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19 July 2025

Structural and Genetic Diversity of Lysis Modules in Bacteriophages Infecting the Genus Streptococcus

,
,
and
1
CHU Bordeaux, Department of Dentistry and Oral Health, University of Bordeaux, F-33000 Bordeaux, France
2
University of Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, UMR 1366, OENO, ISVV, F-33140 Villenave d’Ornon, France
3
CHU Bordeaux, Department of Oral Surgery, University of Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, UMR 1366, OENO, ISVV, F-33000 Bordeaux, France
*
Author to whom correspondence should be addressed.
Genes2025, 16(7), 842;https://doi.org/10.3390/genes16070842
This article belongs to the Section Microbial Genetics and Genomics
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Abstract

Background/Objectives: Bacteriophages infecting the genus Streptococcus play a crucial role in microbial ecology and have potential applications in biotechnology and medicine. Despite their importance, significant gaps remain in our understanding of their lysis modules. This study aims to address these deficiencies by analyzing the genomic diversity and lysis module organization in Streptococcus phages. Methods: A search was conducted in the NCBI RefSeq database to identify phage genomes infecting Streptococcus. A representative panel was selected based on taxonomic diversity. Lysis modules were annotated and visualized, functional domains in endolysins were identified, and holins were characterized. Results: A total of 205 phage genomes were retrieved from the NCBI RefSeq database, of which 185 complete genomes were analyzed. A subset of 34 phages was selected for in-depth analysis, ensuring the representation of taxonomic diversity. The lysis modules were annotated and visualized, revealing five distinct organizations. Among the 256 identified endolysins, 25 distinct architectural organizations were observed, with amidase activity being the most prevalent. Holins were classified into 9 of the 74 families listed in the Transporter Classification Database, exhibiting one to three transmembrane domains. Conclusions: This study provides insights into the structural diversity of lysis modules in Streptococcus phages, paving the way for future research and potential biotechnological applications.

1. Introduction

Antimicrobial resistance (AMR) poses a major global health threat, with antibiotic-resistant bacterial infections estimated to have caused 4.95 million deaths worldwide in 2019 [1]. In response to this growing crisis, phage therapy has re-emerged as a promising alternative or complement to traditional antibiotics.
Bacteriophages, or phages, are viruses that infect bacteria with high specificity, often targeting a single species or even a specific strain [2]. They can be broadly classified as lytic or temperate: lytic phages rapidly lyse and kill their bacterial hosts, whereas temperate phages may integrate into the bacterial genome as prophages. Numerous clinical cases have demonstrated the therapeutic potential of lytic phages, particularly against multi-drug-resistant bacterial infections [3].
One of the most promising components of phage therapy is the exploitation of the lysis module, a set of genes that orchestrate bacterial cell wall degradation at the end of the phage replication cycle. In phages infecting Gram-positive bacteria, such as Streptococcus, the lysis module typically comprises an endolysin, which enzymatically cleaves the peptidoglycan, and a holin, which forms pores in the cytoplasmic membrane to facilitate endolysin access. In contrast, phages infecting Gram-negative hosts often include an additional component, the spanin complex (Rz and Rz1 gene products), responsible for disrupting the outer membrane after peptidoglycan degradation [4]. Variants of this system also exist: some phages use pinholins, which create small lesions in the membrane to activate SAR (Signal–Arrest–Release) endolysins, a type of endolysin tethered to the membrane and released upon membrane depolarization [5]. These mechanistic variations underscore the functional diversity and evolutionary specialization of phage lysis strategies.
Endolysins, in particular, have drawn attention for their high specificity, being able to target selected bacterial genera, species, or even strains [6]. Their therapeutic potential has been notably demonstrated against pathogens such as Streptococcus spp. [7,8,9]. Bacteria from this genus are involved in a broad spectrum of diseases, ranging from mild infections to life-threatening conditions such as pneumonia and meningitis [10,11]. The increasing prevalence of antibiotic-resistant Streptococcus strains highlights the urgent need for alternative treatment options [12,13,14]. Notably, endolysins have also shown efficacy in eliminating intracellular Streptococcus, further expanding their clinical relevance [8].
Beyond their clinical importance, some Streptococcus spp., such as Streptococcus thermophilus, hold significant industrial value due to their use in fermented dairy products like yogurt and cheese, underlining their biotechnological and economic importance [15].
This study aims to conduct a comparative in silico analysis of the lysis modules encoded by phages infecting Streptococcus spp. By examining the genetic organization, domain architecture, and functional diversity of holins as well as endolysins, we seek to provide insights into their functional variability and potential for therapeutic application.

2. Materials and Methods

2.1. Retrieval of Phages Infecting the Streptococcus Genus

A search was performed in the NCBI RefSeq database [16] on 7 March 2025, using the keywords “Streptococcus phage” and “Streptococcus bacteriophage.” Only complete and annotated genomes were retained. Duplicates and evidently incomplete sequences were manually verified and excluded. When available, the bacterial host species was recorded.

2.2. Selection of a Representative Panel

Taxonomic classification (class, family, subfamily, genus, and species) was retrieved from the International Committee on Taxonomy of Viruses (ICTV) database [17] on 22 April 2025. For genera represented by multiple phages, a representative genome was selected based on citation frequency in the literature or the diversity/complexity of the lysis module. Phages unassigned at the genus level were systematically included. The phylogenetic diversity of the final panel was assessed using genome-based distance analyses with VICTOR [18] and VIRIDIC [19]. The resulting tree was visualized using iTOL v6 [20].

2.3. Detection and Annotation of Lysis Module

Phage genomes from the selected panel were annotated using Pharokka v1.7.5 [21] and visualized with LoVis4u version 0.1.2 [22] to identify genes associated with the lysis module. Annotations were cross-checked against RefSeq data. In ambiguous cases, unannotated proteins were analyzed using BLASTp [23] to determine potential homology to known holins or endolysins.

2.4. Detection of Functional Domains in Endolysins

Endolysin sequences were analyzed with phiBIOTICS [24] and SMART [25] to detect enzymatically active domains (EADs) and cell wall-binding domains (CBDs). Additional searches were conducted using HMMER, the Conserved Domain Database (CDD) [26], and MOTIF Search (https://www.genome.jp/tools/motif/, accessed on 28 May 2025), incorporating domain models from Pfam, COG, TIGRFAM, and SMART. An E-value cutoff of <0.01 was applied.

2.5. Characterization of Holins

Identified holins were submitted to BLASTp against the Transporter Classification Database [27] for functional classification. Transmembrane domain (TMD) number and topology were predicted using DeepTMHMM v1.0.42 [28] and confirmed via Protter version 1.0 [29].

