Chimeric receptor-binding proteins for use in bacterial delivery vehicles

Abstract

The present disclosure generally relates to bacterial delivery vehicles for use in the efficient transfer of a desired payload into target bacterial cells. More specifically, the present disclosure relates to bacterial delivery vehicles with a desired host range based on the presence of a chimeric receptor-binding protein (RBP) composed of a fusion between the N-terminal region of the RBP derived from a lambdoid bacteriophage and the C-terminal region of a different RBP.

Description

[Technical Field]

[0001] The present disclosure relates generally to bacterial delivery vehicles for use in the efficient transfer of a desired payload into a target bacterial cell. [Background technology]

[0002] Bacteriophages are parasites that infect and replicate in bacteria. In general, the infection process can be divided into several stages: (i) adsorption, which corresponds to the recognition and binding of the bacterial cell; (ii) injection of the DNA genome into the bacterial cell cytoplasm; (iii) production of a set of viral proteins that can lead to insertion into the host target genome (lysogenic phages) or production of infectious particles (lytic phages); and (iv) release of mature virions from the infected cell, usually by controlled lysis [1].

[0003] Recognition and binding of target cells, the first step required for successful infection, is an essential process in the bacteriophage life cycle. In some cases, bacteriophages have a "broad host range," being able to recognize several strains of the same species, but more commonly they are able to recognize specific antigens that are present only in a few strains of the same species. [2] It is therefore not surprising that this step in the infection process is central to the competition between bacteriophages and bacteria for successful infection.

[0004] As a general mechanism, bacteriophages encode two main sets of proteins involved in the recognition process. The first set is capable of binding to the bacteriophage's primary receptor on the cell surface, an event that triggers DNA release into the cytoplasm. This is usually considered an "irreversible" binding process. [3] Different bacteriophage genera vary in the composition of this set of proteins and may therefore be named differently. For example, in some Siphoviruses, they have what is called the "central tail fiber" or "tail end," which binds irreversibly to the LamB receptor of Escherichia coli. In the Siphoviridae lambda, the "central tail fiber" or "tail end" is composed of the protein gpJ. [4] In some other Siphoviruses, such as T5, proteins located at the very end of the tail mediate this process. In the case of T5, a protein called pb5 recognizes the FhuA receptor. [5] This type of protein can be found in many other bacteriophages. In myoviruses, like T4, irreversible binding to the first receptor or cell surface is generally mediated by a "short tail fiber" also located at the end of the tail tube [5].

[0005] A second set of proteins on bacteriophages (herein referred to as "receptor-binding proteins") encodes the recognition and binding activity of the so-called "secondary receptor" of bacteria. This second receptor scans the surface and the location of the first set of proteins that contact the first receptor, allowing temporary binding of the phage particle to the cell surface. This binding is reversible, allowing the phage to "walk" along the cell surface until it finds the first receptor and initiates the infection process. These protein complexes are sometimes called "L-shaped fibers" (e.g., T5), "lateral tail fibers" (e.g., lambda), "long tail fibers" (e.g., T4), or tail spikes (e.g., phage P22) [5]-[8]. For some phages, such as T4, the presence of this second set of proteins is necessary for the infection process to occur [5]. For some other phages, such as lambda, this second set of proteins is not strictly necessary for the infection process to occur but may enable more effective binding to target cells [7].

[0006] Because adsorption is strictly necessary for successful infection, bacteria can develop diverse ways to avoid being recognized by bacteriophages. For example, they can mutate the primary or secondary receptor to which bacteriophages bind; they can mask this receptor by attaching a protein (receptor masking); or they can grow a physical barrier around them in the form of a bacterial capsule, thus blocking any access to the cell surface [9]. Bacteria can produce many different types of extracellular polymeric capsules

[10] . Bacteriophages, in turn, have evolved different strategies to bypass these defense mechanisms. For example, mutations in tail proteins allow them to use different receptors

[11] . However, the presence of a polymeric capsule around the bacterium requires a different approach, as it blocks all access to any receptors on the cell surface. In these cases, bacteriophages have evolved specific proteins that can enzymatically degrade this capsule and gain access to the cell. These depolymerase activities, in the form of lateral tail fibers, long tail fibers, or tail spikes, are encoded by protein complexes distinct from the primary receptor recognition machinery

[12]

[13]

[14] .

[0007] The concept of bacteriophage host range needs to be redefined when only the adsorption and injection methods are taken into account. Because any incompatibility or defense mechanisms involved in the phage replication cycle are ignored, the "adsorption host range" of a given phage is typically greater than the "classical host range" within which the infection cycle results in newly produced mature virions. The concept of host range differs even more from the classical definition when using packaging phagemids based on a given bacteriophage capsid. Because packaging phagemids do not package the same viral genome, they do not contain the information necessary to replicate viral particles. Therefore, the host range of a packaged phagemid tends to be greater than that of the parent bacteriophage from which it is derived. Therefore, for the development of novel bacterial delivery vehicles designed for the effective delivery of exogenous DNA payloads to target strains, it is paramount to be able to create a delivery vehicle with the desired host range and the ability to bypass bacterial mechanisms that may result in the failure of the packaged phagemid to bind to the bacterial cell surface. [Prior art documents] [Patent documents]

[0008] [Patent Document 1] International Publication No. 2014124226 [Non-patent literature]

