在流行病学研究中,比较从客户卡收集的便和95%乙醇的元基因组性能
Thomas M Kuntz1,2, Ling Liu3, Kai Wang4
1Harvard Chan Microbiome Analysis Core, Harvard T. H. Chan School of Public Health, Boston, Massachusetts.
概括
便卡在大型研究中提供了一种具有成本效益的微生物组评估方法. 虽然通常与乙醇固定样本一致,但分析需要考虑物种级别的微小变化.
科学领域:
- 微生物组研究的研究.
- 流行病学 流行病学
- 大基因组测序的测序.
背景情况:
- 便卡在流行病学研究中用于微生物组分析.
- 评估不同便收集方法的可靠性对于大规模研究至关重要.
研究的目的:
- 为了比较 shotgun metagenomic 测序结果,使用定制便卡收集的便样本与95% 乙醇固定剂进行了比较.
- 评估这两种收集方法在整个社区和个体物种层面上的一致性.
- 评估每个方法在区分结直肠癌相关的种群中的性能.
主要方法:
- 在来自护士健康研究II的32个配对便样本上进行了枪支元基因组测序.
- 参与者自行采集样本,使用定制的便卡或采集 95% 乙醇的收集管.
- 使用相关性分析,多样性指标 (α和β),以及对个体物种和结直肠癌相关的种群的差异丰度测试来评估协议.
主要成果:
- 来自便卡和95%乙醇的甲基基因组在个体内高度相关.
- 在α多样性中没有观察到显著的差异;只有~1%的β多样性变化是由采集方法解释的.
- 虽然大多数物种的相对丰度高度相关 (斯皮尔曼rho=0.96),但239种物种中有10种表现出差异的丰度,包括大肠杆菌和链球菌物种. 在99种结直肠癌相关物种中,有4种也表现出差异的丰度,这与偶然一致.
结论:
- 使用便卡或95%乙醇进行元基因组测序的便样本的自我采集结果基本一致.
- 对少量个体物种观察到不同的丰度,需要仔细考虑数据分析.
- 便卡在流行病学研究中为便样本采集提供了一种经济有效的替代方案,尽管可能需要进行特定的分析调整.
相关概念视频
01:27Principles of Pharmacogenetics: Types of Genetic Variants
143
The human genome is over 99.9% identical between individuals, yet genetic differences exist at millions of bases. The human genome contains approximately 3 million variant positions per individual, many of which are heterozygous, contributing to genetic diversity and individual traits. Genetic variations include single-nucleotide polymorphisms (SNPs), insertions, deletions, and copy number variations (CNVs).SNPs, the most common variation, involve single-base changes in DNA. These can be...
143
01:28Pharmacogenetics of Phase I Enzymes: Cytochrome P450 Isozymes
349
Cytochrome P450 (CYP450) enzymes are a superfamily of heme-containing monooxygenases that play a pivotal role in Phase I drug metabolism by catalyzing oxidation and reduction reactions.These enzymes transform lipophilic xenobiotics into more hydrophilic metabolites, facilitating subsequent Phase II conjugation and eventual excretion. The CYP450 family is classified into families (e.g., CYP1–CYP3) and subfamilies (e.g., CYP2A, CYP2C), based on amino acid sequence homology.CYP450...
349
01:16Pharmacogenetics of Drug Transporters: P-Glycoprotein and Solute Carrier Transporters
189
The pharmacogenetics of drug transporters is increasingly recognized as a critical factor influencing interindividual variability in drug absorption, distribution, and elimination. These membrane-bound proteins regulate drugs' movement across cellular barriers by actively pumping them out (efflux) or facilitating their uptake (influx). Among the major transporter families, ATP-binding cassette (ABC) and solute carrier (SLC) transporters play particularly prominent roles. Genetic polymorphisms...
189
01:11Pharmacogenetics of Drug Targets: β₂-Adrenergic Receptors, Apo E, Thymidylate Synthase
84
Genetic polymorphisms in drug targets have emerged as critical determinants of interindividual variability in drug response and toxicity. Pharmacogenomic investigations increasingly focus on identifying these variations to personalize and optimize therapeutic interventions. A drug target may be a receptor, enzyme, or signaling protein involved in pharmacologic responses or disease-related pathways. While early pharmacogenetic studies focused primarily on drug metabolism, current research...
84
01:29Pharmacogenomics: Identification of New Drug Targets
129
Advances in genomics have profoundly influenced drug discovery by increasing both the speed and accuracy of pharmaceutical development. Pharmacogenomics, which examines how genetic variation influences drug response, facilitates the identification of novel therapeutic targets and enables patient stratification for personalized treatment. These strategies contribute to improved drug efficacy, minimized adverse effects, and more efficient clinical trial design.Mapping genetic differences...
129
01:24Automated Microbial Diagnostics
79
Automated diagnostic analyzers have transformed clinical microbiology by providing rapid and reliable methods for pathogen identification and antibiotic susceptibility testing. Among these systems, the Vitek 2 is widely used because it automates the traditionally labor-intensive processes of microbial identification (ID) and antibiotic susceptibility testing (AST), delivering standardized and timely results that are essential for effective patient care.Microbial Identification with ID CardsThe...
79