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Identification, Recovery, and Refinement of Hitherto Undescribed Population-Level Genomes from the Human Gastrointestinal Tract

Linking taxonomic identity and functional potential at the population-level is important for the study of mixed microbial communities and is greatly facilitated by the availability of microbial reference genomes. While the culture-independent recovery of population-level genomes from environmental s...

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Autores principales: Laczny, Cedric C., Muller, Emilie E. L., Heintz-Buschart, Anna, Herold, Malte, Lebrun, Laura A., Hogan, Angela, May, Patrick, de Beaufort, Carine, Wilmes, Paul
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4914512/
https://www.ncbi.nlm.nih.gov/pubmed/27445992
http://dx.doi.org/10.3389/fmicb.2016.00884
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author Laczny, Cedric C.
Muller, Emilie E. L.
Heintz-Buschart, Anna
Herold, Malte
Lebrun, Laura A.
Hogan, Angela
May, Patrick
de Beaufort, Carine
Wilmes, Paul
author_facet Laczny, Cedric C.
Muller, Emilie E. L.
Heintz-Buschart, Anna
Herold, Malte
Lebrun, Laura A.
Hogan, Angela
May, Patrick
de Beaufort, Carine
Wilmes, Paul
author_sort Laczny, Cedric C.
collection PubMed
description Linking taxonomic identity and functional potential at the population-level is important for the study of mixed microbial communities and is greatly facilitated by the availability of microbial reference genomes. While the culture-independent recovery of population-level genomes from environmental samples using the binning of metagenomic data has expanded available reference genome catalogs, several microbial lineages remain underrepresented. Here, we present two reference-independent approaches for the identification, recovery, and refinement of hitherto undescribed population-level genomes. The first approach is aimed at genome recovery of varied taxa and involves multi-sample automated binning using CANOPY CLUSTERING complemented by visualization and human-augmented binning using VIZBIN post hoc. The second approach is particularly well-suited for the study of specific taxa and employs VIZBIN de novo. Using these approaches, we reconstructed a total of six population-level genomes of distinct and divergent representatives of the Alphaproteobacteria class, the Mollicutes class, the Clostridiales order, and the Melainabacteria class from human gastrointestinal tract-derived metagenomic data. Our results demonstrate that, while automated binning approaches provide great potential for large-scale studies of mixed microbial communities, these approaches should be complemented with informative visualizations because expert-driven inspection and refinements are critical for the recovery of high-quality population-level genomes.
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spelling pubmed-49145122016-07-21 Identification, Recovery, and Refinement of Hitherto Undescribed Population-Level Genomes from the Human Gastrointestinal Tract Laczny, Cedric C. Muller, Emilie E. L. Heintz-Buschart, Anna Herold, Malte Lebrun, Laura A. Hogan, Angela May, Patrick de Beaufort, Carine Wilmes, Paul Front Microbiol Microbiology Linking taxonomic identity and functional potential at the population-level is important for the study of mixed microbial communities and is greatly facilitated by the availability of microbial reference genomes. While the culture-independent recovery of population-level genomes from environmental samples using the binning of metagenomic data has expanded available reference genome catalogs, several microbial lineages remain underrepresented. Here, we present two reference-independent approaches for the identification, recovery, and refinement of hitherto undescribed population-level genomes. The first approach is aimed at genome recovery of varied taxa and involves multi-sample automated binning using CANOPY CLUSTERING complemented by visualization and human-augmented binning using VIZBIN post hoc. The second approach is particularly well-suited for the study of specific taxa and employs VIZBIN de novo. Using these approaches, we reconstructed a total of six population-level genomes of distinct and divergent representatives of the Alphaproteobacteria class, the Mollicutes class, the Clostridiales order, and the Melainabacteria class from human gastrointestinal tract-derived metagenomic data. Our results demonstrate that, while automated binning approaches provide great potential for large-scale studies of mixed microbial communities, these approaches should be complemented with informative visualizations because expert-driven inspection and refinements are critical for the recovery of high-quality population-level genomes. Frontiers Media S.A. 2016-06-21 /pmc/articles/PMC4914512/ /pubmed/27445992 http://dx.doi.org/10.3389/fmicb.2016.00884 Text en Copyright © 2016 Laczny, Muller, Heintz-Buschart, Herold, Lebrun, Hogan, May, de Beaufort and Wilmes. http://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) or licensor 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
Laczny, Cedric C.
Muller, Emilie E. L.
Heintz-Buschart, Anna
Herold, Malte
Lebrun, Laura A.
Hogan, Angela
May, Patrick
de Beaufort, Carine
Wilmes, Paul
Identification, Recovery, and Refinement of Hitherto Undescribed Population-Level Genomes from the Human Gastrointestinal Tract
title Identification, Recovery, and Refinement of Hitherto Undescribed Population-Level Genomes from the Human Gastrointestinal Tract
title_full Identification, Recovery, and Refinement of Hitherto Undescribed Population-Level Genomes from the Human Gastrointestinal Tract
title_fullStr Identification, Recovery, and Refinement of Hitherto Undescribed Population-Level Genomes from the Human Gastrointestinal Tract
title_full_unstemmed Identification, Recovery, and Refinement of Hitherto Undescribed Population-Level Genomes from the Human Gastrointestinal Tract
title_short Identification, Recovery, and Refinement of Hitherto Undescribed Population-Level Genomes from the Human Gastrointestinal Tract
title_sort identification, recovery, and refinement of hitherto undescribed population-level genomes from the human gastrointestinal tract
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4914512/
https://www.ncbi.nlm.nih.gov/pubmed/27445992
http://dx.doi.org/10.3389/fmicb.2016.00884
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