{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T13:04:42Z","timestamp":1785243882077,"version":"3.55.0"},"reference-count":62,"publisher":"American Chemical Society (ACS)","issue":"29","license":[{"start":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T00:00:00Z","timestamp":1784073600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T00:00:00Z","timestamp":1784073600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T00:00:00Z","timestamp":1784073600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"DOI":"10.13039\/100020732","name":"Innovative Research Team of High-level Local University in Shanghai","doi-asserted-by":"publisher","award":["SHSMU-ZLCX20212601"],"award-info":[{"award-number":["SHSMU-ZLCX20212601"]}],"id":[{"id":"10.13039\/100020732","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["22293031"],"award-info":[{"award-number":["22293031"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["22307070"],"award-info":[{"award-number":["22307070"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,7,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Knowledge of the susceptibility of gut bacteria to antibiotics is important for understanding the frequent gut microbiota dysbiosis caused by oral antibiotic administration. However, traditional antimicrobial susceptibility testing (AST) methods are not applicable to unculturable microbes that account for most gut bacteria. Furthermore, they are inapplicable to assess bacterial responses to drugs within a complex microbial community such as the gut microbiota. Here we developed CommAST (Community-level Omni-species Metabolic-activity Antibiotic Susceptibility Testing), a platform profiling multispecies antibiotic susceptibility within complex microbial ecosystems. By treating a microbiota sample with serial concentrations of antibiotics and labeling it with fluorescent D-amino acids, the metabolic status of individual bacterial cells is then quantified by flow cytometry, while their species identity is determined simultaneously via fluorescence in situ hybridization (FISH). CommAST can thus simultaneously determine the minimum inhibitory concentrations for multiple species within a microbial system. When applied to human fecal microbiota, CommAST profiled MICs for 105 drug-bacteria combinations across 27 species. A substantial portion of these were previously uncultured taxa, thereby providing the first antibiotic susceptibility profiles for these species. Notably, we uncovered significant discrepancies between strain-level and community-level MICs, with community-level MICs frequently exceeding their strain-level counterparts. Transcriptomic analysis revealed that enhanced community tolerance stems from synergistic mechanisms, including biofilm protection, metabolic cost-sharing, and coordinated stress responses. Collectively, CommAST establishes an innovative community-level AST platform, enabling a deeper understanding of the mechanisms behind antibiotic-induced gut dysbiosis.<\/jats:p>","DOI":"10.1021\/acs.analchem.6c00243","type":"journal-article","created":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T18:57:12Z","timestamp":1784141832000},"page":"21205-21218","source":"Crossref","is-referenced-by-count":0,"title":["CommAST Enables\nAntibiotic Susceptibility Testing\nat the Gut Microbiota Community Level"],"prefix":"10.1021","volume":"98","author":[{"given":"Chenling","family":"Ding","sequence":"first","affiliation":[{"name":"Shanghai Jiao Tong University School of Medicine , , ,","place":["Shanghai, China, 200127"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weiqi","family":"Wu","sequence":"additional","affiliation":[{"name":"Shanghai Jiao Tong University School of Medicine , , ,","place":["Shanghai, China, 200127"]},{"name":"Shanghai Normal University , , ,","place":["Shanghai, China, 200234"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanqi","family":"Zhang","sequence":"additional","affiliation":[{"name":"Inner Mongolia University , , ,","place":["Hohhot, China, 010021"]},{"name":"Fudan University , , ,","place":["Shanghai, China, 200433"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiacheng","family":"Han","sequence":"additional","affiliation":[{"name":"Fudan