation, where bacteria (Bacillus in MPSo and Microvirga in MPRz) and fungi (Aspergillus in MPSo and Trichoderma in MPRz) represent the main colonisers. The results demonstrate that the presence of MPs causes changes in the soil and rhizosphere microbial community and functions leading to negative effects on plant fitness.
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Affiliation(s)
- Maria Antonietta Ranauda
- Department of Science and Technology, University of Sannio, via de Sanctis snc, 82100, Benevento, Italy
| | - Daniela Zuzolo
- Department of Science and Technology, University of Sannio, via de Sanctis snc, 82100, Benevento, Italy.
| | - Maria Maisto
- Department of Science and Technology, University of Sannio, via de Sanctis snc, 82100, Benevento, Italy
| | - Maria Tartaglia
- Department of Science and Technology, University of Sannio, via de Sanctis snc, 82100, Benevento, Italy
| | - Pierpaolo Scarano
- Department of Science and Technology, University of Sannio, via de Sanctis snc, 82100, Benevento, Italy
| | - Antonello Prigioniero
- Department of Science and Technology, University of Sannio, via de Sanctis snc, 82100, Benevento, Italy
| | - Rosaria Sciarrillo
- Department of Science and Technology, University of Sannio, via de Sanctis snc, 82100, Benevento, Italy
| | - Carmine Guarino
- Department of Science and Technology, University of Sannio, via de Sanctis snc, 82100, Benevento, Italy
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27
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Yan Z, Lei Y, Zhao P, Zhang D, Shen J, Zhang G, Wei R, Liu H, Liu X, He Y, Shen S, Liu D. Natural mating ability is associated with gut microbiota composition and function in captive male giant pandas. Ecol Evol 2024; 14:e11189. [PMID: 38571808 PMCID: PMC10985376 DOI: 10.1002/ece3.11189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/05/2024] [Accepted: 03/12/2024] [Indexed: 04/05/2024] Open
Abstract
The issue of poor sexual performance of some male giant pandas seriously impairs the growth and the genetic diversity of the captive population, yet there is still no clear understanding of the cause of the loss of this ability and its underlying mechanism. In this study, we analyzed the gut microbiota and its function in 72 fecal samples obtained from 20 captive male giant pandas, with an equal allocation between individuals capable and incapable of natural mating. Additionally, we investigated fecal hormone levels and behavioral differences between the two groups. A correlation analysis was then conducted among these factors to explore the influencing factors of their natural mating ability. The results showed significant differences in the composition of gut microbiota between the two groups of male pandas. The capable group had significantly higher abundance of Clostridium sensu stricto 1 (p adjusted = .0021, GLMM), which was positively correlated with fatty acid degradation and two-component system functions (Spearman, p adjusted < .05). Additionally, the capable group showed higher gene abundance in gut microbiota function including purine and pyrimidine metabolism and galactose metabolism, as well as pathways related to biological processes such as ribosome and homologous recombination (DEseq2, p adjusted < .05). We found no significant differences in fecal cortisol and testosterone levels between the two groups, and no difference was found in their behavior either. Our study provides a theoretical and practical basis for further studying the behavioral degradation mechanisms of giant pandas and other endangered mammal species.
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Affiliation(s)
- Zheng Yan
- Department of Ecology, College of Life Sciences, Key Laboratory for Biodiversity and Ecological Engineering of Ministry of EducationBeijing Normal UniversityBeijingHebeiChina
| | - Yinghu Lei
- Research Center for the Qinling Giant PandaShaanxi Rare Wildlife Rescue BaseXi'anShaanxiChina
| | - Pengpeng Zhao
- Research Center for the Qinling Giant PandaShaanxi Rare Wildlife Rescue BaseXi'anShaanxiChina
| | - Danhui Zhang
- Research Center for the Qinling Giant PandaShaanxi Rare Wildlife Rescue BaseXi'anShaanxiChina
| | - Jiena Shen
- Research Center for the Qinling Giant PandaShaanxi Rare Wildlife Rescue BaseXi'anShaanxiChina
| | - Guiquan Zhang
- China Conservation and Research Centre for the Giant PandaWolongSichuanChina
| | - Rongping Wei
- China Conservation and Research Centre for the Giant PandaWolongSichuanChina
| | - Haoqiu Liu
- Department of Ecology, College of Life Sciences, Key Laboratory for Biodiversity and Ecological Engineering of Ministry of EducationBeijing Normal UniversityBeijingHebeiChina
| | - Xiaoyan Liu
- Department of Ecology, College of Life Sciences, Key Laboratory for Biodiversity and Ecological Engineering of Ministry of EducationBeijing Normal UniversityBeijingHebeiChina
| | - Yan He
