Patterns and influencing factors of intestinal microbiota from different groupers

The intestinal microbiota influences nutritional metabolism, immunity, and disease resistance of fish hosts, while the host reciprocally regulates it. The compositional patterns of intestinal microbiota in groupers are influenced by multiple factors, with the core and stable interacting microbiota playing a crucial role in maintaining host growth stability. Asia is renowned for the grouper aquaculture industry, highlighting the importance of studying grouper intestinal microbes for both aquaculture development and conservation efforts.

We integrated and re-analyzed 936 sequencing files of six grouper species (purebred species: Epinephelus akaara, E. coidides, Plectropomus leopardus, and hybrid: E. fuscoguttatus♀ × E. polyphekadion♂, E. lanceolatus♂ × E. fuscoguttatus♀, E. moara♀ × E. lanceolatus♂) from both our experiments and public databases, covering samples from the South China Sea, East China Sea, and Bohai Sea. For aqua-cultured groupers, differences in core intestinal microbiota were mainly determined by host genetics rather than the aquaculture environment. Additionally, a clear purebred-hybrid dichotomy existed in the intestinal microbiota network: hybrids had more intricate, competitive, and stable intestinal microbiota, whereas purebreds possessed simpler yet highly positive intestinal microbiota. Further analysis summarized the common effects of external factors on the core co-occurrence of intestinal microbiota: disease markedly diminished the complexity and positive interactions; antibiotics also weakened microbial community structure; in contrast, probiotics enhanced diversity and stability. Both lipid and plant protein substitutions increased negative interactions and reduced bacterial synergy, with plant protein significantly simplifying the microbiota network. Under varying conditions, the intestinal microbiota balanced between beneficial and potentially harmful two competing guilds. Cluster 1 containing more keystone ASVs was positively correlated with the control group, while Cluster 2 showed a correlation with external factors. Although some factors influenced the core intestinal microbiota, they strived to maintain a balance between two clusters, such as probiotics, plant proteins, and alternative oil groups. In contrast, both disease and antibiotic groups exhibited significant reductions in two clusters, consistent with the marked simplification of core co-occurrence structure.

Generally, understanding the core intestinal microbiota and its changing patterns under influences provides valuable insights into exploring grouper health and improving aquaculture strategies.