TABLE 1.
Properties of seven mycobacteriophages isolated in east Texas, USA, in 2020 and 2021
| Characteristic | Data for phage:a |
||||||
|---|---|---|---|---|---|---|---|
| Duplo | Dynamo | Gilberta | MaCh | Nikao | Phloss | Skinny | |
| Yr found | 2020 | 2021 | 2021 | 2020 | 2020 | 2020 | 2021 |
| Location found | Big Sandy, TX | Longview, TX | Longview, TX | Longview, TX | Longview, TX | Longview, TX | Longview, TX |
| Soil sampling location | 32.588034 N,95.063959 W | 32.46402 N,94.728226 W | 32.468338 N,94.726844 W | 32.465237 N,94.727035 W | 32.54954 N, 94.821309 W | 32.4675 N, 94.725 W | 32.467601 N,94.723749 W |
| Lysate titer (PFU/mL) | 3.0 × 109 | 1.0 × 1010 | 1.0 × 109 | 1.6 × 1010 | 2.17 × 109 | 8.7 × 1011 | 1.18 × 109 |
| Plaque morphology after 48 h at 37°C | Slightly turbid with defined edges | Clear with defined edges | Clear with defined edges | Clear with defined edges | Slightly turbid with defined edges | Clear with defined edges | Clear with defined edges |
| Plaque size (mm) | 3.3 | 0.93 | 1.5 | 2.7 | 1.25 | 2.0 | 1.0 |
| Approx coverage (×) | 1,516 | 1,499 | 5,472 | 705 | 414 | 2,005 | 499 |
| Genome size (bp) | 52,781 | 46,673 | 51,470 | 52,616 | 59,052 | 43,107 | 82,071 |
| GC content (%) | 63.5 | 67.2 | 63.7 | 63.6 | 67.2 | 66.3 | 61.5 |
| Overhang sequence | CGGTCGGTTA | CCCGCCCCCCGA | CGGTCGGTTA | CGGTCGGTTA | CTCGGGGGCAT | CCCGCCGCAATGG | ACCTCCTGCAA |
| Overhang length (bases) | 10 | 12 | 10 | 10 | 11 | 13 | 11 |
| Cluster | A | P | A | A | K | N | M |
| Subcluster | A2 | P1 | A11 | A11 | K1 | M1 | |
| GenBank accession no. | OP297553 | OP434454 | OP297532 | OP297549 | OP297530 | OP297540 | OP297551 |
| SRA accession no. | SRX19690833 | SRX19690834 | SRX19690836 | SRX19690844 | SRX19690847 | SRX19690850 | SRX19690858 |
| Total no. of reads | 560,502 | 485,417 | 1,968,556 | 261,625 | 172,343 | 608,118 | 285,773 |
| No. of predicted genes | 99 | 78 | 99 | 100 | 80 | 70 | 163 |
| No. of predicted tRNAs | 5 | 0 | 1 | 1 | 0 | 0 | 18 |
| tRNA type(s) | Asn, Gln, Glu, Trp, Tyr | Trp | Trp | Trp, Asn, other (Arg/Ala), Tyr, Gln, Pro, Ser, Phe, Met, Arg, His, Leu, Lys, Gly, Val, Thr, Asp, Glu | |||
| No. of genes with predicted functions | 33 | 32 | 36 | 43 | 41 | 28 | 46 |
| % of genes with predicted functions | 33 | 41 | 36 | 43 | 51 | 40 | 28 |
| Key predicted lysogenic life cycle genes | Integrase, excise, immunity repressor | Integrase, excise, immunity repressor | Integrase, immunity repressor | Immunity repressor | Integrase, excise, immunity repressor | Integrase, excise, immunity repressor | Integrase |
| No. of orphams | 2 | 0 | 1 | 0 | 0 | 0 | 2 |
| Capsid size (nm [n value]) | 64.48 (9) | 60.90 (7) | 52.09 (3) | 58.67 (21) | 67.04 (5) | 51.76 (7) | 71.53 (3) |
| Avg tail length (nm [n value]) | 124.23 (9) | 205.57 (6) | 125.54 (3) | 130.93 (21) | 210.16 (5) | 172.04 (7) | 326.19 (3) |
| Isolated by | Skylar M. Weiss, Jimena H. Segovia | Christina A. Holder, Kaitlyn J. Menard, Brady E. Tyler | Hattie R. Mills, Ashlyn B. Collier, Kalista J. Rivera, Claire P. Martinez | Matthew S. Adams, Camryn L. Hill | Kezia K. Happy | Summer L. Apostalo, Gavin J. Meyer | Jenna F. Curran, Kristen N. Rose |
a
All phages were isolated using the enriched isolation method (5) and purified through three sequential 48-h rounds of plating at 37°C. The genomes were sequenced using the Illumina shotgun sequencing method with 150-base single-end reads using the NEB Ultra II Library sequencing kit. All had 3′ sticky overhang genome ends. Genomic termini were identified through buildups of read start positions and variations in genome-wide coverage and verified manually using Consed v29 (14, 15). All phages had a siphovirus morphotype and were predicted to be temperate based on the presence of predicted lysogeny-related genes.