- Department of Ecology, College of Life Sciences, Key Laboratory for Biodiversity and Ecological Engineering of Ministry of EducationBeijing Normal UniversityBeijingHebeiChina
| | - Sijia Shen
- Department of Ecology, College of Life Sciences, Key Laboratory for Biodiversity and Ecological Engineering of Ministry of EducationBeijing Normal UniversityBeijingHebeiChina
| | - Dingzhen Liu
- Department of Ecology, College of Life Sciences, Key Laboratory for Biodiversity and Ecological Engineering of Ministry of EducationBeijing Normal UniversityBeijingHebeiChina
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28
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Zhong S, Sun YQ, Huo JX, Xu WY, Yang YN, Yang JB, Wu WJ, Liu YX, Wu CM, Li YG. The gut microbiota-aromatic hydrocarbon receptor (AhR) axis mediates the anticolitic effect of polyphenol-rich extracts from Sanghuangporus. IMETA 2024; 3:e180. [PMID: 38882491 PMCID: PMC11170970 DOI: 10.1002/imt2.180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 02/20/2024] [Accepted: 02/20/2024] [Indexed: 06/18/2024]
Abstract
Inflammatory bowel disease (IBD) is a significant global health concern. The gut microbiota plays an essential role in the onset and development of IBD. Sanghuangporus (SH), a traditional Chinese medicinal mushroom, has excellent anti-inflammatory effects and is effective at modulating the gut microbiota. Despite these attributes, the specific anticolitic effects of SH and the mechanisms through which the gut microbiota mediates its benefits remain unclear. Herein, we demonstrated that polyphenol-rich extract from SH effectively alleviated the pathological symptoms of dextran sodium sulfate (DSS)-induced colitis in mice by modulating the gut microbiota. Treatment with SH distinctly enriched Alistipes, especially Alistipes onderdonkii, and its metabolite 5-hydroxyindole-3-acetic acid (5HIAA). Oral gavage of live A. onderdonkii or 5HIAA potently mitigated DSS-induced colitis in mice. Moreover, both 5HIAA and SH significantly activated the aromatic hydrocarbon receptor (AhR), and the administration of an AhR antagonist abrogated their protective effects against colitis. These results underscore the potent efficacy of SH in diminishing DSS-induced colitis through the promotion of A. onderdonkii and 5HIAA, ultimately activating AhR signaling. This study unveils potential avenues for developing therapeutic strategies for colitis based on the interplay between SH and the gut microbiota.
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Affiliation(s)
- Shi Zhong
- Institute of Sericulture and Tea Zhejiang Academy of Agricultural Sciences Hangzhou China
| | - Yu-Qing Sun
- Institute of Sericulture and Tea Zhejiang Academy of Agricultural Sciences Hangzhou China
| | - Jin-Xi Huo
- Institute of Sericulture and Tea Zhejiang Academy of Agricultural Sciences Hangzhou China
| | - Wen-Yi Xu
- Beijing QuantiHealth Technology Co., Ltd. Beijing China
| | - Ya-Nan Yang
- School of Chinese Materia Medica Tianjin University of Traditional Chinese Medicine Tianjin China
| | - Jun-Bo Yang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong China
| | - Wei-Jie Wu
- Food Science Institute Zhejiang Academy of Agricultural Sciences Hangzhou China
| | - Yong-Xin Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong China
| | - Chong-Ming Wu
- School of Chinese Materia Medica Tianjin University of Traditional Chinese Medicine Tianjin China
| | - You-Gui Li
- Institute of Sericulture and Tea Zhejiang Academy of Agricultural Sciences Hangzhou China
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29
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Gao Y, Zhang G, Jiang S, Liu Y. Wekemo Bioincloud: A user-friendly platform for meta-omics data analyses. IMETA 2024; 3:e175. [PMID: 38868508 PMCID: PMC10989175 DOI: 10.1002/imt2.175] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 06/14/2024]
Abstract
The increasing application of meta-omics approaches to investigate the structure, function, and intercellular interactions of microbial communities has led to a surge in available data. However, this abundance of human and environmental microbiome data has exposed new scalability challenges for existing bioinformatics tools. In response, we introduce Wekemo Bioincloud-a specialized platform for -omics studies. This platform offers a comprehensive analysis solution, specifically designed to alleviate the challenges of tool selection for users in the face of expanding data sets. As of now, Wekemo Bioincloud has been regularly equipped with 22 workflows and 65 visualization tools, establishing itself as a user-friendly and widely embraced platform for studying diverse data sets. Additionally, the platform enables the online modification of vector outputs, and the registration-independent personalized dashboard system ensures privacy and traceability. Wekemo Bioincloud is freely available at https://www.bioincloud.tech/.
