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ecosystem function. Yet, while thousands of metabolites are produced, only a few molecules have been identified in these associations. Using the ubiquitous microalgae\n                    <jats:italic>Pseudo\u2010nitzschia<\/jats:italic>\n                    sp., as a model, we employed an untargeted metabolomics strategy to assign structural characteristics to the metabolites that distinguished specific diatom\u2010microbiome associations. We cultured five species of\n                    <jats:italic>Pseudo\u2010nitzschia<\/jats:italic>\n                    , including two species that produced the toxin domoic acid, and examined their microbiomes and metabolomes. A total of 4826 molecular features were detected by tandem mass spectrometry. Only 229 of these could be annotated using available mass spectral libraries, but by applying new in silico annotation tools, characterization was expanded to 2710 features. The metabolomes of the\n                    <jats:italic>Pseudo\u2010nitzschia<\/jats:italic>\n                    \u2010microbiome associations were distinct and distinguished by structurally diverse nitrogen compounds, ranging from simple amines and amides to cyclic compounds such as imidazoles, pyrrolidines and lactams. By illuminating the dark metabolomes, this study expands our capacity to discover new chemical targets that facilitate microbial partnerships and uncovers the chemical diversity that underpins algae\u2010bacteria interactions.\n                  <\/jats:p>","DOI":"10.1111\/1462-2920.16242","type":"journal-article","created":{"date-parts":[[2022,10,12]],"date-time":"2022-10-12T04:51:17Z","timestamp":1665550277000},"page":"5408-5424","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":23,"title":["Illuminating the dark metabolome of\n                    <i>Pseudo\u2010nitzschia<\/i>\n                    \u2013microbiome associations"],"prefix":"10.1111","volume":"24","author":[{"given":"Irina","family":"Koester","sequence":"first","affiliation":[{"name":"Scripps Institution of Oceanography University of California San Diego  La Jolla California USA"}]},{"given":"Zachary A.","family":"Quinlan","sequence":"additional","affiliation":[{"name":"Scripps Institution of Oceanography University of California San Diego  La Jolla California USA"}]},{"given":"Louis\u2010F\u00e9lix","family":"Nothias","sequence":"additional","affiliation":[{"name":"Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences University of California San Diego  La Jolla California USA"},{"name":"Skaggs School of Pharmacy and Pharmaceutical Sciences University of California San Diego  La Jolla California USA"}]},{"given":"Margot E.","family":"White","sequence":"additional","affiliation":[{"name":"Scripps Institution of Oceanography University of California San Diego  La Jolla California USA"}]},{"given":"Ariel","family":"Rabines","sequence":"additional","affiliation":[{"name":"Scripps Institution of Oceanography University of California San Diego  La Jolla California USA"},{"name":"Microbial and Environmental Genomics Group J. Craig Venter Institute  La Jolla California USA"}]},{"given":"Daniel","family":"Petras","sequence":"additional","affiliation":[{"name":"Scripps Institution of Oceanography University of California San Diego  La Jolla California USA"},{"name":"Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences University of California San Diego  La Jolla California USA"},{"name":"Skaggs School of Pharmacy and Pharmaceutical Sciences University of California San Diego  La Jolla California USA"}]},{"given":"John K.","family":"Brunson","sequence":"additional","affiliation":[{"name":"Scripps Institution of Oceanography University of California San Diego  La Jolla California USA"},{"name":"Microbial and Environmental Genomics Group J. Craig Venter Institute  La Jolla California USA"}]},{"given":"Kai","family":"D\u00fchrkop","sequence":"additional","affiliation":[{"name":"Chair for Bioinformatics Friedrich Schiller University  Jena Germany"}]},{"given":"Marcus","family":"Ludwig","sequence":"additional","affiliation":[{"name":"Chair for Bioinformatics Friedrich Schiller University  Jena Germany"}]},{"given":"Sebastian","family":"B\u00f6cker","sequence":"additional","affiliation":[{"name":"Chair for Bioinformatics Friedrich Schiller University  Jena Germany"}]},{"given":"Farooq","family":"Azam","sequence":"additional","affiliation":[{"name":"Scripps Institution of Oceanography University of California San Diego  La Jolla California USA"}]},{"given":"Andrew