[0009] [Non-Patent Document 1] Smith et al., 1981, J. Mol. Biol 147:195-197 [Non-patent document 2] Rice, Longden, Bleasby 2000 EMBOSS Trends in Genetics 16: pp. 276-277 [Non-patent document 3] Chemical Reviews 2016, 116 (20) pp. 12655~12687 [Non-patent document 4] Kues, U and Stahl, U 1989, Microbiol Rev 53:491~516 pages [Non-licensed Document 5] Del Solar, 1998, Microhio and Molec Biol. Rev 62:434~464 pages [Non-licensed Document 6] Cotter, Nature Reviews Microbiology 11: 95, 2013 [Non-licensed Document 7] Jinekら、Science 2012 [Non-licensed Document 8] Fonfara, Nucleic Acids Res 42 (4), 2014 [Non-licensed Document 9] Kooninら, Nat Rev Microbiol 15(3), 2017 [Non-licensed Document 10] Henkel (Toxins from Bacteria in EXS. 2010; 100: 1-29) [Non-licensed Document 11] Krupovic, Arch Virol, 2015 [Non-licensed Document 12] Desplats and Krisch, 2003, Res. Microbiol. 154:259~267 pages [Non-licensed Document 13] Bartual, 2010, Proc. Natl. Acad. Sci. 107: 20287~20292 [Non-licensed Document 14] Trojet, 2011, Genome Biol. Evol. 3: 674~686 pages. [Non-licensed Document 15] Matsui, 1997, J. Bacteriol. 179: 1846-1851 [Non-licensed Document 16] Miller, 2003, Microbio. Mol. Biol. Rev. 67:86~156 pages [Non-Patent Document 17] Chen et al., 2017, Appl. Environ. Microbiol. Vl. 83 No. 23 Summary of the Invention [Means for solving the problem]

[0010] As a general mechanism, bacteriophages encode a set of proteins involved in bacterial cell recognition processes. Herein, we describe a novel approach to creating synthetic bacterial delivery vehicles with a desired target host range. In some embodiments, we provide synthetic bacterial delivery vehicles characterized by chimeric receptor-binding proteins (RBPs), where the chimeric RBPs comprise a fusion between the N-terminal domain of an RBP from a lambdoid bacteriophage or lambda bacteriophage and the C-terminal domain of an RBP from a different bacteriophage. The RBPs of such bacteriophages from which the chimeric RBPs are derived may include, for example, "L-shaped fibers," "lateral tail fibers (stf)," "long tail fibers," or "tail spikes," depending on the phage family. As disclosed herein, we have demonstrated that key portions of lambdoid bacteriophage receptor-binding proteins (RBPs), such as the stf protein, can be exchanged with portions of different RBPs. Furthermore, we have identified specific fusion positions in RBPs that allow functional chimeric RBPs to be obtained.

[0011] A chimeric receptor-binding protein (RBP) is one in which the chimeric RBP comprises a fusion between the N-terminal domain of an RBP derived from a lambdoid bacteriophage or a lambda bacteriophage and the C-terminal domain of a different RBP, wherein the N-terminal domain of the RBP is fused to the C-terminal domain of the different RBP within one of the amino acid regions selected from positions 1-150, 320-460, or 495-560 of the N-terminal RBP with respect to the lambda stf sequence (SEQ ID NO: 1), or a similar region of the RBP having homology to one or more of three amino acid regions ranging from positions 1-150, 320-460, and 495-560 of the RBP with respect to the lambda stf sequence. In one particular aspect of the invention, the different RBP domains of the chimeric receptor-binding protein (RBP) are derived from any bacteriophage or any bacteriocin.

[0012] In a particular embodiment, the RBP from a lambdoid bacteriophage or lambda bacteriophage, or a different RBP, contains homology in one or more of three amino acid regions ranging from positions 1 to 150, 320 to 460, and 495 to 560 of the RBP relative to the lambda bacteriophage stf sequence (SEQ ID NO: 1). In particular embodiments, the homology between the lambdoid bacteriophage, lambda bacteriophage, or a different RBP and one or more of the three amino acid regions is approximately 35% identity or greater over 45 amino acids, approximately 50% identity or greater over 30 amino acids, and approximately 90% identity or greater over 18 amino acids relative to the lambda bacteriophage stf sequence (SEQ ID NO: 1). Homology can be determined using alignment tools such as the Smith-Waterman algorithm (Smith et al., 1981, J. Mol. Biol 147:195-197) or EMBOSS Matcher (Rice, Longden, Bleasby 2000 EMBOSS Trends in Genetics 16:276-277).

[0013] In one aspect of the invention, a chimeric RBP comprises an N-terminal domain of an RBP fused to the C-terminal domain of a different RBP within one of the amino acid regions selected from positions 80-150, 320-460, or 495-560 of the N-terminal RBP with respect to the lambda bacteriophage stf sequence (SEQ ID NO: 1). In another embodiment of the invention, a chimeric RBP comprises an N-terminal domain and a C-terminal domain fused within one of the amino acid regions selected from positions 1-150, 320-460, or 495-560 at an insertion site having at least 80% identity to an insertion site selected from the group consisting of amino acids SAGDAS (SEQ ID NO: 178), ADAKKS (SEQ ID NO: 179), MDETNR (SEQ ID NO: 180), SASAAA (SEQ ID NO: 181), and GAGENS (SEQ ID NO: 182).

