food production metagenome
collection_date
2021-12-20
env_broad_scale
Coffee farm
env_local_scale
not applicable
env_medium
coffee mucilage liquid fraction
geo_loc_name_country
Colombia
geo_loc_name
Colombia: Quindio
host
Coffea arabica L.
lat_lon
4.61694 N 75.63306 W
library_strategy
AMPLICON
library_source
METAGENOMIC
Library_Layout
PAIRED
Library_Selection
PCR
Library_Source
METAGENOMIC
platform
ILLUMINA
instrument_model
Illumina MiSeq
design_description
Samples of coffee beans and mucilage were collected at the beginning (CD) and at the end of fermentation (CF) from each of the sampling units (farms), for gDNA extraction, was used a kit DNeasy Powerlyzer Powersoil (QIAGEN). DNA quantification was performed using a spectrophotometer NanoDrop™ 2000-Thermo Scientific™. For the deep sequencing of bacterial 16S rRNA genes, a fragment containing the V3 and V4 variable regions was amplified using the oligonucleotide primers 341F/805R. For fungal diversity, amplification of the ITS2 region was performed using the primers ITS3F/ITS4R. Sequencing was performed on the Illumina MiSeq platform, generating 300bp paired reads each. Sequence quality and classification analyses were performed using MOTHUR version 1.44 platform. Sequences for fungi and bacteria were taxonomically assigned according to the SILVA v138 database, using the VSEARCH method. The phylogenetic classification was performed using the Classifier tool from the RDP database.
filetype
fastq
filename
16SFNACD13R1_1.fastq.gz
filename2
16SFNACD13R1_2.fastq.gz
filename3
16SFNACD13R2_1.fastq.gz
filename4
16SFNACD13R2_2.fastq.gz
filename5
16SFNACD13R3_1.fastq.gz
filename6
16SFNACD13R3_2.fastq.gz
filename7
ITSFNACD13R1_1.fastq.gz
filename8
ITSFNACD13R1_2.fastq.gz
filename9
ITSFNACD13R2_1.fastq.gz
filename10
ITSFNACD13R2_2.fastq.gz
filename11
ITSFNACD13R3_1.fastq.gz
filename12
ITSFNACD13R3_2.fastq.gz
BioSampleModel
MIMARKS.survey
BioSampleModel
MIGS/MIMS/MIMARKS.plant-associated