E.","family":"Allen","sequence":"additional","affiliation":[{"name":"Scripps Institution of Oceanography University of California San Diego  La Jolla California USA"},{"name":"Microbial and Environmental Genomics Group J. Craig Venter Institute  La Jolla California USA"}]},{"given":"Pieter C.","family":"Dorrestein","sequence":"additional","affiliation":[{"name":"Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences University of California San Diego  La Jolla California USA"},{"name":"Skaggs School of Pharmacy and Pharmaceutical Sciences University of California San Diego  La Jolla California USA"}]},{"given":"Lihini I.","family":"Aluwihare","sequence":"additional","affiliation":[{"name":"Scripps Institution of Oceanography University of California San Diego  La Jolla California USA"}]}],"member":"311","published-online":{"date-parts":[[2022,11,16]]},"reference":[{"key":"e_1_2_8_2_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature14488"},{"key":"e_1_2_8_3_1","doi-asserted-by":"publisher","DOI":"10.1128\/MMBR.00007-12"},{"key":"e_1_2_8_4_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1101156"},{"key":"e_1_2_8_5_1","doi-asserted-by":"publisher","DOI":"10.1002\/nt.2620030605"},{"key":"e_1_2_8_6_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.hal.2018.06.001"},{"key":"e_1_2_8_7_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btn603"},{"key":"e_1_2_8_8_1","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00896-20"},{"key":"e_1_2_8_9_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.aau0382"},{"key":"e_1_2_8_10_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro3326"},{"key":"e_1_2_8_11_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.hal.2008.08.008"},{"key":"e_1_2_8_12_1","doi-asserted-by":"publisher","DOI":"10.1093\/icb\/icaa133"},{"key":"e_1_2_8_13_1","doi-asserted-by":"publisher","DOI":"10.4319\/lom.2008.6.230"},{"key":"e_1_2_8_14_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13321-016-0174-y"},{"key":"e_1_2_8_15_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-019-0344-8"},{"key":"e_1_2_8_16_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-020-0740-8"},{"key":"e_1_2_8_17_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1509788112"},{"key":"e_1_2_8_18_1","doi-asserted-by":"publisher","DOI":"10.4319\/lo.2004.49.4.0991"},{"key":"e_1_2_8_19_1","doi-asserted-by":"publisher","DOI":"10.1007\/BF01569683"},{"key":"e_1_2_8_20_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.dsr2.2013.06.022"},{"key":"e_1_2_8_21_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41396-020-00811-y"},{"key":"e_1_2_8_22_1","doi-asserted-by":"publisher","DOI":"10.3390\/md18060313"},{"key":"e_1_2_8_23_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1917265117"},{"key":"e_1_2_8_24_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1462-2920.2005.00759.x"},{"key":"e_1_2_8_25_1","doi-asserted-by":"publisher","DOI":"10.3354\/ame01513"},{"key":"e_1_2_8_26_1","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.01334-20"},{"key":"e_1_2_8_27_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.protis.2019.05.004"},{"key":"e_1_2_8_28_1","doi-asserted-by":"publisher","DOI":"10.1093\/plankt\/18.2.295"},{"key":"e_1_2_8_29_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.hal.2006.06.003"},{"key":"e_1_2_8_30_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-020-0916-7"},{"key":"e_1_2_8_31_1","doi-asserted-by":"publisher","DOI":"10.3354\/ame028229"},{"key":"e_1_2_8_32_1","doi-asserted-by":"publisher","DOI":"10.1002\/lno.11255"},{"key":"e_1_2_8_33_1","doi-asserted-by":"publisher","DOI":"10.1101\/2021.03.09.434501"},{"key":"e_1_2_8_34_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.hal.2004.10.001"},{"key":"e_1_2_8_35_1","doi-asserted-by":"publisher","DOI":"10.2216\/11-37.1"},{"key":"e_1_2_8_36_1","doi-asserted-by":"publisher","DOI":"10.3390\/metabo10030105"},{"key":"e_1_2_8_37_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ecss.2009.04.029"},{"key":"e_1_2_8_38_1","doi-asserted-by":"publisher","DOI":"10.1038\/s42256-020-00234-6"},{"key":"e_1_2_8_39_1","doi-asserted-by":"publisher","DOI":"10.1007\/s003740000304"},{"key":"e_1_2_8_40_1","first-page":"63","article-title":"Synchronous culture of chlorella: II. Changes in content of various vitamins during the course of the algal life cycle","volume":"1","author":"Morimura Y.","year":"1959","journal-title":"Plant & Cell