New insights into molecular characterization and genetic diversity of Eimeria coccidian parasites in bats from diverse geographical regions of Thailand using nanopore-based DNA metabarcoding.

Bats represent over 1400 species globally, accounting for approximately one-fifth of all mammalian diversity, yet their gastrointestinal parasite communities remain understudied. Among these parasites, the genus Eimeria is one of the most commonly documented coccidian groups infecting bats. To date, more than 40 Eimeria spp. have been described from bats worldwide; however, molecular data are limited, and their evolutionary relationships with congeners infecting other vertebrate hosts remain largely unresolved. This study aims to elucidate the evolutionary connections between Eimeria parasites infecting bats and rodents, addressing a key question about shared ancestry and host-switching events across deeply divergent hosts. We investigated the genetic diversity and phylogenetic relationships of Eimeria spp. infecting Thai bats. Ninety-six genomic DNA samples extracted from bat guano, collected across six geographically distinct sites in prior research, were screened using SSU rRNA-PCR and nanopore amplicon sequencing. Host identification based on vertebrate cox1 gene sequencing revealed seven bat species (Pteropus lylei, Taphozous melanopogon, Cynopterus brachyotis, Eonycteris spelaea, Mops plicatus, Hipposideros armiger, and Pteropus vampyrus) along with the Hipposideros larvatus species complex. Haplotype network construction and phylogenetic analyses using Bayesian inference and maximum likelihood identified five putative genetic clusters of Eimeria sequences, including novel Haplogroups 1 and 2 that formed clearly distinct groups. The remaining three clusters showed close genetic affinities to known Eimeria species from bats (Eimeria sp. Bat10 and Eimeria sp. Bat31) and rodents (E. ferrisi). Notably, despite the deep evolutionary divergence between bats and rodents, Eimeria parasites infecting these hosts did not form entirely separate clades. Both phylogenies consistently revealed the polyphyletic nature of bat-derived Eimeria species, with multiple independent lineages interspersed among rodent taxa. This pattern supports hypotheses of shared ancestry or host-switching events, highlighting the complex evolutionary dynamics shaping Eimeria diversity across vertebrate hosts. The widespread distribution and genetic patterns observed in Haplogroup 1 suggest a recent population expansion potentially driven by ecological adaptability and host range dynamics. By focusing on the evolutionary relationships between bat and rodent Eimeria, this study advances our understanding of Eimeria diversity and host-parasite coevolution, emphasizing the importance of integrative molecular approaches in unravelling parasite evolutionary history across vertebrate taxa.