Franciane Cedrola

The rumen ciliate protozoa represent a significant component of the microbial ecosystem in ruminants, contributing to the degradation of complex carbohydrates, intra-ruminal nitrogen recycling, and interactions with methanogenic archaea. Despite their importance, the effects of probiotic supplementation on this community remain poorly understood. This study evaluated the impact of dietary yeast probiotics on the ruminal ciliate community in 16 Holstein × Jersey dairy cows. Animals were assigned to three treatments: a control with placebo (T1), a commercial probiotic yeast (T2), and a test probiotic yeast (T3). Rumen samples were collected and analyzed for ciliate density, diversity, and species composition. No significant differences were found in total or genus-level ciliate densities among treatments; however, species richness and community composition varied. A total of 27 ciliate species were identified. The control group (T1) exhibited the highest richness (26 species), while T3 showed the lowest (20 species). Some species were exclusive to specific treatments, and none were unique to T3, suggesting possible inhibitory effects. These findings highlight the importance of species-level resolution in evaluating probiotic effects and suggest that yeast supplementation may alter protozoal community structure without affecting overall density, with potential implications for rumen function and host productivity.

Rumen ciliates are important constituents of gastrointestinal microbiome of herbivorous mammals. They are traditionally classified based on morphological characteristics. However, molecular markers—mainly the 18S rRNA gene—have increasingly been used to investigate their evolutionary relationships. While the 18S gene provides reliable phylogenetic resolution at higher taxonomic levels, it lacks variability to distinguish closely related taxa. In this study, we evaluated the potential of the internal transcribed spacer (ITS) rDNA region as an alternative or complementary marker to the 18S rRNA gene for phylogenetic reconstruction of rumen ciliates. We generated and analyzed ITS sequences from rumen ciliate species and compared topologies obtained using three datasets: ITS alone, 18S alone, and a concatenated ITS+18S dataset. The concatenated dataset consistently showed improved resolution and support across several key clades, supporting its utility in Trichostomatia phylogeny. Some differences were observed, such as the variable placement of Troglodytella abrassarti, highlighting the importance of multi-marker approaches. Our findings demonstrate that the ITS region is a robust complementary marker that enhances phylogenetic resolution, especially when combined with 18S data.

The subclass Peritrichia encompasses over 1,000 species of ciliates, demonstrating both wide distribution and significant morphological diversity across aquatic environments. Despite their ecological significance and unique biological attributes, genomic information for peritrichs has remained sparse. This study aimed to fill this gap by sequencing the genomes of seven distinct species of peritrich ciliates and employing advanced genomic technologies to investigate their metabolic characteristics, functional diversity and evolutionary relationships. Our analyses revealed a large number of genes annotated across various functional categories, with EggNOG annotations highlighting genes related to post-translational modification, translation and energy metabolism, suggesting a high adaptive and metabolic capacity. Notably, the diversity of CAZymes, particularly glycoside hydrolases, indicates metabolic complexity and the ability to degrade carbohydrates, critical for environmental adaptation and bacterial predation. Additionally, the presence of chitin-degrading enzymes in species like Trichodina acuta points to complex ecological interactions with hosts, with potential implications for natural ecosystems and commercial hatcheries. A concentration of glycosyl transferases found in the Vaginicolidae family suggests an enhanced capacity for glycoconjugate synthesis, possibly linked to lorica formation. The phylogenomic reconstruction was consistent with existing literature, uncovering intricate phylogenetic relationships. Overall, our findings significantly advance the understanding of peritrich ciliates by shedding light on their metabolic potential, ecological adaptability and evolutionary complexity, while also providing a genomic foundation for future ecological and evolutionary studies.

Herbivorous mammals have evolved symbiotic relationships with ciliates, either as mutualists or as parasites. Here, we investigate the ecological roles and metabolic impacts of ciliates across different gastrointestinal environments (rumen, caecum, and large intestine) through a functional genomic analysis. Functional analysis revealed that most rumen and caecum ciliates shared similar metabolic profiles, whereas the parasitic ­Balantioides coli displayed genes associated with energy metabolism and pathogenicity, suggesting a shift from mutualism to parasitism. Carbohydrate-active enzyme profiling showed rumen ciliates to be more metabolically diverse, supporting niche partitioning, enhancing ecological balance in the rumen environment.

Several hundred ciliate species live in animals’ guts as a part of their microbiome. Among them, Muniziella cunhai (Trichostomatia, Pycnotrichidae), the largest described ciliate, is found exclusively associated with Hydrochoerus hydrochaeris (capybara), the largest known rodent reaching up to 90 kg. Here, we present the sequence, structural and functional annotation of this giant microeukaryote macronuclear genome and discuss its phylogenetic placement. The 85 Mb genome is highly AT rich (GC content 25.71 %) and encodes a total of 11 397 protein-coding genes, of which 2793 could have their functions predicted with automated functional assignments. Functional annotation showed that M. cunhai can digest recalcitrant structural carbohydrates, non-structural carbohydrates, and microbial cell walls, suggesting a role in diet metabolization and in microbial population control in the capybara’s intestine. Moreover, the phylogenetic placement of M. cunhai provides insights on the origins of gigantism in the subclass Trichostomatia.

Although the diversity (~35 species) and worldwide distribution of goats (Ruminantia, Bovidae, Caprinae) are significant, studies on the diversity of symbiont ciliates in these mammals are scarce in comparison to other ruminants. The present work is a review and checklist of species based on taxonomic, morphologic, and ecologic studies of rumen ciliate protozoa in goats, presenting geographic distribution and hosts, as well as estimating the macroevolutionary relationships of the species observed in the studies. To that end, all of the available literature on databases was reviewed, the schematic drawings were made based on information present in the original description of the taxa, and the phylogenetic relationships were inferred based on Maximum Likelihood and Bayesian Inference analyses. According to our review, 72 species and 14 genera of ciliates have been associated with goats. Through the analysis of the association between ciliate genera and caprine hosts, it was shown that ciliates are more associated with domestic animals (Capra hircus—14 genera) than wild ones (Rupicapra rupicapra—six genera, Capra ibex—one genus, Capra pyrenaica—one genus). Thirteen countries were identified in the distribution map as having had reports of ciliate species associated with goats. The interaction networks of ciliates and their hosts showed that the species of ciliates associated with goats also occur in other herbivore mammal species. The recovered phylogenetic hypotheses show that the ciliate species in goats form a non-monophyletic group with maximum and minimum ages of ~8.2My and ~2.4My. We have also found that a large portion of the studies on the diversity of ciliates in goats does not employ all necessary techniques in an integrative way, despite it being essential for detailed descriptions and better knowledge of this fraction of biodiversity.

The family Ophryoscolecidae currently comprises 225 species of trichostomatid ciliates, subdivided into three subfamilies (Entodiniinae, Diplodiniinae, and Ophryoscolecinae). The last taxonomic review of the family was performed 55 years ago, but recent morphological and molecular studies indicate the need for a profound review of the systematics of this taxon, since its current taxonomy is insufficient to organize the diversity of the group. Here, we briefly review the systematics of the family Ophryoscolecidae based on information recovered from the literature and new morphological and molecular data. We add four new 18S rDNA sequences of ophryoscolecids to molecular databases, which contributed to improving the comprehension of intrafamily relationships within this group. Finally, we discuss some systematic problems and suggest approaches to resolve such inconsistencies in the future.