[0014] In another aspect, the chimeric RBP comprises the N-terminal domain of an RBP fused to the C-terminal domain of a different RBP, where the different RBP is a protein or group of different proteins that confers an altered host range. In one embodiment, the different RBP is a T4-like or T4 long tail fiber, which is composed of a proximal tail fiber and a distal tail fiber (DTF), and the C-terminal domain of the T4-like or T4 RBP is the distal tail fiber (DTF). In another embodiment, the N-terminal domain of an RBP is fused to a T4-like or T4 distal tail fiber at an insertion site within a T4-like or T4 DTF that has at least 80% identity to an insertion site selected from the group consisting of amino acids ATLKQI (SEQ ID NO: 183), IIQLED (SEQ ID NO: 184), GNIIDL (SEQ ID NO: 185), IATRV (SEQ ID NO: 186), TPGEL (SEQ ID NO: 187), GAIIN (SEQ ID NO: 188), NQIID (SEQ ID NO: 189), GQIVN (SEQ ID NO: 190), and VDRAV (SEQ ID NO: 191). In a specific embodiment, the N-terminal domain of an RBP is fused to a T4-like or T4 distal tail fiber within the region of amino acids 1-90, with a preferred region of amino acids 40-50 of the DTF.

[0015] In certain embodiments, the present disclosure provides certain chimeric RBPs. SEQ ID NOs: 2-61, 123-153, 192, 194-221, 256, and 258 disclose the amino acid sequences of such chimeric RBPs and, in some cases, their corresponding native chaperone proteins (denoted "AP"). Such AP proteins assist in the folding of the chimeric RBPs. In certain embodiments, the RBP comprises the amino acid sequence of SEQ ID NO: 2, 4, 7, 9, 12, 15, 17, 20, 23, 24, 25, 27, 29, 31, 33, 35, 37, 39, 41, 42, 44, 46, 47, 48, 49, 50, 51, 52, 53, 56, 59, 130, 131, 132, 135, 138, 139, 142, 145, 148, 151, 192, 194, 195, 198, 200, 202, 204, 206, 208, 211, 214, 216, 218, or 220.

[0016] In another aspect, the present disclosure provides nucleotide sequences encoding the chimeric RBPs disclosed herein. In certain embodiments, nucleic acids encoding such chimeric RBPs, as well as their corresponding AP proteins, are set forth in SEQ ID NOs: 62-120, 122, 154-177, 222-249, 255, and 257. In certain embodiments, a nucleic acid encoding such a chimeric RBP comprises the nucleotide sequence of SEQ ID NO: 62, 64, 67, 69, 72, 75, 77, 80, 83, 84, 85, 87, 89, 91, 93, 95, 97, 99, 101, 102, 104, 106, 107, 108, 109, 110, 111, 112, 113, 116, 119, 154, 155, 156, 159, 162, 163, 166, 169, 172, 175, 222, 223, 226, 228, 230, 232, 234, 236, 239, 242, 244, 246 or 248.

[0017] In one specific, non-limiting aspect of the present invention, it has been demonstrated that engineering a chimeric RBP to encode a depolymerase activity can dramatically increase the delivery efficiency of a provided bacterial delivery vehicle comprising the chimeric RBP disclosed herein. In one embodiment of the present invention, different RBP domains of the chimeric RBP comprise depolymerase activity for encapsulating bacterial strains. In a specific embodiment, the depolymerase is an endosialidase, such as K1F or K5 endosialidase.

[0018] In one embodiment of the present invention, there is provided a nucleic acid molecule encoding the chimeric RBP disclosed herein. Such nucleic acids may be contained in vectors, such as bacteriophages, plasmids, phagemids, viruses, and other vehicles, that allow for the transfer and expression of the chimeric RBP encoding nucleic acid.

[0019] Bacterial delivery vehicles are provided that enable the transfer of nucleic acid payloads encoding proteins or nucleic acids of interest into desired target bacterial host cells. Such bacterial delivery vehicles are characterized by having a chimeric RBP comprising a fusion between the N-terminal domain of an RBP from a lambdoid bacteriophage or lambda bacteriophage and the C-terminal domain of a different RBP. In an embodiment of the present invention, the bacterial delivery vehicle contains a chimeric RBP comprising a fusion between the N-terminal domain of an RBP from a lambdoid bacteriophage or lambda bacteriophage and the C-terminal domain of a different RBP, wherein the N-terminal domain of the chimeric RBP is fused to the C-terminal domain of the different RBP within one of amino acid regions selected from positions 1-150, 320-460, or 495-560 of the N-terminal domain with respect to the lambda stf sequence (SEQ ID NO: 1). In one aspect, the lambdoid bacteriophage, the RBP from the lambda bacteriophage, and the different RBP contain homology in one or more of three amino acid regions ranging from positions 1-150, 320-460, and 495-560 of the RBP relative to the lambda bacteriophage stf sequence (SEQ ID NO: 1). In particular aspects, the homology is approximately 35% identity or greater for 45 amino acids, approximately 50% identity or greater for 30 amino acids, or approximately 90% identity or greater for 18 amino acids within one or more of the three amino acid regions ranging from positions 1-150, 320-460, and 495-560 of the RBP relative to the lambda bacteriophage stf sequence. In a particular aspect of the invention, the different RBP domains of the chimeric receptor-binding protein (RBP) are derived from a bacteriophage or bacteriocin. In one aspect of the invention, the chimeric RBP comprises the N-terminal domain of an RBP fused to the C-terminal domain of the RBP within one of the amino acid regions selected from positions 80-150, 320-460, or 495-560 of the N-terminal RBP domain with respect to the lambda stf sequence.In another embodiment of the invention, the chimeric RBP comprises the N-terminal domain of the RBP and the C-terminal domain of the RBP fused within a site in the N-terminal RBP domain that has at least 80% identity to a site selected from the group consisting of amino acids SAGDAS (SEQ ID NO: 178), ADAKKS (SEQ ID NO: 179), MDETNR (SEQ ID NO: 180), SASAAA (SEQ ID NO: 181), and GAGENS (SEQ ID NO: 182).

