Phenomics (Cham, Switzerland)最新文献

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The Impact of Lipase H Deficiency on Gut Aging and Lifespan in Drosophila. 脂肪酶H缺乏对果蝇肠道衰老和寿命的影响。
IF 6.2
Phenomics (Cham, Switzerland) Pub Date : 2025-03-11 eCollection Date: 2025-06-01 DOI: 10.1007/s43657-025-00226-9
Ayesha Nisar, Sawar Khan, Yonghan He
{"title":"The Impact of Lipase H Deficiency on Gut Aging and Lifespan in <i>Drosophila</i>.","authors":"Ayesha Nisar, Sawar Khan, Yonghan He","doi":"10.1007/s43657-025-00226-9","DOIUrl":"10.1007/s43657-025-00226-9","url":null,"abstract":"","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"5 3","pages":"326-329"},"PeriodicalIF":6.2,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12390894/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144981694","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
NetNiche: Microbe-Metabolite Network Reconstruction and Microbial Niche Analysis. 微生物-代谢物网络重构和微生物生态位分析。
IF 3.7
Phenomics (Cham, Switzerland) Pub Date : 2025-03-07 eCollection Date: 2025-04-01 DOI: 10.1007/s43657-024-00168-8
Lu Wang, Lequn Wang, Luonan Chen
{"title":"NetNiche: Microbe-Metabolite Network Reconstruction and Microbial Niche Analysis.","authors":"Lu Wang, Lequn Wang, Luonan Chen","doi":"10.1007/s43657-024-00168-8","DOIUrl":"10.1007/s43657-024-00168-8","url":null,"abstract":"<p><p>Metagenomics and metabolomics technologies have been widely used to investigate the microbe-metabolite interactions in vivo. However, the computational methods that accurately infer the microbe-metabolite interactions are lacking. We present a context-aware framework for graph representation learning, NetNiche, which predicts microbe-metabolite and microbe-microbe interactions in an accurate manner, by integrating their abundance data with prior knowledge. We applied NetNiche to datasets on gut and soil microbiome, and demonstrated that NetNiche can outperform the state-of-the-art methods, such as SParse InversE Covariance Estimation for Ecological Association Inference (SPIEC-EASI), Sparse Correlations for Compositional data (SparCC) and microbe-metabolite vectors (mmvec). NetNiche is an effective tool with wide applicability for the multi-omics study of human microbiome.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s43657-024-00168-8.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"5 2","pages":"208-211"},"PeriodicalIF":3.7,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12209087/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144556114","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Regulatory Mechanisms of Gut Homeostasis and Bone Metabolism Interplay in Osteoporosis. 骨质疏松症中肠道稳态和骨代谢相互作用的调节机制。
IF 6.2
Phenomics (Cham, Switzerland) Pub Date : 2025-03-05 eCollection Date: 2025-08-01 DOI: 10.1007/s43657-024-00207-4
Peng Qi, Xin Chen, Hao Liu, Jilong Ma, Zhonghua Qi, Xingwen Xie
{"title":"Regulatory Mechanisms of Gut Homeostasis and Bone Metabolism Interplay in Osteoporosis.","authors":"Peng Qi, Xin Chen, Hao Liu, Jilong Ma, Zhonghua Qi, Xingwen Xie","doi":"10.1007/s43657-024-00207-4","DOIUrl":"https://doi.org/10.1007/s43657-024-00207-4","url":null,"abstract":"<p><p>Osteoporosis, a prevalent metabolic bone disorder characterized by reduced bone mass and compromised bone strength, poses a substantial socioeconomic burden worldwide due to its staggering global incidence. Individuals afflicted with osteoporosis face an elevated risk of debilitating fractures, leading to compromised quality of life, disability, and increased mortality. The gut-bone axis, the intricate bidirectional communication between the gut microbiome and skeletal system, has recently emerged as a focal area in bone health research. Accumulating evidence suggests that gut homeostasis, the delicate balance of gut microbial communities, modulates bone metabolism through diverse mechanisms, potentially driving the pathogenesis of osteoporosis. Conversely, gut dysbiosis, the disruption of this equilibrium, may directly or indirectly perturb bone homeostasis, contributing to the onset and progression of osteoporosis. Elucidating the regulatory interplay between gut homeostasis and bone metabolism in the context of osteoporosis holds promising potential for developing novel preventive and therapeutic strategies, bearing profound theoretical and clinical implications.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"5 4","pages":"435-445"},"PeriodicalIF":6.2,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12457256/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145152310","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Comparative Analysis of Growth Dynamics and Relative Abundances of Gut Microbiota Influenced by Ketogenic Diet. 生酮饮食对肠道菌群生长动态和相对丰度的影响。