3. Results

3.1. Diversity of Phages Infecting the Streptococcus Genus

A total of 205 Streptococcus-associated phages were initially retrieved from RefSeq. After excluding incomplete entries, 185 complete genomes were retained; their NCBI accession numbers are listed in Appendix A.1. A subset of 34 phages was selected for in-depth analysis, representing the observed taxonomic diversity (Figure 1). This selection included phages belonging to different genera when such classification was available, or otherwise phages that remained unclassified at the genus level according to the ICTV database. These 34 phages collectively infect 12 distinct Streptococcus species, although the host species remained unidentified for 1 of them. Notably, 20 phages in this subset were unassigned at the genus level. The four major groups of S. thermophilus-infecting phages were included: Pac (Brussowvirus), Cos (Moineauvirus), 5093 (Vansinderenvirus), and 9871 (Piorkowskivirus) (Appendix A.2).
Figure 1. Phylogenetic tree of the 34 phages selected for their taxonomic diversity. The tree was constructed using pairwise nucleotide alignments between phage genomes, based on a distance matrix computed by VIRIDIC and visualized with iTOL. Branches are colored according to the phages’ taxonomic classification. At the family level: Aliceevansviridae (orange), Madridviridae (fuchsia), and Rountreeviridae (green); at the subfamily level: Ferrettivirinae (purple) and Mcshanvirinae (blue). Branches shown in black indicate phages for which neither the family nor the subfamily is known. Bacterial hosts are represented by colored squares (as indicated in the color key), forming an outer ring.

3.2. Organization of Lysis Modules

Gene annotations revealed the presence of holin and endolysin genes, enabling the delineation of lysis modules in the 34 selected phages (Appendix A.3). Five distinct module organizations (A to E) were identified (Figure 2). These modules contain up to two ORFs each for holins and endolysins.
Figure 2. Schematic representation of the different lysis module organizations identified among the analyzed phages (n = 33). Among the 34 phages examined, 33 harbored a recognizable lysis module. Five distinct organizations, labeled A to E, were defined based on the number and arrangement of lysis-related genes, holins (blue) and endolysins (pink). The number of phages exhibiting each organization is indicated on the right. In organizations A to C, holin genes precede endolysins, whereas in D and E, endolysins come first. Organization C includes an endonuclease gene (gray, diagonally striped) that is variably present between holin and endolysin. Each module is represented in the same transcriptional direction (left to right).
In 85% of phages, holin-encoding ORFs preceded endolysin-encoding ones, while this order was reversed in the remaining 15%. Lysis genes were generally contiguous, though some modules featured intercalated genes. For instance, phage ALQ13.2 (Brussowvirus) harbored an endonuclease and a hypothetical protein between two endolysins. Phage SP-QS1 uniquely lacked a clearly defined lysis module, with holin and endolysin genes separated by 18 unrelated genes, mostly encoding structural or hypothetical proteins.

3.3. Endolysin Architecture

Among the 185 phages, 114 encoded a single endolysin, while 71 encoded two. Endolysin genes ranged from 228 to 1386 bp, yielding a total of 256 distinct endolysins. Within the 34-phage subset, 26 had a single endolysin (Figure 3A).
Figure 3. Diversity and domain architecture of phage endolysins. (A) Phylogenetic tree of the 42 endolysins identified among the 34 selected phages. The tree was built using amino acid sequences aligned with ClustalW pairwise alignment, a slow algorithm, and the BLOSUM matrix). Endolysins are named using the abbreviated name of the originating phage, with the suffix _E when a single endolysin is present, or _E1/_E2 in the case of phages encoding two. For each endolysin, EADs and CBDs, when identified, are represented by colored circles and triangles, respectively (domain color codes are indicated in the figure). Colored squares indicate the bacterial species targeted by the phages encoding these endolysins. (B) Upset plot of the 256 analyzed endolysins. The plot displays the 25 distinct combinations of enzymatic and binding domains, labeled A1 to A25, based on the presence and arrangement of known EADs and CBDs. Each vertical bar represents the number of endolysins sharing a specific combination, while the connected dots below each bar indicate the motifs involved in that combination. On the left, a horizontal bar chart shows the overall frequency of each individual domain motif across all endolysins. A color code is used to distinguish motifs, with similar motifs sharing the same color.
These 256 proteins exhibited 25 architectural types, defined by EAD and CBD composition and arrangement (Figure 3B, Appendix A.4). The most common catalytic activity was amidase (Amidase_5 domain), and the most frequent CBD was ZoocinA_TRD. Seven architectures (A4, A5, A7, A11, A15, A20, and A25) lacked identifiable CBDs; three (A2, A19, and A21) lacked catalytic domains. Architectures were numbered by decreasing frequency (A1 = most common). Some were unique (A14–A25), and five (A5, A8, A14, A16, and A19) were absent from the representative subset.
Architectures lacking catalytic domains were usually co-encoded with catalytically active endolysins. For example, A2 (ZoocinA_TRD only) consistently co-occurred with A1 (Amidase_5 & NLPC_P60 & ZoocinA_TRD). Similarly, A20 (Chap & PlyCA) and A21 (PlyCB) were both encoded by phage C1, reflecting the PlyC endolysin structure.
An exception was phage IPP55, where a lone endolysin belonged to architecture A19. Further analysis using CDD and BLASTP revealed two conserved domains: a PGRP superfamily motif and a pneumo_PspA domain. The protein shared > 99% identity with S. pneumoniae LytA amidase (WP_073176617.1).
Notably, all three S. mutans phages encoding two endolysins lacked any identifiable CBDs.
Generally, catalytic domains were located at the N-terminus, with CBDs at the C-terminus. An exception was architecture A10, where CW7 motifs interrupted the Amidase_5/NLPC_P60 and Glucosaminidase domains. In some endolysins combining Amidase_5 and NLPC_P60, overlapping genes were observed, with the latter starting ~39 nt downstream of the former.

3.4. Characterization of Holins

A total of 340 holins were identified among the 185 phages analyzed. Within the subset of 34 phages, 53 holins were detected, distributed across 9 families (1.E.10, 1.E.11, 1.E.16, 1.E.18, 1.E.19, 1.E.21, 1.E.24, 1.E.26, and 1.E.65) out of the 74 currently listed in the Transporter Classification Database (TCDB). Fourteen holins remained unclassified. Phages encoding two holins always featured proteins from different families, consistent with divergent evolutionary origins (Figure 4).
Figure 4. Phylogenetic tree of the 53 holins identified among the 34 selected phages. The tree was built using amino acid sequences aligned with ClustalW (pairwise alignment, slow algorithm, BLOSUM matrix). Each holin is named using the abbreviated phage name, followed by the suffix _H when a single holin is present, or _H1/_H2 when two are encoded. Nine holin families were identified and are color-coded on the tree branches. Black branches indicate holins with no assigned family. The number of predicted transmembrane domains is shown by blue dots forming the outer ring of the tree.
The number of predicted TMDs was also assessed for all 53 holins and ranged from one to three, depending on the family. The number of TMDs was conserved within each family. Holins from families 1.E.26 and 1.E.65, as well as the unclassified holins, each contained a single TMD. Holins from families 1.E.11, 1.E.18, and 1.E.24 harbored two TMDs, whereas those from the remaining four families exhibited three TMDs.
Interestingly, among the 19 phages encoding two holins, only those infecting S. mutans featured holins with a single TMD in both cases.

