Date Published: October 11, 2018
Publisher: Public Library of Science
Author(s): Bo-Hye Nam, Jisung Jang, Kelsey Caetano-Anolles, Young-Ok Kim, Jung Youn Park, Hawsun Sohn, Sook Hee Yoon, Heebal Kim, Woori Kwak, Kyoung Heon Kim.
Haliotis discus hannai, a species of Pacific abalone, is a highly valuable food source throughout Northeast Asia. As H. discus hannai primarily feed on brown algae and largely extract their energy from algal polysaccharides, understanding the mechanisms by which they digest algal polysaccharides is essential for elucidating their energy metabolism. Gut microbes, as well as the host animal, are involved in the process of polysaccharide degradation. To identify algal polysaccharide-digestion mechanisms and their origin, we analyzed the metagenome and metatranscriptome of abalone visceral extracts. Microbial communities were characterized using the 16S rRNA gene sequences in the metagenome and our results differed significantly from those of previous studies using traditional microbiological methods such as bacterial cultivation and cloning. A greater diversity of bacterial taxa was identified here than was previously identified using cultivation methods. Furthermore, the most abundant bacterial taxa also differed from previous studies, which is not common when comparing the results of bacterial culturing with those of molecular methodologies. Based on the metatranscriptome, overall functions were identified and additional analyses were performed on the coding sequences of algal polysaccharide-digestive enzymes, including alginate lyase. Results of the transcriptomic analyses suggest that alginate lyase in the visceral extracts of H. discus hannai was produced by the host itself, not by visceral bacteria. This is the first next-generation sequencing study performed on abalone to characterize the visceral microbiota and the source of the ability to digest algal polysaccharides by analyzing the metagenome and metatranscriptome together.
Abalone are a group of marine snails which constitute a single genus, Haliotis in the Haliotidae family . Within the genus Haliotis, 57 abalone species are classified principally based on their habitat . One characteristic of abalone is that they consume only macroalgae, primarily red and brown algae . The main food of Haliotis discus hannai is Laminaria japonica, a species of brown algae . As polysaccharides are used for energy storage in brown algae, it is crucial to understand the polysaccharide digestion mechanism of abalone to understand their energy metabolism. Brown algae are composed largely of polysaccharides such as alginates, β-glucans (laminarans), cellulose, heteroglycans, and fucoidans [4, 5]. In particular, alginates constitute up to 40% of the dry mass of brown algae . Therefore, digestive enzymes such as alginate lyase, β-1,3-glucanase, cellulase, and agarase are essential for abalone to obtain nutrients from these algal polysaccharides. The ability of abalone visceral extracts to digest algal polysaccharides has been investigated previously using culturing methods on agar plates. For example, 70% of bacteria isolated from the gut of Haliotis gigantea showed an ability to degrade alginate on agar plates . In H. discus hannai, Vibrio halioticoli, a species of gut microbe, produced acetic acid and volatile short chain fatty acids on a growth medium that included sodium alginate due to alginate degradation by multiple enzymes . Likewise, the gut bacteria of abalone can help it obtain energy by supporting the degradation of algal polysaccharides. Gut bacterial enzymes degrade polysaccharides to smaller components that are more easily absorbed by their host . Bacterial culturing methodologies were useful for identifying several species and evaluating their ability to digest algal polysaccharides. However, the results of culturing methods have not accurately reflected the microbial community due to the differing oxygen conditions of the experimental environment and the anaerobic conditions within the actual gut . Additionally, the artificial high-nutrient content found in the growth media used for these cultivation methods differs significantly from the conditions within the visceral environment, which can greatly affect both the relative abundance of bacteria and the dominant species present . To overcome the limitations of culturing methods, we applied high-throughput sequencing to visceral extracts of H. discus hannai. This is the first next-generation sequencing (NGS) study to use 16S rRNA gene sequences to characterize the abalone visceral microbiota. By analyzing the abalone visceral metagenome, we characterized the bacterial community and bacterial abundance in detail.