Comparing rumen fluid collection methods on fermentation profile and microbial population in lactating dairy cows

[Display omitted] •ST had higher pH and lower NH3-N and total VFA compared with RC.•RC had lower Bacteroidetes and higher Firmicutes compared with ST.•Chao1 and Shannon index were similar between RC and ST. The objective of this study was to compare fermentation profile and microbial diversity from rumen samples collected using a rumen cannula (RC) or stomach tube (ST) in lactating dairy cows. Three ruminally cannulated lactating dairy cows were used in a 3 × 3 Latin square design. The experimental period was 28 d and rumen fluid was collected 4 h after feeding on d 22 and 26 of each experimental period. Treatments were rumen fluid collected from the ST or RC. The pH of rumen contents was measured immediately after fluid collection and samples were analyzed for VFA, ammonia-N (NH3-N) concentration, and microbiome composition. Rumen pH was greater for ST compared with RC (6.88 vs. 6.25). However, NH3-N (15.2 vs. 10.6 mg/dL) and total VFA (121.8 vs. 95.5 mM) were greater for RC compared with ST. The rumen fluid collection methods had no effects on the molar proportion of acetate and propionate; however, the acetate-to-propionate ratio tended to increase with ST compared with RC. The majority of sequences obtained with microbiome analysis belonged to Bacteroidetes, Firmicutes, and Cyanobacteria, regardless of the rumen fluid collection method. However, the abundance of Bacteroidetes was greater and the abundance of Firmicutes was lower for ST compared with RC. No effects were observed on the abundance of phylum Cyanobacteria. The rumen fluid collection methods had no effects on Chao1 and Shannon index. In conclusion, the molar proportion of individual VFA, Chao1, and Shannon index were similar, whereas rumen pH, NH3-N, and total VFA were affected by the rumen fluid collection method.