Isolation and Characterization of Lactobacillus brevis Phages
Abstract
:1. Introduction
2. Materials and Methods
2.1. Bacterial Strains and Cultivation Media
2.2. Phage Isolation and Enrichment
2.3. Phage Detection, Purification and Host Range Analysis
2.4. Phage Concentration and Purification
2.5. Transmission Electron Microscopy
2.6. Phage DNA Extraction and Sequencing
2.7. Phage Structural Proteome and Mass-Spectrometry
2.8. Proteomic Tree
2.9. Phage Activity against Lb. brevis Beer-Spoiling Strains
2.10. Nucleotide Sequence Accession Numbers
3. Results
3.1. Phage Isolation and Host Range Profile
3.2. Phage Morphology
3.3. Lb. brevis Phages Comparative Analysis and Grouping
3.4. Genome Analysis
3.5. Morphogenesis Module
3.6. Structural Proteome
3.7. Phage Activity against Lb. brevis Beer-Spoiling Strains
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Lactobacillus brevis Strains | Isolation Source |
---|---|
ATCC367 [21] | Silage |
UCCLBBS124 | Beer |
UCCLB521 | Brewery |
UCCLB556 | Brewery |
SA-C12 | Silage |
UCCLBBS449 | Beer |
UCCLB94 | Beer |
UCCLB95 | Beer |
RIBM 2-56 | Beer |
Lb. brevis Non-Beer Spoiling Strains | Lb. brevis Beer-Spoiling Strains | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
ATCC367 | UCCLB521 | UCCLB556 | SA-C12 | UCCLBBS124 | UCCLBBS449 | UCCLB94 | UCCLB95 | RIBM 2-56 | ||
Phage | 3-521 | - | + * | - | - | - | - | - | ~ | - |
521B | - | + * | - | - | - | ~ | - | - | - | |
3-SAC12 | - | - | - | + * | - | - | - | - | - | |
SAC12B | - | + | - | + * | - | - | - | - | ~ | |
ATCCB | + * | - | - | - | - | - | - | - | - |
Phage | Sample (Date) | Isolation Source | Genome Size (bp) | ORFs | GC Content (%) | % nt Identity (% coverage) | |
---|---|---|---|---|---|---|---|
Myoviridae | 3-521 | S1 (2017) | Wastewater (Ireland) | 140,816 | 155 | 36.93 | |
521B | S2 (2018) | Wastewater (Ireland) | 136,442 | 188 | 32.27 | 97 (88) with SAC12B | |
SAC12B | S2 (2018) | Wastewater (Ireland) | 136,608 | 191 | 32.41 | 97 (88) with 521B | |
3-SAC12 | S1 (2017) | Wastewater (Ireland) | 41,292 | 61 | 40.01 | ||
Siphoviridae | ATCCB | S2 (2018) | Wastewater (Ireland) | 80,538 | 96 | 30.80 |
Phage | ORF | Putative Function | No. of Peptides | Sequence Coverage (%) |
---|---|---|---|---|
521B | 80 | Probable capsid protein | 8 | 29.4 |
81 | Probable capsid protein | 9 | 28.4 | |
86 | Structural protein | 3 | 16.1 | |
88 | Lipoprotein | 5 | 50.8 | |
106 | Structural protein | 4 | 37.9 | |
121 | Portal protein | 12 | 28.3 | |
122 | Structural protein | 2 | 17.4 | |
123 | Caudovirus prohead protease | 4 | 20.8 | |
125 | Major capsid protein precursor | 19 | 59.7 | |
128 | Capsid protein | 3 | 16.8 | |
130 | Gp91 | 8 | 35 | |
132 | Major tail sheath protein | 16 | 40.4 | |
133 | Tail protein | 5 | 59.9 | |
136 | Tape measure protein | 28 | 31.2 | |
137 | Tail lysin | 12 | 15.1 | |