4. Discussion

This study highlights significant deficiencies in the current taxonomic annotation of Streptococcus phages, with many genomes, particularly within the selected subset, remaining unclassified at the genus level. The lysis modules exhibited considerable diversity, including instances of intercalated ORFs such as endonucleases. Endolysin genomic sequences were generally short, even though they sometimes encode two structurally distinct proteins. This diversity appears to be facilitated by gene overlapping. Amidase activity was the most prevalent enzymatic function observed. While most endolysin gene architectures conformed to the typical N-terminal EAD and C-terminal CBD layout, some deviated from this pattern, including cases with a central CBD or a separate CBD-encoding ORF. Some CBDs also remained uncharacterized. Holins were predominantly found in tandem across the studied phages, although this trend was less pronounced in the subset. The diversity of holins was relatively limited, with those in the subset classified into only 9 of the 74 families currently listed in TCDB, and exhibiting between one and three transmembrane domains depending on the family.
Although all 185 phages were assigned to the class Caudoviricetes, the taxonomic information for several phages, particularly those in the subset, remains incomplete. This is hardly surprising given the trends reported by Turner et al. [30]. Viral taxonomy evolves rapidly, and the ICTV acknowledges that taxonomic assignment may remain partial for certain viruses, particularly when based solely on genomic data without cultivation, or in the context of metagenomic studies [31]. Other factors also complicate viral taxonomy, such as deficiencies in the curation of deposited viral genomes, especially for prophages. For example, phage phiNIH 1.1 (NC_003157.5) shares near-complete genomic identity with phage 315.4 (NC_004587.1), and, according to VIRIDIC analysis (data not shown), should arguably be classified within the same species. The only distinguishing feature is the presence of a gene (NC_003157.5:149-1255) encoding a peptide-methionine (R)-S-oxide reductase (MsrB), located upstream of the integrase gene in phiNIH 1.1 and likely acquired from the S. pyogenes host genome. These challenges underscore the need for improved viral genome curation, and some have proposed the use of artificial intelligence to assist with this task [32].
The findings from this study on the lysis modules of phages infecting Streptococcus species led to the proposal of a classification based on the position and number of ORFs encoding lysins and holins. This classification could be extended to phages infecting Gram-negative bacteria by incorporating the number and position of ORFs encoding spanins [5]. Although lysis-related genes are often contiguous, interspersed ORFs are not uncommon. Among these, endonucleases have been reported, under the designation lysin intergenic locus [33].
Regarding endolysin genomic sequences, the analysis revealed a notable rate of gene overlapping, allowing a single ORF to encode two distinct enzymatic functions. The most common association involved amidase activity (Amidase_5 domain) and endopeptidase activity (NLPC_P60 domain). This genomic arrangement supports the hypothesis of viral genome compression via overprinting, a mechanism widely used by phages to optimize coding efficiency [34,35].
Amidase activity emerged as the dominant enzymatic function in the endolysins of phages infecting the genus Streptococcus, in contrast with endolysins from Staphylococcus phages, where Cysteine, Histidine-dependent Amidohydrolases/Peptidases (CHAP) domains often predominate and amidase domains may play an auxiliary role, possibly contributing to peptidoglycan binding rather than catalysis [36]. This distinction may reflect functional adaptations to differences in host peptidoglycan structure and susceptibility.
The organization of endolysins observed here aligns with the classical architecture described for phages infecting Gram-positive bacteria, typically featuring an N-terminal EAD and a C-terminal CBD [37,38]. However, previously reported exceptions were also identified in this study, such as the well-characterized endolysin PlyC, whose CBD (PlyCB) oligomerizes into an octamer [33], or the presence of a central CBD flanked by EADs at both termini, as described for phage LambdaSa2 lysin and PlySK1249 lysin [39,40]. In some endolysins, particularly from phages infecting S. mutans, only EADs could be identified, which is consistent with a previous review [41]. The 25 architectural organizations described here therefore represent only a subset of the 89 known architectures [42,43].
The frequent presence of tandem holins supports previous observations by Escobedo et al. [44], who reported that the presence of a second holin may improve lytic activity. Nevertheless, further studies are needed to clarify the functional significance of membrane domain organization in holin regulation and activity, as current classification systems do not fully reflect the mechanistic diversity of these proteins [45,46].

5. Conclusions

This study revealed extensive diversity in the lysis modules of Streptococcus phages, with gene overlap and interspersed ORFs contributing to their structural complexity. These findings pave the way for future investigations, including the functional characterization of unannotated CBDs and the refinement of lysin engineering strategies for therapeutic purposes.

Author Contributions

M.S.-J.: writing—original draft, data curation, formal analysis. O.C.: writing—original draft, methodology, data curation, formal analysis. C.L.M.: writing—review and editing, methodology. J.S.: writing—original draft, writing—review and editing, supervision, project administration, conceptualization, methodology, formal analysis. All authors have read and agreed to the published version of the manuscript.

Funding

This research received no external funding.

Institutional Review Board Statement

Not applicable.

Data Availability Statement

The original contributions presented in this study are included in the article. Further inquiries can be directed to the corresponding author.

Conflicts of Interest

The authors declare no conflicts of interest.

Abbreviations

The following abbreviations are used in this manuscript:
CBDCell-wall Binding Domain
CDDConserved Domain Database
CHAPCysteine, Histidine-dependent Amidohydrolases/Peptidases
EADEnzymatically Active Domain
ICTVInternational Committee on Taxonomy of Viruses
ORFOpen Reading Frame
SARSignal–Arrest–Release
TCDBTransporter Classification Database
TMDTransmembrane domain

