Phenomics (Cham, Switzerland)最新文献

{"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}

{"title":"Embracing Interpersonal Variability of Microbiome in Precision Medicine.","authors":"Xin Zhou, Xin Chen, Mark M Davis, Michael P Snyder","doi":"10.1007/s43657-024-00201-w","DOIUrl":"10.1007/s43657-024-00201-w","url":null,"abstract":"","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"5 1","pages":"8-13"},"PeriodicalIF":3.7,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12040794/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144048080","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}

{"title":"Differences in Pathogenetic Mechanism Between Tibetan and Han High-Altitude Polycythemia Based on a Whole Genome-Wide Association Study.","authors":"Zhuoma Basang, Shixuan Zhang, Xianwei Ke, Zhuoma Duoji, La Yang, Danzeng Qiangba, Yang De, Deji Gesang, Zixin Hu, Yanyun Ma, Meng Hao, Ruidong Fan, Li Han, Zeshan Lin, Yi Li, Jiucun Wang, Juan Wu","doi":"10.1007/s43657-024-00180-y","DOIUrl":"10.1007/s43657-024-00180-y","url":null,"abstract":"<p><p>High-altitude polycythemia (HAPC) is a prevalent chronic condition affecting individuals at high altitudes, including both highland and plains populations. This study, involving 2248 participants, explored genetic susceptibility to HAPC among ethnic groups, with 898 HAPC patients (450 Han, 448 Tibetan). The Genome-wide Association Study, encompassing 198 cases (100 Han, 98 Tibetan), identified eight Tibetan HAPC-susceptibility single-nucleotide polymorphisms and four in Han individuals. The common polymorphism locus rs7618658 (<i>SNX4</i>, <i>p</i> _combine < 5 × 10^-8) was validated in both populations. The investigation of Tibetan <i>EPAS1</i> revealed the rs1374749 locus, along with linked loci, as a potential prevalence factor for HAPC. The GGTAC haplotype containing this locus emerged as a Protect haplotype for HAPC (<i>p</i> = 2.461 × 10^-12, OR = 0.344). Enrichment analysis revealed that Tibetans exhibited susceptibility in oxygen-sensing pathways, such as EPAS1, associated with phenotypes like hemoglobin and platelets. In contrast, Han Chinese showed significant sensitivity in cell differentiation and angiogenesis, closely linked to hemoglobin, hematocrit, and platelets.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s43657-024-00180-y.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"5 2","pages":"169-182"},"PeriodicalIF":3.7,"publicationDate":"2025-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12209065/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144556111","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}

{"title":"Precision Dietary Intervention: Gut Microbiome and Meta-metabolome as Functional Readouts.","authors":"Jing Luo, Yulan Wang","doi":"10.1007/s43657-024-00193-7","DOIUrl":"10.1007/s43657-024-00193-7","url":null,"abstract":"<p><p>Gut microbiome, the group of commensals residing within the intestinal tract, is closely associated with dietary patterns by interacting with food components. The gut microbiome is modifiable by the diet, and in turn, it utilizes the undigested food components as substrates and generates a group of small molecule-metabolites that addressed as \"meta-metabolome\" in this review. Profiling and mapping of meta-metabolome could yield insightful information at higher resolution and serve as functional readouts for precision nutrition and formation of personalized dietary strategies. For assessing the meta-metabolome, sample preparation is important, and it should aim for retrieval of gut microbial metabolites as intact as possible. The meta-metabolome can be investigated via untargeted and targeted meta-metabolomics with analytical platforms such as nuclear magnetic resonance spectroscopy and mass spectrometry. Employing flux analysis with meta-metabolomics using available database could further elucidate metabolic pathways that lead to biomarker discovery. In conclusion, integration of gut microbiome and meta-metabolomics is a promising supplementary approach to tailor precision dietary intervention. In this review, relationships among diet, gut microbiome, and meta-metabolome are elucidated, with an emphasis on recent advances in alternative analysis techniques proposed for nutritional research. We hope that this review will provide information for establishing pipelines complementary to traditional approaches for achieving precision dietary intervention.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"5 1","pages":"23-50"},"PeriodicalIF":3.7,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12040796/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144051787","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}

