Meta-Genomic Analysis of Different Bacteria and Their Genomes Found in Raw Buffalo Milk Obtained in Various Farms Using Different Milking Methods
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection
2.2. DNA Extraction
2.3. Metagenomic Sequencing
2.4. Taxonomic Assignment, Functional Annotation and Gene Function Analysis
2.5. Statistical Analysis
3. Results and Discussion
3.1. Effect of Different Milking Methods on the Basal Nutrient Content, SCC and Number of Bacterial Cells of Raw Buffalo Milk
3.2. Milking Methods Influence the Raw Milk Microbiota
3.3. Structure and Composition of the Milk Microbiome of Buffaloes with Different Milking Methods
3.4. Differences in the Relative Abundance Composition of Core Microbiota and Bacteria Potentially Associated with Mastitis at the Genus Level between Milking Methods
3.5. Effect of Milking Methods on Antibiotic Resistance Genes
3.6. Effect of Milking Methods on the Level of Virulence Factors of Pathogenic Bacteria
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Milking Method | Protein (g/100 g) | Fat (g/100 g) | Total Solid (g/100 g) | Solids-Non-Fat g/100 g) | Lactose (g/100 g) | SCC (×104/mL) | CFU (×104 CFU/mL) |
---|---|---|---|---|---|---|---|
HM | 4.55 ± 0.39 a | 7.33 ± 0.46 a | 17.81 ± 1.34 a | 9.77 ± 0.88 a | 4.99 ± 0.39 a | 45.85 ± 31.33 a | 37.06 ± 17.62 a |
MM | 4.50 ± 0.29 a | 7.03 ± 0.68 a | 17.61 ± 0.76 a | 9.99 ± 0.44 a | 5.18 ± 0.20 a | 29.58 ± 15.56 a | 8.37 ± 8.37 b |
Milking Method | Observed. | Simpson | Chao1 | ACE | Shannon | Good’s Coverage |
---|---|---|---|---|---|---|
HM | 830.4444 ± 49.9758 a | 0.8603 ± 0.0713 a | 852.363 ± 35.7754 a | 849.2941 ± 28.6194 a | 3.2567 ± 0.5710 a | 0.9998 ± 0.0003 a |
MM | 665.1667 ± 71.3008 b | 0.7875 ± 0.0994 a | 777.734 ± 53.5937 b | 780.1879 ± 45.1084 b | 2.5035 ± 0.6112 b | 0.9982 ± 0.0011 b |
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Li, L.; Miao, W.; Li, Z.; Huang, L.; Hau, E.; Khan, M.F.; Liu, Q.; Zeng, Q.; Cui, K. Meta-Genomic Analysis of Different Bacteria and Their Genomes Found in Raw Buffalo Milk Obtained in Various Farms Using Different Milking Methods. Genes 2024, 15, 1081. https://doi.org/10.3390/genes15081081
Li L, Miao W, Li Z, Huang L, Hau E, Khan MF, Liu Q, Zeng Q, Cui K. Meta-Genomic Analysis of Different Bacteria and Their Genomes Found in Raw Buffalo Milk Obtained in Various Farms Using Different Milking Methods. Genes. 2024; 15(8):1081. https://doi.org/10.3390/genes15081081
Chicago/Turabian StyleLi, Ling, Wenhao Miao, Zhipeng Li, Li Huang, Enghuan Hau, Muhammad Farhan Khan, Qingyou Liu, Qingkun Zeng, and Kuiqing Cui. 2024. "Meta-Genomic Analysis of Different Bacteria and Their Genomes Found in Raw Buffalo Milk Obtained in Various Farms Using Different Milking Methods" Genes 15, no. 8: 1081. https://doi.org/10.3390/genes15081081