IF 3.7
Phenomics (Cham, Switzerland) Pub Date : 2025-03-04 eCollection Date: 2025-02-01 DOI: 10.1007/s43657-025-00228-7
Mi Tang, Zhidong Zhang, Liyuan Lin, Junling Niu, Guangxun Meng, Wei Wang, Jiwen Wang, Yingyan Wang
{"title":"Comparative Analysis of Growth Dynamics and Relative Abundances of Gut Microbiota Influenced by Ketogenic Diet.","authors":"Mi Tang, Zhidong Zhang, Liyuan Lin, Junling Niu, Guangxun Meng, Wei Wang, Jiwen Wang, Yingyan Wang","doi":"10.1007/s43657-025-00228-7","DOIUrl":"10.1007/s43657-025-00228-7","url":null,"abstract":"<p><p>Although the compositional alterations of gut bacteria in ketogenic diet (KD) have been intensively investigated, the causal relationship between this extreme diet and the microbiota changes is not fully understood. Here, we studied the growth dynamics of intestinal bacteria in KD. We used the CoPTR method to calculate the peak-to-trough ratio (PTR) based on metagenomic sequencing data, serving as an indicator of bacterial growth rates. Notably, <i>Akkermansia muciniphila</i>, a bacterium strongly linked to the therapeutic benefits of KD, exhibited one of the highest growth rates, aligning with its markedly elevated abundance. Our findings also revealed discrepancies in the change patterns of CoPTR values and relative abundances for various bacteria across different diet groups, some of which might be attributed to the exceptionally high or low growth rates of specific species. For some of the species demonstrating obvious differences in growth rates between KD and standard diet, we conducted in vitro culture experiments, supplementing them with diverse nutritional sources to elucidate the underlying mechanisms. The integrative analysis of bacterial abundance and growth dynamics can help deepen our understanding of the gut microbiota changes caused by KD and the therapeutic effects of this special diet.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s43657-025-00228-7.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"5 1","pages":"65-75"},"PeriodicalIF":3.7,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12040800/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144043567","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
MVPCR: Multiplex Visual Detection Strategy Based on Ultrafast PCR for Point-of-Care Pathogens Detection Within 10 Min. MVPCR:基于超快PCR的多重视觉检测策略,用于10分钟内的即时病原体检测。
IF 6.2
Phenomics (Cham, Switzerland) Pub Date : 2025-03-04 eCollection Date: 2025-06-01 DOI: 10.1007/s43657-024-00216-3
Ziqin Zhang, Cui Wu, Linlin Bai, Kaiming Guo, Ting Wang, Dianwei Liu, Mingrui Zhu, Feng Qian, Fang Zhang, Rui Wang
{"title":"MVPCR: Multiplex Visual Detection Strategy Based on Ultrafast PCR for Point-of-Care Pathogens Detection Within 10 Min.","authors":"Ziqin Zhang, Cui Wu, Linlin Bai, Kaiming Guo, Ting Wang, Dianwei Liu, Mingrui Zhu, Feng Qian, Fang Zhang, Rui Wang","doi":"10.1007/s43657-024-00216-3","DOIUrl":"10.1007/s43657-024-00216-3","url":null,"abstract":"<p><p>Pathogens pose significant threats to biosecurity and environmental health due to their potential for widespread outbreaks. Effective pathogen detection requires methods that are rapid, sensitive, specific, and informative. Here, we proposed a multiplex visual detection system that integrated ultrafast polymerase chain reaction (PCR) and molecular beacons, allowing the simultaneous detection of three pathogens in a one-pot reaction. The ultrafast PCR protocol employed cycles of just 7 s each, allowing the entire process-from sampling to result-to be completed within only 10 min. Molecular beacons hybridized with target sequences during ultrafast PCR, generating fluorescence signals that are visually detectable without specialized equipment. Additionally, we developed a compact, portable cartridge integrated with online software for fluorescence visualization and direct result output, eliminating the need for bulky instruments and specialized personnel, thereby facilitating point-of-care testing (POCT). The method demonstrated high specificity and sensitivity, with a limit of detection (LOD) as low as 23 copies per reaction. It achieved a 100% positive detection rate in practical applications, performing comparably to standard PCR. Furthermore, the method effectively identified low concentrations of pathogens in animal infection samples. This ultrafast, highly sensitive, specific, and informative method shows significant potential for POCT applications, including food safety monitoring and clinical diagnostics.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s43657-024-00216-3.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"5 3","pages":"239-251"},"PeriodicalIF":6.2,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12390895/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144981689","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Insights into Causal Associations of Lipid Traits and Lipid-modifying Drug Targets with Uric Acid and Risk of Gout. 洞察脂质特性和脂质修饰药物靶点与尿酸和痛风风险的因果关系。
