Naturally fauna-free (FF) wethers, equipped with ruminal and duodenal cannulas, were used in two groups of eight (Group A) and seven (Group B) animals in six consecutive experimental periods, each lasting for 28 d. The objective was to measure ruminal fermentation traits, and flows of nonammonia nitrogen (NAN), total amino acid (TAA), and bacterial nitrogen (BN) from the stomach after inoculation with individual ciliate protozoa species in each period. The wethers in both groups were fed a diet based on corn silage, haylage, and soybean meal, and they remained FF during the first period. At the beginning of each other period, the wethers were progressively inoculated intraruminally with one individual major species of ruminal ciliate protozoa or total fauna (TF). Thus, Group A was progressively inoculated (+) with Dasytricha ruminantium (DS), Polyplastron multivesiculatum (PP), Isotricha intestinalis (IS), Entodinium caudatum (EN) and TF-type A. Also, Group B was progressively inoculated (+) with IS, DS, Epidinium ecaudatum (EP), Eudiplodinium maggi (EU), and EN. Duodenal digesta and ruminal fluid were collected and sampled in each period on d 26 and 28, respectively, and subjected to chemical analyses. A significantly higher (P < .05) pH (6.4) in ruminal fluid of the Group A wethers was obtained when each DS, DS+PP, DS-PP-IS+EN, and TF population was present in the rumen than when the wethers were FF (6.2). In the Group B wethers, pH (6.1) was lower (P < .05) for the population of IS-DS-EP+EU than for other populations (6.2 to 6.3). The concentration of total VFA in ruminal fluid was higher (P < .05) in the Group B wethers when IS, IS+DS, or IS-DS+EP populations were present in the rumen than when the wethers were FF. The flow of NAN, TAA, and BN from the stomach to the intestinal tract was generally lower for different protozoa populations than for the FF period. Largest decreases (P < .05) in the flow of NAN, TAA, and BN occurred when EN was added into the rumen of wethers in the A and B groups, which already contained populations of DS-PP+IS and IS-DS-EP+EU, respectively. Holotrich protozoa had very little effect on the protein metabolism in the rumen, but cellulolytic protozoa (PP, EP, and EU) and EN decreased the efficiency of protein utilization by the ruminant host.