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Assembly and analytical validation of a metagenomic reference catalog of human gut microbiota based on co-barcoding sequencing
Human gut microbiota is associated with human health and disease, and is known to have the second-largest genome in the human body. The microbiota genome is important for their functions and metabolites; however, accurate genomic access to the microbiota of the human gut is hindered due to the diffi...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10196144/ https://www.ncbi.nlm.nih.gov/pubmed/37213501 http://dx.doi.org/10.3389/fmicb.2023.1145315 |
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author | Huang, Yufen Jiang, Puzi Liang, Zhengjiao Chen, Rouxi Yue, Zhen Xie, Xuefeng Guan, Changge Fang, Xiaodong |
author_facet | Huang, Yufen Jiang, Puzi Liang, Zhengjiao Chen, Rouxi Yue, Zhen Xie, Xuefeng Guan, Changge Fang, Xiaodong |
author_sort | Huang, Yufen |
collection | PubMed |
description | Human gut microbiota is associated with human health and disease, and is known to have the second-largest genome in the human body. The microbiota genome is important for their functions and metabolites; however, accurate genomic access to the microbiota of the human gut is hindered due to the difficulty of cultivating and the shortcomings of sequencing technology. Therefore, we applied the stLFR library construction method to assemble the microbiota genomes and demonstrated that assembly property outperformed standard metagenome sequencing. Using the assembled genomes as references, SNP, INDEL, and HGT gene analyses were performed. The results demonstrated significant differences in the number of SNPs and INDELs among different individuals. The individual displayed a unique species variation spectrum, and the similarity of strains within individuals decreased over time. In addition, the coverage depth analysis of the stLFR method shows that a sequencing depth of 60X is sufficient for SNP calling. HGT analysis revealed that the genes involved in replication, recombination and repair, mobilome prophages, and transposons were the most transferred genes among different bacterial species in individuals. A preliminary framework for human gut microbiome studies was established using the stLFR library construction method. |
format | Online Article Text |
id | pubmed-10196144 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-101961442023-05-20 Assembly and analytical validation of a metagenomic reference catalog of human gut microbiota based on co-barcoding sequencing Huang, Yufen Jiang, Puzi Liang, Zhengjiao Chen, Rouxi Yue, Zhen Xie, Xuefeng Guan, Changge Fang, Xiaodong Front Microbiol Microbiology Human gut microbiota is associated with human health and disease, and is known to have the second-largest genome in the human body. The microbiota genome is important for their functions and metabolites; however, accurate genomic access to the microbiota of the human gut is hindered due to the difficulty of cultivating and the shortcomings of sequencing technology. Therefore, we applied the stLFR library construction method to assemble the microbiota genomes and demonstrated that assembly property outperformed standard metagenome sequencing. Using the assembled genomes as references, SNP, INDEL, and HGT gene analyses were performed. The results demonstrated significant differences in the number of SNPs and INDELs among different individuals. The individual displayed a unique species variation spectrum, and the similarity of strains within individuals decreased over time. In addition, the coverage depth analysis of the stLFR method shows that a sequencing depth of 60X is sufficient for SNP calling. HGT analysis revealed that the genes involved in replication, recombination and repair, mobilome prophages, and transposons were the most transferred genes among different bacterial species in individuals. A preliminary framework for human gut microbiome studies was established using the stLFR library construction method. Frontiers Media S.A. 2023-05-05 /pmc/articles/PMC10196144/ /pubmed/37213501 http://dx.doi.org/10.3389/fmicb.2023.1145315 Text en Copyright © 2023 Huang, Jiang, Liang, Chen, Yue, Xie, Guan and Fang. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Microbiology Huang, Yufen Jiang, Puzi Liang, Zhengjiao Chen, Rouxi Yue, Zhen Xie, Xuefeng Guan, Changge Fang, Xiaodong Assembly and analytical validation of a metagenomic reference catalog of human gut microbiota based on co-barcoding sequencing |
title | Assembly and analytical validation of a metagenomic reference catalog of human gut microbiota based on co-barcoding sequencing |
title_full | Assembly and analytical validation of a metagenomic reference catalog of human gut microbiota based on co-barcoding sequencing |
title_fullStr | Assembly and analytical validation of a metagenomic reference catalog of human gut microbiota based on co-barcoding sequencing |
title_full_unstemmed | Assembly and analytical validation of a metagenomic reference catalog of human gut microbiota based on co-barcoding sequencing |
title_short | Assembly and analytical validation of a metagenomic reference catalog of human gut microbiota based on co-barcoding sequencing |
title_sort | assembly and analytical validation of a metagenomic reference catalog of human gut microbiota based on co-barcoding sequencing |
topic | Microbiology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10196144/ https://www.ncbi.nlm.nih.gov/pubmed/37213501 http://dx.doi.org/10.3389/fmicb.2023.1145315 |
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