{"title":"Impacts of Behavioral Compliance on Weight-Loss and Metabolic Profile in a Smartphone App-Based Lifestyle Intervention or Plus Dietitian Supporting: A Randomized and Controlled Trial Among Chinese.","authors":"Xue Li, Ling Lu, Liang Sun, Yunxia Xie, Kang Huang, Changzheng Yuan, Liying Chen, Xu Lin","doi":"10.1007/s43657-024-00162-0","DOIUrl":"10.1007/s43657-024-00162-0","url":null,"abstract":"<p><p>Mobile health technologies provided innovative solutions for lifestyle interventions and offered reliable methods to evaluate behavioral phenotypes during such interventions. To systematically quantify the impacts of behavioral compliance on weight-loss and metabolic profiles during lifestyle intervention, a total of 395 Chinese adults with overweight/obesity (BMI ≥ 24 kg/m²) or central obesity (waistline ≥ 90 cm for men or ≥ 80 cm for women) were randomly assigned to a smartphone app-based arm (SAA, n = 197) or smartphone app plus dietitian arm (SADA, n = 198) for 6 months. Compliance scores (0-5) were determined based on fulfilling five behavioral tasks: completing online courses, wearing a smart band, and recording weight, food intake, and blood pressure. SADA had greater weight-loss (- 4.94% vs. - 2.28%, <i>p</i> < 0.001) and lower triglyceride, but higher HDL-C levels (both <i>p</i> < 0.05) than SAA after six months. Between-group weight-loss differences were attenuated at compliance scores ≥ 3 (SADA: - 6.30% vs. SAA: - 4.79%, <i>p</i> = 0.07). Mediation analysis suggested that compliance scores explained approximately 30% of the additional weight loss in the SADA (<i>p</i> < 0.001), and self-weighing was the primary mediator (<i>p</i> < 0.05). Higher educational levels, greater initial weight loss, self-perceived simplicity, and satisfaction with the program were potential determinants of intervention compliance. Overall, the superior weight loss and metabolic improvements in the SADA group could be mediated by behavioral compliance, which was possibly influenced by some demographic and intervention response features. Our findings highlighted the roles of behavioral phenotypes and adherence in app-based lifestyle interventions, and added evidence for the future development of more precise strategies in long-term weight management.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s43657-024-00162-0.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"5 2","pages":"154-168"},"PeriodicalIF":3.7,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12209060/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144556112","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}

{"title":"Characteristics of the Corneal Endothelium in Elderly Adults with High Myopia.","authors":"Yinglei Zhang, Shaohua Zhang, Keke Zhang, Yi Lu, Xiangjia Zhu","doi":"10.1007/s43657-024-00186-6","DOIUrl":"10.1007/s43657-024-00186-6","url":null,"abstract":"<p><p>This cross-sectional study aimed to investigate the corneal endothelial characteristics in elderly individuals with high myopia. We assessed corneal endothelial characteristics in 1065 eyes of 1065 elderly patients (549 highly myopic and 516 control eyes) using non-contact specular microscopy. Confirmation of suspected Fuchs endothelial corneal dystrophy (FECD) was performed with slit-lamp and confocal microscopy. Highly myopic eyes exhibited significantly greater central endothelial cell density (ECD) and coefficient of variation (CV) (<i>p</i> = 0.001 and <i>p</i> = 0.002, respectively), and lower average cell area (AVG) and percent of hexagonality (HEX) (<i>p</i> = 0.014 and <i>p</i> < 0.001, respectively) compared to control eyes. After adjusting for age and gender, axial length (AL) was positively correlated with ECD and CV (<i>r</i> = 0.130, <i>p</i> < 0.001 and <i>r</i> = 0.113, <i>p</i> < 0.001, respectively), and was negatively correlated with AVG and HEX (<i>r</i> = - 0.105, <i>p</i> = 0.001 and <i>r</i> = - 0.204, <i>p</i> < 0.001, respectively). FECD prevalence was 4.92% in highly myopic eyes and 3.29% in controls, with more advanced cases in highly myopic eyes (<i>p</i> = 0.036). In conclusion, longer AL was associated with increased corneal ECD, and greater endothelial pleomorphism and polymegethism in elderly patients. Highly myopic eyes appeared to have higher prevalence and severity of FECD. The study was registered on www.clinicaltrials.gov on February 26, 2017, with the registration number NCT03062085.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"4 6","pages":"562-569"},"PeriodicalIF":3.7,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11889312/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143588564","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}