Appendix A

Appendix A.1

Table A1. List of the 185 phages included in the study.
Table A1. List of the 185 phages included in the study.
Phage NameBacterial TargetNCBI RefSeqkbpClassFamilySubfamilyGenusSpecies
Streptococcus phage 20617Streptococcus thermophilusNC_023503.148CaudoviricetesAliceevansviridaeBrussowvirusBrussowvirus 20617
Streptococcus phage ALQ13.2Streptococcus thermophilusNC_013598.135CaudoviricetesAliceevansviridaeBrussowvirusBrussowvirus ALQ132
Streptococcus phage 2972Streptococcus thermophilusNC_007019.134CaudoviricetesAliceevansviridaeBrussowvirusBrussowvirus bv2972
Streptococcus phage 858Streptococcus thermophilusNC_010353.135CaudoviricetesAliceevansviridaeBrussowvirusBrussowvirus bv858
Streptococcus phage 01205Streptococcus thermophilusNC_004303.143CaudoviricetesAliceevansviridaeBrussowvirusBrussowvirus bvO1205
Streptococcus phage CHPC1042Streptococcus thermophilusNC_071061.142CaudoviricetesAliceevansviridaeBrussowvirusBrussowvirus CHPC1042
Streptococcus phage CHPC1109Streptococcus thermophilusNC_071062.133CaudoviricetesAliceevansviridaeBrussowvirusBrussowvirus CHPC1109
Streptococcus phage CHPC1152Streptococcus thermophilusNC_071063.135CaudoviricetesAliceevansviridaeBrussowvirusBrussowvirus CHPC1152
Streptococcus phage CHPC1230Streptococcus thermophilusNC_071064.139CaudoviricetesAliceevansviridaeBrussowvirusBrussowvirus CHPC1230
Streptococcus phage CHPC1246Streptococcus thermophilusNC_071065.136CaudoviricetesAliceevansviridaeBrussowvirusBrussowvirus CHPC1246
Streptococcus phage CHPC1247Streptococcus thermophilusNC_071066.135CaudoviricetesAliceevansviridaeBrussowvirusBrussowvirus CHPC1247
Streptococcus phage CHPC1248Streptococcus thermophilusNC_071067.138CaudoviricetesAliceevansviridaeBrussowvirusBrussowvirus CHPC1248
Streptococcus phage CHPC640Streptococcus thermophilusNC_071068.140CaudoviricetesAliceevansviridaeBrussowvirusBrussowvirus CHPC640
Streptococcus phage CHPC869Streptococcus thermophilusNC_071069.137CaudoviricetesAliceevansviridaeBrussowvirusBrussowvirus CHPC869
Streptococcus phage CHPC931Streptococcus thermophilusNC_071070.136CaudoviricetesAliceevansviridaeBrussowvirusBrussowvirus CHPC931
Streptococcus phage CHPC951Streptococcus thermophilusNC_071071.136CaudoviricetesAliceevansviridaeBrussowvirusBrussowvirus CHPC951
Streptococcus phage CHPC952Streptococcus thermophilusNC_071072.136CaudoviricetesAliceevansviridaeBrussowvirusBrussowvirus CHPC952
Streptococcus phage P4761Streptococcus thermophilusNC_071073.138CaudoviricetesAliceevansviridaeBrussowvirusBrussowvirus P4761
Streptococcus phage P7571Streptococcus thermophilusNC_071074.134CaudoviricetesAliceevansviridaeBrussowvirusBrussowvirus P7571
Streptococcus phage P7951Streptococcus thermophilusNC_071075.134CaudoviricetesAliceevansviridaeBrussowvirusBrussowvirus P7951
Streptococcus phage P7952Streptococcus thermophilusNC_071076.137CaudoviricetesAliceevansviridaeBrussowvirusBrussowvirus P7952
Streptococcus phage P7953Streptococcus thermophilusNC_071077.135CaudoviricetesAliceevansviridaeBrussowvirusBrussowvirus P7953
Streptococcus phage P7954Streptococcus thermophilusNC_071078.135CaudoviricetesAliceevansviridaeBrussowvirusBrussowvirus P7954
Streptococcus phage P7955Streptococcus thermophilusNC_071079.136CaudoviricetesAliceevansviridaeBrussowvirusBrussowvirus P7955
Streptococcus phage P9853Streptococcus thermophilusNC_071080.134CaudoviricetesAliceevansviridaeBrussowvirusBrussowvirus P9853
Streptococcus phage Sfi11Streptococcus thermophilusNC_002214.139CaudoviricetesAliceevansviridaeBrussowvirusBrussowvirus Sfi11
Streptococcus phage SW1151Streptococcus thermophilusNC_071081.135CaudoviricetesAliceevansviridaeBrussowvirusBrussowvirus SW1151
Streptococcus phage SW13Streptococcus thermophilusNC_071082.136CaudoviricetesAliceevansviridaeBrussowvirusBrussowvirus SW13
Streptococcus phage SW14Streptococcus thermophilusNC_071083.135CaudoviricetesAliceevansviridaeBrussowvirusBrussowvirus SW14
Streptococcus phage SW15Streptococcus thermophilusNC_071084.134CaudoviricetesAliceevansviridaeBrussowvirusBrussowvirus SW15
Streptococcus phage SW18Streptococcus thermophilusNC_071085.134CaudoviricetesAliceevansviridaeBrussowvirusBrussowvirus SW18
Streptococcus phage TP-778LStreptococcus thermophilusNC_022776.141CaudoviricetesAliceevansviridaeBrussowvirusBrussowvirus TP778L
Streptococcus phage TP-J34Streptococcus thermophilusNC_020197.145CaudoviricetesAliceevansviridaeBrussowvirusBrussowvirus TPJ34
MAG: Streptococcus phage VS-2018aStreptococcus thermophilusNC_071086.139CaudoviricetesAliceevansviridaeBrussowvirusBrussowvirus VS2018a
Streptococcus phage Abc2Streptococcus thermophilusNC_013645.134CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus Abc2
Streptococcus phage B0Streptococcus thermophilusNC_070655.136CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus B0
Streptococcus phage CHPC1005Streptococcus thermophilusNC_070656.137CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus CHPC1005
Streptococcus phage CHPC1027Streptococcus thermophilusNC_070657.135CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus CHPC1027
Streptococcus phage CHPC1029Streptococcus thermophilusNC_070658.135CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus CHPC1029
Streptococcus phage CHPC1033Streptococcus thermophilusNC_070659.136CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus CHPC1033
Streptococcus phage CHPC1036Streptococcus thermophilusNC_070660.136CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus CHPC1036
Streptococcus phage CHPC1041Streptococcus thermophilusNC_070661.138CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus CHPC1041
Streptococcus phage CHPC1045Streptococcus thermophilusNC_070662.134CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus CHPC1045
Streptococcus phage CHPC1046Streptococcus thermophilusNC_070663.134CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus CHPC1046
Streptococcus phage CHPC1062Streptococcus thermophilusNC_070664.140CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus CHPC1062
Streptococcus phage CHPC1067Streptococcus thermophilusNC_070665.134CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus CHPC1067
Streptococcus phage CHPC1091Streptococcus thermophilusNC_070666.137CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus CHPC1091
Streptococcus phage CHPC1148Streptococcus thermophilusNC_070667.139CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus CHPC1148
Streptococcus phage CHPC1156Streptococcus thermophilusNC_070668.134CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus CHPC1156
Streptococcus phage CHPC572Streptococcus thermophilusNC_070669.137CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus CHPC572
Streptococcus phage CHPC595Streptococcus thermophilusNC_070670.135CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus CHPC595
Streptococcus phage CHPC642Streptococcus thermophilusNC_070671.135CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus CHPC642
Streptococcus phage CHPC663Streptococcus thermophilusNC_070672.138CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus CHPC663
Streptococcus phage CHPC873Streptococcus thermophilusNC_070673.138CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus CHPC873
Streptococcus phage CHPC875Streptococcus thermophilusNC_070674.136CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus CHPC875
Streptococcus phage CHPC877Streptococcus thermophilusNC_070675.139CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus CHPC877
Streptococcus phage CHPC879Streptococcus thermophilusNC_070676.136CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus CHPC879