IF 6.2
Phenomics (Cham, Switzerland) Pub Date : 2025-03-03 eCollection Date: 2025-08-01 DOI: 10.1007/s43657-024-00212-7
Chenfeng Zou, Bei Yang, Jiaying Zhang, Yuying Zhang, Dewei Ye, Hanyu Zhu, Tao Bai, Guozhi Jiang
{"title":"Insights into Causal Associations of Lipid Traits and Lipid-modifying Drug Targets with Uric Acid and Risk of Gout.","authors":"Chenfeng Zou, Bei Yang, Jiaying Zhang, Yuying Zhang, Dewei Ye, Hanyu Zhu, Tao Bai, Guozhi Jiang","doi":"10.1007/s43657-024-00212-7","DOIUrl":"https://doi.org/10.1007/s43657-024-00212-7","url":null,"abstract":"<p><p>Emerging lipid-modifying agents show potential but lack evidence for the management of uric acid and gout. We aimed to explore the causal effects of lipid traits, lipid-modifying drugs on uric acid levels and risk of gout. Two-sample MR analyses were performed to investigate the associations of genetically predicted lipid traits (LDL-C, HDL-C and TG) and lipid-modifying drug targets (PCSK9, HMGCR, NPC1L1, CETP, ABCG5/G8, APOB, LDLR, LPL, ANGPTL3, and APOC3) with uric acid levels and gout risk. Validation analyses were performed using the independent cohort of the UK Biobank. Summary-data-based MR was further conducted to estimate the associations of the expression of drug target genes with the outcomes. Genetically predicted lower HDL-C and higher TG were significantly associated with elevated uric acid levels (<i>β</i> (95% CI): -0.11 [-0.18, -0.04], <i>p</i> = 0.001 for HDL-C; 0.18 [0.09, 0.27], <i>p</i> < 0.001 for TG) and increased risk of gout (OR (95% CI): 0.83 [0.71, 0.97], <i>p</i> = 0.017 for HDL-C; 1.54 [1.25, 1.91], <i>p</i> < 0.001 for TG). Notably, LPL activation among lipid-modifying drug targets demonstrated significant associations with both reduced uric acid levels (<i>β</i> [95% CI]: -0.13 [-0.16, -0.10], <i>p</i> < 0.001) and decreased risk of gout (OR 95% CI: 0.84 [0.76, 0.93], <i>p</i> = 0.001). These findings were corroborated in the UK Biobank dataset. Furthermore, the expression of LPL was significantly associated with lower uric acid levels (<i>β</i> [95% CI]: -0.03 [-0.04, -0.01], <i>p</i> = 0.002). Our results suggest that LPL activation, which reduces TG levels, holds promise as a candidate drug for the treatment and prevention of hyperuricemia and gout.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s43657-024-00212-7.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"5 4","pages":"374-383"},"PeriodicalIF":6.2,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12457272/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145152245","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Progress in Intestinal Homeostasis and Mechanisms of Pancreatic Cancer. 胰腺癌肠道稳态及机制研究进展。
IF 6.2
Phenomics (Cham, Switzerland) Pub Date : 2025-02-23 eCollection Date: 2025-08-01 DOI: 10.1007/s43657-024-00189-3
Zhonghua Qi, Peng Qi, Xiansen Jiang, Ping Qi
{"title":"Progress in Intestinal Homeostasis and Mechanisms of Pancreatic Cancer.","authors":"Zhonghua Qi, Peng Qi, Xiansen Jiang, Ping Qi","doi":"10.1007/s43657-024-00189-3","DOIUrl":"https://doi.org/10.1007/s43657-024-00189-3","url":null,"abstract":"<p><p>Pancreatic cancer is a highly invasive and heterogeneous malignancy, with its incidence witnessed a global escalation in recent years. This tumor type is typically asymptomatic in its early stages, and the anatomical location of the pancreas renders it obscured, frequently leading to late detection. Its highly invasive growth pattern can readily invade surrounding tissues and organs, and pancreatic cancer exhibits poor sensitivity to radiotherapy and chemotherapy. Surgical resection remains the primary treatment modality, but due to delayed diagnosis, most patients lose the opportunity for curative resection. Pancreatic cancer is one of the most challenging malignancies, with a grave prognosis, and its incidence and mortality rates continue to rise annually. In recent years, the interplay between intestinal homeostasis and pancreatic cancer development has emerged as a burgeoning area of research. Intestinal homeostasis is a dynamic equilibrium state formed by the intricate interplay between the intestinal barrier and the intestinal environment (including intestinal microbiota). Further elucidating intestinal homeostasis and its association with pancreatic cancer pathogenesis will aid in exploring novel therapeutic strategies to combat this devastating disease.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"5 4","pages":"446-456"},"PeriodicalIF":6.2,"publicationDate":"2025-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12457279/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145152277","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Topology of gut Microbiota Network and Guild-Based Analysis in Chinese Adults. 中国成年人肠道菌群网络拓扑结构及基于行会的分析