{"title":"Newly Identified Genes Linked to Tetralogy of Fallot.","authors":"Ying Liu, Weinian Shou","doi":"10.1007/s43657-024-00203-8","DOIUrl":"10.1007/s43657-024-00203-8","url":null,"abstract":"","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"4 6","pages":"633-634"},"PeriodicalIF":3.7,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11889324/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143588612","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}

{"title":"<i>MST1R</i> Gene Variants Predispose Individuals to Tetralogy of Fallot.","authors":"Zhiyu Feng, Xianghui Huang, Yuan Gao, Han Gao, Weilan Na, Chaozhong Tan, Shaojie Min, Yuquan Lu, Quannan Zhuang, Siyi Lin, Xiaojing Ma, Weicheng Chen, Weili Yan, Wei Sheng, Guoying Huang","doi":"10.1007/s43657-024-00175-9","DOIUrl":"10.1007/s43657-024-00175-9","url":null,"abstract":"<p><p>Tetralogy of Fallot (TOF) is the most common cyanotic congenital heart malformation. While a few susceptibility genes for TOF have been identified, research on the genetic basis of TOF is limited. The <i>Macrophage stimulating 1 receptor</i> (<i>MST1R</i>) gene encodes the macrophage-stimulating protein receptor with tyrosine phosphatase activity that is involved in immune defense. In this study, we performed whole-exome sequencing (WES) on 10 TOF families and 50 sporadic TOF patients and identified a recessive homozygous missense mutation in <i>MST1R</i>, c.T2009G: p.V670G, in two offspring with TOF in a single family. Targeted sequencing of the <i>MST1R</i> gene showed enrichment for rare variants in 417 TOF patients compared with East Asians in Genome Aggregation Database Version 2 (gnomADv2_EAS). <i>MST1R</i>-deficient human induced pluripotent stem cells (hiPSCs) maintained normal pluripotency but differentiated into non-functional cardiomyocytes (CMs). Taken together, our findings indicate that <i>MST1R</i> may play a critical role in cardiac differentiation and genetic variations in <i>MST1R</i> may be associated with the pathogenesis of TOF.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s43657-024-00175-9.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"4 6","pages":"548-561"},"PeriodicalIF":3.7,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11889330/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143588502","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}

{"title":"Brain Imaging and Phenotyping for the China Phenobank Project.","authors":"Wenjia Bai","doi":"10.1007/s43657-024-00197-3","DOIUrl":"10.1007/s43657-024-00197-3","url":null,"abstract":"","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"4 6","pages":"592-593"},"PeriodicalIF":3.7,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11889274/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143588448","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}

{"title":"Protocol for Simultaneous EEG and fNIRS Measurement in Characterizing Brain State.","authors":"Ligang Zhou, Fang Xiao, Ning Shen, Yalin Wang, Jinbu Tang, Jingchun Luo, Wei Chen, Chen Chen","doi":"10.1007/s43657-023-00148-4","DOIUrl":"10.1007/s43657-023-00148-4","url":null,"abstract":"<p><p>Multi-modal signal measurement is widely used in health monitoring and disease recognition, such as electroencephalography (EEG)-functional magnetic resonance imaging (fMRI), EEG-functional near-infrared spectroscopy (fNIRS), EEG-electrocardiograph (ECG), etc. The concurrent recording of EEG-fNIRS not only measures concentration changes of oxyhemoglobin (HbO₂) and deoxyhemoglobin (HbR) of the cortical microcirculation blood vessels but also records electrical activities of the cerebral cortex in a relatively portable setting compared with EEG-fMRI and other patterns. This protocol proposes a standard operating procedure for the joint EEG-fNIRS measurement, including electrode placement, hardware, and software. In the signal process, artifacts' removal, EEG-fNIRS phenotypes extraction by software and self-developed algorithm ways, and data storage are involved. In addition, solutions to problems that may be encountered in this protocol are also presented. This protocol is expected to broaden the application of joint EEG-fNIRS measurement and gain a deeper understanding of the underlying neural activation pattern and mechanism of the brain.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"5 2","pages":"219-237"},"PeriodicalIF":3.7,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12209161/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144556116","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}