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Data Brief
2024 Jun 01;54:110421. doi: 10.1016/j.dib.2024.110421.
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Sea cucumber (Holothuria glaberrima) intestinal microbiome dataset from Puerto Rico, generated by shotgun sequencing.
Rivera-Lopez EO
,
Nieves-Morales R
,
Melendez-Martinez G
,
Paez-Diaz JA
,
Rodriguez-Carrio SM
,
Rodriguez-Ramos J
,
Morales-Valle L
,
Rios-Velazquez C
.
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The sea cucumber (H. glaberrima) is a species found in the shallow waters near coral reefs and seagrass beds in Puerto Rico. To characterize the microbial taxonomic composition and functional profiles present in the sea cucumber, total DNA was obtained from their intestinal system, fosmid libraries constructed, and subsequent sequencing was performed. The diversity profile displayed that the most predominant domain was Bacteria (76.56 %), followed by Viruses (23.24 %) and Archaea (0.04 %). Within the 11 phyla identified, the most abundant was Proteobacteria (73.16 %), followed by Terrabacteria group (3.20 %) and Fibrobacterota, Chlorobiota, Bacteroidota (FCB) superphylum (1.02 %). The most abundant species were Porvidencia rettgeri (21.77 %), Pseudomonas stutzeri (14.78 %), and Alcaligenes faecalis (5.00 %). The functional profile revealed that the most abundant functions are related to transporters, MISC (miscellaneous information systems), organic nitrogen, energy, and carbon utilization. The data collected in this project on the diversity and functional profiles of the intestinal system of the H. glaberrima provided a detailed view of its microbial ecology. These findings may motivate comparative studies aimed at understanding the role of the microbiome in intestinal regeneration.
Fig. 1. Holothuria glaberrima before and after evisceration. (A)H. glaberrima exhibits an average length ranging from 10 to 15 cm (4 to 6 inches). Its predominant coloration is characterized by shades of black and dark brown [3]. (B) Evisceration process of H. glaberrima after induction with 2 mL of KCl [0.35 M].Credit: Edwin Omar Rivera-Lopez and Carlos Ríos-Velázquez
Fig. 2. Taxonomic diversity of the sea cucumber (Holothuria glaberrima) intestinal metagenome. Utilizing the Centrifuge Metagenomic Classification Tool through NMDC-EDGE showed that there were 5,557,757 classified reads and 314,616 species reads. The most abundant domain was Bacteria (76.56 %), followed by Virus (23.24 %), and Archaea (0.04 %). The most common Phyla out of the 11 found in Bacteria was Proteobacteria (73.16 %), followed by those included in the Terrabacteria group (3.20%) and Fibrobacterota, Chlorobiota, Bacteroidota (FCB) superphylum (1.02 %). The most abundant species were Porvidencia rettgeri (21.77 %), Pseudomonas stutzeri (14.78 %), and Alcaligenes faecalis (5.00 %).
Fig. 3. Functional annotation of the Holothuria glaberrima anatomic regions metagenomic genes. Alluvial plot exhibits the total genes that were annotated and assigned to a KEGG category by DRAM metabolism sheet. The colors represent different types of functional groups. The numbers represent the total number of genes identified per category. Full functional annotation of metagenomes is publicly available via the NMDC EDGE platform and NCBI. From the assembly scaffolds, gene calls resulted in 16,615 total genes. Of those, 9,092 contained a K0 number, used to categorize them metabolically, obtaining 2,480 genes.
