Deep Insights into Gut Microbiota in Four Carnivorous Coral Reef Fishes from the South China Sea

Abstract

Investigations of gut microbial diversity among fish to provide baseline data for wild marine fish, especially the carnivorous coral reef fishes of the South China Sea, are lacking. The present study investigated the gut microbiota of four carnivorous coral reef fishes, including Oxycheilinus unifasciatus, Cephalopholis urodeta, Lutjanus kasmira, and Gnathodentex aurolineatus, from the South China Sea for the first time using high-throughput Illumina sequencing. Proteobacteria, Firmicutes, and Bacteroidetes constituted 98% of the gut microbiota of the four fishes, and 20 of the gut microbial genera recovered in this study represent new reports from marine fishes. Comparative analysis indicated that the four fishes shared a similar microbial community, suggesting that diet type (carnivorous) might play a more important role in shaping the gut microbiota of coral reef fishes than the species of fish. Furthermore, the genera Psychrobacter, Escherichia-Shigella, and Vibrio constituted the core microbial community of the four fishes, accounting for 61-91% of the total sequences in each fish. The lack of the genus Epulopiscium in the four fishes was in sharp contrast to what has been found in coral reef fishes from the Red Sea, in which Epulopiscium was shown to be the most dominant gut microbial genus in seven herbivorous coral reef fishes. In addition, while unique gut microbial genera accounted for a small proportion (8-13%) of the total sequences, many such genera were distributed in each coral reef fish species, including several genera (Endozoicomonas, Clostridium, and Staphylococcus) that are frequently found in marine fishes and 11 new reports of gut microbes in marine fishes. The present study expands our knowledge of the diversity and specificity of gut microbes associated with coral reef fishes.

The Alteration of Intestinal Microbiota Profile and Immune Response in Epinephelus coioides during Pathogen Infection

“…In order to better understand the differential abundance of significantly different microbiomes, we explored the expression profile of microbiomes via Welch’s t -test. The upregulation of Faecalibacterium and Bifidobacterium in control group is consistent with the results of previous microbiota studies [ 84 , 85 , 86 , 87 , 88 ]. Similar studies have shown that Faecalibacterium is predominantly expressed in healthy individuals [ 89 ].…”

The Composition of Intestinal Microbiota From Collichthys lucidus and Its Interaction With Microbiota From Waters Along the Pearl River Estuary in China

“…We observed that Proteobacteria, Actinobacteria, Cyanobacteria, Firmicutes, Bacteroidetes, and Planctomycetes were highly abundant in C. lucidus intestines. These phyla also dominate other fish species (Givens et al, 2015;Gao et al, 2020). We also observed differences between water microbiota and C. lucidus intestinal microbiota from the PRE, while no significant differences were observed in microbial composition in intestines at different habitats in the PRE.…”

“…The presence of such opportunistic pathogens in fish intestines suggests the intestinal tract is a potential pathogen access route (Roeselers et al, 2011;Li et al, 2015). Core intestinal microbiota components were also observed in Salmo salar Dehler et al (2017a), Rudi et al (2018), zebra fish Roeselers et al (2011), European sea-bass (Kokou et al, 2019), carps (grass carp, crucian carp and bighead carp) Wu et al (2012), Li et al (2015), rainbow trout Wong et al (2013), and several other marine fish (Givens et al, 2015;Gao et al, 2020). Based on our data, the core intestinal microbiota of C. lucidus harbored bacteria associated with immune response, nutrient metabolism, probiotic actions, and potential pathogen behaviors.…”

“…Rhodopseudomonas is a photosynthetic bacteria, often recognized as a probiotic species, and associated with growth promoters or immune responses in fish, e.g., R. palustris (Zhou et al, 2010;Wang, 2011;Feckaninova et al, 2017). Escherichia-Shigella is frequently identified in fish intestinal samples, and is known as a potential pathogen (Sun et al, 2019;Zheng et al, 2019;Gao et al, 2020). Acinetobacter is common in fish intestines, the functions of which have been outlined above.…”

Diversity, Relative Abundance, and Functional Genes of Intestinal Microbiota of Tiger Grouper (Epinephelus fuscoguttatus) and Asian Seabass (Lates calcarifer) Reared in A Semi-Closed Hatchery in Dry and Wet Seasons

“…Higher abundance of these bacteria in the tiger grouper's gut suggests that wet season might trigger their abundance, thus stimulating immune response and improving disease resistance in the fish. Moreover, recently Gao et al (2020) reported that class Erysipelotrichi, order Erysipelotrichales and family Erysipelotrichaeae were one of the newest microbes in gut of carnivorous fish. Only Enterococcaceae was found abundant in dry season and this bacterial taxon is a common inhabitant in the gastrointestinal tract of marine fish (Dehler et al, 2017a(Dehler et al, , 2017b.…”