Page 108 - Read Online

Page 16 of 19 Ambros et al. Microbiome Res Rep 2023;2:34 https://dx.doi.org/10.20517/mrr.2023.18

after genome assembly. This could potentially indicate different amounts of viral DNA substrate for
sequencing. Contrary to this argument, L. curvatus phage TMW 1.2272 P1, which caused a strong lysis
event after induction and appeared to generate fully assembled virions as detected via TEM, had a
fragmentized viral genome after assembly as well, despite being the only prophage within L. curvatus strain
TMW 1.2272. The exact reasons for genome fragmentation and the presence of only one phage morphotype
per lysate are still unknown and may need further attention.

CONCLUSION
Our analyses for the commonly used starter organism L. curvatus affirmed the close relationship between
temperate phages and lactobacilli and revealed 50 putatively intact prophages located in 12 discrete
chromosomal loci. Knowledge of conserved regions within phage genomes and integration loci could be
useful to design a prophage detection method (e.g., a PCR-based approach) that is not reliant on induction
experiments. Some of the intact predicted phages contain features, such as genes coding for transposases,
MTases, and tRNAs, which demonstrate their diversity as well as indicate their battle against their host. We
supported our predictive analyses by demonstrating that, after induction treatment with UV light or
mitomycin C, some of these viral sequences can influence the growth of their hosts in varying intensities,
accompanied by the release of new phage progeny with the siphovirus morphotype. Therefore, we suggest
that these lysogens might also have the potential to influence other microbial communities.

DECLARATIONS
Authors’ contributions
Designed, planned and performed the experiments, analysed the data and wrote the manuscript: Ambros
CL
Supervised and participated in the conception of the study and helped in writing the manuscript: Ehrmann
MA
All authors read and approved the final version of the manuscript.

Availability of data and materials
Accession numbers of L. curvatus genomes used in this study are listed below. The outgroups used genomic
data are listed with the respective accession numbers, and/or locus tags in the supplemental material.
L. curvatus genomes (accessible at the NCBI website) used for prophage screening analyses:
CBA3617 (NZ_CP042389), CRL 705 (NZ_AGBU01000145), DRD-164 (JAMRWB000000000), ELA204092
(NZ_JAJJOT010000000), ELA214002 (NZ_JAJJOL010000000), ELA214060 (NZ_JAJJOQ010000000),
E L A 2 1 4 0 6 1 ( N Z _ J A J J O R 0 1 0 0 0 0 0 0 0 ) , E L A 2 1 4 0 6 2 ( N Z _ J A J J O S 0 1 0 0 0 0 0 0 0 ) , E L A 2 1 4 1 1 7
(NZ_JAJJOK010000000), ELA214388 (NZ_JAIULU010000000), FAM25164 (NZ_JAFJMA010000001),
FBA2 (NZ_CP016028), IRG2 (NZ_CP025476), isolate FLEC03 chromosome LCUFL03 (NZ_LT841333),
T
HFS9 (NZ_JAMOHH010000001), JCM 1096 = DSM 20019 (NZ_CP026116), KG6 (NZ_CP022475),
MGYG-HGUT-00020 (NZ_CABIVZ010000001), MRS6 (NZ_CP022474), NFH-Km12 (AP018699),
NRIC0822 (NZ_JTJV01000001), RI-124 (NZ_MKDR01000001), RI-406 (NZ_MKDG01000001), S46
(NZ_SUMW01000010), SRCM103465 (NZ_CP035110), TMW 1.27 (CP016467), TMW 1.401 (CP016216),
TMW 1.407 (CP016218), TMW 1.421 (CP016221), TMW 1.595 (CP016470), TMW 1.624 (CP015490),
TMW 1.1381 (CP015493), TMW 1.1390 (CP015494), TMW 1.1408 (JAHIAF000000000), TMW 1.1928
(NZ_CP031003), TMW 1.2270 (JAHIAD000000000), VRA_2sq_f (NZ_WKLA01000324), WDN19
(NZ_AP024685), WiKim38 (NZ_CP017124), ZJUNIT8 (NZ_CP029966).
L. curvatus genomes provided by this study:
TMW 1.591 (JAHIAT000000000), TMW 1.706 (JAHIAS000000000), TMW 1.1365 (JAHIAR000000000),
TMW 1.1447 (JAHIAQ000000000), TMW 1.2272 (JAHIAP000000000).