Identifying Microbes in Space

2026-07-07 · Source: Towards Data Science · Field: Science & Research — Life Sciences & Biology, Mathematics & Computational Sciences, Space Science & Astronomy · Depth: Intermediate, medium

Summary

This article details the process of identifying microbial species on the International Space Station (ISS) using metagenomics, a technique that analyzes all DNA from a given environment without prior knowledge of its inhabitants. It outlines a workflow starting with downloading sequencing data from Urbaniak et al.'s study (sample F4_S5_P from the European Nucleotide Archive), followed by quality trimming with `fastp`. The core of the analysis uses `kraken2`, a rapid metagenomics tool, to classify DNA sequences by breaking them into $k$-mers and comparing them against a database like the PlusPF-8. The analysis of an ISS dining table sample revealed species such as *Pseudolactococcus raffinolactis*, *Cutibacterium acnes*, *Ralstonia pickettii*, and notably, *Leuconostoc mesenteroides*. The presence of *L. mesenteroides* was traced to kimchi consumed on the ISS in 2008. The article further explains `kraken2`'s mechanism, which employs minimizers and compact hash codes for speed, contrasting it with slower alignment tools like BLAST.

Key takeaway

For research scientists analyzing complex microbial samples, understanding `kraken2`'s $k$-mer and hashing approach is crucial. This method offers significantly faster taxonomic classification than alignment-based tools like BLAST, especially with large datasets. You should consider integrating `kraken2` into your metagenomic workflows for efficient species identification, particularly when dealing with environmental or clinical samples where speed and database-driven matching are paramount. This allows for rapid insights into microbial communities.

Key insights

Metagenomics with tools like `kraken2` rapidly identifies unknown microbial species by comparing DNA sequences to databases using efficient hashing techniques.

Principles

• Metagenomics identifies all species in an environment.
• Exact $k$-mer matching accelerates sequence classification.
• Minimizers and compact hashes optimize database search.

Method

Download raw metagenomic reads, trim and filter for quality using `fastp`, then classify reads taxonomically using `kraken2` against a pre-built database, and analyze reports.

In practice

• Use `fastp` for rapid DNA read quality control.
• Employ `kraken2` for fast metagenomic species identification.
• Select `kraken2` databases with relevant taxa (e.g., fungi/bacteria).

Topics

• Metagenomics
• DNA Sequencing
• Kraken2
• Bioinformatics Tools
• K-mer Analysis
• International Space Station

Code references

• DerrickWood/kraken2
• DAWells/space_mould
• sourmash-bio/sourmash

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Editorial summary, takeaway, and curation by AIssential. Original article published by Towards Data Science.