Is Metagenomic Analysis an Effective Way to Analyze Fish Feeding Habits? A Case of the Yellowfin Sea Bream Acanthopagrus latus (Houttuyn) in Daya Bay

Abstract

Yellowfin seabream, Acanthopagrus latus, is one of the most important species in terms of stock enhancement in China. However, using metagenomic techniques to explore the feeding habits and stomach microbiome of yellowfin seabream is still rare. The objective of this work was to study the feeding habits and stomach microbiome of yellowfin sea bream from Daya Bay through metagenomic analysis of different weight classes (≤50, 50–100, and >100 g). Whole-metagenome shotgun sequencing and morphological observation were used to investigate the stomach contents. The dietary composition and the community composition of the stomach microbiome of A. latus were examined. In this study, 153 species were detected in the eukaryotic composition of the stomach contents of yellowfin sea bream. At the species level, Mytilus edulis was the only species identified by both metagenomic analysis and morphological observation. The proportion of fish and bivalves was over 98%, but the diet changed little with body size. Larimichthys crocea, Scophthalmus maximus, and Seriola dumerili were the most abundant species among all samples. In total, 285 species were identified in the stomach microbiome of yellowfin sea bream. Bacterium 2013Ark19i, bacterium 2013Arg42i and Acinetobacter baumannii, first reported in the stomach contents of yellowfin sea bream, were the most abundant species of the stomach microbiomes. There was no difference in the biodiversity of the stomach microbiomes among the different body sizes. Overall, the composition of the yellowfin sea bream diet mainly consists of fish and bivalves. The use of metagenomics techniques is a promising approach for assessing the feeding habits of yellowfin sea bream. The results derived from this study can provide important information for evaluating the feeding ecology of yellowfin sea bream in Daya Bay.

Diet in phenotypically divergent sympatric species of African weakly electric fish (genus: Campylomormyrus) – a hybrid capture/NGS metabarcoding approach

“…The DNA metabarcoding method provided a clear taxonomic resolution of the partially digested stomach content and potentially detected highly diverse food taxa. This high taxonomic resolution is in line with those of previous dietary studies based on DNA-based approaches (e.g., Harms-Tuohy et al 2016;Pan et al 2021;Rees et al 2020;Sakaguchi et al 2017). The results of this study indicate that the diet ofCampylomormyrus and Gnathonemus species is composed mainly of three types of prey items, i.e., benthic invertebrates, allochthonous invertebrates, and macrophyte material.…”

Diet in phenotypically divergent sympatric species of African weakly electric fish (genus: Campylomormyrus)—A hybrid capture/HTS metabarcoding approach

“…This high taxonomic resolution is in line with those of previous dietary studies also based on DNA-based approaches (e.g. Harms-Tuohy et al, 2016;Pan et al, 2021;Rees et al, 2020;Sakaguchi et al, 2017) here cannot tell the stage of the aquatic insects found in the diet, it is reasonable to assume that the aquatic larvae, rather than the terrestrial imagines, were targeted by Campylomormyrus and Gnathonemus. Indeed, larvae of aquatic insects were reported as food items found in the stomach of mormyrid fish (Blake, 1977;Hyslop, 1986).…”

Impact of environmental micropollutants and diet composition on the gut microbiota of wild european eels (Anguilla anguilla)

“…Most of the current literature on teleost microbiomes was obtained through 16S rRNA barcoding (Llewellyn et al, 2014). In this study, we used whole metagenome sequencing (WMS) that has revealed an effective method for analysing both the feeding habits and gut microbiomes of fish (Pan et al, 2021). In addition to taxa information down to species and even strain levels that are not restricted to procaryotes, the use of WMS can allow analysis of functional potentials of microbiomes.…”