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Genome
Despite the abundance of Endozoicomonas symbionts, only three complete Endozoicomonas genomes are publically available, including E. elysicola, E. montiporae, and E. numazuensis, isolated from a sea slug, coral, and a sponge, respectively. The difficulties in obtaining of Endozoicomonas genome sequencing may be attributed to the difficulty in obtaining cultured isolates from host tissue. The first isolation and sequencing occurred in 2007 by Kurahashi and Yokota, who isolated a strain of Endozoicomonas from a sea slug: Elysia ornata collected in seawater off the coast of Izu-Miyake Island, Japan, at a depth of 15 m. For their sequencing analyses, Kurahashi and Yokota used culture-independent methods of genome sequencing, including meta-genomic binning and single cell genomics.

Endozoicomonas species have large genomes ranging from 4.049 Mb (Endozoicomonas sp. AB1) to 6.69 Mb (E. elysicola DSM22380).

Through various researches, it was discovered that the Endozoicomonas genomes were enriched for genes associated with transporter activity, particularly carbon sugar transport, as well as cell secretion and transposase activity, suggesting that Endozoicomonas have a potential role in the up-cycling of carbohydrates or the supply of proteins to the host. These skills can help Endozoicomonas to quickly adapt to a new host or take advantage of a new niche.

Although none of the Endozoicomonas genomes have the genes for fixing nitrogen directly, E. elysicola, E. numazuensis, and E. montiporae, all have several forms of nitrate reductase, allowing the conversion of nitrate to nitrite and the conversion of nitrite to ammonia, which could then be secreted. Endozoicomonas contain in their own genome also pathway for the assimilation of ammonia through the synthesis of glutamine and glutamate. They can also synthesize other amino acids like alanine, aspartate, cysteine, glycine, homocysteine, homoserine, leucine, lysine, methionine, serine, and threonine. The Endozoicomonas's genomes differ in their capacity to produce these amino acids, which may indicate strain-specific functions.

The Endozoicomonas genus also plays an important role in the coral sulfur cycle. E. acroporae strains cannot only metabolize dimethylsulfoniopropionate (DMSP) to produce dimethylsulfide (DMS), but also use DMSP as a carbon source for growth and survival. Through several researches, the first DMSP-related operon in E. acroporae was also identified, which links DMSP metabolism to the central carbon cycle.