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Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach
Following the trend of studies that investigate microbial ecosystems using different metagenomic techniques, we propose a new integrative systems ecology approach that aims to decipher functional roles within a consortium through the integration of genomic and metabolic knowledge at genome scale. Fo...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley and Sons Inc.
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4767419/ https://www.ncbi.nlm.nih.gov/pubmed/26677108 http://dx.doi.org/10.1002/mbo3.315 |
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author | Bordron, Philippe Latorre, Mauricio Cortés, Maria‐Paz González, Mauricio Thiele, Sven Siegel, Anne Maass, Alejandro Eveillard, Damien |
author_facet | Bordron, Philippe Latorre, Mauricio Cortés, Maria‐Paz González, Mauricio Thiele, Sven Siegel, Anne Maass, Alejandro Eveillard, Damien |
author_sort | Bordron, Philippe |
collection | PubMed |
description | Following the trend of studies that investigate microbial ecosystems using different metagenomic techniques, we propose a new integrative systems ecology approach that aims to decipher functional roles within a consortium through the integration of genomic and metabolic knowledge at genome scale. For the sake of application, using public genomes of five bacterial strains involved in copper bioleaching: Acidiphilium cryptum, Acidithiobacillus ferrooxidans, Acidithiobacillus thiooxidans, Leptospirillum ferriphilum, and Sulfobacillus thermosulfidooxidans, we first reconstructed a global metabolic network. Next, using a parsimony assumption, we deciphered sets of genes, called Sets from Genome Segments (SGS), that (1) are close on their respective genomes, (2) take an active part in metabolic pathways and (3) whose associated metabolic reactions are also closely connected within metabolic networks. Overall, this SGS paradigm depicts genomic functional units that emphasize respective roles of bacterial strains to catalyze metabolic pathways and environmental processes. Our analysis suggested that only few functional metabolic genes are horizontally transferred within the consortium and that no single bacterial strain can accomplish by itself the whole copper bioleaching. The use of SGS pinpoints a functional compartmentalization among the investigated species and exhibits putative bacterial interactions necessary for promoting these pathways. |
format | Online Article Text |
id | pubmed-4767419 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | John Wiley and Sons Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-47674192016-03-07 Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach Bordron, Philippe Latorre, Mauricio Cortés, Maria‐Paz González, Mauricio Thiele, Sven Siegel, Anne Maass, Alejandro Eveillard, Damien Microbiologyopen Original Research Following the trend of studies that investigate microbial ecosystems using different metagenomic techniques, we propose a new integrative systems ecology approach that aims to decipher functional roles within a consortium through the integration of genomic and metabolic knowledge at genome scale. For the sake of application, using public genomes of five bacterial strains involved in copper bioleaching: Acidiphilium cryptum, Acidithiobacillus ferrooxidans, Acidithiobacillus thiooxidans, Leptospirillum ferriphilum, and Sulfobacillus thermosulfidooxidans, we first reconstructed a global metabolic network. Next, using a parsimony assumption, we deciphered sets of genes, called Sets from Genome Segments (SGS), that (1) are close on their respective genomes, (2) take an active part in metabolic pathways and (3) whose associated metabolic reactions are also closely connected within metabolic networks. Overall, this SGS paradigm depicts genomic functional units that emphasize respective roles of bacterial strains to catalyze metabolic pathways and environmental processes. Our analysis suggested that only few functional metabolic genes are horizontally transferred within the consortium and that no single bacterial strain can accomplish by itself the whole copper bioleaching. The use of SGS pinpoints a functional compartmentalization among the investigated species and exhibits putative bacterial interactions necessary for promoting these pathways. John Wiley and Sons Inc. 2015-12-17 /pmc/articles/PMC4767419/ /pubmed/26677108 http://dx.doi.org/10.1002/mbo3.315 Text en © 2015 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution (http://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Original Research Bordron, Philippe Latorre, Mauricio Cortés, Maria‐Paz González, Mauricio Thiele, Sven Siegel, Anne Maass, Alejandro Eveillard, Damien Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach |
title | Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach |
title_full | Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach |
title_fullStr | Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach |
title_full_unstemmed | Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach |
title_short | Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach |
title_sort | putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach |
topic | Original Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4767419/ https://www.ncbi.nlm.nih.gov/pubmed/26677108 http://dx.doi.org/10.1002/mbo3.315 |
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