Active Rumen Bacterial and Protozoal Communities Revealed by RNA-Based Amplicon Sequencing on Dairy Cows Fed Different Diets at Three Physiological Stages
Abstract
:1. Introduction
2. Materials and Methods
2.1. Ethics Statement
2.2. Animal Management, Diet, and Rumen Fluid Sampling
2.3. RNA-Extraction and Synthesis of cDNA
2.4. Targeted Amplicon Sequencing of Bacteria and Protozoa
2.5. Bioinformatic Analysis
2.6. Statistical Analysis
3. Results
3.1. Effect of Physiological Stages of Dairy Cows on the Diversity of Their Active Rumen Microbiota
3.2. Physiological Stage-Dependent Modifications in the Active Rumen Bacterial Communities
3.3. Physiological Stage-Dependent Modifications in the Active Rumen Eukaryotic Communities
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Item | Physiological Stage 1 | ||
---|---|---|---|
LL | DP | PP | |
Ingredients | |||
Meadow hay | 13.1 | 24.6 | 2.5 |
Alfalfa hay | 17.4 | - | 20.6 |
Maize silage | 47.4 | 20.3 | 32.0 |
Wheat straw | - | 37.8 | 1.7 |
Dry sugar beet pulp | - | - | 2.4 |
Protein mix 2 | 10.6 | 16.1 | 17.7 |
Energy mix 3 | 8.9 | - | 19.3 |
Extruded linseed | 1.1 | - | 0.4 |
Fat supplement 4 | - | - | 1.2 |
Vit–min mix 5,6 | 1.4 5 | 1.2 6 | 2.2 5 |
Chemical composition | |||
Dry matter | 50.2 | 63.8 | 55.1 |
Crude protein | 13.1 | 13.0 | 15.7 |
Lipids | 3.4 | 3.2 | 4.2 |
Starch | 21.1 | 7.1 | 24.0 |
NDF | 39.4 | 57.0 | 33.6 |
ADF | 23.4 | 36.0 | 21.1 |
MFU no./kg DM 7 |
Index 1 | Bacteria | Eukaryotes | ||||||||
---|---|---|---|---|---|---|---|---|---|---|
LL | DP | PP | SEM 2 | p-Value 3 | LL | DP | PP | SEM 2 | p-Value 3 | |
Richness | ||||||||||
Chao 1 | 464 b | 692 a | 543 a,b | 36.50 | 0.026 | 47.0 b | 68.0 a | 40.0 b | 3.47 | <0.001 |
Evenness | ||||||||||
Shannon | 0.71 b | 0.84 a | 0.74 b | 0.02 | <0.001 | 0.39 | 0.48 | 0.39 | 0.03 | 0.3000 |
Simpson | 0.93 b | 0.98 a | 0.96 a,b | 0.01 | 0.002 | 0.62 | 0.77 | 0.58 | 0.04 | 0.110 |
Diversity | ||||||||||
Shannon | 4.35 b | 5.50 a | 4.66 b | 0.14 | <0.001 | 1.45 a,b | 2.01 a | 1.43 b | 0.11 | 0.031 |
Inverse Simpson | 16.4 b | 86.6 a | 32.4 a | 8.56 | <0.001 | 3.18 | 4.66 | 3.02 | 0.33 | 0.081 |
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Bailoni, L.; Carraro, L.; Cardin, M.; Cardazzo, B. Active Rumen Bacterial and Protozoal Communities Revealed by RNA-Based Amplicon Sequencing on Dairy Cows Fed Different Diets at Three Physiological Stages. Microorganisms 2021, 9, 754. https://doi.org/10.3390/microorganisms9040754
Bailoni L, Carraro L, Cardin M, Cardazzo B. Active Rumen Bacterial and Protozoal Communities Revealed by RNA-Based Amplicon Sequencing on Dairy Cows Fed Different Diets at Three Physiological Stages. Microorganisms. 2021; 9(4):754. https://doi.org/10.3390/microorganisms9040754
Chicago/Turabian StyleBailoni, Lucia, Lisa Carraro, Marco Cardin, and Barbara Cardazzo. 2021. "Active Rumen Bacterial and Protozoal Communities Revealed by RNA-Based Amplicon Sequencing on Dairy Cows Fed Different Diets at Three Physiological Stages" Microorganisms 9, no. 4: 754. https://doi.org/10.3390/microorganisms9040754