Objective To investigate the characteristics and differences of gut microbial communities between ApoE knockout rabbits and New Zealand rabbits, and to elucidate the potential role of the ApoE gene in regulating intestinal microbiota.

Method ApoE knockout rabbits were successfully generated using CRISPR/Cas9 technology. High throughput sequencing of 16S rRNA gene sequences from fecal samples of ApoE knockout rabbits and New Zealand rabbits was performed on the NovaSeq sequencing platform. Bioinformatics analyses-including quality control, ASV (amplicon sequence variant) clustering, taxonomic annotation, and diversity assessments were conducted to systematically evaluate the differences in gut microbiota diversity, community structure, and functional regulation.

Result Under normal dietary conditions, ApoE knockout rabbits exhibited higher levels of total cholesterol (TC), triglycerides (TG), and low-density lipoprotein cholesterol (LDL-C) in serum compared to New Zealand rabbits, with differences in TC and LDL-C being highly significant (P < 0.01), consistent with hyperlipidemia characteristics. Compared with New Zealand rabbits, ApoE knockout rabbits showed a significant increase in gut microbial ASV abundance (P < 0.01); α diversity indices including Observed_species, Chao1, Shannon, Simpson, and PD_whole_tree were significantly elevated (P < 0.05), indicating increased species richness and diversity. β diversity analysis revealed significant differences, with principal component and principal coordinate analyses explaining 28.84% and 38.20% of the variance respectively, suggesting marked alterations in gut microbial community structure. The Firmicutes/Bacteroidetes ratio (F/B) was significantly increased in ApoE knockout rabbits (P < 0.05), the gut shows an increase in lipopolysaccharide (LPS)-producing bacteria and mucosa-damaging bacteria such as Akkermansia, Alistipes, and Clostridium. Additionally, significant differences were observed in pathways related to basal transcription factor regulation, drug metabolism, and atrazine degradation (P < 0.05).

Conclusion The gut microbial diversity and metabolic pathways in ApoE gene knockout rabbits were altered, indicating that the deletion of the ApoE gene affects the gut microbial ecology and metabolic functions, playing a key role in regulating intestinal microecological balance.