Streptococcus phage CHPC919Streptococcus thermophilusNC_070677.137CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus CHPC919
Streptococcus phage CHPC925Streptococcus thermophilusNC_070678.134CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus CHPC925
Streptococcus phage CHPC927Streptococcus thermophilusNC_070679.137CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus CHPC927
Streptococcus phage CHPC928Streptococcus thermophilusNC_070680.134CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus CHPC928
Streptococcus phage CHPC930Streptococcus thermophilusNC_070681.136CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus CHPC930
Streptococcus phage CHPC950Streptococcus thermophilusNC_070682.135CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus CHPC950
Streptococcus phage CHPC979Streptococcus thermophilusNC_070683.134CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus CHPC979
Streptococcus phage D1024Streptococcus thermophilusNC_070684.137CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus D1024
Streptococcus phage D1811Streptococcus thermophilusNC_070685.134CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus D1811
Streptococcus phage D4276Streptococcus thermophilusNC_070686.139CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus D4276
Streptococcus phage DT1Streptococcus thermophilusNC_002072.234CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus DT1
Streptococcus phage L5A1Streptococcus thermophilusNC_070687.136CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus L5A1
Streptococcus phage M19Streptococcus thermophilusNC_070688.134CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus M19
Streptococcus phage MM25Streptococcus thermophilusNC_070689.134CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus MM25
Streptococcus phage 128Streptococcus thermophilusNC_070651.134CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus mv128
Streptococcus phage 53Streptococcus thermophilusNC_070652.134CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus mv53
Streptococcus phage 7201Streptococcus thermophilusNC_002185.135CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus mv7201
Streptococcus phage 73Streptococcus thermophilusNC_070653.136CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus mv73
Streptococcus phage 7A5Streptococcus thermophilusNC_070654.135CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus mv7A5
Streptococcus phage P0091Streptococcus thermophilusNC_070690.135CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus P0091
Streptococcus phage P3681Streptococcus thermophilusNC_070691.136CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus P3681
Streptococcus phage P3684Streptococcus thermophilusNC_070692.135CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus P3684
Streptococcus phage P5641Streptococcus thermophilusNC_070693.137CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus P5641
Streptococcus phage P5651Streptococcus thermophilusNC_070694.134CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus P5651
Streptococcus phage P7132Streptococcus thermophilusNC_070695.135CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus P7132
Streptococcus phage P7133Streptococcus thermophilusNC_070696.133CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus P7133
Streptococcus phage P7134Streptococcus thermophilusNC_070697.134CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus P7134
Streptococcus phage P7151Streptococcus thermophilusNC_070698.135CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus P7151
Streptococcus phage P7152Streptococcus thermophilusNC_070699.135CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus P7152
Streptococcus phage P7154Streptococcus thermophilusNC_070700.134CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus P7154
Streptococcus phage P7573Streptococcus thermophilusNC_070701.137CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus P7573
Streptococcus phage P7574Streptococcus thermophilusNC_070702.136CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus P7574
Streptococcus phage P7601Streptococcus thermophilusNC_070703.135CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus P7601
Streptococcus phage P7602Streptococcus thermophilusNC_070704.137CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus P7602
Streptococcus phage P7631Streptococcus thermophilusNC_070705.136CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus P7631
Streptococcus phage P7632Streptococcus thermophilusNC_070706.135CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus P7632
Streptococcus phage P7633Streptococcus thermophilusNC_070707.135CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus P7633
Streptococcus phage P9851Streptococcus thermophilusNC_070708.135CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus P9851
Streptococcus phage P9854Streptococcus thermophilusNC_070709.136CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus P9854
Streptococcus phage P9901Streptococcus thermophilusNC_070710.135CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus P9901
Streptococcus phage P9902Streptococcus thermophilusNC_070711.135CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus P9902
Streptococcus phage P9903Streptococcus thermophilusNC_070712.135CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus P9903
Streptococcus phage Sfi19Streptococcus thermophilusNC_000871.137CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus Sfi19
Streptococcus phage Sfi21Streptococcus thermophilusNC_000872.140CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus Sfi21
Streptococcus phage STP1Streptococcus thermophilusNC_070713.135CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus STP1
Streptococcus phage SW1Streptococcus thermophilusNC_070714.134CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus SW1
Streptococcus phage SW11Streptococcus thermophilusNC_070715.136CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus SW11
Streptococcus phage SW12Streptococcus thermophilusNC_070716.135CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus SW12
Streptococcus phage SW2Streptococcus thermophilusNC_070717.137CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus SW2
Streptococcus phage SW3Streptococcus thermophilusNC_070718.137CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus SW3
Streptococcus phage SW5Streptococcus thermophilusNC_070719.136CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus SW5
Streptococcus phage SW6Streptococcus thermophilusNC_070720.134CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus SW6
Streptococcus phage SW7Streptococcus thermophilusNC_070721.135CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus SW7
Streptococcus phage SW8Streptococcus thermophilusNC_070722.133CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus SW8
Streptococcus phage SWK3Streptococcus thermophilusNC_070723.135CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus SWK3
Streptococcus phage SWK6Streptococcus thermophilusNC_070724.134CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus SWK6
Streptococcus phage vB_SthS_VA214Streptococcus thermophilusNC_070725.138CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus VA214
Streptococcus phage vB_SthS_VA460Streptococcus thermophilusNC_070726.141CaudoviricetesAliceevansviridaeMoineauvirusMoineauvirus VA460
Streptococcus phage 5093Streptococcus thermophilusNC_012753.137CaudoviricetesAliceevansviridaeVansinderenvirusVansinderenvirus 5093
