Cucumber Fermentation Microbiome Data from Nanopore Sequencing, 1-90 Days

A metagenomic dataset from a nanopore sequencing study of spontaneously fermenting cucumbers. The data covers cucumbers from organic and commercial cultivation, sampled from the 1st to the 90th day of fermentation. It was authored by Aleksandra Glapa-Nowak and published on figshare in April 2026.

Use Cases

• Tracking microbial community succession over time based on day-to-day sampling mentioned in the description.
• Comparing phage incidence and diversity between organic and commercial cultivation methods as discussed.
• Investigating the role of specific bacteria like Staphylococcus saprophyticus and Staphylococcus schleiferi in fermentation.
• Analyzing the balance between Enterobacteriaceae and lactic acid bacteria in the absence of phages.

Strengths

• Data is derived from nanopore sequencing, a method noted for providing a broader understanding of microbiome diversity.
• Includes a specific time series covering 90 days of fermentation.
• Explicitly reports the occurrence of specific bacterial species with relative abundances (e.g., Staphylococcus schleiferi at 0.03%).

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment.
• The dataset is small (178.0 KB), indicating a limited scope of observations.

Provenance

Source

figshare

Collection Method

Nanopore sequencing of fermenting cucumber samples.

Time Range

Sampling from day 1 to day 90 of fermentation.

Freshness

Last updated 2026-04-28 05:24:07; freshness should be verified.

Geography

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