{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T11:49:46Z","timestamp":1791978586151,"version":"4.4.0"},"reference-count":56,"publisher":"Wiley","license":[{"start":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T00:00:00Z","timestamp":1791936000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T00:00:00Z","timestamp":1791936000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/100006919","name":"Massachusetts Institute of Technology","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006919","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Small Methods"],"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    Raman spectroscopy is a promising tool for microbial identification, yet its implementation in microbiology and clinical workflow is still restricted due to the accompanying additional preparation required to focus on microbial signals. Here, we demonstrate Raman\u2010based bacterial identification directly from unopened, inverted agar plates, the same conditions used during incubation. Our approach enabled sensitive identification using two\n                    <jats:italic>Escherichia coli<\/jats:italic>\n                    variants, differing only in green fluorescent protein (GFP) expression, across diverse media and substrate material conditions, despite the interrogation path traversing 3\u20134\u00a0mm thick background material. We integrated traditional density functional theory (DFT)\u2010based material computation with machine learning analysis, achieving over 97.7% classification accuracy, surpassing the performance of standard measurements from opened plates by 10.8% higher mean accuracy and 0.76% less variance. We further demonstrated Raman mapping\u2010based colony identification via Raman peaks characteristic to GFPmut3 chromophore structure generated by DFT. Our approach is robust to changes in algorithms or substrate materials and promises real\u2010time, non\u2010perturbative monitoring of bacterial growth, biofilm formation, and antimicrobial resistance development.\n                  <\/jats:p>","DOI":"10.1002\/smtd.71013","type":"journal-article","created":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T11:01:46Z","timestamp":1791975706000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Non\u2010Perturbative Bacterial Identification Directly From Solid Agar Plates Using Raman Micro\u2010Spectroscopy and Machine Learning"],"prefix":"10.1002","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5689-1445","authenticated-orcid":false,"given":"Jeong Hee","family":"Kim","sequence":"first","affiliation":[{"name":"Department of Mechanical Engineering Massachusetts Institute of Technology  Cambridge Massachusetts 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of MGH Massachusetts Institute of Technology and Harvard  Cambridge Massachusetts USA"},{"name":"Jameel Clinic for AI &amp; Healthcare Massachusetts Institute of Technology  Cambridge Massachusetts USA"},{"name":"Institute for Medical Engineering and Science Massachusetts Institute of Technology  Cambridge Massachusetts USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,10,14]]},"reference":[{"key":"e_1_2_8_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.tifs.2018.05.020"},{"key":"e_1_2_8_3_1","doi-asserted-by":"publisher","DOI":"10.1111\/1541\u20104337.12618"},{"key":"e_1_2_8_4_1","doi-asserted-by":"publisher","DOI":"10.1002\/adma.202313389"},{"key":"e_1_2_8_5_1","doi-asserted-by":"publisher","DOI":"10.1111\/febs.16705"},{"key":"e_1_2_8_6_1","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1007\/978-981-16-2225-0_20","volume-title":"Application of Microbes in Environmental and Microbial 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