Intestinal microbial diversity is higher in Pacific abalone (Haliotis discus hannai) with slower growth rates

Mi-JinChoi^a,1, Young Dae Oh^b, Han Kyu Lim^b,c, Jong-Myoung Kim^a

Department of Fisheries Biology, PuKyong National University, Busan 48513, Republic of Korea.

Abstract

Microbial communities within animal intestines reflect various aspects of host physiological and metabolic status, including growth, feeding, and immunity. To find microbial indicators associated with faster abalone growth and hence the economics of abalone aquaculture, we performed a metabarcoding analysis of the intestinal microbial community in Pacific abalone (Haliotis discus hannai) with different growth rates. Two groups of Pacific abalone of different sizes were selected from a population that originated from the same fertilization batch grown in indoor tanks for 750 days post-fertilization: small (S; 4.24 ± 1.89 g; n = 8) and large (L; 24.47 ± 4.65 g; n = 8). We then performed DNA isolation using intestines dissected from the Pacific abalone in both groups, followed by polymerase chain reaction amplification of the 16S rRNA gene. Overall, an average of 75,643 reads, of which 415.8–424.9 bp were obtained via Illumina MiSeq analysis. Taxonomic classification of the 16S rRNA gene identified up to 1032 operational taxonomic units (OTUs) per group and more than 807 microbial genera were detected at least twice from all intestinal metabarcoding DNA samples analyzed. Principal coordinate analysis indicated that there was a clear distinction between groups. The most dominant genus among the intestinal samples in both size groups was Mycoplasma, followed by Psychrilyobacter, Vibrio, and Algibacter. The microbial genus that were more prevalent in large than small abalone were Mycoplasma (32.3635 ± 4.356%), followed by Psychrilyobacter (17.305 ± 8.179) and unclassified species belonging to Mycoplasmataceae (2.930 ± 0.794%), and Rhodospirillaceae (2.555 ± 0.486%). The microbial genera more prevalent in small abalone were as follows: Algibacter (4.944 ± 0.969%), Shewanella (3.037 ± 0.589%), and Haloferula (2.810 ± 0.445). A higher ratio of Firmicutes to Bacteroidetes was observed in large abalone (1.067 ± 0.694) than in small abalone (0.027 ± 0.013). The species richness within each group was assessed based on OTUs (L: 371.38 ± 136.40, S: 837.63 ± 138.99, P ≤ 0.001), the Chao1 index (L: 380.31 ± 141.03, S: 860.18 ± 151.01), and abundance-based coverage estimator values (L: 391.89 ± 147.17, S: 888.19 ± 163.38). Species diversity was compared between groups based on the Shannon index (L: 2.82 ± 0.5, S: 4.41 ± 0.11, P ≤ 0.001). These results indicated that microbial species diversity was higher in small abalone with slower growth rates. Understanding changes in the characteristics of intestinal microbial populations in Pacific abalones, and the relationship thereof with growth rates, will provide a basis for developing a microbiota-based strategy for abalone aquaculture.

Keywords: Pacific abalone, Metabarcoding, Microbial diversity, Microbiome.