Organ-specific microbiomes reveal strong bacterial compartmentalization in two tropical squid species

Beyond the well-established symbiosis between the bobtail squid light organ and the bioluminescent bacterium Aliivibrio fischeri, the microbiomes associated with other cephalopod tissues remain poorly characterized. Here, we examined bacterial communities associated with major organs (e.g. skin, gut, gills and nidamental gland) in two Southeast Asian squid species, Uroteuthis chinensis and Sepioteuthis lessoniana. Because host species and environmental/temporal factors were fully confounded in our sampling design, we focused on characterizing microbiome compartmentalization across organs rather than on disentangling their relative contributions. Bacterial communities were strongly structured by anatomical compartment, with each organ harboring a distinct microbiome. In U. chinensis, gill communities were dominated by Endozoicomonas, whereas the gut microbiome of S. lessoniana was dominated by Mycoplasma. Nidamental glands from both species were enriched in Ruegeria and Pikeienuella, while skin communities displayed marked interspecific differences: U. chinensis skin was enriched in Sphingomonadales and Vibrionales, whereas S. lessoniana exhibited a more diverse mix including Micrococcales, Hyphomicrobiales, and Flavobacteriales. Together, these results provide a first descriptive characterization of microbiome organization across major squid organs and establish a baseline for future studies investigating the ecological and functional roles of host-associated bacteria in cephalopods.