Microbial Evolution — Data Braids

Reference genome and taxonomy database for evolutionary biology and microbial community analysis. The anchor datasets for wetSpring.

LTEE REL606 genome

Reference genome for E. coli B strain REL606 — the ancestral strain of Lenski’s Long-Term Evolution Experiment (LTEE). 4.6M bp, 4,432 genes. The starting point for tracking 75,000+ generations of evolution in the longest-running evolution experiment in history.

What’s Possible

• Anchor for LTEE evolutionary dynamics analysis (wetSpring breseq pipeline)
• Combine with SILVA 138.1 for phylogenetic context of evolved populations
• Feed lithoSpore for self-verifying genomic artifacts
• Map mutations across 75K generations to functional annotations in UniProt

The Braid

sweetGrass braid.create produced a W3C PROV-O JSON-LD attestation:

{
  "@context": "https://www.w3.org/ns/prov#",
  "@id": "urn:braid:ltee-rel606-westgate-20260728",
  "prov:wasGeneratedBy": {
    "@type": "prov:Activity",
    "prov:used": "https://www.ncbi.nlm.nih.gov/nuccore/CP000819.1",
    "prov:wasAssociatedWith": "did:eco:westgate"
  },
  "prov:wasAttributedTo": "did:eco:westgate",
  "prov:generatedAtTime": "2026-07-28T...",
  "eco:license": "Public Domain",
  "eco:blake3_root": "...",
  "eco:file_count": 1,
  "eco:size_bytes": 6082560
}

SILVA 138.1 (16S ref)

16S rRNA reference taxonomy database. Gold standard for microbial community classification via amplicon sequencing. Used by DADA2, QIIME2, and every major microbiome analysis pipeline.

What’s Possible

• Classify microbial communities from 16S amplicon data (wetSpring GPU-accelerated DADA2 pipeline)
• Combine with LTEE REL606 for evolutionary context of E. coli populations

The Braid

sweetGrass braid.create produced a W3C PROV-O JSON-LD attestation:

{
  "@context": "https://www.w3.org/ns/prov#",
  "@id": "urn:braid:silva-138-westgate-20260729",
  "prov:wasGeneratedBy": {
    "@type": "prov:Activity",
    "prov:used": "https://www.arb-silva.de/download/archive/",
    "prov:wasAssociatedWith": "did:eco:westgate"
  },
  "prov:wasAttributedTo": "did:eco:westgate",
  "prov:generatedAtTime": "2026-07-29T...",
  "eco:license": "CC-BY-4.0",
  "eco:blake3_root": "...",
  "eco:file_count": 1,
  "eco:size_bytes": 197132288
}

See Also

• Environmental — NOAA, USGS (environmental context)
• Proteomics — UniRef90 (protein-level evolution)