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Page 8 of 19 Kok et al. Microbiome Res Rep 2023;2:30 https://dx.doi.org/10.20517/mrr.2023.16

Table 4. Details of 26 Paenibacillus larvae phages discovered, sequenced and annotated
Geographic Bacteria isolated Genome length No. of GC content Cluster Accession
region on (bp) genes (%) No.
ABAtENZ Hamilton Pl-PFR-2017 44,419 82 42.97 Vegas OP503968
AJG77 Wanaka Pl-PFR-2017 44,417 82 42.98 Vegas OP503969
ApiWellbeing Masterton Pl-F1A 44,429 82 43.01 Vegas OP503970
BarryFoster_Benicio Whangarei Pl-F1A 44,421 82 42.98 Vegas OP503543
Bloomfield Haast Pl-PFR-2017 44,419 82 42.98 Vegas OP503971
Bob Matakana Island F2B 43,553 80 43.03 Vegas OP503972
Callan West Taratahi Pl-PFR-2006 44,768 77 39.69 Harrison OP503989
Carlos Carterton Pl-F1A 44,430 83 42.98 Vegas OP503973
Dante Elgin Pl-WAI 44,420 82 42.98 Vegas OP503974
Dash West Taratahi Pl-PFR-2006 44,599 79 39.39 Harrison OP503990
FutureBee Hamilton Pl-TP 44,417 83 42.98 Vegas OP503975
GaryLarson Willowby Pl-F2B 44,420 82 42.98 Vegas OP503976
GIW2016 Wanaka Pl-PFR-2017 43,555 80 43.01 Vegas OP503977
Jacinda Haast Pl-PFR-2017 44,419 82 42.97 Vegas OP503978
Lena Rotorua Pl-PFR-2017 44,420 82 42.97 Vegas OP503979
Lilo Pukekawa Pl-F1A 40,941 70 40.33 Harrison OP503991
Logan Tolaga Bay Pl-PFR-2017 44,419 82 42.99 Vegas OP503980
LunBun Gisborne Pl-F1A 44,421 82 42.97 Vegas OP494865
NHScienceFair Albany F1A 44,419 82 42.98 Vegas OP503981
Ollie Marton Pl-PFR-2017 44,420 83 42.98 Vegas OP503982
Rae.2Bee1 Fairton Pl-TP 44,420 82 42.97 Vegas OP503983
Rosalind Westport F1A 43,556 80 43.00 Vegas OP503984
Ted Napier Pl-PFR-2017 44,419 82 42.99 Vegas OP503985
TonyLawson77 Palmerston North Pl-F1A 44,420 82 42.96 Vegas OP503986
UtuhinaGold_Zacery Rotorua Pl-PFR-2017 44,420 82 42.97 Vegas OP503987
WildCape Gisborne Pl-F1A 44,430 82 43.00 Vegas OP503988

P. Larvae: Paenibacillus larvae.

prevented us from progressing to genome sequencing and electron microscopy as our typical methods
require 10 mL . We therefore developed the Rapid Adaptive Mutation of Phage-UP or RAMP-UP protocol
9
-1
to increase phage titer by mutation, which can work in as little as four days .
[30]
Upon sequencing, we discovered the New Zealand phages were between 40-44 kbp in length with 70-83
genes per genome. The phages belong to two of the four major genomically determined clusters of P. larvae
phages; three belong to the Harrison cluster and 23 belong to the Vegas cluster [Table 4]. Clusters were
determined by average nucleotide identity (ANI); if two phages have ANI greater than or equal to 60%, they
are placed in the same cluster . All New Zealand P. larvae phages are linear and use the 3’ cohesive end
[19]
DNA packaging mechanism, similar to the majority of previously described P. larvae phages . The New
[19]
Zealand P. larvae phages are lytic in vitro, despite the presence of annotated integrases in their genomes, the
presence of which suggests the capacity for a temperate lifestyle. Phage Dash (Harrison Cluster) has an
integrase at GP38 and phage ABAtENZ (Vegas Cluster) has an integrase at GP32 [Figure 3]. The presence
of integrases, and the absence of evidence of a temperate lifecycle in the laboratory, is consistent across the