Comparative Rumen Metagenome and CAZyme Profiles in Cattle and Buffaloes: Implications for Methane Yield and Rumen Fermentation on a Common Diet
Abstract
:1. Introduction
2. Materials and Methods
2.1. Ethical Approval
2.2. Animal Feeding and Management
2.3. Ruminal Digesta Collection
2.4. DNA Extraction
2.5. Shotgun Metagenome Sequencing
2.6. Bioinformatics Analysis
2.7. Gene Prediction and CAZyme Annotation
2.8. Protozoal Enumeration
2.9. Enteric CH4 Emission
2.10. Chemical Composition, Nutrient Intake, and Digestibility
2.11. VFA and Ammonia
2.12. Statistical Analysis
3. Results
3.1. Alpha and Beta Diversity
3.2. Rumen Metagenome
3.3. CAZyme Abundance
3.4. Protozoal Population
3.5. Daily Enteric CH4 Emissions and CH4 Yield
3.6. Nutrient Intake, Digestibility, and Rumen Fermentation
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Conflicts of Interest
References
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Attributes | Cattle | Buffaloes | p-Value |
---|---|---|---|
Daily enteric CH4 (g/d) | 280 ± 16.2 | 136 ± 4.40 | <0.0001 |
CH4 (g/100 kg BW) | 52.8 ± 3.45 | 45.0 ± 3.20 | 0.125 |
CH4 yield (g/kg DMI) | 25.1 ± 1.59 | 23.9 ± 1.10 | 0.612 |
Total protozoa (×107 cells/mL) | 9.58 ± 0.78 | 10.8 ± 0.47 | 0.191 |
Entodiniomorphs (×107 cells/mL) | 8.91 ± 0.93 | 10.7 ± 0.48 | 0.112 |
Holotrichs (×107 cells/mL) | 0.661 ± 0.36 | 0.131 ± 0.02 | 0.170 |
Attribute | Cattle | Buffaloes | p-Value |
---|---|---|---|
Intake | |||
Dry matter (kg/d) | 11.2 ± 0.30 | 5.88 ± 0.53 | <0.0001 |
Dry matter (kg/100 kg BW) | 2.11 ± 0.08 | 1.91 ± 0.13 | 0.231 |
Organic matter (kg/d) | 10.8 ± 0.28 | 5.59 ± 0.51 | <0.0001 |
Organic matter (kg/100 kg BW) | 2.04 ± 0.10 | 1.82 ± 0.12 | 0.191 |
Crude protein (kg/d) | 1.34 ± 0.038 | 0.620 ± 0.063 | <0.0001 |
Neutral detergent fibre (kg/d) | 5.81 ± 0.16 | 3.18 ± 0.31 | <0.0001 |
Acid detergent fibre (kg/d) | 3.23 ± 0.11 | 1.82 ± 0.19 | <0.0001 |
Apparent digestibility (%) | |||
Dry matter | 63.4 ± 1.11 | 62.3 ± 0.80 | 0.449 |
Organic matter | 66.3 ± 1.12 | 65.1 ± 0.54 | 0.365 |
Crude protein | 70.1 ± 1.16 | 66.7 ± 1.45 | 0.095 |
Neutral detergent fibre | 55.0 ± 1.42 | 54.4 ± 1.09 | 0.723 |
Acid detergent fibre | 46.5 ± 2.24 | 49.0 ± 1.65 | 0.386 |
Attributes | Cattle | Buffaloes | p-Value |
---|---|---|---|
TVFA (mmol) | 68.6 ± 4.42 | 78.3 ± 8.23 | 0.627 |
Ammonia (mg/dL) | 7.93 ± 1.06 | 8.87 ± 0.69 | 0.479 |
Individual VFA | |||
Acetate (mmol) | 49.5 ± 2.34 | 54.3 ± 5.69 | 0.732 |
Propionate (mmol) | 10.3 ± 2.42 | 13.2 ± 1.04 | 0.300 |
Butyrate (mmol) | 4.99 ± 0.88 | 6.17 ± 0.93 | 0.554 |
Iso-butyrate (mmol) | 1.44 ± 0.48 | 1.63 ± 0.51 | 0.794 |
Valerate (mmol) | 1.42 ± 0.30 | 1.87 ± 0.17 | 0.227 |
Iso-valerate (mmol) | 0.881 ± 0.34 | 1.08 ± 0.36 | 0.695 |
A/P ratio | 4.70 | 4.08 | 0.219 |
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Malik, P.K.; Trivedi, S.; Kolte, A.P.; Mohapatra, A.; Biswas, S.; Bhattar, A.V.K.; Bhatta, R.; Rahman, H. Comparative Rumen Metagenome and CAZyme Profiles in Cattle and Buffaloes: Implications for Methane Yield and Rumen Fermentation on a Common Diet. Microorganisms 2024, 12, 47. https://doi.org/10.3390/microorganisms12010047
Malik PK, Trivedi S, Kolte AP, Mohapatra A, Biswas S, Bhattar AVK, Bhatta R, Rahman H. Comparative Rumen Metagenome and CAZyme Profiles in Cattle and Buffaloes: Implications for Methane Yield and Rumen Fermentation on a Common Diet. Microorganisms. 2024; 12(1):47. https://doi.org/10.3390/microorganisms12010047
Chicago/Turabian StyleMalik, Pradeep K., Shraddha Trivedi, Atul P. Kolte, Archit Mohapatra, Siddharth Biswas, Ashwin V. K. Bhattar, Raghavendra Bhatta, and Habibar Rahman. 2024. "Comparative Rumen Metagenome and CAZyme Profiles in Cattle and Buffaloes: Implications for Methane Yield and Rumen Fermentation on a Common Diet" Microorganisms 12, no. 1: 47. https://doi.org/10.3390/microorganisms12010047
APA StyleMalik, P. K., Trivedi, S., Kolte, A. P., Mohapatra, A., Biswas, S., Bhattar, A. V. K., Bhatta, R., & Rahman, H. (2024). Comparative Rumen Metagenome and CAZyme Profiles in Cattle and Buffaloes: Implications for Methane Yield and Rumen Fermentation on a Common Diet. Microorganisms, 12(1), 47. https://doi.org/10.3390/microorganisms12010047