Evaluation of the Spoilage-Related Bacterial Profiles of Vacuum-Packaged Chilled Ostrich Meat by Next-Generation DNA Sequencing Approach
Abstract
:1. Introduction
2. Material and Methods
2.1. Meat Samples
2.2. Microbiological Analysis
2.3. 16S rDNA Amplicon Sequencing
2.3.1. DNA Extraction
2.3.2. PCR Amplification of 16S rDNA Genes
2.3.3. Library Preparation and Sequencing
2.3.4. Sequencing Data Analysis
2.4. Statistical Analysis
3. Results
3.1. Bacterial Enumeration of Initial and VP Meat
3.2. 16S rDNA Sequencing Data of VP Meat
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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Microbial Group | Culture Medium | Incubation | References | |
---|---|---|---|---|
Temp. (°C) | Time (h) | |||
Presumptive Photobacterium sp. a | Marine Agar (Difco Becton Dickinson Sparks MD. USA) | 15 | 72 | [27] |
Lactic acid bacteria (LAB) a | Man. Rogosa. Sharpe (MRS) agar (Merck, Darmstadt, Germany) | 30 | 72 | ISO 15214:1998 |
Brochothrix spp. b | Streptomycin, sulphate thallous acetate agar (STAA) (Oxoid Basingstoke, UK) | 25 | 48 | ISO 13722:2017 |
Pseudomonas spp. b | Pseudomonas agar supplemented with cetrimide. fucidin. cephalosporin (CFC) (Merck, Darmstadt, Germany) | 25 | 72 | ISO 13720:2010 |
Enterobacteriaceaec | Violet red bile glucose agar (VRBGA) (Graso Biotech., Poland) | 37 | 24 | ISO 21528-2:2017 |
Meat | Colony Count (log CFU/g) | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Photobacterium spp. | LAB | Brochotrix spp. | Pseudomonas spp. | Enterobacteriaceae | ||||||
Storage Days | ||||||||||
Initial | 14 Days | Initial | 14 Days | Initial | 14 Days | Initial | 14 Days | Initial | 14 Days | |
Batch I | 4.95 ± 0.13 aA | 7.40 ± 0.08 bA | 3.10 ± 0.30 aA | 6.15 ± 0.00 bB | 1.80 ± 0.45 aA | 2.66 ± 0.24 aA | <1.00 aA | 1.48 ± 0.67 aA | 2.47 ± 0.51 aA | 5.02 ± 0.03 bA |
Batch II | 5.12 ± 0.05 aA | 7.65 ± 0.05 bAB | 2.75 ± 0.15 aA | 5.70 ± 0.48 bAB | 1.82 ± 0.47 aA | 3.27 ± 0.43 aAB | 1.87 ± 0.12 aB | 1.73 ± 0.18 aA | 2.91 ± 0.41 aA | 5.62 ± 0.30 bA |
Batch III | 4.15 ± 1.05 aA | 7.85 ± 0.08 bB | 3.56 ± 0.68 aA | 4.78 ± 0.10 aA | 2.02 ± 0.08 aA | 4.73 ± 0.45 bB | 0.54 ± 0.66 aAB | 1.65 ± 0.07 aA | 1.70 ± 0.06 aA | 5.56 ± 0.07 bA |
Family/Genus | Steak I | Steak II | Steak III | Fillet I | Fillet II | Fillet III | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
N | % | N | % | N | % | N | % | N | % | N | % | |
Vibrionaceae/Photobacterium | 60,540.0 | 85.63 | 52,126.0 | 87.71 | 52,997.0 | 47.22 | 65,651.0 | 83.47 | 41,658.0 | 91.77 | 62,198.0 | 65.31 |
Carnobacteriaceae/Carnobacterium | 494.0 | 0.70 | 1,550.0 | 2.61 | 17,533.0 | 15.62 | 1013.0 | 1.29 | 1520.0 | 3.35 | 8749.0 | 9.19 |
Carnobacteriaceae/Other | - | - | - | - | 22,224.0 | 19.80 | - | - | - | - | 9852.0 | 10.35 |
Lactobacillaceae/Lactobacillus | 3320.0 | 4.70 | 4,078.0 | 6.86 | 2474.0 | 2.20 | 2125.0 | 2.70 | 1051.0 | 2.32 | 1924.0 | 2.02 |
Enterobacteriaceae/Serratia | - | - | - | - | - | - | 657.0 | 0.84 | - | - | - | - |
Enterobacteriaceae/Other | - | - | 494.0 | 0.83 | 5564.0 | 4.96 | - | - | 594.0 | 1.31 | 3061.0 | 3.21 |
Streptococcaceae/Lactococcus | - | - | - | - | 3023.0 | 2.69 | - | - | - | - | 3785.0 | 3.97 |
