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Functional and taxonomic classification of a greenhouse water drain metagenome
Microbiome sequencing has become the standard procedure in the study of new ecological and human-constructed niches. To our knowledge, this is the first report of a metagenome from the water of a greenhouse drain. We found that the greenhouse is not a diverse niche, mainly dominated by Rhizobiales a...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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BioMed Central
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6173933/ https://www.ncbi.nlm.nih.gov/pubmed/30323887 http://dx.doi.org/10.1186/s40793-018-0326-y |
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author | López-Leal, Gamaliel Cornejo-Granados, Fernanda Hurtado-Ramírez, Juan Manuel Mendoza-Vargas, Alfredo Ochoa-Leyva, Adrian |
author_facet | López-Leal, Gamaliel Cornejo-Granados, Fernanda Hurtado-Ramírez, Juan Manuel Mendoza-Vargas, Alfredo Ochoa-Leyva, Adrian |
author_sort | López-Leal, Gamaliel |
collection | PubMed |
description | Microbiome sequencing has become the standard procedure in the study of new ecological and human-constructed niches. To our knowledge, this is the first report of a metagenome from the water of a greenhouse drain. We found that the greenhouse is not a diverse niche, mainly dominated by Rhizobiales and Rodobacterales. The analysis of the functions encoded in the metagenome showed enrichment of characteristic features of soil and root-associated bacteria such as ABC-transporters and hydrolase enzymes. Additionally, we found antibiotic resistances genes principally for spectinomycin, tetracycline, and aminoglycosides. This study aimed to identify the bacteria and functional gene composition of a greenhouse water drain sample and also provide a genomic resource to search novel proteins from a previously unexplored niche. All the metagenome proteins and their annotations are available to the scientific community via http://microbiomics.ibt.unam.mx/tools/metagreenhouse/. |
format | Online Article Text |
id | pubmed-6173933 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-61739332018-10-15 Functional and taxonomic classification of a greenhouse water drain metagenome López-Leal, Gamaliel Cornejo-Granados, Fernanda Hurtado-Ramírez, Juan Manuel Mendoza-Vargas, Alfredo Ochoa-Leyva, Adrian Stand Genomic Sci Metagenome Report Microbiome sequencing has become the standard procedure in the study of new ecological and human-constructed niches. To our knowledge, this is the first report of a metagenome from the water of a greenhouse drain. We found that the greenhouse is not a diverse niche, mainly dominated by Rhizobiales and Rodobacterales. The analysis of the functions encoded in the metagenome showed enrichment of characteristic features of soil and root-associated bacteria such as ABC-transporters and hydrolase enzymes. Additionally, we found antibiotic resistances genes principally for spectinomycin, tetracycline, and aminoglycosides. This study aimed to identify the bacteria and functional gene composition of a greenhouse water drain sample and also provide a genomic resource to search novel proteins from a previously unexplored niche. All the metagenome proteins and their annotations are available to the scientific community via http://microbiomics.ibt.unam.mx/tools/metagreenhouse/. BioMed Central 2018-10-05 /pmc/articles/PMC6173933/ /pubmed/30323887 http://dx.doi.org/10.1186/s40793-018-0326-y Text en © The Author(s). 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Metagenome Report López-Leal, Gamaliel Cornejo-Granados, Fernanda Hurtado-Ramírez, Juan Manuel Mendoza-Vargas, Alfredo Ochoa-Leyva, Adrian Functional and taxonomic classification of a greenhouse water drain metagenome |
title | Functional and taxonomic classification of a greenhouse water drain metagenome |
title_full | Functional and taxonomic classification of a greenhouse water drain metagenome |
title_fullStr | Functional and taxonomic classification of a greenhouse water drain metagenome |
title_full_unstemmed | Functional and taxonomic classification of a greenhouse water drain metagenome |
title_short | Functional and taxonomic classification of a greenhouse water drain metagenome |
title_sort | functional and taxonomic classification of a greenhouse water drain metagenome |
topic | Metagenome Report |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6173933/ https://www.ncbi.nlm.nih.gov/pubmed/30323887 http://dx.doi.org/10.1186/s40793-018-0326-y |
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