Physiology"},{"key":"e_1_2_8_41_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmicrobiol.2016.5"},{"key":"e_1_2_8_42_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-020-0933-6"},{"key":"e_1_2_8_43_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmars.2017.00405"},{"key":"e_1_2_8_44_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.chemosphere.2020.129450"},{"key":"e_1_2_8_45_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-11-395"},{"key":"e_1_2_8_46_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0231902"},{"key":"e_1_2_8_47_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00248-006-9162-5"},{"key":"e_1_2_8_48_1","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.02274-06"},{"key":"e_1_2_8_49_1","doi-asserted-by":"publisher","DOI":"10.1111\/jpy.12898"},{"key":"e_1_2_8_50_1","doi-asserted-by":"publisher","DOI":"10.1007\/BF02922978"},{"key":"e_1_2_8_51_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.1239303"},{"key":"e_1_2_8_52_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2012088117"},{"key":"e_1_2_8_53_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1516878112"},{"key":"e_1_2_8_54_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2016.01433"},{"key":"e_1_2_8_55_1","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2013.138"},{"key":"e_1_2_8_56_1","doi-asserted-by":"publisher","DOI":"10.1007\/s11306-007-0082-2"},{"key":"e_1_2_8_57_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1218344"},{"key":"e_1_2_8_58_1","volume-title":"Identifying marine phytoplankton","author":"Tomas C.R.","year":"1997"},{"key":"e_1_2_8_59_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.hal.2011.10.025"},{"key":"e_1_2_8_60_1","doi-asserted-by":"publisher","DOI":"10.1111\/1462-2920.14344"},{"key":"e_1_2_8_61_1","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3597"},{"key":"e_1_2_8_62_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-019-0375-9"},{"key":"e_1_2_8_63_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmars.2020.582161"},{"key":"e_1_2_8_64_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2017.01985"},{"key":"e_1_2_8_65_1","doi-asserted-by":"crossref","unstructured":"Williams R.J. Lyman C.M. Goodyear G.H. Truesdail J.H. andHoladay D.(1933)\u201cPantothenic acid \u201d a growth determinant of universal biological occurrence.","DOI":"10.1021\/ja01334a049"}],"updated-by":[{"DOI":"10.1111\/1462-2920.16433","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2023,6,5]],"date-time":"2023-06-05T00:00:00Z","timestamp":1685923200000}}],"container-title":["Environmental Microbiology"],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/1462-2920.16242","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1111\/1462-2920.16242","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/sfamjournals.onlinelibrary.wiley.com\/doi\/am-pdf\/10.1111\/1462-2920.16242","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/sfamjournals.onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/1462-2920.16242","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,30]],"date-time":"2025-10-30T23:51:15Z","timestamp":1761868275000},"score":0.0,"resource":{"primary":{"URL":"https:\/\/sfamjournals.onlinelibrary.wiley.com\/doi\/10.1111\/1462-2920.16242"}},"issued":{"date-parts":[[2022,11]]},"references-count":64,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2022,11]]}},"alternative-id":["10.1111\/1462-2920.16242"],"URL":"https:\/\/doi.org\/10.1111\/1462-2920.16242","archive":["Portico"],"ISSN":["1462-2912","1462-2920"],"issn-type":[{"value":"1462-2912","type":"print"},{"value":"1462-2920","type":"electronic"}],"published":{"date-parts":[[2022,11]]},"assertion":[{"value":"2022-04-04","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2022-10-09","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2022-11-16","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]},{"indexed":{"date-parts":[[2026,3,22]],"date-time":"2026-03-22T12:28:48Z","timestamp":1774182528627,"version":"3.50.1"},"reference-count":0,"publisher":"Proceedings of the National Academy of Sciences","issue":"25","license":[{"start":{"date-parts":[[2023,6,15]],"date-time":"2023-06-15T00:00:00Z","timestamp":1686787200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["IOS-1656475"],"award-info":[{"award-number":["IOS-1656475"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["IOS-1656481"],"award-info":[{"award-number":["IOS-1656481"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000936","name":"Gordon and Betty Moore Foundation","doi-asserted-by":"publisher","award":["GBMF7622"],"award-info":[{"award-number":["GBMF7622"]}],"id":[{"id":"10.13039\/100000936","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"HHS | National Institutes of Health","doi-asserted-by":"publisher","award":["P41 