A simple microbiome in the European common cuttlefish, Sepia officinalis

Abstract

The European common cuttlefish, Sepia officinalis, is used extensively in biological and biomedical research yet its microbiome remains poorly characterized. We analyzed the microbiota of the digestive tract, gills, and skin in mariculture-raised S. officinalis using a combination of 16s rRNA amplicon sequencing and fluorescence spectral imaging. Sequencing revealed a highly simplified microbiota consisting largely of two single bacterial amplicon sequence variants (ASVs) of Vibrionaceae and Piscirickettsiaceae. The esophagus was dominated by a single ASV of the genus Vibrio. Imaging revealed a striking organization of bacteria distributed in a discrete layer that lines the esophagus. Imaging with specific probes confirmed the identity of these bacteria as Vibrionaceae. This Vibrio was also abundant in the microbiota of the stomach, cecum, and intestine, but occurred at lower density and in the lumen rather than in a discrete layer; it was present in only trace proportions in tank water and in the microbiome of shrimp that were used as feed for the cuttlefish. These Vibrio were resilient to treatment of animals with the commonly-used antibiotic, enrofloxacin. The gills were colonized by a single ASV in the family Piscirickettsiaceae, which imaging visualized as small clusters of cells. We conclude that bacteria belonging to the Gammaproteobacteria, especially Vibrionaceae, are the major symbionts of the cuttlefish Sepia officinalis cultured from eggs in captivity, and that the esophagus and gills are major colonization sites.\n\nIMPORTANCEMicrobes can play critical roles in the physiology of their animal hosts, as evidenced in cephalopods by the role of Vibrio (Aliivibrio) fischeri in the light organ of the bobtail squid and the role of Alpha- and Gammaproteobacteria in the reproductive system and egg defense in a variety of cephalopods. We sampled the cuttlefish microbiome throughout the digestive tract, gills, and skin and found dense colonization of an unexpected site, the esophagus, by a microbe of the genus Vibrio, as well as colonization of gills by Piscirickettsiaceae. We found these associations to be resilient to the treatment of animals with a common antibiotic, enrofloxacin. This finding expands the range of organisms and body sites known to be associated with Vibrio and is of potential significance for understanding host-symbiont associations as well as for understanding and maintaining the health of cephalopods in mariculture.