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Article

Microbial Composition and Genes for Key Metabolic Attributes in the Gut Digesta of Sea Urchins Lytechinus variegatus and Strongylocentrotus purpuratus Using Shotgun Metagenomics

by
Joseph A. Hakim
1,†,
George B. H. Green
1,
Stephen A. Watts
1,
Michael R. Crowley
2,
Casey D. Morrow
3,* and
Asim K. Bej
1,*
1
Department of Biology, The University of Alabama at Birmingham, 1300 University Blvd., Birmingham, AL 35294, USA
2
Department of Genetics, Heflin Center Genomics Core, School of Medicine, The University of Alabama at Birmingham, 705 South 20th Street, Birmingham, AL 35294, USA
3
Department of Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham, 1918 University Blvd., Birmingham, AL 35294, USA
*
Authors to whom correspondence should be addressed.
†
Current Address: School of Medicine (M.D.), The University of Alabama at Birmingham, 1670 University Blvd, Birmingham, AL 35233, USA.
Curr. Issues Mol. Biol. 2021, 43(2), 978-995; https://doi.org/10.3390/cimb43020070
Submission received: 21 July 2021 / Revised: 11 August 2021 / Accepted: 18 August 2021 / Published: 26 August 2021
(This article belongs to the Section Bioinformatics and Systems Biology)
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Abstract

This paper describes the microbial community composition and genes for key metabolic genes, particularly the nitrogen fixation of the mucous-enveloped gut digesta of green (Lytechinus variegatus) and purple (Strongylocentrotus purpuratus) sea urchins by using the shotgun metagenomics approach. Both green and purple urchins showed high relative abundances of Gammaproteobacteria at 30% and 60%, respectively. However, Alphaproteobacteria in the green urchins had higher relative abundances (20%) than the purple urchins (2%). At the genus level, Vibrio was dominant in both green (~9%) and purple (~10%) urchins, whereas Psychromonas was prevalent only in purple urchins (~24%). An enrichment of Roseobacter and Ruegeria was found in the green urchins, whereas purple urchins revealed a higher abundance of Shewanella, Photobacterium, and Bacteroides (q-value < 0.01). Analysis of key metabolic genes at the KEGG-Level-2 categories revealed genes for amino acids (~20%), nucleotides (~5%), cofactors and vitamins (~6%), energy (~5%), carbohydrates (~13%) metabolisms, and an abundance of genes for assimilatory nitrogen reduction pathway in both urchins. Overall, the results from this study revealed the differences in the microbial community and genes designated for the metabolic processes in the nutrient-rich sea urchin gut digesta, suggesting their likely importance to the host and their environment.
Keywords: echinoderm; gut microbiome; high-throughput sequencing; MG-RAST; KEGG; RefSeq; bioinformatics echinoderm; gut microbiome; high-throughput sequencing; MG-RAST; KEGG; RefSeq; bioinformatics

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MDPI and ACS Style

Hakim, J.A.; Green, G.B.H.; Watts, S.A.; Crowley, M.R.; Morrow, C.D.; Bej, A.K. Microbial Composition and Genes for Key Metabolic Attributes in the Gut Digesta of Sea Urchins Lytechinus variegatus and Strongylocentrotus purpuratus Using Shotgun Metagenomics. Curr. Issues Mol. Biol. 2021, 43, 978-995. https://doi.org/10.3390/cimb43020070

AMA Style

Hakim JA, Green GBH, Watts SA, Crowley MR, Morrow CD, Bej AK. Microbial Composition and Genes for Key Metabolic Attributes in the Gut Digesta of Sea Urchins Lytechinus variegatus and Strongylocentrotus purpuratus Using Shotgun Metagenomics. Current Issues in Molecular Biology. 2021; 43(2):978-995. https://doi.org/10.3390/cimb43020070

Chicago/Turabian Style

Hakim, Joseph A., George B. H. Green, Stephen A. Watts, Michael R. Crowley, Casey D. Morrow, and Asim K. Bej. 2021. "Microbial Composition and Genes for Key Metabolic Attributes in the Gut Digesta of Sea Urchins Lytechinus variegatus and Strongylocentrotus purpuratus Using Shotgun Metagenomics" Current Issues in Molecular Biology 43, no. 2: 978-995. https://doi.org/10.3390/cimb43020070

APA Style

Hakim, J. A., Green, G. B. H., Watts, S. A., Crowley, M. R., Morrow, C. D., & Bej, A. K. (2021). Microbial Composition and Genes for Key Metabolic Attributes in the Gut Digesta of Sea Urchins Lytechinus variegatus and Strongylocentrotus purpuratus Using Shotgun Metagenomics. Current Issues in Molecular Biology, 43(2), 978-995. https://doi.org/10.3390/cimb43020070

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