{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T13:52:32Z","timestamp":1791208352265,"version":"4.1.0"},"reference-count":128,"publisher":"American Society for Microbiology","license":[{"start":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T00:00:00Z","timestamp":1791158400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T00:00:00Z","timestamp":1791158400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R35GM150870"],"award-info":[{"award-number":["R35GM150870"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["mBio"],"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Metabolomics provides a direct window into microbial function by capturing the small molecules that reflect cellular activity and microbial interactions. Here, we highlight its diverse applications for microbiologists across both\n                      <jats:italic toggle=\"yes\">in vitro<\/jats:italic>\n                      and\n                      <jats:italic toggle=\"yes\">in vivo<\/jats:italic>\n                      models under dynamic biological and nutritional conditions, including variations in community complexity, medium composition, and exposure to exogenous compounds such as antibiotics. Through representative case studies, we demonstrate how metabolomics provides critical insights into microbial physiology and inter-organismal interactions. We also showcase examples of multiomics integration, in which metabolomics is combined with complementary approaches to enhance data interpretation and strengthen biological conclusions. Finally, we discuss key challenges in metabolomics data analysis and highlight emerging strategies to overcome these limitations.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/mbio.01913-26","type":"journal-article","created":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T13:00:51Z","timestamp":1791205251000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Metabolomics in microbiology: interrogating microbial physiology and interactions"],"prefix":"10.1128","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-8544-0196","authenticated-orcid":true,"given":"M\u00f3nica","family":"Monge-Lor\u00eda","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01zkghx44","id-type":"ROR","asserted-by":"publisher"}],"name":"School of Chemistry and Biochemistry, Georgia Institute of Technology","place":["Atlanta, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew C.","family":"McAvoy","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01zkghx44","id-type":"ROR","asserted-by":"publisher"}],"name":"School of Chemistry and Biochemistry, Georgia Institute of Technology","place":["Atlanta, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2760-7123","authenticated-orcid":true,"given":"Neha","family":"Garg","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01zkghx44","id-type":"ROR","asserted-by":"publisher"}],"name":"School of Chemistry and Biochemistry, Georgia Institute of Technology","place":["Atlanta, USA"]},{"id":[{"id":"https:\/\/ror.org\/01zkghx44","id-type":"ROR","asserted-by":"publisher"}],"name":"Center for Microbial Dynamics and Infection, Georgia Institute of Technology","place":["Atlanta, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","published-online":{"date-parts":[[2026,10,5]]},"reference":[{"key":"e_1_3_2_2_2","volume-title":"Molecular biology of the gene","author":"Watson JD","year":"1987","unstructured":"Watson JD, Hopkins NH, Roberts JW, Steitz JA, Weiner AM. 1987. Molecular biology of the gene. 4th ed. Benjamin\/Cummings, Menlo Park, CA.","edition":"4"},{"key":"e_1_3_2_3_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41392-018-0024-7"},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.1038\/nchembio0705-64"},{"key":"e_1_3_2_5_2","doi-asserted-by":"publisher","DOI":"10.1007\/s10295-019-02136-y"},{"key":"e_1_3_2_6_2","doi-asserted-by":"publisher","DOI":"10.1021\/ac60352a007"},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00072-12"},{"key":"e_1_3_2_8_2","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2025.1607258"},{"key":"e_1_3_2_9_2","doi-asserted-by":"publisher","DOI":"10.4187\/respcare.06697"},{"key":"e_1_3_2_10_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12890-016-0339-5"},{"key":"e_1_3_2_11_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.01138-07"},{"key":"e_1_3_2_12_2","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.03042-19"},{"key":"e_1_3_2_13_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1419677112"},{"key":"e_1_3_2_14_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-00421-4"},{"key":"e_1_3_2_15_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.03609-12"},{"key":"e_1_3_2_16_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00250-21"},{"key":"e_1_3_2_17_2","doi-asserted-by":"publisher","DOI":"10.1021\/acschembio.2c00529"},{"key":"e_1_3_2_18_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00044-13"},{"key":"e_1_3_2_19_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2022.855331"},{"key":"e_1_3_2_20_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2017.02618"},{"key":"e_1_3_2_21_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.lwt.2024.116254"},{"key":"e_1_3_2_22_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2018.00668"},{"key":"e_1_3_2_23_