University , , ,","place":["Shanghai, China, 200433"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5539-4532","authenticated-orcid":true,"given":"Wei","family":"Wang","sequence":"additional","affiliation":[{"name":"Fudan University , , ,","place":["Shanghai, China, 200433"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0122-8360","authenticated-orcid":true,"given":"Jia","family":"Song","sequence":"additional","affiliation":[{"name":"Shanghai Jiao Tong University School of Medicine , , ,","place":["Shanghai, China, 200092"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuan","family":"Gao","sequence":"additional","affiliation":[{"name":"Shanghai Jiao Tong University School of Medicine , , ,","place":["Shanghai, China, 200127"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan","family":"Gao","sequence":"additional","affiliation":[{"name":"Shanghai Jiao Tong University School of Medicine , , ,","place":["Shanghai, China, 200127"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2374-5342","authenticated-orcid":true,"given":"Chaoyong","family":"Yang","sequence":"additional","affiliation":[{"name":"Shanghai Jiao Tong University School of Medicine , , ,","place":["Shanghai, China, 200127"]},{"name":"Xiamen University , , ,","place":["Xiamen, China, 361005"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,7,15]]},"reference":[{"key":"2026072808080555200_cit1","doi-asserted-by":"publisher","first-page":"499","DOI":"10.1038\/s41586-019-0965-1","article-title":"A new genomic blueprint\nof the human gut microbiota","volume":"568","author":"Almeida","year":"2019","journal-title":"Nature"},{"key":"2026072808080555200_cit2","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1038\/s41579-020-0433-9","article-title":"Gut microbiota in human\nmetabolic health and disease","volume":"19","author":"Fan","year":"2021","journal-title":"Nat. Rev. Microbiol."},{"key":"2026072808080555200_cit3","doi-asserted-by":"publisher","first-page":"565","DOI":"10.1038\/s41575-022-00605-x","article-title":"The gut\nmicrobiome as a modulator\nof healthy ageing","volume":"19","author":"Ghosh","year":"2022","journal-title":"Nat. Rev. Gastroenterol.\nHepatol."},{"key":"2026072808080555200_cit4","doi-asserted-by":"publisher","DOI":"10.1126\/science.aat9351","article-title":"T cell-mediated regulation of the\nmicrobiota protects against obesity","volume":"365","author":"Petersen","year":"2019","journal-title":"Science"},{"issue":"9","key":"2026072808080555200_cit5","doi-asserted-by":"publisher","first-page":"3870","DOI":"10.1021\/acs.analchem.3c05327","article-title":"11-plex DLeu\nisobaric\nlabeling enables quantitative assessment of brain region protein association\nnetworks impacted by the gut microbiome","volume":"96","author":"Han","year":"2024","journal-title":"Anal.\nChem."},{"key":"2026072808080555200_cit6","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-45332-w","article-title":"The gut microbiome-prostate\ncancer\ncrosstalk is modulated by dietary polyunsaturated long-chain fatty\nacids","volume":"15","author":"Lachance","year":"2024","journal-title":"Nat. Commun."},{"key":"2026072808080555200_cit7","doi-asserted-by":"publisher","first-page":"1339","DOI":"10.1038\/s41591-024-02963-2","article-title":"Microbiome\nconfounders and quantitative profiling challenge predicted microbial\ntargets in colorectal cancer development","volume":"30","author":"Tito","year":"2024","journal-title":"Nat.\nMed."},{"issue":"6","key":"2026072808080555200_cit8","doi-asserted-by":"publisher","first-page":"786","DOI":"10.1016\/j.chom.2024.05.009","article-title":"Response, resistance,\nand recovery of gut bacteria to human-targeted drug exposure","volume":"32","author":"de la Cuesta-Zuluaga","year":"2024","journal-title":"Cell Host Microbe"},{"key":"2026072808080555200_cit9","doi-asserted-by":"publisher","first-page":"S209","DOI":"10.1093\/infdis\/jiaa497","article-title":"The Gut Microbiome\nas a reservoir for antimicrobial resistance","volume":"223","author":"Anthony","year":"2021","journal-title":"J. Infect. Dis."},{"key":"2026072808080555200_cit10","doi-asserted-by":"publisher","first-page":"299","DOI":"10.1038\/s41579-020-0327-x","article-title":"Innovative and\nrapid antimicrobial susceptibility testing systems","volume":"18","author":"van Belkum","year":"2020","journal-title":"Nat. Rev. Microbiol."