[0020] In certain embodiments, the present disclosure provides bacterial delivery vehicles comprising chimeric RBPs. SEQ ID NOs: 2-61, 123-153, 192, 194-221, 257, 256, and 258 disclose the amino acid sequences of such chimeric RBPs and, in some cases, their corresponding native chaperone proteins (denoted "AP"). Such AP proteins assist in the folding of the chimeric RBPs. In certain embodiments, the RBP comprises the amino acid sequence of SEQ ID NO: 2, 4, 7, 9, 12, 15, 17, 20, 23, 24, 25, 27, 29, 31, 33, 35, 37, 39, 41, 42, 44, 46, 47, 48, 49, 50, 51, 52, 53, 56, 59, 130, 131, 132, 135, 138, 139, 142, 145, 148, 151, 178, 179, 182, 184, 186, 188, 190, 192, 194, 195, 198, 200, 202, 204, 206, 208, 211, 214, 216, 218, or 220.

[0021] In one aspect, the present disclosure also provides nucleotide sequences encoding the chimeric RBPs disclosed herein. In certain embodiments, nucleic acids encoding such chimeric RBPs, as well as the corresponding AP proteins, are set forth in SEQ ID NOs: 62-120, 122, 154-177, 222-249, 255, and 257. In certain embodiments, a nucleic acid encoding such a chimeric RBP comprises the nucleotide sequence of SEQ ID NO: 62, 64, 67, 69, 72, 75, 77, 80, 83, 84, 85, 87, 89, 91, 93, 95, 97, 99, 101, 102, 104, 106, 107, 108, 109, 110, 111, 112, 113, 116, 119, 154, 155, 156, 159, 162, 163, 166, 169, 172, 175, 222, 224, 227, 229, 231, 233, 235, 237, 240, 243, 245, 247 or 249.

[0022] In other specific embodiments, to increase the delivery efficiency of the bacterial delivery vehicles disclosed herein, the distinct RBP domains of the chimeric RBP comprise a domain with depolymerase activity against the encapsulated bacterial strain. In specific embodiments, the depolymerase is an endosialidase, such as K1F or K5 endosialidase.

[0023] The bacterial delivery vehicles provided herein enable the transfer of nucleic acid payloads encoding one or more proteins or nucleic acids of interest into desired target bacterial host cells. In certain embodiments of the present invention, the nucleic acid of interest is selected from the group consisting of a Cas nuclease gene, a Cas9 nuclease gene, a guide RNA, a CRISPR locus, a toxin gene, a gene expressing an enzyme such as a nuclease or kinase, a TALEN, a ZFN, a meganuclease, a recombinase, a bacterial receptor, a membrane protein, a structural protein, a secreted protein, a gene expressing resistance to antibiotics or drugs in general, a gene expressing a toxin protein or a toxic factor, and a gene expressing a virulence protein or a virulence factor, or any combination thereof. In embodiments of the present invention, the nucleic acid payload encodes a therapeutic protein. In other embodiments, the nucleic acid payload encodes an antisense nucleic acid molecule. In some embodiments, the nucleic acid payload encodes two nucleic acids of interest, one a nuclease gene, e.g., a Cas nuclease gene, and one any other nucleic acid of interest. In one aspect, the bacterial delivery vehicle allows for the transfer of a nucleic acid payload encoding a nuclease that targets cleavage of the host bacterial cell genome or a host bacterial cell plasmid. In some aspects, the cleavage occurs in an antibiotic resistance gene. In another embodiment of the invention, the nuclease that mediates cleavage of the host bacterial cell genome is designed to stimulate a homologous recombination event for insertion of the nucleic acid of interest into the bacterial cell's genome.

[0024] The present invention also provides pharmaceutical or veterinary compositions comprising one or more bacterial delivery vehicles disclosed herein and a pharmaceutically acceptable carrier. Methods for treating a bacterial infection are also provided, comprising administering a provided pharmaceutical or veterinary composition to a subject having a bacterial infection in need of treatment. The present invention also relates to pharmaceutical or veterinary compositions disclosed herein for use in treating a bacterial infection, and the use of a pharmaceutical or veterinary composition disclosed herein for the manufacture of a medicament in treating a bacterial infection. Methods for reducing the amount of pathogenic and / or antibiotic-resistant bacteria in a bacterial population are also provided, comprising contacting the bacterial population with a bacterial delivery vehicle disclosed herein. The present invention also relates to pharmaceutical or veterinary compositions disclosed herein for use in reducing the amount of pathogenic and / or antibiotic-resistant bacteria in a bacterial population, and the use of a pharmaceutical or veterinary composition disclosed herein for the manufacture of a medicament for reducing the amount of pathogenic and / or antibiotic-resistant bacteria in a bacterial population.