IF 3.7
Phenomics (Cham, Switzerland) Pub Date : 2025-02-21 eCollection Date: 2025-02-01 DOI: 10.1007/s43657-024-00211-8
Jiongxing Fu, Danxia Yu, Wei Zheng, Yu Jiang, Lei Wang, Hui Cai, Qinghua Xia, Xiao-Ou Shu, Wanghong Xu
{"title":"Topology of gut Microbiota Network and Guild-Based Analysis in Chinese Adults.","authors":"Jiongxing Fu, Danxia Yu, Wei Zheng, Yu Jiang, Lei Wang, Hui Cai, Qinghua Xia, Xiao-Ou Shu, Wanghong Xu","doi":"10.1007/s43657-024-00211-8","DOIUrl":"10.1007/s43657-024-00211-8","url":null,"abstract":"<p><p>Gut microbiota with co-abundant behaviors is considered belonging to the same guild in micro-ecosystem. In this study, we established co-abundance networks of operational taxonomic units (OTUs) among 2944 Chinese adults from the Shanghai Men's and Women's Health Studies and observed a positive connection-dominated scale-free network using Sparse Correlations for Compositional data (SparCC). The closeness centrality was negatively correlated with other degree-based topological metrics in the network, indicating the isolated modularization of the bacteria. A total of 130 guilds were constructed, with a high modularity of 0.68, and retaining more diversity of OTUs than genus classification. The scores of guild structure similarity for comparisons between all, the healthy and the unhealthy subjects were higher than those derived from randomized permutations, suggesting a robust guild structure. We further used the constructed 130 guilds as the aggregation units to identify gut microbiota that may be associated with type 2 diabetes, and found that the OTUs in 21 significant guilds relevant to diabetes belonged to 19 of 41 (46.3%) previously reported genera (derived from Disbiome database), while only 10 (24.4%) showed different abundances between diabetes patients and healthy subjects in genus-based analysis. Our study reveals modularization of gut microbiota as guilds in Chinese populations, and demonstrates advantages of guild-based analysis in identifying diabetes-related gut bacteria. The analytical method based on microbial networks should be widely used to deepen our understanding of the role of gut microbiota in human health.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s43657-024-00211-8.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"5 1","pages":"91-108"},"PeriodicalIF":3.7,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12040777/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144051802","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Impact of DNA Extraction Methods on Gut Microbiome Profiles: A Comparative Metagenomic Study. DNA提取方法对肠道微生物组的影响:一项比较宏基因组研究。
IF 3.7
Phenomics (Cham, Switzerland) Pub Date : 2025-02-20 eCollection Date: 2025-02-01 DOI: 10.1007/s43657-025-00232-x
Yanni Pu, Xiaofeng Zhou, Hao Cai, Tao Lou, Chenglin Liu, Mengmeng Kong, Zhonghan Sun, Yanren Wang, Ruyi Zhang, Yuxuan Zhu, Lin Ye, Yuanting Zheng, Baoli Zhu, Zhexue Quan, Guoping Zhao, Yan Zheng
{"title":"Impact of DNA Extraction Methods on Gut Microbiome Profiles: A Comparative Metagenomic Study.","authors":"Yanni Pu, Xiaofeng Zhou, Hao Cai, Tao Lou, Chenglin Liu, Mengmeng Kong, Zhonghan Sun, Yanren Wang, Ruyi Zhang, Yuxuan Zhu, Lin Ye, Yuanting Zheng, Baoli Zhu, Zhexue Quan, Guoping Zhao, Yan Zheng","doi":"10.1007/s43657-025-00232-x","DOIUrl":"10.1007/s43657-025-00232-x","url":null,"abstract":"<p><p>In gut microbial research, DNA extraction remarkably influences study outcomes and biological interpretations. Rapid advancements in the research scale and technological upgrades necessitate evaluating new methods to ensure reliability and precision in microbial community profiling. We systematically evaluated the performance of eight recent and commonly used extraction methods using a microbial mock community (MMC) and fecal samples from two healthy volunteers, incorporating bacterial, archaeal, and fungal constituents. Performance metrics included nucleic acid assessment, microbial profile assessment, and scalability for large-scale studies, leveraging shotgun metagenomics for in-depth analysis. Despite variations in DNA quantity and quality, all methods yielded sufficient DNA for shotgun metagenomic sequencing. In the MMC