On the 28th day of the feeding regimen, a single rumen sample (both solid and liquid fractions) from each Holstein and Jersey cow was collected at 1300 h via esophageal tubing. The esophageal tubing apparatus was prepared by coupling one end of the esophageal tube to a metal strainer as described by Raun and Burroughs (1962) (link) and the other end was connected to a 125-mL Nalgene bottle (Thermo Scientific Inc., Waltham, MA, USA) using a “Tee” connection. The remaining end of the “Tee” was connected to a Masterflex vacuum pump (model 7015-10; Cole Parmer, Vernon Hills, IL) (Figure S1 ). Rumen samples were collected by passing the tube containing the metal strainer through a Frick speculum into the ventral sac. The first 200-mL of rumen fluid were discarded to minimize saliva contamination. Then 40-mL of rumen fluid were collected and placed into a 50-mL propylene conical tube (Thermo Scientific Inc., Waltham, MA, USA). After removal of the esophageal tube, particles attached to the metal strainer were recovered and added into the conical tube to collect a sample more adequately representative of the rumen content and then samples were snap-frozen in liquid nitrogen. Across samples, particles ranged from 10 to 15% of the total sample. Between sampling, the metal strainer and Frick speculum were thoroughly washed with warm water and water was run through the stomach tube to prevent cross contamination from the previous animal. Additionally, the removal of the first 200-mL also prevented any cross contamination.
Immediately after the collection of the esophageal sampling, another sample was collected from the Holstein cows via the rumen cannula. Ruminal contents were collected from the dorsal, ventral, and caudal areas of the rumen. The digesta were mixed and a representative sample was collected and snap-frozen in liquid nitrogen for bacterial community analysis. All samples collected via esophageal tubing or via the cannula were stored in an -80°C freezer until used for DNA extraction and bacterial community analysis.
Immediately after the collection of the esophageal sampling, another sample was collected from the Holstein cows via the rumen cannula. Ruminal contents were collected from the dorsal, ventral, and caudal areas of the rumen. The digesta were mixed and a representative sample was collected and snap-frozen in liquid nitrogen for bacterial community analysis. All samples collected via esophageal tubing or via the cannula were stored in an -80°C freezer until used for DNA extraction and bacterial community analysis.
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