138 | Structural component of the tail fibre | 8 | 10 | |
140 | Structural protein | 2 | 15.1 | |
141 | Structural protein | 5 | 42.2 | |
142 | Baseplate protein | 3 | 23.1 | |
143 | Baseplate J-like protein | 6 | 15.1 | |
144 | Baseplate protein | 7 | 9.4 | |
146 | Tail protein | 15 | 34.1 | |
147 | Putative adsorption protein | 9 | 22.2 | |
156 | DNA starvation/stationary phase protein | 6 | 48 | |
185 | Structural protein | 3 | 38.5 | |
3-521 | 10 | dUTP diphosphatase | 2 | 9.9 |
19 | Zn-dependent protease | 5 | 23.7 | |
52 | Portal protein | 3 | 7.9 | |
53 | Prohead protease | 1 | 8.3 | |
55 | Major capsid protein | 19 | 51.1 | |
57 | Phage capsid and scaffold | 19 | 18.6 | |
60 | Structural protein | 4 | 20.1 | |
65 | Tail sheath protein | 14 | 25 | |
66 | Putative tail protein | 6 | 53.3 | |
69 | Tape measure protein | 14 | 17.4 | |
70 | Tail lysin protein | 16 | 21.1 | |
71 | gp673 | 2 | 1.7 | |
72 | Structural protein | 3 | 15.3 | |
76 | Baseplate protein | 4 | 3 | |
77 | Structural protein | 2 | 18 | |
78 | Tail protein | 22 | 24.5 | |
79 | Tail associated protein | 23 | 20.1 | |
98 | Nucleoside 2-deoxyribosyltransferase | 2 | 12.4 | |
101 | Structural protein | 1 | 6.1 | |
106 | Structural protein | 7 | 62 | |
108 | Tail protein | 1 | 18 | |
117 | Adenyltransferase | 6 | 16.9 | |
119 | ADP-ribose pyrophosphatase | 1 | 5.3 | |
124 | Structural protein | 6 | 15.7 | |
126 | AAA superfamily ATPase | 9 | 26.2 | |
128 | Phosphatase | 4 | 5.4 | |
3-SAC12 | 1 | Terminase small subunit | 1 | 6.6 |
3 | Portal protein | 13 | 31.4 | |
5 | Major capsid protein | 4 | 26.3 | |
6 | Capsid protein | 9 | 26.7 | |
10 | Putative head-tail adaptor | 1 | 9.8 | |
11 | Structural protein | 1 | 9 | |
12 | Sheath protein | 3 | 11.8 | |
13 | Structural protein | 2 | 22.4 | |
17 | Structural protein | 4 | 13.6 | |
ATCCB | 70 | Baseplate protein | 6 | 9.2 |
79 | Major tail protein | 6 | 50.2 | |
86 | Major capsid protein | 8 | 25.9 | |
87 | Prohead protease | 2 | 7.5 |
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Feyereisen, M.; Mahony, J.; Lugli, G.A.; Ventura, M.; Neve, H.; Franz, C.M.A.P.; Noben, J.-P.; O’Sullivan, T.; van Sinderen, D. Isolation and Characterization of Lactobacillus brevis Phages. Viruses 2019, 11, 393. https://doi.org/10.3390/v11050393
Feyereisen M, Mahony J, Lugli GA, Ventura M, Neve H, Franz CMAP, Noben J-P, O’Sullivan T, van Sinderen D. Isolation and Characterization of Lactobacillus brevis Phages. Viruses. 2019; 11(5):393. https://doi.org/10.3390/v11050393
Chicago/Turabian StyleFeyereisen, Marine, Jennifer Mahony, Gabriele A. Lugli, Marco Ventura, Horst Neve, Charles M. A. P. Franz, Jean-Paul Noben, Tadhg O’Sullivan, and Douwe van Sinderen. 2019. "Isolation and Characterization of Lactobacillus brevis Phages" Viruses 11, no. 5: 393. https://doi.org/10.3390/v11050393