Enterococcaceae/Vagococcus | - | - | - | - | - | - | - | - | 101.0 | 0.22 | - | - |
Leuconostocaceae/Weissella | 530.0 | 0.75 | 650.0 | 1.09 | - | - | 720.0 | 0.92 | 67.0 | 0.15 | - | - |
Shewanellaceae/Shewanella | 1241.0 | 1.76 | - | - | - | - | 859.0 | 1.09 | - | - | - | - |
Bacteroidaceae/Bacteroides | 492.0 | 0.70 | - | - | - | - | - | - | - | - | - | - |
Unidentified | 2607.0 | 3.69 | 250.0 | 0.42 | 7546.0 | 6.72 | 4745.0 | 6.03 | 5050.0 | 5.30 |
Family/Genus | Batch I (August) | Batch II (October) | Batch III (March) | Relative Abundances (I + II + III) * |
---|---|---|---|---|
(%) | (%) | (%) | (%) | |
Vibrionaceae/Photobacterium | 84.55 | 89.74 | 56.27 | 76.85 |
Carnobacteriaceae/other | - | - | 15.08 | 15.08 |
Carnobacteriaceae/Carnobacterium | 1.00 | 2.98 | 12.21 | 5.39 |
Enterobacteriaceae/other | - | - | 4.09 | 4.09 |
Lactobacillaceae/Lactobacillus | 3.7 | 4.7 | 2.11 | 3.50 |
Streptococcaceae/Lactococcus | - | - | 3.33 | 3.33 |
Shewanellaceae/Shewanella | 1.43 | - | - | 1.43 |
Enterococcaceae/Vagococcus | - | 1.35 | - | 1.35 |
Leuconostocaceae/Weissella | 0.84 | 0.62 | - | 0.73 |
Enterobacteriaceae/Serratia | 0.84 | - | - | 0.84 |
Bacteroidaceae/Bacteroides | 0.7 | - | - | 0.70 |
Unclassified | 4.86 | 0.475 | 6.01 | 3.78 |
Family/Genus | Batch I (August) | Batch II (October) | Batch III (March) |
---|---|---|---|
Vibrionaceae/Photobacterium | 84.55 ± 1.53 Cb | 89.74 ± 2.87 Cb | 56.09 ± 12,81 Da |
Bacteroidaceae/Bacteroides | 0.35 ± 0.49 Aa | 0 ± 0 Aa | 0 ± 0 Aa |
Carnobacteriaceae/Carnobacterium | 1,00 ± 0,42 Aa | 2.98 ± 0.52 ABa | 12.21 ± 4.6 BCb |
Lactobacillaceae/Lactobacillus | 3.70 ± 1.41 Ba | 4.61 ± 3.18 Ba | 2.11 ± 0.13 Aa |
Carnobacteriaceae/Other | 0 ± 0 Aa | 0 ± 0 Aa | 15.08 ± 6.68 Cb |
Enterobacteriaceae/Other | 0 ± 0 Aa | 0 ± 0 Aa | 4.09 ± 1.24 ABb |
Enterobacteriaceae/Serratia | 0.84 ± 0.59 Aa | 0 ± 0 Aa | 0 ± 0 Aa |
Enterococcaceae/Vagococcus | 0 ± 0 Aa | 1.35 ± 1.9 Aa | 0 ± 0 Aa |
Streptococcaceae/Lactococcus | 0 ± 0 Aa | 0 ± 0 Aa | 3.33 ± 0.91 ABb |
Leuconostocaceae/Weissella | 0.84 ± 0.12 Aa | 0.62 ± 0.66 Aa | 0.10 ± 0.01 Aa |
Shewanellaceae/Shewanella | 1.43 ± 0.47 Ab | 0 ± 0 Aa | 0 ± 0 Aa |
Unidentified | 4.86 ± 1.65 Bb | 0.21 ± 0.3 Aa | 6.01 ± 1.00 ABCb |
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Juszczuk-Kubiak, E.; Dekowska, A.; Sokołowska, B.; Połaska, M.; Lendzion, K. Evaluation of the Spoilage-Related Bacterial Profiles of Vacuum-Packaged Chilled Ostrich Meat by Next-Generation DNA Sequencing Approach. Processes 2021, 9, 803. https://doi.org/10.3390/pr9050803
Juszczuk-Kubiak E, Dekowska A, Sokołowska B, Połaska M, Lendzion K. Evaluation of the Spoilage-Related Bacterial Profiles of Vacuum-Packaged Chilled Ostrich Meat by Next-Generation DNA Sequencing Approach. Processes. 2021; 9(5):803. https://doi.org/10.3390/pr9050803
Chicago/Turabian StyleJuszczuk-Kubiak, Edyta, Agnieszka Dekowska, Barbara Sokołowska, Marzena Połaska, and Krzysztof Lendzion. 2021. "Evaluation of the Spoilage-Related Bacterial Profiles of Vacuum-Packaged Chilled Ostrich Meat by Next-Generation DNA Sequencing Approach" Processes 9, no. 5: 803. https://doi.org/10.3390/pr9050803