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Within host\u2013ectoparasite holobionts, the dialogue between the two microbiomes offers powerful clues to ecological balance, disease dynamics and evolution. Because each holobiont is structurally and functionally compartmentalised, microbes exchanged at the interface can elicit highly local, niche-specific effects that ripple through the system. This review synthesises evidence for microbiota-to-microbiota interactions in four models:\n                    <jats:italic>Varroa<\/jats:italic>\n                    mite\u2013honeybee, tick\u2013vertebrate, bat fly\u2013bat and mosquito\u2013vertebrate pairs. In all cases, microbes move passively during feeding or contact, then colonise, replicate and modulate physiology and immunity, exerting a longer-lasting influence than transient biochemical cues. We further introduce the idea of indirect modulation, whereby abiotic or biotic factors act on a recipient holobiont through the intermediary of transferred microbes, underscoring the adaptive plasticity of holobiont networks. Bidirectional cross-talk forms self-reinforcing feedback loops that can redefine a microbe as pathogen, symbiont or immunomodulator, and tune its virulence according to context. These mechanisms shape disease transmission, resistance traits and the overall health of both partners. A deeper grasp of such cross-holobiont dynamics will pave the way for microbiota-based vaccines, targeted microbiome engineering and other innovative tools for human, veterinary and environmental health.\n                  <\/jats:p>","DOI":"10.1186\/s13071-025-07026-0","type":"journal-article","created":{"date-parts":[[2025,9,24]],"date-time":"2025-09-24T15:32:13Z","timestamp":1758727933000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Holobiont\u2013holobiont interactions across host\u2013ectoparasite systems"],"prefix":"10.1186","volume":"18","author":[{"given":"\u0160tef\u00e1nia","family":"Ski\u010dkov\u00e1","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karol\u00edna","family":"Svobodov\u00e1","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Myriam","family":"Kratou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexandra","family":"Corduneanu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana Laura","family":"Cano-Arg\u00fcelles","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Just\u00e9","family":"A\u017eelyt\u0117","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miray","family":"Tonk-R\u00fcgen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vikt\u00f3ria","family":"Majl\u00e1thov\u00e1","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dasiel","family":"Obregon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elianne","family":"Piloto-Sardi\u00f1as","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vaidas","family":"Palinauskas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alejandro","family":"Cabezas-Cruz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,9,24]]},"reference":[{"key":"7026_CR1","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1186\/s40168-018-0445-0","volume":"6","author":"MA Hassani","year":"2018","unstructured":"Hassani MA, Dur\u00e1n P, Hacquard S. 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