},{"key":"2026072808080555200_cit11","unstructured":"NCCLS.\n          .  Methods\nfor Antimicrobial\nSusceptibility Testing of Anaerobicbacteria; Approved Standard-Sixth\nEdition; NCCLS, 2004."},{"key":"2026072808080555200_cit12","unstructured":"CLSI.\n          .  Methods for Dilution\nAntimicrobial Susceptibility Tests Forbacteria that Grows Aerobically,\n9th ed.; Clinical and Laboratory Standards\nInstitute, 2012."},{"key":"2026072808080555200_cit13","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-022-01272-5","article-title":"Opportunities and challenges of using metagenomic data to bring uncultured\nmicrobes into cultivation","volume":"10","author":"Liu","year":"2022","journal-title":"Microbiome"},{"issue":"267","key":"2026072808080555200_cit14","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.3009650","article-title":"A rapid antimicrobial susceptibility\ntest based on single-cell morphological analysis","volume":"6","author":"Choi","year":"2014","journal-title":"Sci. Transl. Med."},{"issue":"10","key":"2026072808080555200_cit15","doi-asserted-by":"publisher","first-page":"2297","DOI":"10.1039\/C5LC00311C","article-title":"Direct detection\nand\ndrug-resistance profiling of bacteremias using inertial microfluidics","volume":"15","author":"Hou","year":"2015","journal-title":"Lab Chip"},{"key":"2026072808080555200_cit16","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-18902-x","article-title":"A fast impedance-based\nantimicrobial susceptibility\ntest","volume":"11","author":"Spencer","year":"2020","journal-title":"Nat. Commun."},{"issue":"19","key":"2026072808080555200_cit17","doi-asserted-by":"publisher","first-page":"6957","DOI":"10.1021\/acs.analchem.1c05006","article-title":"Metabolism-triggered\ncolorimetric sensor array for fingerprinting and antibiotic susceptibility\ntesting of bacteria","volume":"94","author":"Gao","year":"2022","journal-title":"Anal. Chem."},{"key":"2026072808080555200_cit18","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-46213-y","article-title":"Accurate and\nrapid antibiotic susceptibility testing using a machine learning-assisted\nnanomotion technology platform","volume":"15","author":"Sturm","year":"2024","journal-title":"Nat. Commun."},{"issue":"3","key":"2026072808080555200_cit19","doi-asserted-by":"publisher","DOI":"10.1128\/jcm.00276-21","article-title":"Update from the European Committee\non Antimicrobial Susceptibility\nTesting (EUCAST)","volume":"60","author":"Giske","year":"2022","journal-title":"J. Clin. Microbiol."},{"issue":"3","key":"2026072808080555200_cit20","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2209043119","article-title":"Community\ninteractions drive the\nevolution of antibiotic tolerance in bacteria","volume":"120","author":"Mizrahi","year":"2023","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2026072808080555200_cit21","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-36252-2","article-title":"Cross-protection and cross-feeding\nbetween Klebsiella pneumoniae and Acinetobacter baumannii promotes their co-existence","volume":"14","author":"Semenec","year":"2023","journal-title":"Nat. Commun."},{"key":"2026072808080555200_cit22","doi-asserted-by":"publisher","DOI":"10.1128\/cmr.00024-23","article-title":"Biofilm antimicrobial\nsusceptibility testing: where are we and where could we be going?","volume":"36","author":"Coenye","year":"2023","journal-title":"Clin. Microbiol. Rev."},{"key":"2026072808080555200_cit23","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2025.1560569","article-title":"Advancements in AI-driven\ndrug sensitivity testing research","volume":"15","author":"Liao","year":"2025","journal-title":"Front. Cell.\nInfect. 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Developmental roadmap for\nantimicrobial susceptibility testing systems","volume":"17","author":"van Belkum","year":"2019","journal-title":"Nat. Rev. Microbiol."},{"key":"2026072808080555200_cit28","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-33659-1","article-title":"Rapid antibiotic\nsusceptibility\ntesting and species identification for mixed samples","volume":"13","author":"Kandavalli","year":"2022","journal-title":"Nat. Commun."