دورية أكاديمية
Single-gene long-read sequencing illuminates Escherichia coli strain dynamics in the human intestinal microbiome.
| العنوان: | Single-gene long-read sequencing illuminates Escherichia coli strain dynamics in the human intestinal microbiome. |
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| المؤلفون: | Hu D; School of Life and Environmental Sciences, Charles Perkins Centre, University of Sydney, Camperdown, NSW 2006, Australia., Fuller NR; The Boden Institute, Charles Perkins Centre, University of Sydney, Camperdown, NSW 2006, Australia; Metabolism and Obesity Services, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia., Caterson ID; School of Life and Environmental Sciences, Charles Perkins Centre, University of Sydney, Camperdown, NSW 2006, Australia; The Boden Institute, Charles Perkins Centre, University of Sydney, Camperdown, NSW 2006, Australia; Metabolism and Obesity Services, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia., Holmes AJ; School of Life and Environmental Sciences, Charles Perkins Centre, University of Sydney, Camperdown, NSW 2006, Australia., Reeves PR; School of Life and Environmental Sciences, Charles Perkins Centre, University of Sydney, Camperdown, NSW 2006, Australia. Electronic address: peter.reeves@sydney.edu.au. |
| المصدر: | Cell reports [Cell Rep] 2022 Jan 11; Vol. 38 (2), pp. 110239. |
| نوع المنشور: | Journal Article; Research Support, Non-U.S. Gov't |
| اللغة: | English |
| بيانات الدورية: | Publisher: Cell Press Country of Publication: United States NLM ID: 101573691 Publication Model: Print Cited Medium: Internet ISSN: 2211-1247 (Electronic) NLM ISO Abbreviation: Cell Rep Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: [Cambridge, MA] : Cell Press, c 2012- |
| مواضيع طبية MeSH: | Escherichia coli/*metabolism , Gastrointestinal Microbiome/*genetics , Transcriptome/*genetics, Adult ; DNA, Bacterial/genetics ; Escherichia coli/genetics ; Escherichia coli Proteins/metabolism ; Feces/microbiology ; Female ; Flagellin/genetics ; Flagellin/metabolism ; Gastrointestinal Microbiome/physiology ; Gene Expression/genetics ; Genetic Variation/genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Intestines ; Male ; Microbiota/genetics ; Middle Aged ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods |
| مستخلص: | Gut microbiome is of major interest due to its close relationship to health and disease. Bacteria usually vary in gene content, leading to functional variations within species, so resolution higher than species-level methods is needed for ecological and clinical relevance. We design a protocol to identify strains in selected species with high discrimination and in high numbers by amplicon sequencing of the flagellin gene. We apply the protocol to fecal samples from a human diet trial, targeting Escherichia coli. Across the 119 samples from 16 individuals, there are 1,532 amplicon sequence variants (ASVs), but only 32 ASVs are dominant in one or more fecal samples, despite frequent dominant strain turnover. Major strains in an intestine are found to be commonly accompanied by a large number of satellite cells, and many are identified as potential extraintestinal pathogens. The protocol could be used to track epidemics or investigate the intra- or inter-host diversity of pathogens. Competing Interests: Declaration of interests The authors declare no competing interests. (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.) |
| فهرسة مساهمة: | Keywords: E. coli strain diversity; amplicon sequence variation (ASV); human gut microbiome; strain-level metagenomic profiling |
| المشرفين على المادة: | 0 (DNA, Bacterial) 0 (Escherichia coli Proteins) 0 (RNA, Ribosomal, 16S) 12777-81-0 (Flagellin) |
| تواريخ الأحداث: | Date Created: 20220112 Date Completed: 20220214 Latest Revision: 20220214 |
| رمز التحديث: | 20240829 |
| DOI: | 10.1016/j.celrep.2021.110239 |
| PMID: | 35021078 |
| قاعدة البيانات: | MEDLINE |
Full Text Finder | تدمد: | 2211-1247 |
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| DOI: | 10.1016/j.celrep.2021.110239 |