📜 From Pothakos 2020 “Temporal shotgun metagenomics of an Ecuadorian coffee fermentation process highlights the predominance of lactic acid bacteria”
This study presents a temporal shotgun metagenomic analysis of an Arabica wet coffee fermentation process conducted at a coffee plantation research station near Nanegal, Ecuador (elevation 1329 m). The project was designed to complement previous microbiological and metabolomic studies of the same fermentation process by providing an in-depth, genome-level analysis of the microbial community structure and functional capabilities. The research examined reproducible wet coffee processing practices, where ripe coffee cherries (Coffea arabica L. var. Typica) were mechanically depulped and fermented underwater in a concrete tank (1 m × 2 m × 2 m).
The primary objectives were to delineate the structure and function of the microbiome, investigate temporal shifts in community composition, track microbial sources from the plantation environment, identify core and transient microbiota, and determine the metabolic roles of distinct microbial species during fermentation.
The study generated approximately 54 million high-quality metagenomic sequences representing 16 Gbp of data, which were analyzed following removal of ~8 million plant DNA sequences from Coffea canephora.
| Sample | Time Point | Description |
|---|---|---|
| F0 | 0 h | Start of fermentation (baseline) |
| F8 | 8 h | Early fermentation phase |
| F16 | 16 h | End of standard fermentation; mucilage removal complete |
| F24 | 24 h | Extended fermentation begins |
| F36 | 36 h | Mid-extended fermentation |
| F64 | 64 h | End of extended fermentation |
The reads were deposited to public repositories under this accession number: PRJEB24129. This project contains indeed six sequenced samples:
We will use - like the authors of the original paper - genome GCA_036785865.1, that we can download using datasets, a CLI tool from NCBI.