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Affiliation(s)
- Yunyun Gao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Guoxing Zhang
- Shenzhen Wekemo Technology Group Co., Ltd.ShenzhenChina
| | - Shunyao Jiang
- Shenzhen Wekemo Technology Group Co., Ltd.ShenzhenChina
| | - Yong‐Xin Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
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30
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Lin D, Xu JY, Wang L, Du S, Zhu D. Long-term application of organic fertilizer prompting the dispersal of antibiotic resistance genes and their health risks in the soil plastisphere. ENVIRONMENT INTERNATIONAL 2024; 183:108431. [PMID: 38217904 DOI: 10.1016/j.envint.2024.108431] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 01/15/2024]
Abstract
Microplastic (MP) pollution is a rapidly growing global environmental concern that has led to the emergence of a new environmental compartment, the plastisphere, which is a hotspot for the accumulation of antibiotic resistance genes (ARGs) and human bacterial pathogens (HBPs). However, studies on the effects of long-term organic fertilizer application on the dispersal of ARGs and virulence factor genes (VFGs) in the plastisphere of farmland soil have been limited. Here, we performed a field culture experiment by burying nylon bags filled with MPs in paddy soil that had been treated with different fertilizers for over 30 years to explore the changes of ARGs and VFGs in soil plastisphere. Our results show that the soil plastisphere amplified the ARG and VFG pollution caused by organic fertilization by 1.5 and 1.4 times, respectively. And it also led to a 2.7-fold increase in the risk of horizontal gene transfer. Meanwhile, the plastisphere tended to promote deterministic process in the community assembly of HBPs, with an increase of 1.4 times. Network analysis found a significant correlation between ARGs, VFGs, and bacteria in plastisphere. Correlation analysis highlight the important role of mobile genetic elements (MGEs) and bacterial communities in shaping the abundance of ARGs and VFGs, respectively. Our findings provide new insights into the health risk associated with the soil plastisphere due ARGs and VFGs derived from organic fertilizers.
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Affiliation(s)
- Da Lin
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Jia-Yang Xu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Lu Wang
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Shuai Du
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China.
| | - Dong Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China.
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31
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Bu Y, Feng L, Xu D, Zhang S, Liang L, Si J, Lu Y, Liu Q, Yan G, Wang Y, Lan G, Liang J. Changes in Gut Microbiota Associated with Parity in Large White Sows. Animals (Basel) 2023; 14:112. [PMID: 38200843 PMCID: PMC10778104 DOI: 10.3390/ani14010112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
As one of the most critical economic traits, the litter performance of sows is influenced by their parity. Some studies have indicated a connection between the gut microbiota and the litter performance of animals. In this study, we examined litter performance in 1363 records of different parities of Large White sows. We observed a marked decline in TNB (Total Number Born) and NBH (Number of Healthy Born) We observed a marked decline in TNB (Total Number Born) and NBH (Number of Healthy Born) among sows with parity 7 or higher. To gain a deeper understanding of the potential role of gut microbiota in this phenomenon, we conducted 16S rRNA amplicon sequencing of fecal DNA from 263 Large White sows at different parities and compared the changes in their gut microbiota with increasing parity. The results revealed that in comparison to sows with a parity from one to six, sows with a parity of seven or higher exhibited decreased alpha diversity in their gut microbiota. There was an increased proportion of pathogenic bacteria (such as Enterobacteriaceae, Streptococcus, and Escherichia-Shigella) and a reduced proportion of SCFA-producing families (such as Ruminococcaceae), indicating signs of inflammatory aging. The decline in sow function may be one of the primary reasons for the reduction in their litter performance.
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Affiliation(s)
- Yage Bu
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (Y.B.); (L.F.); (D.X.); (S.Z.); (L.L.); (J.S.); (Y.L.); (Q.L.); (G.Y.); (Y.W.); (G.L.)
| | - Lingli Feng
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (Y.B.); (L.F.); (D.X.); (S.Z.); (L.L.); (J.S.); (Y.L.); (Q.L.); (G.Y.); (Y.W.); (G.L.)
| | - Di Xu
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (Y.B.); (L.F.); (D.X.); (S.Z.); (L.L.); (J.S.); (Y.L.); (Q.L.); (G.Y.); (Y.W.); (G.L.)
| | - Shuai Zhang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (Y.B.); (L.F.); (D.X.); (S.Z.); (L.L.); (J.S.); (Y.L.); (Q.L.); (G.Y.); (Y.W.); (G.L.)
| | - Liang Liang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (Y.B.); (L.F.); (D.X.); (S.Z.); (L.L.); (J.S.); (Y.L.); (Q.L.); (G.Y.); (Y.W.); (G.L.)
| | - Jinglei Si
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (Y.B.); (L.F.); (D.X.); (S.Z.); (L.L.); (J.S.); (Y.L.); (Q.L.); (G.Y.); (Y.W.); (G.L.)