GM103484"],"award-info":[{"award-number":["P41 GM103484"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"HHS | National Institutes of Health","doi-asserted-by":"publisher","award":["R01 GM107550"],"award-info":[{"award-number":["R01 GM107550"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"HHS | National Institutes of Health","doi-asserted-by":"publisher","award":["P01 CA125066"],"award-info":[{"award-number":["P01 CA125066"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100013407","name":"Netherlands eScience Center","doi-asserted-by":"publisher","award":["ASDI.2017.030"],"award-info":[{"award-number":["ASDI.2017.030"]}],"id":[{"id":"10.13039\/100013407","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.pnas.org"],"crossmark-restriction":true},"short-container-title":["Proc. Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2023,6,20]]},"abstract":"<jats:p>\n            Fungus-growing ants depend on a fungal mutualist that can fall prey to fungal pathogens. This mutualist is cultivated by these ants in structures called fungus gardens. Ants exhibit weeding behaviors that keep their fungus gardens healthy by physically removing compromised pieces. However, how ants detect diseases of their fungus gardens is unknown. Here, we applied the logic of Koch\u2019s postulates using environmental fungal community gene sequencing, fungal isolation, and laboratory infection experiments to establish that\n            <jats:italic>Trichoderma<\/jats:italic>\n            spp. can act as previously unrecognized pathogens of\n            <jats:italic>Trachymyrmex septentrionalis<\/jats:italic>\n            fungus gardens. Our environmental data showed that\n            <jats:italic>Trichoderma<\/jats:italic>\n            are the most abundant noncultivar fungi in wild\n            <jats:italic>T. septentrionalis<\/jats:italic>\n            fungus gardens. We further determined that metabolites produced by\n            <jats:italic>Trichoderma<\/jats:italic>\n            induce an ant weeding response that mirrors their response to live\n            <jats:italic>Trichoderma<\/jats:italic>\n            . Combining ant behavioral experiments with bioactivity-guided fractionation and statistical prioritization of metabolites in\n            <jats:italic>Trichoderma<\/jats:italic>\n            extracts demonstrated that\n            <jats:italic>T. septentrionalis<\/jats:italic>\n            ants weed in response to peptaibols, a specific class of secondary metabolites known to be produced by\n            <jats:italic>Trichoderma<\/jats:italic>\n            fungi. Similar assays conducted using purified peptaibols, including the two previously undescribed peptaibols trichokindins VIII and IX, suggested that weeding is likely induced by peptaibols as a class rather than by a single peptaibol metabolite. In addition to their presence in laboratory experiments, we detected peptaibols in wild fungus gardens. 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We aimed to determine whether beta-lactamase activity is detectable in urine specimens to enable faster identification of resistance.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>Urine specimens from patients with extended spectrum beta lactamase (ESBL)-expressing urinary infections were incubated with beta lactam antibiotics. Beta lactam hydrolysis was determined by mass spectrometry methods.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Ceftriaxone hydrolysis was observed in 45 of 45 ESBL-containing specimens from patients not treated with a beta lactamase inhibitor before specimen collection. Ceftriaxone hydrolysis was not observed in 108 of 108 non-ESBL-containing specimens. Spiking studies show that beta lactam hydrolysis can be observed within 30 minutes. Beta lactam hydrolysis is evidenced by mass spectrometry preceded by either liquid chromatography or matrix-assisted laser desorption ionization specimen processing methods.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusion<\/jats:title>\n                  <jats:p>Clinically significant beta lactamase activity is detectable directly from urine specimens. The described methods would enable the detection of beta lactam resistance 24 to 48 hours sooner than culture based methods.