Novel systems analysis elucidates the influence of personalized variation in microbiome composition on metronidazole efficacy in bacterial vaginosis

Novel systems analysis elucidates the influence of personalized variation in microbiome composition on metronidazole efficacy in bacterial vaginosis | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Help Center Sign In Submit a Preprint Cite Share Download PDF Article Novel systems analysis elucidates the influence of personalized variation in microbiome composition on metronidazole efficacy in bacterial vaginosis Christina Lee, Ryan Cheu, Melissa Lemke, Andrew Gustin, Michael France, and 6 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-66397/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 01 Dec, 2020 Read the published version in Nature Communications → Version 1 posted You are reading this latest preprint version Abstract Bacterial vaginosis (BV) is a syndrome of the female reproductive tract associated with adverse reproductive outcomes and characterized by a shift from a Lactobacillus (LB)-dominant vaginal microbiota to a polymicrobial, anaerobic microbiota, consistently colonized by strains of Gardnerella vaginalis (Gv). The first-line treatment for BV is metronidazole (MNZ); however, treatment failure and recurrence rates remain high. To gain insight into complex interactions between target species (Gv) and non-target Lactobacillus species (Lactobacillus iners (Li)) with MNZ and understand their respective roles in efficacy, we developed an ordinary differential equation model that predicts bacterial growth as a function of drug uptake, metabolism, proliferation, and MNZ sensitivity. Model findings revealed a critical factor in MNZ efficacy may be Li sequestration of MNZ, and that efficacy decreases when the relative abundance of Li is higher pre-treatment. These results were validated in Gv and Li co-cultures (p < 0.001), and in two clinical cohorts, finding women with recurrent BV had significantly lower pre-treatment levels of BV-associated bacteria relative to Lactobacillus spp. (p = 0.0366; p = 0.0484). Overall, model results support a mechanism where non-target Lactobacillus species sequester MNZ from BV-associated target species, such as Gv, promoting BV recurrence by reducing MNZ bioavailability. General Microbiology Systems Biology systems analysis bacterial vaginosis (BV) metronidazole efficacy Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Full Text Additional Declarations Yes there is potential Competing Interest. JR is co-founder of LUCA Biologics, a biotechnology company focusing on translating microbiome research into live biotherapeutic drugs for women's health. All other authors declare no competing interests. Cite Share Download PDF Status: Published Journal Publication published 01 Dec, 2020 Read the published version in Nature Communications → Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. 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Also discoverable on Platform About Our Team In Review Editorial Policies Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-66397","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":1904241,"identity":"b138e46e-0966-4560-8b4d-5b2891c461f4","order_by":0,"name":"Christina Lee","email":"","orcid":"","institution":"University of Michigan","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Christina","middleName":"","lastName":"Lee","suffix":""},{"id":1904242,"identity":"ce0311fb-b57d-4846-9018-2a59c5594f71","order_by":1,"name":"Ryan Cheu","email":"","orcid":"","institution":"University of Miami","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Ryan","middleName":"","lastName":"Cheu","suffix":""},{"id":1904243,"identity":"fe35e15a-bfc4-4052-b175-a770973732ee","order_by":2,"name":"Melissa Lemke","email":"","orcid":"https://orcid.org/0000-0003-1860-4550","institution":"University of Michigan–Ann Arbor","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Melissa","middleName":"","lastName":"Lemke","suffix":""},{"id":1904244,"identity":"646d565d-e0f5-41cb-b889-f02975c136f8","order_by":3,"name":"Andrew Gustin","email":"","orcid":"https://orcid.org/0000-0002-8760-8320","institution":"University of Washington","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Andrew","middleName":"","lastName":"Gustin","suffix":""},{"id":1904245,"identity":"f85d0c3b-690c-44e5-b795-70afed30e102","order_by":4,"name":"Michael France","email":"","orcid":"","institution":"University of