# Pathogenic piscine intestinal coccidia infection alters gut microbiome in juvenile Asian seabass (Lates calcarifer)

## TL;DR

This study shows that coccidia infection in juvenile Asian seabass changes their gut microbiome, increasing harmful bacteria and reducing beneficial ones.

## Contribution

The study identifies specific bacterial genera affected by coccidial infection in fish gut microbiomes.

## Key findings

- Infected fish showed higher microbial diversity and shifts in gut bacteria composition.
- Pathogenic genera like Clostridium and Escherichia-Shigella increased in infected fish.
- Uninfected fish had higher levels of environmental and opportunistic bacteria like Bacillus and Vibrio.

## Abstract

Piscine intestinal coccidiosis has been associated with increased susceptibility to secondary bacterial infections, potentially through disruption of the gut microbiota. While many gut bacteria are commensal, infection-related alterations in microbial composition may favor the proliferation of opportunistic taxa. However, the specific effects of intestinal coccidial infections on the gut microbiome of fish remain insufficiently described.

This study examined the influence of intestinal coccidial infection on gut microbiota composition and the relative abundance of potentially pathogenic bacteria in juvenile Asian seabass (Lates calcarifer). Intestinal samples from seven coccidia-infected and five uninfected fish were analyzed using 16S rRNA gene sequencing. Infected fish demonstrated greater microbial diversity and marked compositional shifts across multiple taxonomic levels. Relative abundances of genera with reported pathogenic potential, such as Clostridium, Lactococcus, and Kurthia, as well as zoonotic bacteria including Helicobacter and Escherichia-Shigella, were elevated in the infected group. Conversely, uninfected fish harbored higher levels of genera such as Bacillus, Vibrio, Acinetobacter, and Streptococcus, which are commonly associated with environmental niches and opportunistic colonization. Coccidial infection was also linked to microbial imbalance, reflected in reduced Proteobacteria-to-Bacteroidota (P:B) and Proteobacteria-to-Firmicutes (P:F) ratios, alongside histopathological evidence of intestinal inflammation.

Intestinal coccidiosis in juvenile Asian seabass is associated with open niche gut characterized by altered microbial diversity and increased abundance of bacterial genera with pathogenic potential. These findings suggest that coccidial infection may contribute to an elevated risk of secondary infections, underscoring the relevance of gut microbiome monitoring in fish health management. Further studies are warranted to clarify host–parasite–microbiome interactions and their implications for aquaculture health.

The online version contains supplementary material available at 10.1186/s12917-025-05168-y.