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Shipworms are marine bivalve molluscs, known for their wood boring abilities. They use modified shells to bore into and grind wood, which is then digested. The shipworm's ability to feed on lignocellulose is dependent on the presence of endosymbiotic bacteria that live in the animal's gills inside specialized eukaryotic cells called bacteriocytes. These bacteria provide the animal with hydrolytic enzymes for wood digestion, which are translocated from the gills to the caecum, the main site of wood digestion. Unlike other lignocellulose degrading organisms, which harbour symbiotic microbes in their digestive tract, the shipworm caecum hosts only few bacteria but contains a large amount of carbohydrate active enzymes (CAZymes) of both endogenous and bacterial origin. This study investigates the anatomical, physiological and molecular basis of wood digestion in the shipworm Lyrodus pedicellatus. A combination of meta-transcriptomics, meta-proteomics and microscopic studies of the shipworm digestive organs were used, coupled with recombinant production and characterisation of some of the most expressed lignocellulolytic enzymes. This multidisciplinary analysis revealed how two structures, the food groove (a mucus stream utilised by filter feeding molluscs to transport food particles from the gills to the digestive system) and the crystalline style (a rotating structure hosted in the stomach involved in extra-cellular digestion) have been co-opted in shipworms to translocate bacteria and their enzymes from the gills to the caecum, to facilitate wood digestion. The transcriptomic and proteomic results indicate that bacterial lignocellulolytic enzymes are expressed in the gills, while the endogenous enzymes are mainly produced by the digestive glands, with complementary CAZy classes being expressed by the bacteria and the shipworms, indicating a subdivision of roles. Five bacterial CAZymes were recombinantly expressed and characterised, showing activity on cellulose, galacto-glucomannan and xylan. This study provides new insights into the mechanisms of wood digestion in shipworms, which may have biotechnological relevance.