Maryland, Baltimore","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Michael","middleName":"","lastName":"France","suffix":""},{"id":1904246,"identity":"5ec44e52-acba-4396-b866-c952d9a9631f","order_by":5,"name":"Benjamin Hampel","email":"","orcid":"","institution":"University of Zurich","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Benjamin","middleName":"","lastName":"Hampel","suffix":""},{"id":1904247,"identity":"9902af95-aecd-4f85-9dd8-dcad8d82d4d6","order_by":6,"name":"Andrea Thurman","email":"","orcid":"","institution":"Eastern Virginia Medical School","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Andrea","middleName":"","lastName":"Thurman","suffix":""},{"id":1904248,"identity":"a7531fd2-ee55-4959-bcd4-b7cec9fe9f18","order_by":7,"name":"Gustavo Doncel","email":"","orcid":"","institution":"Eastern Virginia Medical 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Arnold","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAAwklEQVRIiWNgGAWjYBACCQkwZcHYDyQPMDaASOK0SDDObCBZywaQSqK0SM5ufva5oEJCdvON7MQDP3cwyPHdSMCvRVrmmPHsGWckjLfdyN1wsPcMg7EkIS1yEgnGzLxtEokgLYcZ2xgSNxDWkv4ZrGXzDIiWeoJapCVyILZskIBoSTAgpEVyzpliZh6gX2aceQv0S5uE4cwzD/BrkbjdvpmZp8JGtr89d/OHn2028nzHCdiCYQRpykfBKBgFo2AUYAcAr0NI8CP0z5YAAAAASUVORK5CYII=","orcid":"","institution":"University of Michigan–Ann Arbor","correspondingAuthor":true,"submittingAuthor":false,"prefix":"","firstName":"Kelly","middleName":"","lastName":"Arnold","suffix":""}],"badges":[],"createdAt":"2020-08-26 18:23:56","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-66397/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-66397/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1038/s41467-020-19880-w","type":"published","date":"2020-12-01T05:00:00+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":2225378,"identity":"45815cac-61a4-49a8-a4d7-c5f30281e269","added_by":"auto","created_at":"2020-09-03 16:13:22","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":214728,"visible":true,"origin":"","legend":"Model schematic for bacterial growth dynamics in BV with MNZ treatment. (a) MNZ is internalized by both G. vaginalis (Gv) and L. iners (Li) at rates kint-GV and kint-LI, cells are proliferating at kgrow-GV and kgrow-LI and MNZ inhibits growth by kkill-GV and kkill-LI. For G. vaginalis, a potential mechanism of MNZ resistance is the bacterial-mediated interactions to the drug leading to the formation of metabolites (kmet). (b) Sensitivity of Gv growth with 500 μg/ml MNZ when parameters directly related to Gv growth are varied 0.001x to 1,000x baseline values. Percent maximal growth refers to the final cell count compared to the carrying capacity of the culture, or the maximum cell count the unperturbed culture can reach at 48h based on initial cell counts (c) Sensitivity of Gv growth with 500 μg/ml MNZ when parameters related to Li survival are varied 0.001x to 1,000x baseline values. (d) Max growth of Gv (left) and Li (right) when the initial ratio of Gv to Li is varied with 500 μg/ml MNZ treatment. (e) Max growth of Gv when MNZ internalization rate of Li is varied at three different population compositions with 500 μg/ml MNZ treatment.","description":"","filename":"F1.png","url":"https://assets-eu.researchsquare.com/files/rs-66397/v1/F1.png"},{"id":2225379,"identity":"5711eb33-432f-4af6-8ca3-e0d54e54b881","added_by":"auto","created_at":"2020-09-03 16:13:22","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":323908,"visible":true,"origin":"","legend":"A higher initial Gv:Li ratio improves MNZ treatment efficacy. (a) Surface plot to illustrate predicted percent maximal growth of Gv (z-axis) when concentration of MNZ (x-axis) and the ratio of Gv:Li (y-axis) are varied in simultaneously. Arrows indicate the concentration of MNZ and ratios of Gv:Li used for model validation. (b) Percent maximal growth of Li after simultaneous variation of MNZ dose and Gv:Li ratio. (c-d) Comparison of model simulations to experimental data for 500 μg/ml MNZ at 1000x and 0.001x Gv:Li (* p \u003c 0.05, ** p \u003c 0.01, *** p \u003c 0.001, unpaired two-tailed t-test, error bars represent standard deviation).","description":"","filename":"F2.png","url":"https://assets-eu.researchsquare.com/files/rs-66397/v1/F2.png"},{"id":2225380,"identity":"10a6ab80-b97a-4f61-9601-891e43706fc7","added_by":"auto","created_at":"2020-09-03 16:13:22","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":362582,"visible":true,"origin":"","legend":"Initial Gv:Li ratios dictate final microbial populations. (a) Surface plot illustrates model predictions for proportion of Li relative to Gv 48h at different starting Gv:Li ratios (x-axis) and at different doses of MNZ (y-axis). Experimental validation was performed in in vitro co-cultures of Li and Gv (n = 36) and is plotted on the surface, with mean and ± standard deviation represented by nodes and vertical lines (b) Phase diagram of microbial growth dynamics 48hrs after exposure to various MNZ doses, dots indicate experimental conditions evaluated. There are four possibilities: Both Gv and Li populations are increased after treatment, both Gv and Li populations are decreased, only the Gv population is increased and only the Li population is increased. Pie charts indicate the fraction of experimental samples that agree with the predicted trends (right).","description":"","filename":"F3.png","url":"https://assets-eu.researchsquare.com/files/rs-66397/v1/F3.png"},{"id":2225381,"identity":"bb1cad90-dc54-434a-8fbf-c74ea80c766a","added_by":"auto","created_at":"2020-09-03 16:13:22","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":373592,"visible":true,"origin":"","legend":"High pre-treatment BV:LB ratio is predicted to reduce MNZ efficacy in more complex microbial environments regardless of strain variability. (A) Original model structure validated in Fig. 2 (B) Two species model with negative interaction between other Lactobacillus sp. (oLB) and Gv (c) Four species model of Gv and Li with additional representative bacteria for BV-associated bacteria and Lactobacillus sp. (d) Four species model with inter-species interactions. Within BV-associated bacteria and Lactobacillus sp. interactions were simulated from mutualistic (both benefit) to commensal (one benefits, the other is neutral). Inhibitory (amensal) interactions are included between D-lactic acid producing bacteria, other Lactobacillus sp., with both BV-associated bacteria (e-h) post-MNZ treatment (48h, 500 μg/ml) Lactobacillus sp. relative abundances at. 0.6x and 100x BV-associated bacteria to Lactobacillus sp (BV:LB) ratios. Each point represents a parameter set randomly sampled from physiological ranges in Tables S2 and S3 (i) Significantly sensitive parameters (assessed by partial rank correlation) for each model structure (a-d) as determined by the global sensitivity and uncertainty analysis.","description":"","filename":"F4.png","url":"https://assets-eu.researchsquare.com/files/rs-66397/v1/F4.png"},{"id":2225382,"identity":"0c2fe242-1e20-4800-9962-ae1513b4fec1","added_by":"auto","created_at":"2020-09-03 16:13:22","extension":"png","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":105891,"visible":true,"origin":"","legend":"Increased initial BV:LB ratios associated with successful treatment of BV. (a – b) clinical results for the UMB-HMP cohort describing the (a) log base 10 transform of initial BV-associated bacteria relative abundance to Lactobacillus sp. relative abundance (b) initial Gv:Li ratio. (c – d) Clinical results for the CONRAD BV cohort (c) log base 10 transform of initial BV-associated bacteria relative abundance to Lactobacillus sp. relative abundance. (d) initial Gv:Li ratio. Lines depict the 25th, 50th and 75th percentiles, multiple unpaired one-tailed t-test p-values were adjusted using Benjamini and Hochberg correction.","description":"","filename":"F5.png","url":"https://assets-eu.researchsquare.com/files/rs-66397/v1/F5.png"},{"id":2225385,"identity":"343bf15b-bbfb-4dab-a8d6-36e1bc6aad7a","added_by":"auto","created_at":"2020-09-03 16:13:24","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":3456920,"visible":true,"origin":"","legend":"","description":"","filename":"LeeCheuRevisedBVMNZManuscript824CL.pdf","url":"https://assets-eu.researchsquare.com/files/rs-66397/v1_stamped.pdf"},{"id":2225383,"identity":"2eb72711-a01c-487f-bbef-fd882dde7bb9","added_by":"auto","created_at":"2020-09-03 16:13:22","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":3335843,"visible":true,"origin":"","legend":"","description":"","filename":"LeeCheuRevisedBVMNZManuscript824CL.pdf","url":"https://assets-eu.researchsquare.com/files/rs-66397/v1/LeeCheuRevisedBVMNZManuscript824CL.pdf"},{"id":15784933,"identity":"9066088d-77bf-41ed-bda4-50e4e80878e4","added_by":"auto","created_at":"2021-11-22 15:50:13","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":2523489,"visible":true,"origin":"","legend":"","description":"","filename":"LeeCheuBVMNZManuscriptnohighlighting.pdf","url":"https://assets-eu.researchsquare.com/files/rs-66397/v1_covered.pdf"},{"id":13528195,"identity":"e972a6eb-f71f-48d9-8344-2ebe0966080b","added_by":"auto","created_at":"2021-09-17 00:59:12","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":2518474,"visible":true,"origin":"","legend":"","description":"","filename":"LeeCheuBVMNZManuscriptnohighlighting.pdf","url":"https://assets-eu.researchsquare.com/files/rs-66397/v1_covered.pdf"}],"financialInterests":"\u003cb\u003eYes\u003c/b\u003e there is potential Competing Interest.