[0025] For a better understanding of the subject matter disclosed herein, and to illustrate how it may be carried out in practice, embodiments will now be described, by way of non-limiting example, with reference to the accompanying drawings, in which: With particular reference to the drawings, it is emphasized that the features shown are by way of example and for purposes of illustration of embodiments of the invention. [Brief explanation of the drawings]

[0026] [Figure 1]Figure 1 demonstrates delivery in wild-type E. coli strains by lambda and OMPF-lambda packaged phagemids. Lambda packaged phagemids were diluted 1:5 in LB plus 5 mM CaCl, and 10 μL was added to each well. 90 μL of cells grown to an OD of approximately 0.5 were then added to each phagemid-containing well, incubated at 37°C for 30 minutes, and 10 μL was spotted onto LB agar supplemented with chloramphenicol. Left panel, wild-type lambda packaged phagemid; right panel, OMPF-lambda variants. Circles indicate strains showing altered delivery compared to lambda wild-type. [Figure 2] Figure 2 shows wild-type lambda and lambda-stf-K1F chimeric delivery vehicles in the K1+ strain. Lambda-packaged phagemids were serially diluted 10x in LB plus 5 mM CaCl2, and 10 μL was added to each well. Cells grown to an OD600 of approximately 0.5 were then added to each phagemid dilution, incubated at 37°C for 30 minutes, and 10 μL was plated onto LB supplemented with chloramphenicol. Top panel, UTI89 strain; bottom panel, S88 strain. Left panel, wild-type lambda-packaged phagemid; right panel, stf-K1F lambda-packaged phagemid. [Figure 3] Figure 3 shows wild-type lambda and lambda-stf-K5 chimeric delivery vehicles in the K5+ strain. Lambda packaging phagemids were serially diluted 10x in LB plus 5 mM CaCl, and 10 μL was added to each well. ECOR55 cells grown to an OD of approximately 0.5 were then added to each phagemid dilution, incubated at 37°C for 30 minutes, and 10 μL plated onto LB supplemented with chloramphenicol. Left panel, wild-type lambda packaging phagemid; right panel, stf-K15 lambda packaging phagemid. [Figure 4]Figure 4 shows wild-type lambda, lambda-stf-AG22, and lambda-stf-SIEA11 chimeric delivery vehicles in various encapsulation strains (O and K capsules). Lambda phagemid was diluted 1:5 in LB plus 5 mM CaCl, and 10 μL was added to each well. 90 μL of cells grown to an OD of approximately 0.5 were then added to each phagemid-containing well, incubated at 37°C for 30 minutes, and 10 μL was spotted onto LB agar supplemented with chloramphenicol. Left panel, wild-type lambda phagemid; middle panel, lambda stf-SIEA11 variant; right panel, lambda-stf-AG22 variant. Circles indicate strains showing altered delivery compared to lambda wild-type. [Figure 5] Figure 5 shows the delivery of wild-type lambda and stf chimeras with different insertion sites in various encapsulation strains (O and K capsules). Lambda-packaged phagemids were diluted 1:5 in LB plus 5 mM CaCl, and 10 μL was added to each well. 90 μL of cells grown to an OD of approximately 0.5 were then added to each phagemid-containing well, incubated at 37°C for 30 minutes, and 10 μL was spotted onto LB agar supplemented with chloramphenicol. A) Left panel, wild-type lambda-packaged phagemid; remaining panels, three different ADAKKS-stf variants. B) Left panel, wild-type lambda-packaged phagemid; remaining panels, three different SASAAA-stf variants. C) Left panel, wild-type lambda-packaged phagemid; remaining panels, three different MDETNR-stf variants. For all panels, circles indicate strains with altered delivery efficiency compared to lambda wildtype. [Figure 6] Figure 6 shows a phmmer search performed in a representative proteome database (rp75) using a 50 aa sliding window (step 10). The number of significant hits (E-value < 0.01) is reported. [Figure 7] Figure 7 shows the structure of the engineered lambda stf-T4-like DTF chimera. Semicircle indicates RBS site; T symbol, transcription terminator; arrow, promoter. [Figure 8] Figure 8 shows the screening of phagemid particles carrying the chimeric lambda stf-T4-like DTF. A collection of 96 different wild-type E. coli strains, covering different serotypes, was transduced with the lambda-based phagemid and plated on Cm LB agar. Left panel, wild-type lambda stf; middle panel, chimeric lambda-stf-WW13; right panel, chimeric lambda-stf-PP-1. [Figure 9] Figure 9 shows the screening of phagemid particles carrying the chimeric lambda stf-T4-like DTF. A collection of 96 different wild-type E. coli strains, covering different serotypes, was transduced with the lambda-based phagemid and plated on Cm LB agar. Left panel, wild-type lambda stf; middle panel, chimeric lambda-stf-WW55; right panel, chimeric lambda-stf-WW34. [Figure 10] Figure 10 shows the screening of phagemid particles carrying chimeric lambda stf-T4-like DTFs. All dots indicate universal insertion sites for DTFs, located within the amino acid range from 1 to 90 relative to the WW13 amino acid sequence. A collection of 96 different wild-type E. coli strains, encompassing different serotypes, were transduced with the lambda-based phagemids and plated on Cm LB agar (names at the top). [Figure 11] Figure 11 shows a dot scoring system for quantifying delivery efficiency: density 0:5 or less colonies; density 1: more than 5 colonies but not enough to define a distinct circular drop; density 2: some colonies but the background is clearly visible and some colonies are still separated; density 3: many colonies, the background is still visible but the colonies are separated and difficult to recognize; density 4: spots are almost completely dense and the background is only slightly visible in some parts of the drop; density 5: spots appear to be completely dense and the background cannot be seen. [Figure 12]Figure 12 shows raw dot titration of delivery particles carrying chimeric stfs in 40 human strains from the ECOR collection. Below each panel is the name of the chimeric stf. Above each dot is the one- to two-letter code used to identify the strain in Figure 13. [Figure 13] Figure 13 shows the bar-formatted delivery data from Figure 12, ranging from 0 (no entry, gray background) to 5 (maximum delivery). The length of the bar is proportional to the entry score, ranging from 1 (smallest bar) to 5 (longest bar). DETAILED DESCRIPTION OF THE INVENTION

[0027] Disclosed herein is a novel approach to engineer synthetic bacterial delivery vehicles with desired target host ranges. The synthetic bacterial delivery vehicles are characterized by chimeric receptor-binding proteins (RBPs), which contain a fusion between the N-terminal domain of a lambdoid bacteriophage or an RBP derived from a lambda bacteriophage and the C-terminal domain of a different RBP. We demonstrate herein that key portions of lambdoid RBPs, such as the stf protein, can be exchanged for portions of different RBPs. Furthermore, we identify specific fusion moieties of the receptor-binding proteins that allow for functional chimeric RBPs to be obtained.

