Page 13 - Read Online

O’Connell et al. Microbiome Res Rep 2023;2:21 https://dx.doi.org/10.20517/mrr.2023.17 Page 7 of 21

Table 1. The MP clusters represented in the RefSeq dataset, based on the information available on the Actinobacteriophage
Database (https://phagesdb.org/hosts/genera/1/?sequenced=True) and/or literature searches
Cluster Number of Phage Number of Subclusters
A 256 19
B 63 12
C 31 2
D 5 2
E 25 0
F 157 5
G 18 5
H 6 2
I 6 2
J 11 0
K 66 7
L 22 4
M 7 2
N 19 0
O 5 0
P 24 6
Q 1 0
R 2 0
S 2 0
T 2 0
U 1 0
V 1 0
X 1 0
Y 2 0
Z 2 0
AA 1 0
AB 2 0
AC 3 0
AD 1 0
Singletons 6 n/a
Unknown 3 n/a

The total number of phage MP in each cluster as well as the total number of subclusters represented within the cluster are also indicated.

phylogenetic trees to provide evidence for the existence of the novel genera. Subsequently, the queried
subclusters are indicated within the VIRIDIC alignments and dendrograms to highlight anomalies with
current subcluster assignments that may be clarified by the creation of more subclusters (or the removal of
one, in the case of cluster G).

Cluster A - Ten novel genera and two novel subclusters
The total number of genomes included in the dataset that belong to cluster A is 256. These are organised
into 19 subclusters based on the existing Actinobacteriophage database classifications. There is a large
number of MP assigned to the genus Fromanvirus [Supplementary Table 1]. The MP Froman belongs to
subcluster A1, which VIRIDIC groups into a single genus, so this genus shall be considered the true
Fromanvirus genus. Amongst the remaining “Fromanviruses”, initially, 11 novel genera were identified
based on a threshold of ≥ 70% nucleotide similarity as illustrated in the VIRIDIC output [Figure 2A].
However, following inspection of the proteomic analysis performed with Gegenees, it appears that the best