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/labmed\/lmab068","type":"journal-article","created":{"date-parts":[[2021,7,13]],"date-time":"2021-07-13T19:09:58Z","timestamp":1626203398000},"page":"128-137","source":"Crossref","is-referenced-by-count":1,"title":["Mass Spectrometry\u2013Based Detection of Beta Lactam Hydrolysis Enables Rapid Detection of Beta Lactamase Mediated Antibiotic Resistance"],"prefix":"10.1093","volume":"53","author":[{"given":"Raymond T","family":"Suhandynata","sequence":"first","affiliation":[{"name":"Department of Pathology, UC San Diego Health , San Diego, California , US"}]},{"given":"Kyle","family":"Lund","sequence":"additional","affiliation":[{"name":"Department of Pathology, UC San Diego Health , San Diego, California , US"}]},{"given":"Andr\u00e9s M","family":"Caraballo-Rodr\u00edguez","sequence":"additional","affiliation":[{"name":"Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California , San Diego, La Jolla, California , US"}]},{"given":"Sharon L","family":"Reed","sequence":"additional","affiliation":[{"name":"Department of Pathology, UC San Diego Health , San Diego, California , US"}]},{"given":"Pieter C","family":"Dorrestein","sequence":"additional","affiliation":[{"name":"Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California , San Diego, La Jolla, California , US"}]},{"given":"Robert L","family":"Fitzgerald","sequence":"additional","affiliation":[{"name":"Department of Pathology, UC San Diego Health , San Diego, California , US"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8073-5941","authenticated-orcid":false,"given":"Nicholas J","family":"Bevins","sequence":"additional","affiliation":[{"name":"Department of Pathology, UC San Diego Health , San Diego, California , US"}]}],"member":"286","published-online":{"date-parts":[[2021,8,17]]},"reference":[{"issue":"2","key":"2023020501013241500_CIT0001","doi-asserted-by":"crossref","first-page":"67","DOI":"10.3109\/08941939.2012.664099","article-title":"History of antibiotics. 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Nuclear magnetic resonance (NMR) spectroscopy is widely used in metabolomics studies for identification and quantification of metabolites. However, the accurate identification of individual metabolites is still a challenging process with higher peak intensity or similar chemical shifts from different metabolites. In this study, we applied a convolutional neural network (CNN) to\n                    <jats:sup>1<\/jats:sup>\n                    H\u2010\n                    <jats:sup>13<\/jats:sup>\n                    C HSQC NMR spectra to achieve accurate peak identification in complex mixtures. The results reveal that the neural network was successfully trained on metabolite identification from these 2D NMR spectra and achieved very good performance compared with other NMR\u2010based metabolomic tools.\n                  <\/jats:p>","DOI":"10.1002\/mrc.5240","type":"journal-article","created":{"date-parts":[[2021,12,20]],"date-time":"2021-12-20T10:18:36Z","timestamp":1639995516000},"page":"1070-1075","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":29,"title":["SMART\u2010Miner: A convolutional neural network\u2010based metabolite identification from\n                    <sup>1<\/sup>\n                    H\u2010\n                    <sup>13<\/sup>\n                    C HSQC spectra"],"prefix":"10.1002","volume":"60","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2473-8360","authenticated-orcid":false,"given":"Hyun Woo","family":"Kim","sequence":"first","affiliation":[{"name":"Center for Marine Biotechnology and 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Among these molecules, nonribosomal peptides (NRPs) represent a diverse class of natural products that include antibiotics, immunosuppressants, and anticancer agents. Recent breakthroughs in natural product discovery have revealed the chemical structure of several thousand NRPs. However, biosynthetic gene clusters (BGCs) encoding them are known only for a few hundred compounds. Here, we developed Nerpa, a computational method for the high-throughput discovery of novel BGCs responsible for producing known NRPs. After searching 13,399 representative bacterial genomes from the RefSeq repository against 8368 known NRPs, Nerpa linked 117 BGCs to their products. We further experimentally validated the predicted BGC of ngercheumicin from Photobacterium galatheae via mass spectrometry. Nerpa supports searching new genomes against thousands of known NRP structures, and novel molecular structures against tens of thousands of bacterial genomes. The availability of these tools can enhance our understanding of NRP synthesis and the function of their biosynthetic enzymes.