Intestinal Parasite Community Dynamics in the Critically Endangered Chinese Alligator (Alligator sinensis): Multifactorial Insights From 18S rRNA Amplicon Sequencing.

The intestinal parasite communities of vertebrates are shaped by complex interactions among biological, environmental, and anthropogenic factors. However, such dynamics remain poorly characterized in endangered the Chinese Alligator (Alligator sinensis). Here, we conducted a high-throughput 18S rRNA amplicon survey of intestinal parasites in 149 fecal samples from the critically endangered Chinese alligators, spanning two geographic localities, four feeding regimens, three developmental stages, and 3 months. We identified 1524 eukaryotic parasite OTUs and 6606 nematode OTUs, revealing significant geographic variation in parasite composition, with higher richness in Wuhu than in Xuancheng populations. PERMANOVA further confirmed significant locality-level differences in parasite community structure for both eukaryotic and nematode assemblages. Feeding regimen strongly influenced parasite diversity and community composition, with nematode communities exhibiting particularly pronounced responses, showing the lowest abundance and diversity in alligators maintained on a standardized catfish-carp diet and highest in those fed diverse prey. Eukaryotic parasite richness declined markedly with host age, while nematode diversity showed pronounced depression in August. At finer taxonomic resolution, multiple parasite phyla and genera exhibited dynamic, factor-specific responses to locality, diet, age, and sampling month, highlighting strong ecological filtering effects. Linear Discriminant Analysis Effect Size analysis uncovered specific parasite taxa associated with distinct factors. Our results firstly demonstrate the structure of parasite communities in A. sinensis, and clarified how they are shaped by interacting ecological and management factors, providing critical baseline data for future research.