Streptococcus phage CHPC1198Streptococcus thermophilusNC_071053.133CaudoviricetesAliceevansviridaeVansinderenvirusVansinderenvirus CHPC1198
Streptococcus phage CHPC1151Streptococcus thermophilusNC_071057.133CaudoviricetesAliceevansviridaeVansinderenvirusVansinderenvirus CHPC1232
Streptococcus phage CHPC1282Streptococcus thermophilusNC_071058.134CaudoviricetesAliceevansviridaeVansinderenvirusVansinderenvirus CHPC1282
Streptococcus phage P0092Streptococcus thermophilusNC_071056.134CaudoviricetesAliceevansviridaeVansinderenvirusVansinderenvirus P0092
Streptococcus phage P0093Streptococcus thermophilusNC_071054.134CaudoviricetesAliceevansviridaeVansinderenvirusVansinderenvirus P0093
Streptococcus phage P0095Streptococcus thermophilusNC_071059.135CaudoviricetesAliceevansviridaeVansinderenvirusVansinderenvirus P0095
Streptococcus phage SW19Streptococcus thermophilusNC_071060.135CaudoviricetesAliceevansviridaeVansinderenvirusVansinderenvirus SW19
Streptococcus phage SW24Streptococcus thermophilusNC_071055.132CaudoviricetesAliceevansviridaeVansinderenvirusVansinderenvirus SW24
Streptococcus phage SW27Streptococcus thermophilusNC_071052.133CaudoviricetesAliceevansviridaeVansinderenvirusVansinderenvirus SW27
Streptococcus phage SW4Streptococcus thermophilusNC_071051.134CaudoviricetesAliceevansviridaeVansinderenvirusVansinderenvirus SW4
Streptococcus phage Cp-1Streptococcus pneumoniaeNC_001825.119CaudoviricetesMadridviridae CepunavirusCepunavirus Cp1
Streptococcus phage Cp-7Streptococcus pneumoniaeNC_042114.119CaudoviricetesMadridviridae CepunavirusCepunavirus Cp7
Streptococcus phage C1Group C StreptococciNC_004814.116CaudoviricetesRountreeviridae FischettivirusFischettivirus C1
Streptococcus phage phiARI0004Streptococcus pneumoniaeNC_031920.141Caudoviricetes FerrettivirinaeHinxtonvirusHinxtonvirus ARI0004
Streptococcus phage phiARI0031Streptococcus pneumoniaeNC_031910.141Caudoviricetes FerrettivirinaeHinxtonvirusHinxtonvirus ARI0031
Streptococcus phage phiARI0462Streptococcus pneumoniaeNC_031942.140Caudoviricetes FerrettivirinaeHinxtonvirusHinxtonvirus ARI0062
Streptococcus phage phiARI0468-1Streptococcus pneumoniaeNC_031929.141Caudoviricetes FerrettivirinaeHinxtonvirusHinxtonvirus ARI04681
Streptococcus phage DCC1738Streptococcus pneumoniaeNC_024361.138Caudoviricetes FerrettivirinaeHinxtonvirusHinxtonvirus DCC1738
Streptococcus phage IC1Streptococcus pneumoniaeNC_024370.139Caudoviricetes FerrettivirinaeHinxtonvirusHinxtonvirus IC1
Streptococcus phage K13Streptococcus pneumoniaeNC_024357.139Caudoviricetes FerrettivirinaeHinxtonvirusHinxtonvirus K13
Streptococcus phage phiARI0131-1Streptococcus pneumoniaeNC_031901.142Caudoviricetes FerrettivirinaeSpinunavirusSpinunavirus ARI01311
Streptococcus phage phiARI0460-1Streptococcus pneumoniaeNC_031913.141Caudoviricetes FerrettivirinaeSpinunavirusSpinunavirus ARI04601
Streptococcus phage phiARI0468-2Streptococcus pneumoniaeNC_031923.142Caudoviricetes FerrettivirinaeSpinunavirusSpinunavirus ARI04682
Streptococcus phage phiARI0923Streptococcus pneumoniaeNC_030946.133Caudoviricetes McshanvirinaeAdrianbuildvirusAdrianbuildvirus ARI0923
Streptococcus phage SpSL1Streptococcus pneumoniaeNC_027396.133Caudoviricetes McshanvirinaeAdrianbuildvirusAdrianbuildvirus SpSL1
Streptococcus phage phiARI0131-2Streptococcus pneumoniaeNC_031941.134Caudoviricetes McshanvirinaeMedawarvirusMedawarvirus ARI01312
Streptococcus phage PH10Streptococcus oralisNC_012756.131Caudoviricetes McshanvirinaePhadecavirusPhadecavirus PH10
Streptococcus phage phiBHN167Streptococcus pneumoniaeNC_022791.137Caudoviricetes  PaclarkvirusPaclarkvirus BHN167
Streptococcus phage IPP14Streptococcus pneumoniaeNC_070925.137Caudoviricetes  PaclarkvirusPaclarkvirus IPP14
Streptococcus phage IPP39Streptococcus pneumoniaeNC_070926.137Caudoviricetes  PaclarkvirusPaclarkvirus IPP39
Streptococcus phage IPP48Streptococcus pneumoniaeNC_070928.137Caudoviricetes  PaclarkvirusPaclarkvirus IPP48
Streptococcus phage IPP52Streptococcus pneumoniaeNC_070929.136Caudoviricetes  PaclarkvirusPaclarkvirus IPP52
Streptococcus phage IPP54Streptococcus pneumoniaeNC_070923.138Caudoviricetes  PaclarkvirusPaclarkvirus IPP54
Streptococcus phage IPP55Streptococcus pneumoniaeNC_070924.137Caudoviricetes  PaclarkvirusPaclarkvirus IPP55
Streptococcus phage IPP65Streptococcus pneumoniaeNC_070922.139Caudoviricetes  PaclarkvirusPaclarkvirus IPP65
Streptococcus phage IPP66Streptococcus pneumoniaeNC_070930.137Caudoviricetes  PaclarkvirusPaclarkvirus IPP66
Streptococcus pneumoniae bacteriophage MM1Streptococcus pneumoniaeNC_003050.240Caudoviricetes  PaclarkvirusPaclarkvirus MM1
Streptococcus phage SpGS-1Streptococcus pneumoniaeNC_070927.137Caudoviricetes  PaclarkvirusPaclarkvirus SpGS-1
Streptococcus phage CHPC577Streptococcus thermophilusNC_070901.135Caudoviricetes  PiorkowskivirusPiorkowskivirus CHPC577
Streptococcus phage CHPC926Streptococcus thermophilusNC_070900.130Caudoviricetes  PiorkowskivirusPiorkowskivirus CHPC926
Streptococcus virus 9871Streptococcus thermophilusNC_031069.132Caudoviricetes  PiorkowskivirusPiorkowskivirus pv9871
Streptococcus virus 9872Streptococcus thermophilusNC_031094.133Caudoviricetes  PiorkowskivirusPiorkowskivirus pv9872
Streptococcus virus 9874Streptococcus thermophilusNC_031023.132Caudoviricetes  PiorkowskivirusPiorkowskivirus pv9874
Streptococcus phage SW16Streptococcus thermophilusNC_070899.132Caudoviricetes  PiorkowskivirusPiorkowskivirus SW16
Streptococcus phage SW22Streptococcus thermophilusNC_070898.131Caudoviricetes  PiorkowskivirusPiorkowskivirus SW22
Streptococcus phage SP-QS1Streptococcus pneumoniaeNC_021868.158Caudoviricetes  SaphexavirusSaphexavirus SPQS1
Streptococcus phage A25Streptococcus pyogenesNC_028697.133Caudoviricetes  StonewallvirusStonewallvirus A25
Streptococcus phage APCM01Streptococcus mutansNC_029030.131Caudoviricetes    
Streptococcus phage Dp-1Streptococcus pneumoniaeNC_015274.156Caudoviricetes    
Streptococcus phage M102Streptococcus mutansNC_012884.131Caudoviricetes    
Streptococcus phage M102ADStreptococcus mutansNC_028984.130Caudoviricetes    
Streptococcus phage P9Streptococcus equiNC_009819.140Caudoviricetes    
Streptococcus phage PH15Streptococcus gordoniiNC_010945.139Caudoviricetes    
Streptococcus phage phi3396Streptococcus dysgalactiaeNC_009018.138Caudoviricetes    
Streptococcus phage phiNIH1.1Streptococcus pyogenesNC_003157.543Caudoviricetes    
Streptococcus phage phiNJ2Streptococcus suisNC_019418.137Caudoviricetes    
Streptococcus phage SM1Streptococcus mitisNC_004996.134Caudoviricetes    
Streptococcus phage SMPStreptococcus suisNC_008721.236Caudoviricetes    
Streptococcus phage Str-PAP-1Streptococcus parauberisNC_028666.136Caudoviricetes    
Streptococcus phage T12Streptococcus pyogenesNC_028700.137Caudoviricetes    
Streptococcus phage YMC-2011Streptococcus salivariusNC_018285.140Caudoviricetes    
Streptococcus pyogenes phage 315.3Streptococcus pyogenesNC_004586.134Caudoviricetes    
Streptococcus virus 9873Streptococcus thermophilusNC_047763.132Caudoviricetes    
Streptococcus prophage 315.1Streptococcus pyogenesNC_004584.139Caudoviricetes    
Streptococcus prophage 315.2Streptococcus pyogenesNC_004585.141Caudoviricetes    
Streptococcus prophage 315.4Streptococcus pyogenesNC_004587.141Caudoviricetes    
Streptococcus prophage 315.5Streptococcus pyogenesNC_004588.138Caudoviricetes    
Streptococcus prophage 315.6Streptococcus pyogenesNC_004589.140Caudoviricetes    
Streptococcus prophage EJ-1Streptococcus pneumoniaeNC_005294.142Caudoviricetes    
Taxonomic information according to ICTV is provided when available.

