用于微生物生态学分析的肠道微生物群采样及细菌16S rRNA基因的靶向扩增。
Sampling of intestinal microbiota and targeted amplification of bacterial 16S rRNA genes for microbial ecologic analysis.
作者信息
Tong Maomeng, Jacobs Jonathan P, McHardy Ian H, Braun Jonathan
机构信息
Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at the University of California at Los Angeles, Los Angeles, California.
Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at the University of California at Los Angeles, Los Angeles, California.
出版信息
Curr Protoc Immunol. 2014 Nov 3;107:7.41.1-7.41.11. doi: 10.1002/0471142735.im0741s107.
Abstract
Dysbiosis of host-associated commensal microbiota is emerging as an important factor in risk and phenotype of immunologic, metabolic, and behavioral diseases. Accurate analysis of microbial composition and functional state in humans or mice requires appropriate collection and pre-processing of biospecimens. Methods to sample luminal and mucosal microbiota from human or mouse intestines and to profile microbial phylogenetic composition using 16S rRNA sequencing are presented here. Data generated using the methods in this unit can be used for downstream quantitative analysis of microbial ecology.
摘要
宿主相关共生微生物群的失调正成为免疫、代谢和行为疾病风险及表型的一个重要因素。准确分析人类或小鼠体内的微生物组成和功能状态需要对生物样本进行适当的采集和预处理。本文介绍了从人类或小鼠肠道中采集管腔和黏膜微生物群以及使用16S rRNA测序分析微生物系统发育组成的方法。使用本单元所述方法生成的数据可用于微生物生态学的下游定量分析。
相似文献
1
Sampling of intestinal microbiota and targeted amplification of bacterial 16S rRNA genes for microbial ecologic analysis.用于微生物生态学分析的肠道微生物群采样及细菌16S rRNA基因的靶向扩增。
Curr Protoc Immunol. 2014 Nov 3;107:7.41.1-7.41.11. doi: 10.1002/0471142735.im0741s107.
2
High throughput sequencing reveals distinct microbial populations within the mucosal and luminal niches in healthy individuals.高通量测序揭示了健康个体黏膜和管腔生态位内不同的微生物群落。
Gut Microbes. 2015;6(3):173-81. doi: 10.1080/19490976.2015.1044711.
3
Characterising the Canine Oral Microbiome by Direct Sequencing of Reverse-Transcribed rRNA Molecules.通过逆转录rRNA分子的直接测序对犬口腔微生物群进行特征分析。
PLoS One. 2016 Jun 8;11(6):e0157046. doi: 10.1371/journal.pone.0157046. eCollection 2016.
4
Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing.采用两步法PCR和新一代16S rRNA基因测序进行微生物群分析
J Vis Exp. 2019 Oct 15(152). doi: 10.3791/59980.
5
Analyses of Intestinal Microbiota: Culture versus Sequencing.肠道微生物群分析：培养法与测序法
ILAR J. 2015;56(2):228-40. doi: 10.1093/ilar/ilv017.
6
Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification.使用16S rRNA基因扩增技术重建古代微生物群落所面临的内在挑战。
Sci Rep. 2015 Nov 13;5:16498. doi: 10.1038/srep16498.
7
High-throughput 16S rRNA gene sequencing reveals alterations of intestinal microbiota in myalgic encephalomyelitis/chronic fatigue syndrome patients.高通量 16S rRNA 基因测序揭示肌痛性脑脊髓炎/慢性疲劳综合征患者肠道微生物组的改变。
Anaerobe. 2013 Aug;22:50-6. doi: 10.1016/j.anaerobe.2013.06.002. Epub 2013 Jun 19.
8
Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing.基于16S rRNA扩增子测序的粪便微生物特征分析指导方案
J Vis Exp. 2018 Mar 19(133):56845. doi: 10.3791/56845.
9
Analysis of the mouse gut microbiome using full-length 16S rRNA amplicon sequencing.使用全长 16S rRNA 扩增子测序分析小鼠肠道微生物组。
Sci Rep. 2016 Jul 14;6:29681. doi: 10.1038/srep29681.
10
Evaluation of Full-Length Versus V4-Region 16S rRNA Sequencing for Phylogenetic Analysis of Mouse Intestinal Microbiota After a Dietary Intervention.评价膳食干预后小鼠肠道微生物群系统发育分析时全长 16S rRNA 测序与 V4 区 16S rRNA 测序的效果。
Curr Microbiol. 2022 Jul 30;79(9):276. doi: 10.1007/s00284-022-02956-9.
引用本文的文献
1
Sex-based associations between neighborhood disadvantage and brain-gut alterations in individuals with irritable bowel syndrome.肠易激综合征患者中，邻里劣势与脑-肠改变之间基于性别的关联。
Biol Sex Differ. 2025 Aug 11;16(1):61. doi: 10.1186/s13293-025-00739-y.
2
Biogeographical distribution of gut microbiome composition and function is partially recapitulated by fecal transplantation into germ-free mice.通过将粪便移植到无菌小鼠体内，部分重现了肠道微生物组组成和功能的生物地理分布。
ISME J. 2025 Jan 2;19(1). doi: 10.1093/ismejo/wrae250.
