Comparison of Two Sampling Techniques for Evaluating Ruminal Fermentation and Microbiota in the Planktonic Phase of Rumen Digesta in Dairy Cows

The objective of this experiment was to compare ruminal fluid samples collected through rumen cannula (RC) or using an oral stomach tube (ST) for measurement of ruminal fermentation and microbiota variables. Six ruminally cannulated lactating Holstein cows fed a standard diet were used in the study. Rumen samples were collected at 0, 2, 4, 6, 8, and 12 h after the morning feeding on two consecutive days using both RC and ST techniques. Samples were filtered through two layers of cheesecloth and the filtered ruminal fluid was used for further analysis. Compared with RC, ST samples had 7% greater pH; however, the pattern in pH change after feeding was similar between sampling methods. Total volatile fatty acids (VFA), acetate and propionate concentrations in ruminal fluid were on average 23% lower for ST compared with RC. There were no differences between RC and ST in VFA molar proportions (except for isobutyrate), ammonia and dissolved hydrogen (dH2) concentrations, or total protozoa counts, and there were no interactions between sampling technique and time of sampling. Bacterial ASV richness was higher in ST compared with RC samples; however, no differences were observed for Shannon diversity. Based on Permanova analysis, bacterial community composition was influenced by sampling method and there was an interaction between sampling method and time of sampling. A core microbiota comprised of Prevotella, S24-7, unclassified Bacteroidales and unclassified Clostridiales, Butyrivibrio, unclassified Lachnospiraceae, unclassified Ruminococcaceae, Ruminococcus, and Sharpea was present in both ST and RC samples, although their relative abundance varied and was influenced by an interaction between sampling time and sampling method. Overall, our results suggest that ruminal fluid samples collected using ST (at 180 to 200 cm depth) are not representative of rumen pH, absolute values of VFA concentrations, or bacterial communities >2 h postfeeding when compared to samples of ruminal fluid collected using RC. However, ST can be a feasible sampling technique if the purpose is to study molar proportions of VFA, protozoa counts, dH2, and ammonia concentrations.



Work Title Comparison of Two Sampling Techniques for Evaluating Ruminal Fermentation and Microbiota in the Planktonic Phase of Rumen Digesta in Dairy Cows
Open Access
  1. Camila Lage
  2. Susanna Raeisaenen
  4. Krum Nedelkov
  5. Xianjiang Chen
  7. Molly Fetter
  8. Nagaraju Indugu
  9. Joseph Bender
  10. Bonnie Vecchiarelli
  11. Meagan Hennessy
  12. Dipti Pitta
  13. Alexander Hristov
  1. non-invasive sampling techniques
  2. stomach tube method
  3. rumen microbiome
  4. rumen cannula
  5. rumen fermentation
  6. stomach tube
License CC BY 4.0 (Attribution)
Work Type Article
  1. Frontiers Media S.A
Publication Date December 23, 2020
Publisher Identifier (DOI)
  1. 10.3389/fmicb.2020.618032
Deposited March 09, 2021




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  • Created
  • Added Creator Camila Lage
  • Added Creator Susanna Raeisaenen
  • Added Creator Krum Nedelkov
  • Added Creator Xianjiang Chen
  • Added Creator JOONPYO OH
  • Added Creator Molly Fetter
  • Added Creator Nagaraju Indugu
  • Added Creator Joseph Bender
  • Added Creator Bonnie Vecchiarelli
  • Added Creator Meagan Hennessy
  • Added Creator Dipti Pitta
  • Added Creator Alexander Hristov
  • Added de Assis Lage et al 2020 (published).pdf
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