},{"issue":"31","key":"2026072808080555200_cit29","doi-asserted-by":"publisher","first-page":"10874","DOI":"10.1021\/ja505668f","article-title":"Reconstitution\nof peptidoglycan cross-linking leads to improved fluorescent\nprobes of cell wall synthesis","volume":"136","author":"Lebar","year":"2014","journal-title":"J. Am. Chem.\nSoc."},{"key":"2026072808080555200_cit30","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1038\/nprot.2014.197","article-title":"Synthesis\nof fluorescent D-amino acids and their use for probing peptidoglycan\nsynthesis and bacterial growth in situ","volume":"10","author":"Kuru","year":"2015","journal-title":"Nat.\nProtoc."},{"issue":"29","key":"2026072808080555200_cit31","doi-asserted-by":"publisher","first-page":"11923","DOI":"10.1002\/anie.202004703","article-title":"Quantification of bacterial\nmetabolic activities in the gut by D-amino acid-based in vivo labeling","volume":"59","author":"Lin","year":"2020","journal-title":"Angew. Chem., Int. Ed."},{"issue":"6","key":"2026072808080555200_cit32","doi-asserted-by":"publisher","DOI":"10.1002\/adhm.202101736","article-title":"D-amino acid-based metabolic labeling\nenables a fast antibiotic susceptibility test of both isolated bacteria\nand bronchoalveolar lavage fluid","volume":"11","author":"Gao","year":"2022","journal-title":"Adv. Healthcare\nMater."},{"issue":"11","key":"2026072808080555200_cit33","doi-asserted-by":"publisher","first-page":"1314","DOI":"10.1039\/D2CB00163B","article-title":"Fluorescent\nmetabolic labeling-based\nquick antibiotic susceptibility test for anaerobic bacteria","volume":"3","author":"Gao","year":"2022","journal-title":"RSC Chem. Biol."},{"key":"2026072808080555200_cit34","doi-asserted-by":"publisher","first-page":"204","DOI":"10.1016\/j.trsl.2016.08.002","article-title":"Gut microbiome\ninteractions with drug metabolism, efficacy,\nand toxicity","volume":"179","author":"Wilson","year":"2017","journal-title":"Transl. Res."},{"issue":"1","key":"2026072808080555200_cit35","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41385-018-0053-0","article-title":"Interbacterial mechanisms\nof colonization resistance\nand the strategies pathogens use to overcome them","volume":"12","author":"Sorbara","year":"2019","journal-title":"Mucosal Immunol."},{"issue":"23","key":"2026072808080555200_cit36","doi-asserted-by":"publisher","first-page":"3161","DOI":"10.1093\/bioinformatics\/bts597","article-title":"KASpOD-a web\nservice for highly specific and explorative oligonucleotide design","volume":"28","author":"Parisot","year":"2012","journal-title":"Bioinformatics"},{"key":"2026072808080555200_cit37","doi-asserted-by":"publisher","first-page":"120","DOI":"10.1038\/s41586-021-03986-2","article-title":"Unravelling\nthe collateral damage of antibiotics on gut bacteria","volume":"599","author":"Maier","year":"2021","journal-title":"Nature"},{"issue":"3","key":"2026072808080555200_cit38","doi-asserted-by":"publisher","first-page":"1199","DOI":"10.1128\/AAC.01771-09","article-title":"Antimicrobial susceptibility\nof clinically\nrelevant Gram-positive anaerobic cocci collected over a three-year\nperiod in the Netherlands","volume":"55","author":"Veloo","year":"2011","journal-title":"Antimicrob. Agents\nChemother."},{"issue":"9","key":"2026072808080555200_cit39","doi-asserted-by":"publisher","first-page":"3996","DOI":"10.1128\/AAC.00908-08","article-title":"In vitro activities of telavancin and six comparator agents\nagainst anaerobic bacterial isolates","volume":"53","author":"Finegold","year":"2009","journal-title":"Antimicrob.\nAgents Chemother."},{"issue":"9","key":"2026072808080555200_cit40","doi-asserted-by":"publisher","first-page":"2005","DOI":"10.1128\/AAC.36.9.2005","article-title":"Vancomycin\nresistance gene vanC is specific to Enterococcus gallinarum","volume":"36","author":"Leclercq","year":"1992","journal-title":"Antimicrob.\nAgents Chemother."},{"issue":"9","key":"2026072808080555200_cit41","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.02487-19","article-title":"A roadblock-and-kill\nmechanism of action model for\nthe DNA-targeting antibiotic ciprofloxacin","volume":"64","author":"Ojkic","year":"2020","journal-title":"Antimicrob. Agents Chemother."