3
Stress-Resilience Impacts Psychological Wellbeing: Evidence from Brain-Gut Microbiome Interactions.应激适应力对心理健康的影响：来自脑-肠-微生物组相互作用的证据。
Nat Ment Health. 2024 Aug;2(8):935-950. doi: 10.1038/s44220-024-00266-6. Epub 2024 Jun 21.
4
Gastrointestinal Microbiota in Gastric Cancer: Potential Mechanisms and Clinical Applications-A Literature Review.胃癌中的胃肠道微生物群：潜在机制与临床应用——文献综述
Cancers (Basel). 2024 Oct 21;16(20):3547. doi: 10.3390/cancers16203547.
5
ZIP8 A391T Crohn's Disease-Linked Risk Variant Induces Colonic Metal Ion Dyshomeostasis, Microbiome Compositional Shifts, and Inflammation.ZIP8 A391T 克罗恩病相关风险变异导致结肠金属离子稳态失调、微生物组组成变化和炎症。
Dig Dis Sci. 2024 Oct;69(10):3760-3772. doi: 10.1007/s10620-024-08647-8. Epub 2024 Sep 25.
6
Bariatric-induced microbiome changes alter MASLD development in association with changes in the innate immune system.肥胖诱导的微生物群变化与先天性免疫系统的变化相关，从而改变代谢相关脂肪性肝病的发展。
Front Microbiol. 2024 Aug 9;15:1407555. doi: 10.3389/fmicb.2024.1407555. eCollection 2024.
7
Enhanced CTLA-4 blockade anti-tumor immunity with APG-157 combination in a murine head and neck cancer.CTLA-4 阻断增强抗肿瘤免疫作用与 APG-157 联合治疗鼠头颈部肿瘤。
Cancer Med. 2024 May;13(9):e7212. doi: 10.1002/cam4.7212.
8
Diet and the gut microbiome in patients with Parkinson's disease.帕金森病患者的饮食与肠道微生物群
NPJ Parkinsons Dis. 2024 Apr 22;10(1):89. doi: 10.1038/s41531-024-00681-7.
9
Ambient long-term exposure to organophosphorus pesticides and the human gut microbiome: an observational study.环境中长期暴露于有机磷农药与人类肠道微生物组：一项观察性研究。
Environ Health. 2024 Apr 16;23(1):41. doi: 10.1186/s12940-024-01078-y.
10
Are fecal samples an appropriate proxy for amphibian intestinal microbiota?粪便样本是否是两栖动物肠道微生物群的合适替代物？
Ecol Evol. 2024 Jan 31;14(2):e10862. doi: 10.1002/ece3.10862. eCollection 2024 Feb.
本文引用的文献
1
HIV Infection is associated with compositional and functional shifts in the rectal mucosal microbiota.HIV 感染与直肠黏膜微生物群落的组成和功能变化有关。
Microbiome. 2013 Oct 12;1(1):26. doi: 10.1186/2049-2618-1-26.
2
Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships.整合分析人类肠道黏膜表面的微生物组和代谢组揭示了精细的相互关系。
Microbiome. 2013 Jun 5;1(1):17. doi: 10.1186/2049-2618-1-17.
3
A modular organization of the human intestinal mucosal microbiota and its association with inflammatory bowel disease.人类肠道黏膜微生物群的模块化组织及其与炎症性肠病的关联。
PLoS One. 2013 Nov 19;8(11):e80702. doi: 10.1371/journal.pone.0080702. eCollection 2013.
4
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences.基于 16S rRNA 标记基因序列对微生物群落进行功能预测分析。
Nat Biotechnol. 2013 Sep;31(9):814-21. doi: 10.1038/nbt.2676. Epub 2013 Aug 25.
5
Gut microbiota disturbance during antibiotic therapy: a multi-omic approach.抗生素治疗期间的肠道微生物失调：一种多组学方法。
Gut. 2013 Nov;62(11):1591-601. doi: 10.1136/gutjnl-2012-303184. Epub 2012 Dec 12.
6
Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease.整合宏基因组/宏蛋白质组学揭示了克罗恩病的人类宿主-微生物群特征。
PLoS One. 2012;7(11):e49138. doi: 10.1371/journal.pone.0049138. Epub 2012 Nov 28.
7
Using QIIME to analyze 16S rRNA gene sequences from microbial communities.使用QIIME分析来自微生物群落的16S rRNA基因序列。
Curr Protoc Microbiol. 2012 Nov;Chapter 1:Unit 1E.5.. doi: 10.1002/9780471729259.mc01e05s27.
8
Host-gut microbiota metabolic interactions.宿主-肠道微生物群代谢相互作用。
Science. 2012 Jun 8;336(6086):1262-7. doi: 10.1126/science.1223813. Epub 2012 Jun 6.
9
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms.Illumina HiSeq 和 MiSeq 平台上的超高通量微生物群落分析。
ISME J. 2012 Aug;6(8):1621-4. doi: 10.1038/ismej.2012.8. Epub 2012 Mar 8.
10
A metaproteomic approach to study human-microbial ecosystems at the mucosal luminal interface.采用宏蛋白质组学方法研究黏膜腔界面的人类微生物生态系统。
PLoS One. 2011;6(11):e26542. doi: 10.1371/journal.pone.0026542. Epub 2011 Nov 21.
Zotero 插件