{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/116181"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/116181","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Mechanistic modeling of complex microbial communities","abstract":"Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2022-11-15 without embargo terms","abstract_html":"Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2022-11-15 without embargo terms","abstract_has_math":false,"creators":["Dubinkina, Veronika"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Bioengineering","degree_department":null,"school":null,"contributors":["Maslov, Sergei","Donovan, Sharon M.","O'Dwyer, James","Irudayaraj, Joseph Maria Kumar"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2022,"date_issued":"2022-08","date_published":"2022-08","updated_at":"2026-07-22T22:24:55Z","subjects":["consumer-resource models","microbial community","dynamical modeling"],"languages":["en","eng"],"rights":["Copyright 2022 Veronika Dubinkina"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/2142/116181","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Maslov, Sergei","Donovan, Sharon M.","O'Dwyer, James","Irudayaraj, Joseph Maria Kumar"]},{"key":"dc:creator","label":"Author","values":["Dubinkina, Veronika"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2022-08","2022-07-15"]},{"key":"dc:type","label":"Dc Type","values":["text","Thesis"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Bioengineering"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Ph.D."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["consumer-resource models","microbial community","dynamical modeling"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en","eng"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2022 Veronika Dubinkina"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://hdl.handle.net/2142/116181"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2022-11-15 without embargo terms","The student, Veronika Dubinkina, accepted the attached license on 2022-07-04 at 15:00.","The student, Veronika Dubinkina, submitted this Dissertation for approval on 2022-07-05 at 20:45.","This Dissertation was approved for publication on 2022-07-15 at 10:19.","DSpace SAF Submission Ingestion Package generated from Vireo submission #18137 on 2022-11-15 at 17:38:06","Microbial communities have many practical applications in human health, agriculture, industry, and civil engineering. Yet the attempts to explain patterns observed in them resulted in the understanding that complexity of these ecosystems should be attributed not only to the microbial species present, but also to the metabolites they consume and secrete. These metabolites shape microbial communities as they underlie competitive exclusion and mediate inter-species interactions. Models that explicitly incorporate nutrients have proven to be useful in gaining insights into principles governing various microbial communities due to their mechanistic nature. This dissertation aims to contribute to these efforts by developing consumer-resource models capturing different patterns of metabolite consumption and studying their effects on microbial interactions, community assembly, stability and resilience. We first studied a model for the community of diauxically shifting microbes, where every community member consumes one resource at a time. Using a game-theoretical as well as dynamic approach we demonstrated that coexistence of such species means that their resource preferences should be complementary and community members are selected based on their top choices. We then developed a model considering another limit: each species requires several essential resources for growth. This assumption leads to the existence of multistable states and complicates community assembly process. We also used fundamental ecological rules captured in such models to leverage existing multi-omics data and infer relevant parameters characterizing consumption and production of metabolites by various species. By developing models that incorporate key factors contributing to microbial growth, such as environmental state, we can expect to capture the right level of detail that permits the use of acquired understanding in practical tasks, e.g. design of viable strategies to control and manipulate complex microbial communities."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Mechanistic modeling of complex microbial communities"]}]}],"canonical_facts":{"dc:contributor":["Maslov, Sergei","Donovan, Sharon M.","O'Dwyer, James","Irudayaraj, Joseph Maria Kumar"],"dc:creator":["Dubinkina, Veronika"],"dc:date":["2022-08","2022-07-15"],"dc:description":["Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2022-11-15 without embargo terms","The student, Veronika Dubinkina, accepted the attached license on 2022-07-04 at 15:00.","The student, Veronika Dubinkina, submitted this Dissertation for approval on 2022-07-05 at 20:45.","This Dissertation was approved for publication on 2022-07-15 at 10:19.","DSpace SAF Submission Ingestion Package generated from Vireo submission #18137 on 2022-11-15 at 17:38:06","Microbial communities have many practical applications in human health, agriculture, industry, and civil engineering. Yet the attempts to explain patterns observed in them resulted in the understanding that complexity of these ecosystems should be attributed not only to the microbial species present, but also to the metabolites they consume and secrete. These metabolites shape microbial communities as they underlie competitive exclusion and mediate inter-species interactions. Models that explicitly incorporate nutrients have proven to be useful in gaining insights into principles governing various microbial communities due to their mechanistic nature. This dissertation aims to contribute to these efforts by developing consumer-resource models capturing different patterns of metabolite consumption and studying their effects on microbial interactions, community assembly, stability and resilience. We first studied a model for the community of diauxically shifting microbes, where every community member consumes one resource at a time. Using a game-theoretical as well as dynamic approach we demonstrated that coexistence of such species means that their resource preferences should be complementary and community members are selected based on their top choices. We then developed a model considering another limit: each species requires several essential resources for growth. This assumption leads to the existence of multistable states and complicates community assembly process. We also used fundamental ecological rules captured in such models to leverage existing multi-omics data and infer relevant parameters characterizing consumption and production of metabolites by various species. By developing models that incorporate key factors contributing to microbial growth, such as environmental state, we can expect to capture the right level of detail that permits the use of acquired understanding in practical tasks, e.g. design of viable strategies to control and manipulate complex microbial communities."],"dc:format":["application/pdf"],"dc:identifier":["https://hdl.handle.net/2142/116181"],"dc:language":["en","eng"],"dc:rights":["Copyright 2022 Veronika Dubinkina"],"dc:subject":["consumer-resource models","microbial community","dynamical modeling"],"dc:title":["Mechanistic modeling of complex microbial communities"],"dc:type":["text","Thesis"],"thesis:degree_discipline":["Bioengineering"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Ph.D."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:24:55Z"}