},{"issue":"3","key":"2026072808080555200_cit42","doi-asserted-by":"publisher","first-page":"610","DOI":"10.1111\/jcpt.13369","article-title":"Meropenem use and therapeutic\ndrug monitoring in clinical practice: a literature review","volume":"46","author":"Steffens","year":"2021","journal-title":"J. Clin. Pharm. Ther."},{"issue":"1","key":"2026072808080555200_cit43","doi-asserted-by":"publisher","first-page":"650","DOI":"10.1128\/AAC.03719-14","article-title":"Metallo-\u03b2-lactamase-producing\nbacteroides species can shield other members of the gut microbiota\nfrom antibiotics","volume":"59","author":"Stiefel","year":"2015","journal-title":"Antimicrob. Agents Chemother."},{"issue":"4","key":"2026072808080555200_cit44","first-page":"694","article-title":"The use of vancomycin with its therapeutic and adverse\neffects: a review","volume":"19","author":"Bruniera","year":"2015","journal-title":"Eur. Rev. Med. Pharmacol.\nSci."},{"key":"2026072808080555200_cit45","doi-asserted-by":"publisher","first-page":"1759","DOI":"10.2147\/DDDT.S164515","article-title":"Linezolid: a review of its properties,\nfunction, and use in critical care","volume":"12","author":"Hashemian","year":"2018","journal-title":"Drug Des.\nDev. Ther."},{"key":"2026072808080555200_cit46","doi-asserted-by":"publisher","first-page":"202","DOI":"10.1007\/s00284-004-4431-3","article-title":"Antibiotic susceptibility of Lactobacillus and Bifidobacterium species\nfrom the human gastrointestinal tract","volume":"50","author":"Delgado","year":"2005","journal-title":"Curr.\nMicrobiol."},{"issue":"9","key":"2026072808080555200_cit47","doi-asserted-by":"publisher","first-page":"1167","DOI":"10.1017\/S0031182017002025","article-title":"A review on\nmetronidazole: an old warhorse in antimicrobial chemotherapy","volume":"146","author":"Leitsch","year":"2019","journal-title":"Parasitology"},{"issue":"2","key":"2026072808080555200_cit48","doi-asserted-by":"publisher","first-page":"337","DOI":"10.3201\/eid0702.010239","article-title":"Emerging\nmechanisms of fluoroquinolone resistance","volume":"7","author":"Hooper","year":"2001","journal-title":"Emerg.\nInfect. Dis."},{"key":"2026072808080555200_cit49","doi-asserted-by":"publisher","first-page":"668","DOI":"10.1038\/s41596-023-00926-4","article-title":"High-throughput anaerobic screening for identifying compounds acting\nagainst gut bacteria in monocultures or communities","volume":"19","author":"Mu\u0308ller","year":"2024","journal-title":"Nat. Protoc."},{"issue":"3","key":"2026072808080555200_cit50","doi-asserted-by":"publisher","first-page":"812","DOI":"10.1038\/s41396-021-01130-6","article-title":"Inter-species interactions alter\nantibiotic efficacy\nin bacterial communities","volume":"16","author":"Bottery","year":"2022","journal-title":"ISME J."},{"issue":"1","key":"2026072808080555200_cit51","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1016\/j.biotechadv.2018.11.006","article-title":"Quorum sensing inhibitors\nas antipathogens: biotechnological applications","volume":"37","author":"Kalia","year":"2019","journal-title":"Biotechnol. Adv."},{"key":"2026072808080555200_cit52","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2021.747834","article-title":"Acidic\nmicroenvironment determines\nantibiotic susceptibility and biofilm formation of Pseudomonas aeruginosa","volume":"12","author":"Lin","year":"2021","journal-title":"Front.\nMicrobiol."},{"key":"2026072808080555200_cit53","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1038\/s41564-018-0313-5","article-title":"Phylogenetic\nbarriers to horizontal transfer of antimicrobial peptide resistance\ngenes in the human gut microbiota","volume":"4","author":"Kintses","year":"2019","journal-title":"Nat. Microbiol."},{"key":"2026072808080555200_cit54","doi-asserted-by":"publisher","first-page":"2285","DOI":"10.1038\/s41564-019-0550-2","article-title":"Persistent\nmetagenomic signatures of early-life hospitalization and antibiotic\ntreatment in the infant gut microbiota and resistome","volume":"4","author":"Gasparrini","year":"2019","journal-title":"Nat. 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