Appendix A.2

Table A2. List of the 34 selected phages.
Table A2. List of the 34 selected phages.
PhageShort Name for
Figure Readability		Bacterial TargetNCBI RefSeq
Accession		kbpClassFamilySubfamilyGenusSpecies
Streptococcus phage ALQ13.2ALQ13.2Streptococcus thermophilusNC_013598.135CaudoviricetesAliceevansviridae BrussowvirusBrussowvirus ALQ132Pac group
Streptococcus phage P7573P7573Streptococcus thermophilusNC_070701.137CaudoviricetesAliceevansviridae MoineauvirusMoineauvirus P7573Cos group
Streptococcus phage 50935093Streptococcus thermophilusNC_012753.137CaudoviricetesAliceevansviridae VansinderenvirusVansinderenvirus 50935093 group
Streptococcus phage Cp-1Cp-1Streptococcus pneumoniaeNC_001825.119CaudoviricetesMadridviridae CepunavirusCepunavirus Cp1 
Streptococcus phage C1C1Group C StreptococciNC_004814.116CaudoviricetesRountreeviridae FischettivirusFischettivirus C1 
Streptococcus phage K13K13Streptococcus pneumoniaeNC_024357.139CaudoviricetesFerrettivirinaeHinxtonvirusHinxtonvirus K13 
Streptococcus phage phiARI0468-2phiARI0468-2Streptococcus pneumoniaeNC_031923.142CaudoviricetesFerrettivirinaeSpinunavirusSpinunavirus ARI04682 
Streptococcus phage SpSL1SpSL1Streptococcus pneumoniaeNC_027396.133CaudoviricetesMcshanvirinaeAdrianbuildvirusAdrianbuildvirus SpSL1 
Streptococcus phage phiARI0131-2phiARI0131-2Streptococcus pneumoniaeNC_031941.134CaudoviricetesMcshanvirinaeMedawarvirusMedawarvirus ARI01312 
Streptococcus phage PH10PH10Streptococcus oralisNC_012756.131CaudoviricetesMcshanvirinaePhadecavirusPhadecavirus PH10 
Streptococcus pneumoniae bacteriophage MM1MM1Streptococcus pneumoniaeNC_003050.240Caudoviricetes PaclarkvirusPaclarkvirus MM1 
Streptococcus virus 98719871Streptococcus thermophilusNC_031069.132Caudoviricetes PiorkowskivirusPiorkowskivirus pv98719871 group
Streptococcus phage SP-QS1SP-QS1Streptococcus pneumoniaeNC_021868.158Caudoviricetes SaphexavirusSaphexavirus SPQS1 
Streptococcus phage A25A25Streptococcus pyogenesNC_028697.133Caudoviricetes StonewallvirusStonewallvirus A25 
Streptococcus phage APCM01APCM01Streptococcus mutansNC_029030.131CaudoviricetesAliceevansviridaeNo ICTV assignationNo ICTV assignationNo ICTV assignation 
Streptococcus phage M102M102Streptococcus mutansNC_012884.131CaudoviricetesAliceevansviridaeNo ICTV assignationNo ICTV assignationNo ICTV assignation 
Streptococcus phage M102ADM102ADStreptococcus mutansNC_028984.130CaudoviricetesAliceevansviridaeNo ICTV assignationNo ICTV assignationNo ICTV assignation 
Streptococcus phage PH15PH15Streptococcus gordoniiNC_010945.139CaudoviricetesAliceevansviridaeNo ICTV assignationNo ICTV assignationNo ICTV assignation 
Streptococcus phage YMC-2011YMC-2011Streptococcus salivariusNC_018285.140CaudoviricetesAliceevansviridaeNo ICTV assignationNo ICTV assignationNo ICTV assignation 
Streptococcus phage Dp-1Dp-1Streptococcus pneumoniaeNC_015274.156CaudoviricetesNo ICTV assignationNo ICTV assignationNo ICTV assignationNo ICTV assignation 
Streptococcus prophage EJ-1EJ-1Streptococcus pneumoniaeNC_005294.142CaudoviricetesNo ICTV assignationNo ICTV assignationNo ICTV assignationNo ICTV assignation 
Streptococcus phage P9P9Streptococcus equiNC_009819.140CaudoviricetesNo ICTV assignationNo ICTV assignationNo ICTV assignationNo ICTV assignation 
Streptococcus phage phi3396phi3396Streptococcus dysgalactiaeNC_009018.138CaudoviricetesNo ICTV assignationNo ICTV assignationNo ICTV assignationNo ICTV assignation 
Streptococcus phage phiNJ2phiNJ2Streptococcus suisNC_019418.137CaudoviricetesNo ICTV assignationNo ICTV assignationNo ICTV assignationNo ICTV assignation 
Streptococcus phage SM1SM1Streptococcus mitisNC_004996.134CaudoviricetesNo ICTV assignationNo ICTV assignationNo ICTV assignationNo ICTV assignation 
Streptococcus phage SMPSMPStreptococcus suisNC_008721.236CaudoviricetesNo ICTV assignationNo ICTV assignationNo ICTV assignationNo ICTV assignation 
Streptococcus phage Str-PAP-1Str-PAP-1Streptococcus parauberisNC_028666.136CaudoviricetesNo ICTV assignationNo ICTV assignationNo ICTV assignationNo ICTV assignation 
Streptococcus phage T12T12Streptococcus pyogenesNC_028700.137CaudoviricetesNo ICTV assignationNo ICTV assignationNo ICTV assignationNo ICTV assignation 
Streptococcus pyogenes phage 315.3315.3Streptococcus pyogenesNC_004586.134CaudoviricetesNo ICTV assignationNo ICTV assignationNo ICTV assignationNo ICTV assignation 
Streptococcus prophage 315.1315.1Streptococcus pyogenesNC_004584.139CaudoviricetesNo ICTV assignationNo ICTV assignationNo ICTV assignationNo ICTV assignation 
Streptococcus prophage 315.2315.2Streptococcus pyogenesNC_004585.141CaudoviricetesNo ICTV assignationNo ICTV assignationNo ICTV assignationNo ICTV assignation 
Streptococcus prophage 315.4315.4Streptococcus pyogenesNC_004587.141CaudoviricetesNo ICTV assignationNo ICTV assignationNo ICTV assignationNo ICTV assignation 
Streptococcus prophage 315.5315.5Streptococcus pyogenesNC_004588.138CaudoviricetesNo ICTV assignationNo ICTV assignationNo ICTV assignationNo ICTV assignation 
Streptococcus prophage 315.6315.6Streptococcus pyogenesNC_004589.140CaudoviricetesNo ICTV assignationNo ICTV assignationNo ICTV assignationNo ICTV assignation 
The abbreviated names used in graphical representations are indicated.

