Differences and correlation analysis of feeding habits and intestinal microbiome in Schizopygopsis microcephalus and Ptychobarbus kaznakovi in the upper reaches of Yangtze River

The alpha diversity results indicated that <i>S. microcephalus</i> exhibited higher intestinal microbiota and feeding diversity compared to <i>P. kaznakovi</i>. Furthermore, the beta diversity results revealed significant differences in both intestinal microbiota and eukaryotic communities between the two species. The dominant bacterial phyla in both <i>S. microcephalus</i> and <i>P. kaznakovi</i> included Proteobacteria, Firmicutes, Actinobacteriota, Chloroflexi, and Verrucomicrobiota; however, Firmicutes was significantly more abundant in <i>P. kaznakovi</i> (<i>P</i> = 0.006), while Actinobacteriota was significantly higher (<i>P</i> = 0.019) in <i>S. microcephalus</i> at the phylum level. The primary food sources for <i>S. microcephalus</i> and <i>P. kaznakovi</i> were identified as Streptophyta (54.41%, 77.50%) and Cercozoa (8.67%, 1.94%), with Bacillariophyta (25.65%) was also the main food of constituting a major component of the diet for <i>S. microcephalus</i>. These differences suggested that <i>S. microcephalus</i> and <i>P. kaznakovi</i> occupy distinct dietary niches. To further explore the relationship between gut microbiota and feeding habits, we identified significant correlations between various food components and the gut microbial community through co-occurrence networks. This study enhances our understanding of the co-evolution and co-adaptation between host gut microbiota and feeding behaviors in sympatric fish species.