Abstract Background Balantioides coli is a zoonotic intestinal protozoan distributed at the human–animal interface, with pigs recognized as its principal hosts and reservoirs. Despite its broad occurrence, gaps remain regarding its genetic diversity and its interactions with associated microbial communities. This study investigated the genetic and phylogenetic diversity of B. coli and the impact of in vitro culture on the structure of these communities using Sanger and next-generation sequencing (NGS) in xenic isolates and their original fecal samples. Methods A total of 39 fecal samples from pigs were collected between 2023 and 2024 from 15 farms located in the states of Rio de Janeiro and Minas Gerais, Brazil. Samples were subjected to direct microscopy, xenic culture, Sanger sequencing of the ITS1–5.8SrDNA–ITS2 region, and NGS targeting the 18S and 16S rRNA regions. Results Direct examination revealed a higher frequency of trophozoites (64.1%) compared with cysts (48.7%). In vitro isolation was successful from fecal samples obtained from pigs at all farms. Molecular ITS analysis confirmed the presence of B. coli in both isolates and fecal samples, with predominance of the B0 variant. Metabarcoding revealed that the abundance and genetic diversity of other eukaryotes did not differ significantly between feces and cultures (p > 0.05), although fecal samples exhibited greater taxonomic richness, particularly Blastocystis spp. and Entamoeba spp., including E. suis , E. polecki , E. moshkovskii , and E. hartmanni . In contrast, prokaryotic communities showed significant differences (p ≤ 0.05). In correspondence analyses, the eukaryotic dataset showed a diffuse distribution of B. coli ASVs, without marked associations with other eukaryotic taxa. In contrast, the prokaryotic dataset showed more structured associations, with a large cluster of B. coli ASVs grouped near bacterial genera such as Bacteroides , Pseudomonas , and Escherichia–Shigella . Conclusions Balantioides coli remained genetically stable after in vitro establishment, with predominance of the B0 variant in both fecal samples and xenic cultures. Xenic culture preserved part of the eukaryotic diversity but significantly restructured the prokaryotic community, selecting bacterial taxa potentially linked to parasite persistence under in vitro conditions. These findings indicate that B. coli persists within a complex intestinal microbial consortium rather than as an isolated protozoan.
Class et al. (Tue,) studied this question.