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Despite its epidemiological importance, the molecular and microbial determinants of\n                    <jats:italic>A. darlingi<\/jats:italic>\n                    susceptibility to\n                    <jats:italic>P. vivax<\/jats:italic>\n                    remain poorly understood. Here, we investigated vector-parasite-microbiota interactions using experimental infections with field-derived\n                    <jats:italic>P. vivax<\/jats:italic>\n                    gametocytaemic blood, which produced two distinct infection phenotypes: low and high oocyst burdens. Transcriptomic profiling of mosquito midguts across key parasite developmental timepoints revealed that low-infection mosquitoes mounted an early and sustained response characterised by activation of detoxification pathways, redox regulation, aromatic amino acid catabolism, and purine depletion, likely coordinated through neurophysiological cues, which collectively create a metabolically restrictive environment for parasite development. These physiological changes were accompanied by reduced bacterial diversity and enrichment of Enterobacteriales and Pseudomonadales, taxa previously linked to anti-\n                    <jats:italic>Plasmodium<\/jats:italic>\n                    activity. Conversely, high-infection mosquitoes exhibited limited metabolic reprogramming, expansion of Flavobacteriales, and transcriptional signatures consistent with permissive physiological states, potentially associated with reproductive trade-offs. Importantly, low infection outcomes consistently arose from bloodmeals with the lowest gametocyte densities, suggesting that host- and parasite-derived components of the bloodmeal act as early conditioning factors that prime the mosquito midgut for either resistance or susceptibility. These findings reframe\n                    <jats:italic>A. darlingi<\/jats:italic>\n                    vector competence to\n                    <jats:italic>P. vivax<\/jats:italic>\n                    not as a fixed immune trait but as a dynamic outcome of early redox, metabolic, and microbial interactions. They also highlight ecological and physiological targets for transmission-blocking strategies and reinforce the importance of studying vector-parasite interactions in regionally relevant systems.\n                  <\/jats:p>","DOI":"10.1371\/journal.ppat.1013823","type":"journal-article","created":{"date-parts":[[2025,12,23]],"date-time":"2025-12-23T18:35:34Z","timestamp":1766514934000},"page":"e1013823","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":2,"title":["Metabolic reprogramming and gut microbiota ecology drive divergent Plasmodium vivax infection outcomes in Anopheles darlingi"],"prefix":"10.1371","volume":"21","author":[{"given":"Bianca Cechetto","family":"Carlos","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kamila","family":"Voges","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pedro Henrique de Andrade","family":"Affonso","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amie","family":"Jaye","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carlos","family":"Tong Rios","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bruno","family":"Tinoco-Nunes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Diego Peres","family":"Alonso","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julia A.","family":"Cai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert M.","family":"MacCallum","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marta","family":"Moreno","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dina","family":"Vlachou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jayme A.","family":"Souza-Neto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3323-1687","authenticated-orcid":true,"given":"George K.","family":"Christophides","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2025,12,23]]},"reference":[{"key":"ppat.1013823.ref001","article-title":"World malaria report 2024","year":"2024"},{"issue":"1","key":"ppat.1013823.ref002","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1186\/s40249-022-00945-5","article-title":"Reaching the malaria elimination goal in Brazil: a spatial analysis and time-series study","volume":"11","author":"GZ Laporta","year":"2022","journal-title":"Infect Dis Poverty"},{"issue":"7","key":"ppat.1013823.ref003","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1089\/vbz.2019.2527","article-title":"First Observation of Experimental Plasmodium vivax Infection of Three Malaria Vectors from the Brazilian Amazon","volume":"20","author":"MdS Ara\u00fajo","year":"2020","journal-title":"Vector Borne Zoonotic Dis"},{"issue":"1","key":"ppat.1013823.ref004","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1080\/20477724.2019.1581463","article-title":"A comprehensive analysis of malaria transmission in Brazil","volume":"113","author":"BC Carlos","year":"2019","journal-title":"Pathog Glob Health"},{"issue":"1","key":"ppat.1013823.ref005","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1186\/s13071-020-3924-7","article-title":"Evidence for family-level variation of phenotypic traits in response to temperature of Brazilian Nyssorhynchus darlingi","volume":"13","author":"VM Chu","year":"2020","journal-title":"Parasit Vectors"},{"issue":"8","key":"ppat.1013823.ref006","doi-asserted-by":"crossref","first-page":"705","DOI":"10.1016\/j.pt.2020.05.011","article-title":"When Is a Plasmodium-Infected Mosquito an Infectious Mosquito?","volume":"36","author":"W Graumans","year":"2020","journal-title":"Trends Parasitol"},{"key":"ppat.1013823.ref007","first-page":"223","article-title":"Chapter Eight - The Complement System of Malaria Vector Mosquitoes.","volume-title":"Advances in Insect Physiology. 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interactions affect development of Plasmodium falciparum in Africa","volume":"4","author":"AM Mendes","year":"2008","journal-title":"PLoS Pathog"},{"issue":"2","key":"ppat.1013823.ref027","doi-asserted-by":"crossref","first-page":"61","DOI":"10.3390\/metabo11020061","article-title":"Amino Acid Metabolism in Apicomplexan Parasites","volume":"11","author":"A Krishnan","year":"2021","journal-title":"Metabolites"},{"issue":"18","key":"ppat.1013823.ref028","doi-asserted-by":"crossref","first-page":"8365","DOI":"10.1021\/acs.jmedchem.9b00182","article-title":"Plasmodium Purine Metabolism and Its Inhibition by Nucleoside and Nucleotide Analogues","volume":"62","author":"T Cheviet","year":"2019","journal-title":"J Med Chem"},{"key":"ppat.1013823.ref029","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1016\/j.dci.2016.09.012","article-title":"The Anopheles FBN9 immune factor mediates Plasmodium species-specific defense through transgenic fat body expression","volume":"67","author":"ML Sim\u00f5es","year":"2017","journal-title":"Dev Comp Immunol"},{"issue":"2","key":"ppat.1013823.ref030","article-title":"Plasmodium Para-Aminobenzoate Synthesis and Salvage Resolve Avoidance of Folate Competition and Adaptation to Host Diet","volume":"26","author":"JM Matz","year":"2019","journal-title":"Cell Rep"},{"issue":"5","key":"ppat.1013823.ref031","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1006391","article-title":"Microbiota-induced peritrophic matrix regulates midgut homeostasis and prevents systemic infection of malaria vector mosquitoes","volume":"13","author":"FH Rodgers","year":"2017","journal-title":"PLoS Pathog"},{"key":"ppat.1013823.ref032","doi-asserted-by":"crossref","first-page":"34084","DOI":"10.1038\/srep34084","article-title":"A natural Anopheles-associated Penicillium chrysogenum enhances mosquito susceptibility to Plasmodium infection","volume":"6","author":"YI Angler\u00f3-Rodr\u00edguez","year":"2016","journal-title":"Sci 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