Phenomics (Cham, Switzerland)最新文献

{"title":"Implication of Gut Mycobiome and Virome in Type-2 Diabetes Mellitus: Uncovering the Hidden Players.","authors":"Mona Kriti, Raj Ojha, Samradhi Singh, Devojit Kumar Sarma, Vinod Verma, Ashok Kumar Yadav, Ravinder Nagpal, Manoj Kumar","doi":"10.1007/s43657-024-00199-1","DOIUrl":"https://doi.org/10.1007/s43657-024-00199-1","url":null,"abstract":"<p><p>Type-2 diabetes mellitus (T2DM) is a global epidemic with significant societal costs. The gut microbiota, including its metabolites, plays a pivotal role in maintaining health, while gut dysbiosis is implicated in several metabolic disorders, including T2DM. Although data exists on the relationship between the gut bacteriome and metabolic disorders, further attention is needed for the mycobiome and virome. Recent advancements have begun to shed light on these connections, offering potential avenues for preventive measures. However, more comprehensive investigations are required to untangle the interrelations between different microbial kingdoms and their role in T2DM development or mitigation. This review presents a simplified overview of the alterations in the gut bacteriome in T2DM and delves into the current understanding of the mycobiome and virome's role in T2DM, along with their interactions with the cohabiting bacteriome. Subsequently, it explores into the age-related dynamics of the gut microbiome and the changes observed in the microbiome composition with the onset of T2DM. Further, we explore the basic workflow utilized in gut microbiome studies. Lastly, we discuss potential therapeutic interventions in gut microbiome research, which could contribute to the amelioration of the condition, serve as preventive measures, or pave the way towards personalized medicine.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"5 1","pages":"51-64"},"PeriodicalIF":3.7,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12040793/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144052910","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":"Development of Next Generation Probiotics for Cardiometabolic Diseases.","authors":"Muhammed Tanweer Khan, Fredrik Bäckhed","doi":"10.1007/s43657-025-00230-z","DOIUrl":"https://doi.org/10.1007/s43657-025-00230-z","url":null,"abstract":"","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"5 1","pages":"18-22"},"PeriodicalIF":3.7,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12040764/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144055335","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":"Relational Stability: A New Strategy for Defining the Human Core Microbiome.","authors":"Liping Zhao","doi":"10.1007/s43657-025-00236-7","DOIUrl":"https://doi.org/10.1007/s43657-025-00236-7","url":null,"abstract":"","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"5 1","pages":"14-17"},"PeriodicalIF":3.7,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12040776/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144055457","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":"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":"https://doi.org/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}

{"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":"https://doi.org/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}

{"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":"https://doi.org/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":"https://doi.org/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":"Precision Dietary Intervention: Gut Microbiome and Meta-metabolome as Functional Readouts.","authors":"Jing Luo, Yulan Wang","doi":"10.1007/s43657-024-00193-7","DOIUrl":"https://doi.org/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":"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}