microbial profile assessment, the QIAamp PowerFecal pro Kit (PF) and DNeasy PowerSoil HTP kit (PS) methods exhibited higher similarity with the theoretical composition and lower variability across technical replicates compared to other methods. For fecal samples, the extraction method accounted for 21.4% of the overall microbiome variation and significantly affected the abundances of 32% of detected microbial species. Methods using mechanical lysis with small beads, such as PF and PS, demonstrated better efficiency, indicated by increased microbial diversity in extracting DNA from Gram-positive bacteria. Furthermore, the PF and PS methods are notably simple to execute and automation-friendly, though relatively costly. Our study underscores the importance of maintaining consistency in DNA extraction methods for reliable comparative metagenomic analyses. We recommend PF and PS methods as optimal for expansive gut metagenomic research, emphasizing the critical role of mechanical lysis in DNA extraction.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s43657-025-00232-x.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"5 1","pages":"76-90"},"PeriodicalIF":3.7,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12040788/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144058224","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Lipoprotein Subfractions Predict All-cause and Cardiovascular Mortality in CKD Patients Undergoing Hemodialysis: A Prospective Cohort Study Based on NMR Metabolomics. 脂蛋白亚组分预测血液透析CKD患者的全因死亡率和心血管死亡率:一项基于核磁共振代谢组学的前瞻性队列研究。
IF 6.2
Phenomics (Cham, Switzerland) Pub Date : 2025-02-20 eCollection Date: 2025-08-01 DOI: 10.1007/s43657-024-00179-5
Qingxia Huang, Han Zhang, Ziyan Shen, Jing Chen, Xuesen Cao, Linghan Xu, Cheng Zhu, Shiqi Lv, Xixi Yu, Xiaoqiang Ding, Huiru Tang, Xiaoyan Zhang
{"title":"Lipoprotein Subfractions Predict All-cause and Cardiovascular Mortality in CKD Patients Undergoing Hemodialysis: A Prospective Cohort Study Based on NMR Metabolomics.","authors":"Qingxia Huang, Han Zhang, Ziyan Shen, Jing Chen, Xuesen Cao, Linghan Xu, Cheng Zhu, Shiqi Lv, Xixi Yu, Xiaoqiang Ding, Huiru Tang, Xiaoyan Zhang","doi":"10.1007/s43657-024-00179-5","DOIUrl":"https://doi.org/10.1007/s43657-024-00179-5","url":null,"abstract":"<p><p>Lipoprotein metabolism is markedly altered in chronic kidney disease (CKD). Studies on the association between nuclear magnetic resonance (NMR) derived lipoprotein subfraction signature and mortality in CKD patients undergoing hemodialysis are limited. NMR based metabolomics was performed on the baseline plasma samples from 368 maintenance hemodialysis patients. Survival analyses were used to investigate the effect of lipoproteins on all-cause mortality and cardiovascular disease (CVD) mortality. Prediction models were further developed using stepwise regression combined cox proportional-hazards model. During the average follow-up of 45.1 months, we observed 144 all-cause deaths and 67 CVD deaths. After adjustment for 14 important covariates, we identified 18 and 35 lipoprotein parameters associated with all-cause mortality and CVD mortality, separately. Cholesterol in total low-density lipoprotein (LDL-C) and total high-density lipoprotein (HDL-C) were correlated with neither all-cause death nor CVD death. For lipoprotein subfractions, triglyceride levels in large very-low density lipoprotein (VLDL) were positively correlated only with all-cause mortality. Lipids (triglyceride, cholesterol and phospholipid) in medium VLDL, cholesterol/total lipids in intermediate-density lipoprotein (IDL) and free cholesterol/total lipids in small high-density lipoprotein (HDL) were positively associated with both all-cause and CVD mortality. The addition of lipoprotein parameters to traditional risk factors significantly improved the mortality risk prediction: the area under the receiver operating characteristic curve (AUC) was improved from 0.811 to 0.842 (<i>p</i>-value = 0.020) for all-cause mortality and 0.806 to 0.854 (<i>p</i>-value = 0.005) for CVD mortality. Our results highlight the lipoprotein subfractions related to all-cause and CVD mortality of maintenance hemodialysis patients, and the lipoproteins-driven prediction models significantly outperform traditional risk factors.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s43657-024-00179-5.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"5 4","pages":"361-373"},"PeriodicalIF":6.2,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12457243/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145152256","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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