Appendix A.3

Genes 16 00842 g0a1
Figure A1. Nucleotide alignment of the 34 selected phages. Alignment was performed using the Lovis4u softwarev0.0.12. ORF functions are shown using a color-coded scheme.

Appendix A.4

Table A3. Summary of the architectures identified among the 256 endolysins.
Table A3. Summary of the architectures identified among the 256 endolysins.
ArchitectureCountEADCBDPhages List
A1120Amidase_5 & NLPC_P60 ZoocinA_TRDCHPC1151_E1, CHPC572_E1, CHPC1027_E1, SW27_E1, P7134_E1, P0093_E1, P0092_E1, CHPC1282_E1, SW14_E1, CHPC1033_E1, SW12_E1, SW24_E, STP1_E1, SW6_E1, P7955_E1, P7573_E1, P7571_E1, P0091_E, L5A1_E, SW4_E1, P9854_E1, CHPC927_E1, CHPC926_E1, CHPC925_E1, SW1151_E1, CHPC950_E1, CHPC1248_E1, CHPC1247_E1, CHPC1246_E1, CHPC1230_E1, CHPC1046_E1, SW11_E1, CHPC877_E, 128_E, P7133_E, MM25_E, 5093_E, CHPC979_E, CHPC928_E, P7602_E, P7633_E, P7601_E, P7632_E, P7631_E, SW7_E, P3684_E, CHPC875_E, CHPC1091_E, CHPC930_E, CHPC1067_E, 7A5_E, SW3_E, B0_E, P3681_E, SW15_E, P7574_E, SW19_E1, CHPC952_E, CHPC931_E1, CHPC869_E1, SW8_E1, P5651_E1, CHPC1029_E1, CHPC1042_E1, P9851_E1, P9853_E1, CHPC640_E1, P7152_E1, SW18_E1, 9874_E1, CHPC1041_E1, D4276_E1, P0095_E1, CHPC1005_E1, CHPC879_E, vB_SthS_VA460_E2, MAG-VS-2018a_E, CHPC663_E1, 20617_E, 858_E1, 2972_E1, P7151_E1, CHPC1156_E1, vB_SthS_VA214_E2, CHPC642_E, P7132_E, SWK3_E, CHPC1036_E, CHPC1045_E, SWK6_E, P7154_E, CHPC1148_E, 7201_E, CHPC1198_E1, CHPC577_E1, 9871_E1, SW22_E1, SW16_E, 9873_E1, M19_E, 53_E, CHPC1152_E, SW5_E, P9901_E, SW2_E, CHPC951_E, Abc2_E, 73_E, D1811_E1, D1024_E1, ALQ13.2_E1, 9872_E1, DT1_E1, TP-778L_E, TP-J34_E, Sfi19_E, CHPC919_E, Sfi21_E, Sfi11_E, 1205_E
A265 ZoocinA_TRDvB_SthS_VA460_E1, 858_E2, CHPC1246_E2, CHPC1230_E2, 9874_E2, CHPC663_E2, P7571_E2, CHPC1033_E2, CHPC1027_E2, CHPC931_E2, CHPC869_E2, SW4_E2, CHPC1282_E2, CHPC1198_E2, SW27_E2, SW11_E2, P9854_E2, P9851_E2, P7134_E2, P0093_E2, P0092_E2, CHPC1248_E2, CHPC1247_E2, CHPC1151_E2, 2972_E2, P9853_E2, CHPC926_E2, 9871_E2, SW22_E2, SW1151_E2, CHPC1042_E2, CHPC1029_E2, vB_SthS_VA214_E1, P4761_E2, 9873_E2, 9872_E2, SW19_E2, D1811_E2, D1024_E2, CHPC595_E2, DT1_E2, CHPC1156_E2, CHPC927_E2, P0095_E2, CHPC925_E2, CHPC640_E2, CHPC1041_E2, SW14_E2, D4276_E2, SW8_E2, CHPC950_E2, CHPC1046_E2, SW12_E2, ALQ13.2_E2, P7151_E2, CHPC577_E2, STP1_E2, CHPC572_E2, P7955_E2, P7573_E2, SW6_E2, SW18_E2, P7152_E2, P5651_E2, CHPC1005_E2
A319Amidase_2Choline_bind_1 & Choline_bind_2 & Choline_bind_3SpSL1_E, EJ-1_E, phiARI0462_E, phiARI0460-1_E, phiARI0131-1_E, phiARI0131-2_E, phiARI0923_E, phiARI0004_E, phiARI0468-2_E, phiARI0468-1_E, phiARI0031_E, IPP48_E, phiBHN167_E, IPP14_E, IPP52_E, IC1_E, IPP39_E, IPP54_E, SpGS-1_E
A46Glyco_hydro_25 APCM01_E1, M102_E1, M102AD_E1, P7951_E, P5641_E, CHPC1062_E
A56CHAP & Glyco_hydro_25 P7954_E, SW13_E, P7953_E, P7952_E, SW1_E, CHPC873_E
A66Glucosaminidase & CHAPSH3_5P9_E, 315.6_E2, 315.2_E, 315.1_E, phiNIH1.1_E, 315.4_E
A74CHAP SP-QS1_E, APCM01_E2, M102_E2, M102AD_E2
A84Amidase_5 & NLPC_P60 & Glyco_hydro_75ZoocinA_TRDP4761_E1, CHPC595_E1, P9903_E, P9902_E
A93CHAPSH3_5T12_E, 315.5_E, phiNJ2_E
A103Amidase_5 & NLPC_P60 & Glucosaminidase CW7315.3_E, SMP_E, A25_E
A113Amidase_2 K13_E, DCC1738_E, IPP66_E
A122CHAPSH3_3 & SH3_5YMC-2011_E, phi3396_E
A132Amidase_2Choline_bind_1 & Choline_bind_3MM1_E, IPP65_E
A141Glyco_hydro_25LysM & LysM_RLK & LysM3_LYK4_5 & LysM3_NFPCHPC1109_E
A151Glucosaminidase 315.6_E1
A161Glyco_hydro_25CW7Cp-7_E
A171Glyco_hydro_25Choline_bind_1 & Choline_bind_2 & Choline_bind_3Cp-1_E
A181Glyco_hydro_25Choline_bind_1 & Choline_bind_2 & Choline_bind_3 & Choline_bind_4PH10_E
A191 Choline_bind_1 & Choline_bind_2 & Choline_bind_3IPP55_E
A201PlyCA_N & CHAP C1 E1
A211 C1_PlyCBC1 E2
A221Amidase_5ZoocinA_TRDPH15_E
A231Amidase_5Choline_bind_1 & Choline_bind_3SM1_E
A241Amidase_5 & NLPC_P60Choline_bind_1 & Choline_bind_2 & Choline_bind_3 Dp-1_E
A251CHAP & Amidase_2 Str-PAP-1_E
Each identified endolysin is associated with its domain architecture. Endolysins from phages included in the 34-phage subset are highlighted in bold.

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