[0028] As used herein, a receptor binding protein or RBP is a polypeptide that recognizes, and optionally binds to and / or modifies or degrades a substrate located on the bacterial outer envelope, including, but not limited to, structures such as the bacterial outer membrane, LPS, capsule, protein receptors, channels, flagella, pili, etc., secretion system. The substrate can be, but is not limited to, any carbohydrate or modified carbohydrate, any lipid or modified lipid, any protein or modified protein, any amino acid sequence, and any combination thereof. As used herein, a lambda-like bacteriophage refers to any bacteriophage that encodes an RBP that has amino acid sequence homology of about 35% identity or greater for 45 amino acids, about 50% identity or greater for 30 amino acids, or about 90% identity or greater for 18 amino acids in one or more of three amino acid regions ranging from positions 1-150, 320-460, and 495-560 with respect to the lambda bacteriophage stf sequence of SEQ ID NO: 1, independently of other amino acid sequences encoded by the bacteriophage.

[0029] The present disclosure provides chimeric receptor-binding proteins (RBPs), which comprise a fusion between the N-terminal domain of an RBP from a lambdoid bacteriophage or lambda bacteriophage and the C-terminal domain of an RBP from a different bacteriophage. The RBP from such a bacteriophage, from which the chimeric RBP is derived, may comprise, for example, an "L-shaped fiber," a "lateral tail fiber (stf)," a "long tail fiber," or a "tail spike." As disclosed herein, we have demonstrated that key portions of lambdoid bacteriophage receptor-binding proteins (RBPs), such as the stf protein, can be exchanged with portions of different RBPs. Furthermore, we have identified specific fusion moieties in RBPs that allow functional chimeric RBPs to be obtained. Such chimeric RBPs include those with altered host range and / or biological activity, such as depolymerase activity.

[0030] A chimeric receptor-binding protein (RBP) is one in which the chimeric RBP comprises a fusion between the N-terminal domain of an RBP derived from a lambdoid bacteriophage or a lambda bacteriophage and the C-terminal domain of a different RBP, wherein the N-terminal domain of the RBP is fused to the C-terminal domain of the different RBP within one of the amino acid regions selected from positions 1-150, 320-460, or 495-560 of the N-terminal RBP with respect to the lambda stf sequence (SEQ ID NO: 1), or a similar region of the RBP having homology to one or more of three amino acid regions ranging from positions 1-150, 320-460, or 495-560 of the RBP with respect to the lambda stf sequence. In a specific aspect of the invention, the different RBP of the chimeric receptor-binding protein (RBP) is derived from any bacteriophage or any bacteriocin.

[0031] In a particular embodiment, the RBP from a lambdoid bacteriophage, lambda bacteriophage, or a different RBP contains homology to one or more of three amino acid regions ranging from positions 1 to 150, 320 to 460, and 495 to 560 of the RBP relative to the lambda bacteriophage stf sequence (SEQ ID NO: 1). In particular embodiments, the homology between the lambdoid bacteriophage, lambda bacteriophage, or a different RBP and the one or more amino acid regions is approximately 35% identity or greater over 45 amino acids, approximately 50% identity or greater over 30 amino acids, and approximately 90% identity or greater over 18 amino acids. Homology can be determined using alignment tools such as the Smith-Waterman algorithm (Smith et al., 1981, J. Mol. Biol 147:195-197) or EMBOSS Matcher (Rice, Longden, Bleasby 2000 EMBOSS Trends in Genetics 16:276-277). In one aspect of the invention, the chimeric RBP comprises the N-terminal domain of a chimeric RBP fused to the C-terminal domain of the chimeric RBP within one of the amino acid regions selected from positions 80-150, 320-460, or 495-560 with respect to the lambda bacteriophage stf sequence (SEQ ID NO: 1). In another embodiment of the invention, the chimeric RBP comprises an N-terminal domain and a C-terminal domain fused within one of three amino acid regions at an insertion site having at least 80% identity to an insertion site selected from the group consisting of amino acids SAGDAS (SEQ ID NO: 178), ADAKKS (SEQ ID NO: 179), MDETNR (SEQ ID NO: 180), SASAAA (SEQ ID NO: 181), and GAGENS (SEQ ID NO: 182).

[0032] In certain embodiments, the present invention provides chimeric RBPs. SEQ ID NOs: 2-61, 123-153, 192, 194-221, 256, and 258 disclose the amino acid sequences of such chimeric RBPs and, in some cases, their corresponding native chaperone proteins (denoted "AP"). Such AP proteins assist in the folding of the chimeric RBPs. In certain embodiments, the RBP comprises the amino acid sequence of SEQ ID NO: 2, 4, 7, 9, 12, 15, 17, 20, 23, 24, 25, 27, 29, 31, 33, 35, 37, 39, 41, 42, 44, 46, 47, 48, 49, 50, 51, 52, 53, 56, 59, 130, 131, 132, 135, 138, 139, 142, 145, 148, 151, 192, 194, 195, 198, 200, 202, 204, 206, 208, 211, 214, 216, 218, or 220.

