Fall 2017

Document Type

Master's Thesis (Open Access)

Degree Name

Master of Science (M.S.)


Moss Landing Marine Laboratories


Growth and gut microbiome composition of Red abalone, Haliotis rufescens, fed different diets were compared after six months. The diet treatments were starvation and three fresh macroalgal diets (Macrocystis pyrifera, Palmaria mollis, and Ulva lactuca). Abalone shell length and wet in-shell mass were measured for growth comparisons across treatments. Contents of the buccal cavity, intestine, and stomach, as well as seawater and macroalgal tissue samples, were also collected monthly for 16S rRNA Illumina MiSeq sequencing. Shell length and wet in-shell mass showed significant difference among treatments (two-way ANOVA test, F(2,74)=4.26, p=0.019) and months (two-way ANOVA test, F(4,74)=15.54, p<0.0001). The metabarcoding assay detected 17981 unique operational taxonomic units (OTUs) from all samples. Gut microbiome composition was significantly different across treatments at class (PERMANOVA test, F(3,203)=18.02, p=0.001) and genus (PERMANOVA test, F(3,203)=15.23, p=0.001) levels at a rarefaction depth of 13065 reads per sample. Gut microbiome composition was significantly different in the 3 gut regions at class (PERMANOVA test, F(2,203)=91.66, p=0.001) and genus (PERMANOVA test, F(2,203)=64.08, p=0.001) levels. Proteobacteria, Bacteroidetes, Fusobacteria, and Cyanobacteria were dominant taxa in most of the samples. SIMPER dissimilarity analysis showed that microbiomes similarities among diets ranged from 44.33% to 47.67% at the class level. Microbiome composition was more similar (57.33%) between the stomach and intestine samples than between mouth and stomach samples (40.61%) and between mouth and intestine samples (47.95%) at the class level. To date, this is the first study comparing gut microbiome compositions in red abalone under various macroalgal diets using Illumina sequencing technique. This work will enhance our understanding of the gut microbiome composition in red abalone which is essential for abalone farmers to support the production of quality juveniles for aquaculture and restoration purposes.