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2024.05.035"},{"key":"e_1_3_2_24_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2047-9"},{"key":"e_1_3_2_25_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-026-68556-4"},{"key":"e_1_3_2_26_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-023-06906-8"},{"key":"e_1_3_2_27_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2024.02.019"},{"key":"e_1_3_2_28_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-023-01570-0"},{"key":"e_1_3_2_29_2","doi-asserted-by":"publisher","DOI":"10.1080\/19490976.2023.2172671"},{"key":"e_1_3_2_30_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.it.2025.12.008"},{"key":"e_1_3_2_31_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2024.05.005"},{"key":"e_1_3_2_32_2","doi-asserted-by":"publisher","DOI":"10.1021\/acschembio.4c00562"},{"key":"e_1_3_2_33_2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.biochem.4c00706"},{"key":"e_1_3_2_34_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2023.112540"},{"key":"e_1_3_2_35_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.05.001"},{"key":"e_1_3_2_36_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-026-02299-2"},{"key":"e_1_3_2_37_2","doi-asserted-by":"publisher","DOI":"10.1111\/nph.70112"},{"key":"e_1_3_2_38_2","doi-asserted-by":"publisher","DOI":"10.1111\/1462-2920.13858"},{"key":"e_1_3_2_39_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2212930119"},{"key":"e_1_3_2_40_2","doi-asserted-by":"publisher","DOI":"10.1093\/ismeco\/ycaf133"},{"key":"e_1_3_2_41_2","doi-asserted-by":"publisher","DOI":"10.1093\/ismeco\/ycaf142"},{"key":"e_1_3_2_42_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-17612-8"},{"key":"e_1_3_2_43_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-025-61432-7"},{"key":"e_1_3_2_44_2","doi-asserted-by":"publisher","DOI":"10.1080\/10643389.2023.2212569"},{"key":"e_1_3_2_45_2","doi-asserted-by":"publisher","DOI":"10.1093\/ismejo\/wrae049"},{"key":"e_1_3_2_46_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41396-021-01153-z"},{"key":"e_1_3_2_47_2","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.81604"},{"key":"e_1_3_2_48_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.3001093"},{"key":"e_1_3_2_49_2","doi-asserted-by":"publisher","unstructured":"Pakkir Shah AK Griesshammer A Stincone P Kalinski J-C Walter A Wang M Maier L Petras D. 2026. A functional metabolomics framework to track microbiome drug metabolism. bioRxiv. doi:10.64898\/2026.01.30.702925","DOI":"10.64898\/2026.01.30.702925"},{"key":"e_1_3_2_50_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.tim.2025.01.006"},{"key":"e_1_3_2_51_2","doi-asserted-by":"publisher","DOI":"10.1093\/ismejo\/wraf283"},{"key":"e_1_3_2_52_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41396-021-01125-3"},{"key":"e_1_3_2_53_2","doi-asserted-by":"publisher","DOI":"10.1186\/s40538-024-00651-4"},{"key":"e_1_3_2_54_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2025.02.007"},{"key":"e_1_3_2_55_2","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00269-18"},{"key":"e_1_3_2_56_2","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.87039"},{"key":"e_1_3_2_57_2","doi-asserted-by":"publisher","DOI":"10.1038\/s44259-025-00168-2"},{"key":"e_1_3_2_58_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkac363"},{"key":"e_1_3_2_59_2","doi-asserted-by":"publisher","DOI":"10.15252\/msb.20167028"},{"key":"e_1_3_2_60_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1812066116"},{"key":"e_1_3_2_61_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.3002781"},{"key":"e_1_3_2_62_2","doi-asserted-by":"publisher","DOI":"10.1089\/ars.2021.0043"},{"key":"e_1_3_2_63_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2022.10.008"},{"key":"e_1_3_2_64_2","doi-asserted-by":"publisher","DOI":"10.1089\/ars.2017.7300"},{"key":"e_1_3_2_65_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-35277-3"},{"key":"e_1_3_2_66_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2025.07.008"},{"key":"e_1_3_2_67_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-022-01686-6"},{"key":"e_1_3_2_68_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2024.03.014"},{"key":"e_1_3_2_69_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.2000862"},{"key":"e_1_3_2_70_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-18049-9"},{"key":"e_1_3_2_71_2","doi-asserted-by":"publisher","DOI":"10.1111\/imm.12930"},{"key":"e_1_3_2_72_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmet.2014.10.016"},{"key":"e_1_3_2_73_2","doi-asserted-by":"publisher","DOI":"10.1021\/acsinfecdis.9b00286"},{"key":"e_1_3_2_74_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.copbio.2025.103373"},{"key":"e_1_3_2_75_2","doi-asserted-by":"publisher","DOI":"10.1155\/2015\/723515"},{"key":"e_1_3_2_76_2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jnatprod.7b00737"},{"key":"e_1_3_2_77_2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jnatprod.4c00214"},{"key":"e_1_3_2_78_2","doi-asserted-by":"publisher","DOI":"10.1021\/jacs.4c09582"},{"key":"e_1_3_2_79_2","doi-asserted-by":"publisher","DOI":"10.1039\/d1np00036e"},{"key":"e_1_3_2_80_2","doi-asserted-by":"publisher","DOI":"10.1007\/s10142-025-01645-7"},{"key":"e_1_3_2_81_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1714381115"},{"key":"e_1_3_2_82_2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jnatprod.6c00213"},{"key":"e_1_3_2_83_2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jnatprod.6c00045"},{"key":"e_1_3_2_84_2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jnatprod.3c00750"},{"key":"e_1_3_2_85_2","doi-asserted-by":"publisher","unstructured":"Monge-Lor\u00eda