\nJR is co-founder of LUCA Biologics, a biotechnology company focusing on translating microbiome research into live biotherapeutic drugs for women's health. All other authors declare no competing interests.","formattedTitle":"Novel systems analysis elucidates the influence of personalized variation in microbiome composition on metronidazole efficacy in bacterial vaginosis","fulltext":[{"header":"Full Text","content":"\u003cp\u003eThis preprint is available for \u003ca href='/article/rs-66397/latest.pdf' target='_blank'\u003edownload as a PDF\u003c/a\u003e.\u003c/p\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"nature-portfolio","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"","title":"Nature Portfolio","twitterHandle":"","acdcEnabled":false,"dfaEnabled":false,"editorialSystem":"ejp","reportingPortfolio":"","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"systems analysis, bacterial vaginosis (BV), metronidazole efficacy","lastPublishedDoi":"10.21203/rs.3.rs-66397/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-66397/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"Bacterial vaginosis (BV) is a syndrome of the female reproductive tract associated with adverse reproductive outcomes and characterized by a shift from a Lactobacillus (LB)-dominant vaginal microbiota to a polymicrobial, anaerobic microbiota, consistently colonized by strains of Gardnerella vaginalis (Gv). The first-line treatment for BV is metronidazole (MNZ); however, treatment failure and recurrence rates remain high. To gain insight into complex interactions between target species (Gv) and non-target Lactobacillus species (Lactobacillus iners (Li)) with MNZ and understand their respective roles in efficacy, we developed an ordinary differential equation model that predicts bacterial growth as a function of drug uptake, metabolism, proliferation, and MNZ sensitivity. Model findings revealed a critical factor in MNZ efficacy may be Li sequestration of MNZ, and that efficacy decreases when the relative abundance of Li is higher pre-treatment. These results were validated in Gv and Li co-cultures (p \u003c 0.001), and in two clinical cohorts, finding women with recurrent BV had significantly lower pre-treatment levels of BV-associated bacteria relative to Lactobacillus spp. (p = 0.0366; p = 0.0484). Overall, model results support a mechanism where non-target Lactobacillus species sequester MNZ from BV-associated target species, such as Gv, promoting BV recurrence by reducing MNZ bioavailability.","manuscriptTitle":"Novel systems analysis elucidates the influence of personalized variation in microbiome composition on metronidazole efficacy in bacterial vaginosis","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2020-09-03 16:13:20","doi":"10.21203/rs.3.rs-66397/v1","editorialEvents":[],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"nature-communications","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"NCOMMS","sideBox":"Learn more about [Nature Communications](http://www.nature.com/ncomms/)","snPcode":"","submissionUrl":"https://mts-ncomms.nature.com/","title":"Nature Communications","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"ejp","reportingPortfolio":"Nature Communications","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"d6b88954-a7f1-42fe-a987-f5b5277f9574","owner":[],"postedDate":"September 3rd, 2020","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[{"id":426800,"name":"General Microbiology"},{"id":426801,"name":"Systems Biology"}],"tags":[],"updatedAt":"2021-11-22T15:48:54+00:00","versionOfRecord":{"articleIdentity":"rs-66397","link":"https://doi.org/10.1038/s41467-020-19880-w","journal":{"identity":"nature-communications","isVorOnly":false,"title":"Nature Communications"},"publishedOn":"2020-12-01 05:00:00","publishedOnDateReadable":"December 1st, 2020"},"versionCreatedAt":"2020-09-03 16:13:20","video":"","vorDoi":"10.1038/s41467-020-19880-w","vorDoiUrl":"https://doi.org/10.1038/s41467-020-19880-w","workflowStages":[]},"version":"v1","identity":"rs-66397","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-66397","identity":"rs-66397","version":["v1"]},"buildId":"wLkW0s4AflPzk-lpfg-fK","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}