<\/jats:p>","DOI":"10.3390\/metabo11100693","type":"journal-article","created":{"date-parts":[[2021,10,11]],"date-time":"2021-10-11T09:16:42Z","timestamp":1633943802000},"page":"693","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":18,"title":["Nerpa: A Tool for Discovering Biosynthetic Gene Clusters of Bacterial Nonribosomal Peptides"],"prefix":"10.3390","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9544-6344","authenticated-orcid":false,"given":"Olga","family":"Kunyavskaya","sequence":"first","affiliation":[{"name":"Center for Algorithmic Biotechnology, Saint Petersburg State University, Saint Petersburg 199004, Russia"},{"name":"Scientific Center for Information Technologies and Artificial Intelligence, Sirius University of Science and Technology, Sochi 354340, Russia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6185-0821","authenticated-orcid":false,"given":"Azat M.","family":"Tagirdzhanov","sequence":"additional","affiliation":[{"name":"Center for Algorithmic Biotechnology, Saint Petersburg State University, Saint Petersburg 199004, Russia"},{"name":"Scientific Center for Information Technologies and Artificial Intelligence, Sirius University of Science and Technology, Sochi 354340, Russia"},{"name":"Department of Higher Mathematics, Saint Petersburg Electrotechnical University \u201cLETI\u201d, Saint Petersburg 197376, Russia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5499-2728","authenticated-orcid":false,"given":"Andr\u00e9s Mauricio","family":"Caraballo-Rodr\u00edguez","sequence":"additional","affiliation":[{"name":"Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6711-6719","authenticated-orcid":false,"given":"Louis-F\u00e9lix","family":"Nothias","sequence":"additional","affiliation":[{"name":"Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3003-1030","authenticated-orcid":false,"given":"Pieter C.","family":"Dorrestein","sequence":"additional","affiliation":[{"name":"Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2937-9259","authenticated-orcid":false,"given":"Anton","family":"Korobeynikov","sequence":"additional","affiliation":[{"name":"Center for Algorithmic Biotechnology, Saint Petersburg State University, Saint Petersburg 199004, Russia"},{"name":"Scientific Center for Information Technologies and Artificial Intelligence, Sirius University of Science and Technology, Sochi 354340, Russia"},{"name":"Department of Mathematics and Mechanics, Saint Petersburg State University, Saint Petersburg 199004, Russia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3980-2505","authenticated-orcid":false,"given":"Hosein","family":"Mohimani","sequence":"additional","affiliation":[{"name":"Computational Biology Department, School of Computer Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5855-3519","authenticated-orcid":false,"given":"Alexey","family":"Gurevich","sequence":"additional","affiliation":[{"name":"Center for Algorithmic Biotechnology, Saint Petersburg State University, Saint Petersburg 199004, Russia"},{"name":"Scientific Center for Information Technologies and Artificial Intelligence, Sirius University of Science and Technology, Sochi 354340, Russia"}]}],"member":"1968","published-online":{"date-parts":[[2021,10,11]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"828","DOI":"10.3389\/fphar.2017.00828","article-title":"Nonribosomal peptides from marine microbes and their antimicrobial and anticancer potential","volume":"8","author":"Agrawal","year":"2017","journal-title":"Front. 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H.; Valeriote, F. A.; Polin, L.; Panchapor, C.; Pugh, S.; White, K.; Lowichik, N.; Knight, J.; Bissery, M. C.; Wozniak, A.; LoRusso, P.; Biernat, L.; Polin, D.; Knight, L.; Biggar, S.; Looney, D.; Demchik, L.; Jones, J.; Jones, L.; Blair, S.; Palmer, K.; Essenmacher, S.; Lisow, L.; Mattes, K. C.; Cavanaugh, P. F.; Rake, J. B.; Baker, L. In Cytotoxic Anticancer Drugs: Models and Concepts for Drug Discovery and Development,  Proceedings of the Twenty-Second Annual Cancer Symposium Detroit, Michigan, USA, April 26\u201328, 1990; Valeriote, F. A., Corbett, T. H., Baker, L. H. Eds.; Chapter 3, pp 35\u201387."},{"key":"ref13\/cit13","doi-asserted-by":"publisher","DOI":"10.1016\/j.phytochem.2015.11.011"},{"key":"ref14\/cit14","doi-asserted-by":"publisher","DOI":"10.1021\/np200077f"},{"key":"ref15\/cit15","unstructured":"Gustafson, K. R. In  Handbook of Marine Natural Products; Fattorusso, E., Gerwick, W. H., Taglialatela-Scafati, O., Eds. 