PS13-21. Microbial Community Composition, Fermentation Profile, and Methane Emissions Throughout the Gastrointestinal Tract of Adult Ruminants.

Abstract The bovine gastrointestinal tract (GIT) contains functionally distinct compartments with varying physicochemical conditions. However, links between spatial microbial structure and fermentative potential remain limited. This study investigated the microbial diversity, community composition, and fermentation kinetics across five GIT compartments. Digesta were collected post-evisceration from the rumen, abomasum, small intestine (SI), cecum, and large intestine (LI) of Angus-Holstein cattle (n = 8). Microbial composition was assessed via sequencing of the 16S rRNA gene, and fermentation kinetics were estimated after 24 hours of incubation (ANKOM RF) using a modified Gompertz model. Gas composition (H2, CH4, and CO2) was analyzed by gas chromatography, and volatile fatty acids (VFA) concentrations were determined by HPLC. Data were analyzed using linear mixed-effects models in R, with GIT compartment as a fixed effect and animal as a random effect. Tukey’s post hoc test was used for multiple comparisons, and significance was considered at P < 0.05. Fermentation kinetics differed by compartment, with the abomasum showing the longest lag time (3.18 h) but the greatest cumulative gas (408 mL; P < 0.05). CH4 was highest in the rumen (99,870 ppm), whereas H2 and CO2 varied modestly across sections (P < 0.001). Initial pH was lowest in the abomasum (4.24) and rumen (5.35) and increased to near-neutral values in the intestines (P < 0.001). VFA concentration and composition differed among compartments (P < 0.013). Total VFA were highest in the rumen (136.20 mmol/L) and cecum (130.10 mmol/L) and lowest in the abomasum (79.80 mmol/L). Acetate proportions were greater in the SI (55.95%) and LI (54.17%) than in the rumen (45.17%; P = 0.001), whereas propionate was highest in the rumen (31.38%) and lowest in the abomasum (22.01%; P = 0.013). The acetate-to-propionate ratio did not differ (P = 0.190) across GIT compartments. Butyrate and valerate were significantly enriched in the abomasum (18.89%), while the SI (5.74%) showed the lowest proportions (P < 0.001). Branched-chain VFA showed trends toward compartmental differences (P = 0.058). Microbial alpha diversity differed by location (P < 0.05), with the highest diversity in the cecum, followed by the LI and rumen, and beta-diversity confirmed distinct community structures (P < 0.05). Prevotellamassilia was significantly enriched in all gastrointestinal compartments compared to the rumen, including the abomasum (LFC=4.49; P = 0.002), cecum (LFC=4.96; P < 0.001), large intestine (LFC=4.77; P = 0.011), and small intestine (LFC=5.79; P < 0.001). Limosilactobacillus was enriched in the abomasum (LFC=4.44; P = 0.034), while members of the Enterobacteriaceae family (Gammaproteobacteria) showed higher abundance in the small intestine (LFC=5.78; P = 0.001). Additionally, Turicibacter was enriched in the cecum (LFC=5.21; P = 0.039). Overall, this study reveals compartment-specific variation in microbial diversity, community composition, and fermentation kinetics throughout the bovine gastrointestinal tract. These patterns reflect connections between local conditions and microbial function, with distinct fermentative roles played by the rumen and the hindgut.