Functional and taxonomic classification of a greenhouse water drain metagenome

• Main Authors: Gamaliel López-Leal, Fernanda Cornejo-Granados, Juan Manuel Hurtado-Ramírez, Alfredo Mendoza-Vargas, Adrian Ochoa-Leyva
• Format: Article
• Language: English
• Published: BMC 2018-10-01
• Series: Standards in Genomic Sciences
• Subjects: Shotgun sequencing; Greenhouse; Metagenome; Environmental sample; Water drain
• Online Access: http://link.springer.com/article/10.1186/s40793-018-0326-y

Abstract 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/.