{
  "abstract": "Quantitative microbial metabolomics requires rapid quenching and highly standardized extraction, yet these pre-analytical steps remain labor-intensive and difficult to reproduce, limiting time-resolved intracellular measurements under controlled bioreactor cultivation. Here, we present an integrated robotic platform that couples parallel fermenter operation with circulation-based sampling, immediate cold-alcohol quenching, automated refrigerated centrifugation, interface-aware supernatant removal, and solvent extraction with controlled heating and mixing, followed by plate-based storage for liquid chromatography–tandem mass spectrometry (LC–MS/MS). To benchmark the precision of the automated preparation module, we compared repeated LC–MS/MS measurements of a single extract with measurements of independently processed samples subjected to post-quench automated harvesting, extraction, and transfer. The analysis was restricted to 76 analytes consistently detected in all replicates of both datasets. The mean coefficients of variation increased from 6.92% for repeated LC–MS/MS measurements to 8.82% for automated preparation, corresponding to a modest increase of 1.90 percentage points. These results indicate that post-quench automated preparation introduces a small but measurable additional source of variability while maintaining mean analytical variation below 10%. We then performed time-course endo- and exometabolomics across four widely used Escherichia coli lineages (BW25113, BL21­(DE3), W, and C). Principal component analysis resolved strain-specific trajectories throughout batch growth and revealed strain-specific metabolic phenotypes, including coordinated accumulation of sugar phosphates and 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway intermediates in strain C, and comparatively high intracellular pools of branched-chain amino acids in strain W. This platform enables standardized and traceable automated preparation for dense, time-resolved metabolomics and provides directly measurable phenotypes for host selection and metabolic engineering.",
  "abstract_shown": true,
  "affiliations": [
    "Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan",
    "Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan",
    "Research Center for Solar Energy Chemistry, Graduate School of Engineering Science, The University of Osaka, Toyonaka, Osaka 560-8531, Japan",
    "RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan",
    "Department of Chemical Science and Engineering, Faculty of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan",
    "Solutions Center of Excellence, Analytical & Measuring Instruments Division, Shimadzu Corporation, 1, Nishinokyo Kuwabara-cho, Nakagyo-ku, Kyoto 604-8511, Japan"
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 9,
  "authors": [
    {
      "affs": [
        0,
        1,
        2
      ],
      "name": "Kenya Tanaka",
      "orcid": "0000-0002-6506-3788"
    },
    {
      "affs": [
        1
      ],
      "name": "Takahiro Bamba",
      "orcid": "0009-0009-2679-2900"
    },
    {
      "affs": [
        1
      ],
      "name": "Musashi Takenaka"
    },
    {
      "affs": [
        0
      ],
      "name": "Yoshimi Hori"
    },
    {
      "affs": [
        0
      ],
      "name": "Takanobu Yoshida"
    },
    {
      "affs": [
        0
      ],
      "name": "Mami Matsuda"
    },
    {
      "affs": [
        0,
        1,
        3,
        4
      ],
      "name": "Akihiko Kondo",
      "orcid": "0000-0003-1527-5288"
    },
    {
      "affs": [
        5
      ],
      "name": "Yoshihiro Hayakawa"
    },
    {
      "affs": [
        0,
        1,
        3,
        4
      ],
      "name": "Tomohisa Hasunuma",
      "orcid": "0000-0002-8382-2362"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/bqxwg4xs4myks.bib",
  "cited_by": 0,
  "doi": "10.1021/acs.analchem.6c01820",
  "fulltext_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13737998/",
  "id": "bqxwg4xs4myks",
  "issns": [
    "0003-2700",
    "1520-6882"
  ],
  "landing_url": "https://doi.org/10.1021/acs.analchem.6c01820",
  "language": "en",
  "licence": "CC-BY-NC-ND-4.0",
  "licence_label": "CC BY-NC-ND 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "Article"
    ],
    [
      "openalex",
      "1312|Metabolomics and Mass Spectrometry Studies"
    ]
  ],
  "openalex": "W7222969781",
  "pdf_url": null,
  "pmcid": "PMC13737998",
  "pmid": "42975179",
  "published": "2026-10-19",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/bqxwg4xs4myks.ris",
  "sources": [
    {
      "first_seen": "2026-11-09T12:23:04Z",
      "native_id": "PMC13737998",
      "source": "pmc",
      "url": "https://doi.org/10.1021/acs.analchem.6c01820"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Metabolomics and Mass Spectrometry Studies",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Automated Quenching and Extraction for High-Precision Metabolomics Uncovers Distinct Metabolome Trajectories across Escherichia coli Lineages",
  "title_text": "Automated Quenching and Extraction for High-Precision Metabolomics Uncovers Distinct Metabolome Trajectories across Escherichia coli Lineages",
  "type": "peer-reviewed",
  "updated_at": "2026-11-09T12:23:04Z",
  "url": "https://research.draconitic.com/paper/bqxwg4xs4myks",
  "venue": "Analytical Chemistry",
  "versions": []
}