Abstract
Sea urchins, in many instances, are collected from the wild, maintained in the laboratory aquaculture environment, and used as model animals for various scientific investigations. It has been increasingly evident that diet-driven dysbiosis of the gut microbiome could affect animal health and physiology, thereby impacting the outcome of the scientific studies. In this study, we compared the gut microbiome between naturally occurring (ENV) and formulated diet-fed laboratory aquaculture (LAB) sea urchin Lytechinus variegatus by amplicon sequencing of the V4 region of the 16S rRNA gene and bioinformatics tools. Overall, the ENV gut digesta had higher taxa richness with an abundance of Propionigenium, Photobacterium, Roseimarinus, and Flavobacteriales. In contrast, the LAB group revealed fewer taxa richness, but noticeable abundances of Arcobacter, Agarivorans, and Shewanella. However, Campylobacteraceae, primarily represented by Arcobacter spp., was commonly associated with the gut tissues of both ENV and LAB groups whereas the gut digesta had taxa from Gammaproteobacteria, particularly Vibrio spp. Similarly, the co-occurrence network displayed taxonomic organizations interconnected by Arcobacter and Vibrio as being the key taxa in gut tissues and gut digesta, respectively. Predicted functional analysis of the gut tissues microbiota of both ENV and LAB groups showed a higher trend in energy-related metabolisms, whereas amino acids, carbohydrate, and lipid metabolisms heightened in the gut digesta. This study provides an outlook of the laboratory-formulated diet-fed aquaculture L. variegatus gut microbiome and predicted metabolic profile as compared to the naturally occurring animals, which should be taken into consideration for consistency, reproducibility, and translatability of scientific studies.
Highlights
IntroductionOrganisms from all domains of life cohabit in the nearshore marine ecosystems worldwide, where they thrive by modulating their community structure with the fluctuating biotic and abiotic factors, food sources, and other perturbances, such as natural calamities and human activities [1,2,3]
The raw sequence count of the V4 segment of the 16S rRNA generated from the paired-end Illumina MiSeq across all samples yielded 1,433,598 reads following quality checking (Supplementary Table S1)
The sequence dataset used in this study was analyzed using the QIIME2/Amplicon sequence variants (ASVs) tools, which have been described as superior tools on multiple fronts, such as the recovery of sequences, by avoiding spurious taxa assignments as well as providing more accurate diversity estimates as compared to previously reported tools, including QIIME1 (v1.9.1)
Summary
Organisms from all domains of life cohabit in the nearshore marine ecosystems worldwide, where they thrive by modulating their community structure with the fluctuating biotic and abiotic factors, food sources, and other perturbances, such as natural calamities and human activities [1,2,3]. The resiliency of these ecosystems in such changing environments is often contingent upon the composition and metabolic activities of microbial communities that help sustain some of the crucial trophic functions [2].
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