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Teneral flies (newly eclosed adults) are especially susceptible to parasite establishment and development, yet our understanding of why remains fragmentary. The tsetse gut microbiome is dominated by two Gammaproteobacteria, an essential and ancient mutualist <jats:italic>Wigglesworthia glossinidia<\/jats:italic> and a commensal <jats:italic>Sodalis glossinidius<\/jats:italic>. Here, we characterize and compare the metatranscriptome of teneral <jats:italic>Glossina morsitans<\/jats:italic> to that of <jats:italic>G. brevipalpis<\/jats:italic> and describe unique immunological, physiological, and metabolic landscapes that may impact vector competence differences between these two species.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>An active expression profile was observed for <jats:italic>Wigglesworthia<\/jats:italic> immediately following host adult metamorphosis. Specifically, \u2018translation, ribosomal structure and biogenesis\u2019 followed by \u2018coenzyme transport and metabolism\u2019 were the most enriched clusters of orthologous genes (COGs), highlighting the importance of nutrient transport and metabolism even following host species diversification. Despite the significantly smaller <jats:italic>Wigglesworthia<\/jats:italic> genome more differentially expressed genes (DEGs) were identified between interspecific isolates (<jats:italic>n<\/jats:italic>\u00a0=\u2009326, ~\u200955% of protein coding genes) than between the corresponding <jats:italic>Sodalis<\/jats:italic> isolates (<jats:italic>n<\/jats:italic>\u00a0=\u2009235, ~\u20095% of protein coding genes) likely reflecting distinctions in host co-evolution and adaptation. DEGs between <jats:italic>Sodalis<\/jats:italic> isolates included genes involved in chitin degradation that may contribute towards trypanosome susceptibility by compromising the immunological protection provided by the peritrophic matrix. Lastly, <jats:italic>G. brevipalpis<\/jats:italic> tenerals demonstrate a more immunologically robust background with significant upregulation of IMD and melanization pathways.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>These transcriptomic differences may collectively contribute to vector competence differences between tsetse species and offers translational relevance towards the design of novel vector control strategies.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12864-021-07729-5","type":"journal-article","created":{"date-parts":[[2021,5,31]],"date-time":"2021-05-31T08:04:21Z","timestamp":1622448261000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["The holobiont transcriptome of teneral tsetse fly species of varying vector competence"],"prefix":"10.1186","volume":"22","author":[{"given":"Miguel","family":"Medina Munoz","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Caitlyn","family":"Brenner","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dylan","family":"Richmond","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Noah","family":"Spencer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2732-7540","authenticated-orcid":false,"given":"Rita V. 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