First molecular detection and phylogenetic characterization of Balantioides coli in lowland tapir (Tapirus terrestris).

As a vulnerable species to extinction, Tapirus terrestris has scarce data on gastrointestinal parasites, particularly regarding the occurrence of zoonotic ciliates such as Balantioides coli. Therefore, gastrointestinal parasites were investigated in this host using parasitological, in vitro culture, and molecular approaches. A total of 45 fecal samples were analyzed from animals under human care and from free-ranging or reintroduced individuals in southeastern Brazil. Overall parasite positivity reached 68.9%, varying among sampling sites. Protozoa from the phylum Ciliophora represented the most frequent group, occurring in 60% of samples (p ≤ 0.05). Nematode forms were identified in 31.1% of samples, predominantly as strongylid-type eggs, as well as eggs consistent with Trichuris spp. (4.4%) and members of the family Spiruridae (4.4%). Coccidian oocysts were detected in 20% of samples and were morphometrically compatible with the genus Eimeria. In vitro culture enabled the successful isolation of 20 ciliate strains, and PCR amplification targeting the ITS1-5.8SrDNA-ITS2 region confirmed B. coli in 24 samples, including isolates obtained directly from feces and in vitro cultures, corresponding to an infection rate of 53.3%. Sequence identity ranged from 98.08% to 100% compared to GenBank references. Phylogenetic analysis grouped all sequences within the B. coli clade and identified genetic variants A0 (50%), B0 (37.5%), and B1 (8.3%). Variant A0 predominated and was detected in both ex situ and in situ populations, whereas B0 and B1 showed more restricted distributions. Additionally, amoebae of the genus Entamoeba were detected in 17.8% of samples. These findings represent the first molecular confirmation of B. coli infection in T. terrestris and reinforce the epidemiological relevance of this host in the circulation of zoonotic protozoa across different ecological contexts.