A Simple Microbiome in the European Common Cuttlefish, Sepia officinalis

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 using a combination of 16S rRNA amplicon sequencing, quantitative PCR (qPCR), and fluorescence spectral imaging. Sequencing revealed a highly simplified microbiota consisting largely of two single bacterial amplicon sequence variants (ASVs) of and . The esophagus was dominated by a single ASV of the genus . Imaging revealed bacteria in the family distributed in a discrete layer that lines the esophagus. This was also the primary ASV found in the microbiota of the stomach, cecum, and intestine, but occurred at lower abundance, as determined by qPCR, and was found only scattered in the lumen rather than in a discrete layer via imaging analysis. Treatment of animals with the commonly used antibiotic enrofloxacin led to a nearly 80% reduction of the dominant ASV in the esophagus but did not significantly alter the relative abundance of bacteria overall between treated versus control animals. Data from the gills were dominated by a single ASV in the family , which imaging visualized as small clusters of cells. We conclude that bacteria belonging to the are the major symbionts of the cuttlefish cultured from eggs in captivity and that the esophagus and gills are major colonization sites. Microbes can play critical roles in the physiology of their animal hosts, as evidenced in cephalopods by the role of ( ) in the light organ of the bobtail squid and the role of - and 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 , as well as colonization of gills by . This finding expands the range of organisms and body sites known to be associated with and is of potential significance for understanding host-symbiont associations, as well as for understanding and maintaining the health of cephalopods in mariculture.