[0033] In one aspect, the present disclosure also provides nucleotide sequences encoding the chimeric RBPs disclosed herein. In certain embodiments, nucleic acids encoding such chimeric RBPs, as well as the corresponding AP proteins, are set forth in SEQ ID NOs: 62-120, 122, 154-177, 222-249, 255, and 257. In certain embodiments, the nucleic acid encoding the chimeric RBP comprises the nucleotide sequence of SEQ ID NO: 62, 64, 67, 69, 72, 75, 77, 80, 83, 84, 85, 87, 89, 91, 93, 95, 97, 99, 101, 102, 104, 106, 107, 108, 109, 110, 111, 112, 113, 116, 119, 154, 155, 156, 159, 162, 163, 166, 169, 172, 175, 222, 224, 227, 229, 231, 233, 235, 237, 240, 243, 245, 247 or 249.

[0034] In one specific, non-limiting aspect of the present invention, it has been demonstrated that engineering a chimeric RBP to encode a depolymerase activity can dramatically increase the delivery efficiency of a provided bacterial delivery vehicle comprising the chimeric RBP disclosed herein. In one embodiment of the present invention, different RBP domains of the chimeric RBP comprise depolymerase activity for encapsulating bacterial strains. In certain embodiments, the depolymerase is an endosialidase, such as K1F or K5 endosialidase.

[0035] Nucleic acid molecules encoding the chimeric RBPs disclosed herein are provided. Such nucleic acids can be contained in vectors, such as bacteriophages, plasmids, phagemids, viruses, and other vehicles, that allow for the transfer and expression of the chimeric RBP encoding nucleic acid.

[0036] Bacterial delivery vehicles are provided that enable the transfer of nucleic acid payloads encoding proteins or nucleic acids of interest into desired target bacterial host cells. Such bacterial delivery vehicles are characterized by having a chimeric RBP comprising a fusion between the N-terminal domain of an RBP from a lambdoid bacteriophage or lambda bacteriophage and the C-terminal domain of a different RBP. In an embodiment of the present invention, the bacterial delivery vehicle contains a chimeric RBP comprising a fusion between the N-terminal domain of an RBP from a lambdoid bacteriophage or lambda bacteriophage and the C-terminal domain of a different RBP, wherein the N-terminal domain of the chimeric RBP is fused to the C-terminus of the different RBP within one of amino acid regions selected from positions 1-150, 320-460, or 495-560 of the N-terminal domain of the RBP with respect to the lambda stf sequence (SEQ ID NO: 1). In one aspect, the lambdoid bacteriophage, the RBP from the lambda bacteriophage, and the different RBP contain homology in one or more of three amino acid regions ranging from positions 1-150, 320-460, and 495-560 of the N-terminal RBP with respect to the lambda bacteriophage stf sequence (SEQ ID NO: 1). In particular aspects, the homology is approximately 35% identity or greater for 45 amino acids, approximately 50% identity or greater for 30 amino acids, or approximately 90% identity or greater for 18 amino acids within one or more of three amino acid regions ranging from positions 1-150, 320-460, and 495-560 of the N-terminal RBP with respect to the lambda bacteriophage stf sequence (SEQ ID NO: 1). In a particular aspect of the invention, the different RBP domains of the chimeric receptor-binding protein (RBP) are derived from a bacteriophage or bacteriocin. In one aspect of the invention, the chimeric RBP comprises the N-terminal domain of an RBP fused to the C-terminal domain of the RBP within one of the amino acid regions selected from positions 80-150, 320-460, or 495-560 of the RBP with respect to the lambda stf sequence (SEQ ID NO: 1).In another embodiment of the invention, the chimeric RBP comprises the N-terminal domain of the RBP and the C-terminal domain of the RBP fused within a site of the N-terminus RBP having at least 80% identity to a site selected from the group consisting of amino acids SAGDAS (SEQ ID NO: 178), ADAKKS (SEQ ID NO: 179), MDETNR (SEQ ID NO: 180), SASAAA (SEQ ID NO: 181), and GAGENS (SEQ ID NO: 182).

[0037] In certain embodiments, the present disclosure provides bacterial delivery vehicles comprising chimeric RBPs. SEQ ID NOs: 2-153, 192, 194-221, 256, and 258 disclose the amino acid sequences of such chimeric RBPs and, in some cases, their corresponding native chaperone proteins (denoted "AP"). Such AP proteins assist in the folding of the chimeric RBPs. In certain embodiments, the RBP comprises the amino acid sequence of SEQ ID NO: 2, 4, 7, 9, 12, 15, 17, 20, 23, 24, 25, 27, 29, 31, 33, 35, 37, 39, 41, 42, 44, 46, 47, 48, 49, 50, 51, 52, 53, 56, 59, 130, 131, 132, 135, 138, 139, 142, 145, 148, 151, 192, 194, 195, 198, 200, 202, 204, 206, 208, 211, 214, 216, 218, or 220.

[0038] In one aspect, the present disclosure also provides nucleotide sequences encoding the chimeric RBPs disclosed herein. In certain embodiments, nucleic acids encoding such chimeric RBPs, as well as the corresponding AP proteins, are set forth in SEQ ID NOs: 62-120, 122, and 154-177. In certain embodiments, the nucleic acid encoding the chimeric RBP comprises the nucleotide sequence of SEQ ID NO: 62, 64, 67, 69, 72, 75, 77, 80, 83, 84, 85, 87, 89, 91, 93, 95, 97, 99, 101, 102, 104, 106, 107, 108, 109, 110, 111, 112, 113, 116, 119, 154, 155, 156, 159, 162, 163, 166, 169, 172, 175, 222, 223, 226, 228, 230, 232, 234, 236, 239, 242, 244, 246 or 248.