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Plant Sci."],"abstract":"<jats:p>Natural products produced by plants are one of the most investigated natural sources, which substantially contributed to the development of the natural products field. Even though these compounds are widely explored, the literature still lacks comprehensive investigations aiming to explore the evolution of secondary metabolites produced by plants, especially if classical methodologies are employed. The development of sensitive hyphenated techniques and computational tools for data processing has enabled the study of large datasets, being valuable assets for chemosystematic studies. Here, we describe a strategy for chemotaxonomic investigations using the Malpighiaceae botanical family as a model. Our workflow was based on MS\/MS untargeted metabolomics, spectral searches, and recently described <jats:italic>in silico<\/jats:italic> classification tools, which were mapped into the latest molecular phylogeny accepted for this family. The metabolomic analysis revealed that different ionization modes and extraction protocols significantly impacted the chemical profiles, influencing the chemotaxonomic results. Spectral searches within public databases revealed several clades or genera-specific molecular families, being potential chemical markers for these taxa, while the <jats:italic>in silico<\/jats:italic> classification tools were able to expand the Malpighiaceae chemical space. The classes putatively annotated were used for ancestral character reconstructions, which recovered several classes of metabolites as homoplasies (i.e., non-exclusive) or synapomorphies (i.e., exclusive) for all sampled clades and genera. Our workflow combines several approaches to perform a comprehensive evolutionary chemical study. We expect it to be used on further chemotaxonomic investigations to expand chemical knowledge and reveal biological insights for compounds classes in different biological groups.<\/jats:p>","DOI":"10.3389\/fpls.2022.854842","type":"journal-article","created":{"date-parts":[[2022,4,14]],"date-time":"2022-04-14T12:25:35Z","timestamp":1649939135000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":28,"title":["Untargeted Metabolomics Sheds Light on the Diversity of Major Classes of Secondary Metabolites in the Malpighiaceae Botanical Family"],"prefix":"10.3389","volume":"13","author":[{"given":"Helena","family":"Mannochio-Russo","sequence":"first","affiliation":[]},{"given":"Rafael F.","family":"de Almeida","sequence":"additional","affiliation":[]},{"given":"Wilhan D. G.","family":"Nunes","sequence":"additional","affiliation":[]},{"given":"Paula C. P.","family":"Bueno","sequence":"additional","affiliation":[]},{"given":"Andr\u00e9s M.","family":"Caraballo-Rodr\u00edguez","sequence":"additional","affiliation":[]},{"given":"Anelize","family":"Bauermeister","sequence":"additional","affiliation":[]},{"given":"Pieter C.","family":"Dorrestein","sequence":"additional","affiliation":[]},{"given":"Vanderlan S.","family":"Bolzani","sequence":"additional","affiliation":[]}],"member":"1965","published-online":{"date-parts":[[2022,4,14]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"2388","DOI":"10.1016\/j.phytochem.2005.07.011","article-title":"Unusual naphthoquinones, catechin and triterpene from Byrsonima microphylla","volume":"66","author":"Aguiar","year":"2005","journal-title":"Phytochemistry"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"132","DOI":"10.1016\/j.phytochem.2019.03.027","article-title":"Evolution of phytochemical diversity in Pilocarpus (Rutaceae)","volume":"163","author":"Allevato","year":"2019","journal-title":"Phytochemistry"},{"key":"ref3","first-page":"210","article-title":"The origin of the Malpighiaceae-The evidence from morphology","volume":"64","author":"Anderson","year":"1990","journal-title":"Mem. 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Bot."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"e01216","DOI":"10.1128\/mSystems.01216-20","article-title":"EMPress enables tree-guided, interactive, and exploratory analyses of multi-omic data sets","volume":"6","author":"Cantrell","year":"2021","journal-title":"mSystems"},{"key":"ref25","doi-asserted-by":"publisher","first-page":"986","DOI":"10.1021\/np040058h","article-title":"Cytotoxic triterpenoids from Acridocarpus vivy from the Madagascar rain forest","volume":"67","author":"Cao","year":"2004","journal-title":"J. Nat. Prod."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"644","DOI":"10.1021\/np0304666","article-title":"Isolation of nor-secofriedelanes from the sedative extracts of Galphimia glauca","volume":"67","author":"Cardoso Taketa","year":"2004","journal-title":"J. Nat. 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