- Guangxi State Farms Yongxin Animal Husbandry Group Co., Ltd., Nanning 530022, China
| | - Yujie Lu
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (Y.B.); (L.F.); (D.X.); (S.Z.); (L.L.); (J.S.); (Y.L.); (Q.L.); (G.Y.); (Y.W.); (G.L.)
| | - Qiaoling Liu
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (Y.B.); (L.F.); (D.X.); (S.Z.); (L.L.); (J.S.); (Y.L.); (Q.L.); (G.Y.); (Y.W.); (G.L.)
| | - Gang Yan
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (Y.B.); (L.F.); (D.X.); (S.Z.); (L.L.); (J.S.); (Y.L.); (Q.L.); (G.Y.); (Y.W.); (G.L.)
| | - Yubin Wang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (Y.B.); (L.F.); (D.X.); (S.Z.); (L.L.); (J.S.); (Y.L.); (Q.L.); (G.Y.); (Y.W.); (G.L.)
| | - Ganqiu Lan
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (Y.B.); (L.F.); (D.X.); (S.Z.); (L.L.); (J.S.); (Y.L.); (Q.L.); (G.Y.); (Y.W.); (G.L.)
| | - Jing Liang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (Y.B.); (L.F.); (D.X.); (S.Z.); (L.L.); (J.S.); (Y.L.); (Q.L.); (G.Y.); (Y.W.); (G.L.)
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32
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Gao Y, Li D, Liu YX. Microbiome research outlook: past, present, and future. Protein Cell 2023; 14:709-712. [PMID: 37219087 PMCID: PMC10599639 DOI: 10.1093/procel/pwad031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 05/09/2023] [Indexed: 05/24/2023] Open
Affiliation(s)
- Yunyun Gao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Danyi Li
- R-Institute Co. Ltd., Beijing 100011, China
| | - Yong-Xin Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
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Salas-Espejo E, Terrón-Camero LC, Ruiz JL, Molina NM, Andrés-León E. Exploring the Microbiome in Human Reproductive Tract: High-Throughput Methods for the Taxonomic Characterization of Microorganisms. Semin Reprod Med 2023; 41:125-143. [PMID: 38320576 DOI: 10.1055/s-0044-1779025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
Microorganisms are important due to their widespread presence and multifaceted roles across various domains of life, ecology, and industries. In humans, they underlie the proper functioning of multiple systems crucial to well-being, including immunological and metabolic functions. Emerging research addressing the presence and roles of microorganisms within human reproduction is increasingly relevant. Studies implementing new methodologies (e.g., to investigate vaginal, uterine, and semen microenvironments) can now provide relevant insights into fertility, reproductive health, or pregnancy outcomes. In that sense, cutting-edge sequencing techniques, as well as others such as meta-metabolomics, culturomics, and meta-proteomics, are becoming more popular and accessible worldwide, allowing the characterization of microbiomes at unprecedented resolution. However, they frequently involve rather complex laboratory protocols and bioinformatics analyses, for which researchers may lack the required expertise. A suitable pipeline would successfully enable both taxonomic classification and functional profiling of the microbiome, providing easy-to-understand biological interpretations. However, the selection of an appropriate methodology would be crucial, as it directly impacts the reproducibility, accuracy, and quality of the results and observations. This review focuses on the different current microbiome-related techniques in the context of human reproduction, encompassing niches like vagina, endometrium, and seminal fluid. The most standard and reliable methods are 16S rRNA gene sequencing, metagenomics, and meta-transcriptomics, together with complementary approaches including meta-proteomics, meta-metabolomics, and culturomics. Finally, we also offer case examples and general recommendations about the most appropriate methods and workflows and discuss strengths and shortcomings for each technique.
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Affiliation(s)
- Eduardo Salas-Espejo
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada, Spain
| | - Laura C Terrón-Camero
- Bioinformatics Unit, Institute of Parasitology and Biomedicine "López-Neyra" (IPBLN), CSIC, Granada, Spain
| | - José L Ruiz
- Bioinformatics Unit, Institute of Parasitology and Biomedicine "López-Neyra" (IPBLN), CSIC, Granada, Spain
| | - Nerea M Molina
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada, Spain
| | - Eduardo Andrés-León
- Bioinformatics Unit, Institute of Parasitology and Biomedicine "López-Neyra" (IPBLN), CSIC, Granada, Spain
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