The Raw Milk Microbiota from Semi-Subsistence Farms Characteristics by NGS Analysis Method
Abstract
:1. Introduction
2. Results and Discussion
2.1. Taxonomic Analysis of the Milk Microbiome
2.2. Lactic Fermentation Bacteria
2.3. Spoiled Milk Bacteria
2.4. Pathogenic Bacteria Causing Mastitis
2.5. Analysis of Biodiversity
2.6. Analysis of Functional Potential and Antibiotic Resistance
3. Materials and Methods
3.1. Characteristics of Farms and Collection of Samples
3.2. Isolation of DNA
3.3. PCR Amplification and NGS Sequencing
3.4. Bioinformatic Analysis
3.5. Prediction the Functional Profile from Targeted Metagenomic Data
3.6. Statistical Analysis
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Sample Availability
References
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Milk from Farm A | Milk from Farm B | Milk from Farm C | |
---|---|---|---|
Number of OTUs | 5490 ± 78 | 4486 ± 94 | 3488 ± 58 |
Chao-1 bias-corrected | 5503 ± 14 | 4597 ± 18 | 3508 ± 14 |
Shannon entropy | 8.59 ± 0.45 | 7.02 ± 0.36 | 6.33 ± 0.39 |
Phylogenetic diversity | 10.23 ± 0.61 | 8.98 ± 0.49 | 7.12 ± 0.44 |
KO Identifier | Gene Name |
---|---|
K01467 | beta-lactamase class C (ampC) |
K02171 | BlaI family transcriptional regulator, penicillinase repressor (blaI) |
K02172 | bla regulator protein blaR1 (blaR1) |
K02545 | penicillin-binding protein 2 prime (mecA) |
K02546 | BlaI family transcriptional regulator, methicillin resistance regulatory protein (mecI) |
K02547 | methicillin resistance protein (mecR1) |
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Hornik, B.; Czarny, J.; Staninska-Pięta, J.; Wolko, Ł.; Cyplik, P.; Piotrowska-Cyplik, A. The Raw Milk Microbiota from Semi-Subsistence Farms Characteristics by NGS Analysis Method. Molecules 2021, 26, 5029. https://doi.org/10.3390/molecules26165029
Hornik B, Czarny J, Staninska-Pięta J, Wolko Ł, Cyplik P, Piotrowska-Cyplik A. The Raw Milk Microbiota from Semi-Subsistence Farms Characteristics by NGS Analysis Method. Molecules. 2021; 26(16):5029. https://doi.org/10.3390/molecules26165029
Chicago/Turabian StyleHornik, Bartosz, Jakub Czarny, Justyna Staninska-Pięta, Łukasz Wolko, Paweł Cyplik, and Agnieszka Piotrowska-Cyplik. 2021. "The Raw Milk Microbiota from Semi-Subsistence Farms Characteristics by NGS Analysis Method" Molecules 26, no. 16: 5029. https://doi.org/10.3390/molecules26165029