M Brady C Wu H Aron A Garg N. 2026. Discovery of metallophore diversity in Microbulbifer in mixed culture with a coral pathogen using computational mass spectrometry and genome mining. bioRxiv. doi:10.64898\/2026.03.11.711190","DOI":"10.64898\/2026.03.11.711190"},{"key":"e_1_3_2_86_2","doi-asserted-by":"publisher","DOI":"10.1021\/jacs.5c18527"},{"key":"e_1_3_2_87_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2016.02.020"},{"key":"e_1_3_2_88_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-025-10079-x"},{"key":"e_1_3_2_89_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41589-018-0193-2"},{"key":"e_1_3_2_90_2","doi-asserted-by":"publisher","DOI":"10.1021\/acschembio.9b00049"},{"key":"e_1_3_2_91_2","doi-asserted-by":"publisher","DOI":"10.1002\/anie.201901342"},{"key":"e_1_3_2_92_2","doi-asserted-by":"publisher","DOI":"10.1021\/acschembio.2c00588"},{"key":"e_1_3_2_93_2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.biochem.4c00659"},{"key":"e_1_3_2_94_2","doi-asserted-by":"publisher","DOI":"10.1021\/acscentsci.5c00969"},{"key":"e_1_3_2_95_2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jnatprod.5c00776"},{"key":"e_1_3_2_96_2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.orglett.2c02092"},{"key":"e_1_3_2_97_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4939-2377-9_13"},{"key":"e_1_3_2_98_2","doi-asserted-by":"publisher","DOI":"10.1002\/bmb.2004.494032020331"},{"key":"e_1_3_2_99_2","doi-asserted-by":"publisher","DOI":"10.1080\/05704920902717872"},{"key":"e_1_3_2_100_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-021-01197-1"},{"key":"e_1_3_2_101_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.trac.2008.01.007"},{"key":"e_1_3_2_102_2","doi-asserted-by":"publisher","DOI":"10.1002\/0471142727.mb3004s114"},{"key":"e_1_3_2_103_2","doi-asserted-by":"publisher","DOI":"10.1002\/elps.200800512"},{"key":"e_1_3_2_104_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.aca.2011.09.042"},{"key":"e_1_3_2_105_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.trac.2019.04.022"},{"key":"e_1_3_2_106_2","doi-asserted-by":"publisher","DOI":"10.1038\/s44303-024-00025-3"},{"key":"e_1_3_2_107_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1206855109"},{"key":"e_1_3_2_108_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1424409112"},{"key":"e_1_3_2_109_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1145557"},{"key":"e_1_3_2_110_2","doi-asserted-by":"publisher","DOI":"10.1038\/s43705-023-00318-5"},{"key":"e_1_3_2_111_2","doi-asserted-by":"publisher","DOI":"10.1128\/msystems.01183-25"},{"key":"e_1_3_2_112_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-025-29411-6"},{"key":"e_1_3_2_113_2","doi-asserted-by":"publisher","DOI":"10.1631\/jzus.B1300149"},{"key":"e_1_3_2_114_2","doi-asserted-by":"publisher","DOI":"10.3390\/metabo7040053"},{"key":"e_1_3_2_115_2","doi-asserted-by":"publisher","DOI":"10.1002\/0471250953.bi1411s37"},{"key":"e_1_3_2_116_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv1042"},{"key":"e_1_3_2_117_2","doi-asserted-by":"publisher","DOI":"10.1007\/s11306-022-01963-y"},{"key":"e_1_3_2_118_2","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3597"},{"key":"e_1_3_2_119_2","doi-asserted-by":"publisher","DOI":"10.1002\/jms.1777"},{"key":"e_1_3_2_120_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-020-0942-5"},{"key":"e_1_3_2_121_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac868"},{"key":"e_1_3_2_122_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-019-0344-8"},{"key":"e_1_3_2_123_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1509788112"},{"key":"e_1_3_2_124_2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.analchem.1c01465"},{"key":"e_1_3_2_125_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-022-01486-3"},{"key":"e_1_3_2_126_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-020-0740-8"},{"key":"e_1_3_2_127_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-020-0933-6"},{"key":"e_1_3_2_128_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41596-020-0317-5"},{"key":"e_1_3_2_129_2","doi-asserted-by":"publisher","DOI":"10.1016\/bs.mie.2021.09.012"}],"container-title":["mBio"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/mbio.01913-26","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/mbio.01913-26","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T13:00:53Z","timestamp":1791205253000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/mbio.01913-26"}},"subtitle":[],"editor":[{"given":"Marvin","family":"Whiteley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,10,5]]},"references-count":128,"alternative-id":["10.1128\/mbio.01913-26"],"URL":"https:\/\/doi.org\/10.1128\/mbio.01913-26","relation":{},"ISSN":["2150-7511"],"issn-type":[{"value":"2150-7511","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,5]]},"assertion":[{"value":"2026-10-05","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e01913-26"}}