High-Throughput 16S rRNA Gene Sequencing of Butter Microbiota Reveals a Variety of Opportunistic Pathogens
Abstract
:1. Introduction
2. Materials and Methods
2.1. Samples
2.2. Plating and Microbial Enrichment
2.3. DNA Isolation
2.4. DNA Barcoding
2.5. High-Throughput Sequencing
3. Results
4. Discussion
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Bacteria | Butter Sample | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | |
Geobacillus spp. | |||||||||||||||||||||
Stenotrophomonas spp. | |||||||||||||||||||||
Thermus thermophilus | |||||||||||||||||||||
Cedecea davisae | |||||||||||||||||||||
Tatumella citrea | |||||||||||||||||||||
Lactobacillus spp. | |||||||||||||||||||||
Lactococcus spp. | |||||||||||||||||||||
Streptococcus spp. | |||||||||||||||||||||
Acinetobacter spp. | |||||||||||||||||||||
Anoxybacillus spp. | |||||||||||||||||||||
Xanthomonas bromi | |||||||||||||||||||||
Pseudoxanthomonas spp. | |||||||||||||||||||||
Propionibacterium acnes | |||||||||||||||||||||
Leuconostoc spp. | |||||||||||||||||||||
Pseudomonas spp. | |||||||||||||||||||||
Massilia varians | |||||||||||||||||||||
Ochrobactrum spp. | |||||||||||||||||||||
Bacillus cereus group | |||||||||||||||||||||
Chryseobacterium spp. | |||||||||||||||||||||
Trabulsiella spp. | |||||||||||||||||||||
Shewanella japonica | |||||||||||||||||||||
Haemophilus sputorum | |||||||||||||||||||||
Pantoea spp. | |||||||||||||||||||||
Gibbsiella spp. | |||||||||||||||||||||
Brevundimonas spp. | |||||||||||||||||||||
<1% -no color | 1–10% | 21–30% | 21–30% | 31–40% | 41–50% | 51–60% | >61% |
Opportunistic Pathogen | Found in Samples, % (10–100 Reads Per ASV) | Found in Samples, % (100–500 Reads Per ASV) | Found in Samples, % (>500 Reads Per ASV) |
---|---|---|---|
Bacillus cereus group | 100 | 66.7 | 52.4 |
Pseudomonas aeruginosa | 38.1 | 23.8 | 9.6 |
Cronobacter spp. | 57.2 | 42.9 | 14.3 |
Escherichia coli | 61.9 | 28.6 | 14.3 |
Listeria innocua | 38.1 | 14.3 | 4.8 |
Citrobacter spp. | 14.3 | 9.5 | 4.8 |
Enterococcus spp. | 90.5 | 66.7 | 14.3 |
Klebsiella pneumoniae | 28.6 | 28.6 | 14.3 |
Butter Sample | Amount of Bacteria, CFU/g | Bacteria Identified in the Sample |
---|---|---|
2 | 3.0 × 105 | Bacillus pumilus, Acinetobacter guillouiae, Rothia sp., Rahnella aquatilis, Pseudomonas sp. |
3 | 3.0 × 104 | Bacillus thuringiensis, Neisseria sp., Moraxella osloensis |
4 | 2.0 × 104 | Enterococcus sp., Zimmermannella faecalis, Pseudomonas sp. |
6 | 5.0 × 104 | Lysinibacillus sp., Carnobacterium maltaromaticum, Pseudomonas sp. |
12 | 7.0 × 105 | Enterococcus italicus, Pseudomonas sp., Kocuria salsicia, Cronobacter sakazakii, |
18 | 1.0 × 106 | Enterobacter cloacae, Staphylococcus epidermidis, Lysinibacillus sp., Micrococcus sp. |
Bacteria | Butter Sample | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | |
Lactobacillus kisonensis | |||||||||||||||||||||
Lactobacillus senioris | |||||||||||||||||||||
Lactobacillus diolivorans | |||||||||||||||||||||
Lactobacillus kefiri | |||||||||||||||||||||
Lactobacillus parakefiri | |||||||||||||||||||||
Lactobacillus delbrueckii | |||||||||||||||||||||
Lactococcus taiwanensis | |||||||||||||||||||||
Lactococcus chungangensis | |||||||||||||||||||||
Lactococcus plantarum | |||||||||||||||||||||
Lactococcus raffinolactis | |||||||||||||||||||||
Streptococcus infantarius | |||||||||||||||||||||
Streptococcus vestibularis | |||||||||||||||||||||
Streptococcus porcorum | |||||||||||||||||||||
Streptococcus hongkongensis | |||||||||||||||||||||
Leuconostoc pseudomesenteroides | |||||||||||||||||||||
0% -no color | <0.1% | 0.1–1% | 2–15% | 16–30% | 31–45% | 46–60% | 61–75% |
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Syromyatnikov, M.Y.; Kokina, A.V.; Solodskikh, S.A.; Panevina, A.V.; Popov, E.S.; Popov, V.N. High-Throughput 16S rRNA Gene Sequencing of Butter Microbiota Reveals a Variety of Opportunistic Pathogens. Foods 2020, 9, 608. https://doi.org/10.3390/foods9050608
Syromyatnikov MY, Kokina AV, Solodskikh SA, Panevina AV, Popov ES, Popov VN. High-Throughput 16S rRNA Gene Sequencing of Butter Microbiota Reveals a Variety of Opportunistic Pathogens. Foods. 2020; 9(5):608. https://doi.org/10.3390/foods9050608
Chicago/Turabian StyleSyromyatnikov, Mikhail Y., Anastasia V. Kokina, Sergey A. Solodskikh, Anna V. Panevina, Evgeny S. Popov, and Vasily N. Popov. 2020. "High-Throughput 16S rRNA Gene Sequencing of Butter Microbiota Reveals a Variety of Opportunistic Pathogens" Foods 9, no. 5: 608. https://doi.org/10.3390/foods9050608