How environmental microbes colonize the fish gut ‘island’ ecosystem and which ecological process drives the microbial community assembly remain unknown. A recent study conducted by Dr. YAN Qingyun and his colleagues from Institute of Hydrobiology of Chinese Academy of Sciences reveal that environmental filtering is the major process governing the fish gut microbiota, but its contribution to the community assembly decreases with host development. This study was published online in Environmental Microbiology.

To understand the community assembly in fish gut ecosystem, researchers studied three major aquaculture fish species in China (i.e., herbivorous Ctenopharyngodon idellus, carnivorous Siniperca chuatsi, and Silurus meridionalis) from the larval stage to the adult stage. They use the high-throughput sequencing to assess the taxonomic compositions and phylogenetic diversity of gut microbiota across host development. The major ecological processes and their contributions to the microbial community assembly and turnover were then determined by null model test, phylogenetic-based mean nearest taxon distance (MNTD), and βMNTD in combination of Bray-Curtis-based Raup-Crick (RC_bray) distance analyses.

Research results indicate that taxonomic diversity of gut microbiota in the three examined freshwater fish species showed clear stage-specific patterns. Further phylogenetic analyses suggest that host gut environmental filtering led to the assembly of microbial communities in the fish gut ‘island’ ecosystem. However, the phylogenetic clustering of local communities and deterministic processes driving community turnover became less distinct as the fish developed. The relative importance of ecological processes that govern the community turnover of gut microbiota also found to be different in larva and adult. In brief, determinism (selection and dispersal) levels in the larvae (especially in the carnivorous S. chuatsi and S. meridionalis) were stronger than those found in the adults, whereas stochasticity (drift) levels significantly increased in the adults.

This study provides insights into community assembly studies in mammalian gut ecosystems. It was mainly conducted by the cooperation of the research groups led by Prof. YU Yuhe and Prof. WANG Yaping at Institute of Hydrobiology of Chinese Academy of Sciences, and Prof. ZHOU Jizhong at Institute for Environmental Genomics, University of Oklahoma.

The study was funded by the National Natural Science Foundation of China, and the Youth Innovation Promotion Association of the Chinese Academy of Sciences.