[0039] In other specific embodiments, to increase the delivery efficiency of the bacterial delivery vehicles disclosed herein, the different RBP domains of the chimera include a domain with depolymerase activity against the encapsulated bacterial strain. In specific embodiments, the depolymerase is an endosialidase, such as K1F or K5 endosialidase.

[0040] The bacterial delivery vehicles provided herein allow for the transfer of a nucleic acid payload encoding a protein or nucleic acid of interest into a desired target bacterial host cell. As used herein, the term "delivery vehicle" refers to any means that allows for the transfer of a payload into bacteria. Several types of delivery vehicles are encompassed by the present invention, including, but not limited to, bacteriophage scaffolds, viral scaffolds, chemical-based delivery vehicles (e.g., cyclodextrins, calcium phosphate, cationic polymers, cationic liposomes), protein- or peptide-based delivery vehicles, lipid-based delivery vehicles, nanoparticle-based delivery vehicles, non-chemical-based delivery vehicles (e.g., transformation, electroporation, sonoporation, optical transfection), particle-based delivery vehicles (e.g., gene guns, magnetofection, imparefection, biolistics, cell-penetrating peptides), or donor bacteria (conjugation).

[0041] Any combination of delivery vehicles is also encompassed by the present invention. A delivery vehicle may also refer to a bacteriophage-derived scaffold and may be derived from a natural, evolved, or engineered capsid. In some embodiments, the delivery vehicle is a payload, as bacteria are naturally capable of absorbing payloads from their environment.

[0042] As used herein, the term "payload" refers to any one or more nucleic acid sequences and / or amino acid sequences, or a combination of both (e.g., but not limited to, peptide nucleic acid or peptide oligonucleotide conjugates), that are transferred to a bacterium by a delivery vehicle. The term "payload" can also refer to a plasmid, vector, or cargo. A payload can be a phagemid or phasmid derived from a natural, evolved, or engineered bacteriophage genome. A payload may also consist of only a portion of a phagemid or phasmid derived from a natural, evolved, or engineered bacteriophage genome.

[0043] As used herein, the term "nucleic acid" refers to a sequence of at least two nucleotides covalently linked together, which may be single-stranded or double-stranded, or contain portions of both single-stranded and double-stranded sequences. Nucleic acids of the present invention may be naturally occurring, recombinant, or synthetic. Nucleic acids may be in the form of circular or linear sequences, or a combination of both forms. Nucleic acids may be DNA, both genomic and cDNA, or RNA, or a combination of both. Nucleic acids may contain any combination of deoxyribonucleotides and ribonucleotides, and any combination of bases, including uracil, adenine, thymine, cytosine, guanine, inosine, xanthine, hypoxanthine, isocytosine, 5-hydroxymethylcytosine, and isoguanine. Other examples of modified bases that can be used in the present invention are detailed in Chemical Reviews 2016, 116 (20), pp. 12655-12687. The term "nucleic acid" also encompasses any nucleic acid analogs that may contain other backbones, including, but not limited to, phosphoramide, phosphorothioate, phosphorodithioate, O-methyl phosphoramidite linkages and / or deoxyribonucleotide and ribonucleotide nucleic acids. Any combination of the above characteristics of nucleic acids is also encompassed by the present invention.

[0044] In this document, "approximately" when specifying homology or identity means + / - 10% of the number, preferably + / - 5% of the number. Approximately 100 then means between 90 and 110, preferably between 95 and 105.

[0045] Origins of replication known in the art have been identified from species-specific plasmid DNA (e.g., CoIE1, R1, pT181, pSC101, pMB1, R6K, RK2, p15a, etc.), from bacterial viruses (e.g., φX174, M13, F1 and P4), and from bacterial chromosomal origins of replication (e.g., oriC). In one embodiment, a phagemid according to the present disclosure comprises a bacterial origin of replication that is functional in the target bacterium.

[0046] Alternatively, the plasmids according to the present disclosure do not contain any functional bacterial origin of replication or contain an origin of replication that is inactive in the target bacterium, and therefore cannot replicate by themselves when introduced into the bacterium by a bacterial viral particle.

[0047] In one embodiment, the origin of replication on the packaged plasmid is inactive in the target bacterium, meaning that the origin of replication is not functional in the bacterium targeted by the bacterial viral particle, thus preventing unwanted plasmid replication.

[0048] In one embodiment, the plasmid contains a bacterial origin of replication that is functional in the bacteria used for production of bacterial viral particles.

[0049] Plasmid replication depends on host enzymes and plasmid regulatory cis- and trans-determinants. For example, some plasmids contain determinants recognized in almost all Gram-negative bacteria and function correctly in each host during replication initiation and control. Other plasmids retain this ability only in some bacteria (Kues, U and Stahl, U 1989, Microbiol Rev 53:491-516).

[0050] Plasmids replicate by three general mechanisms: theta, strand displacement, and rolling circle replication initiated at origins of replication (reviewed by Del Solar et al., 1998, Microhio and Molec Biol. Rev 62:434-464). These origins of replication contain sites necessary for the interaction of plasmid- and / or host-encoded proteins.

[0051] The origin of replication used in the plasmids of the present disclosure may be of medium copy number, such as the colE1 ori from pBR322 (15-20 copies per cell) or R6K plasmid (15-20 copies per cell), or may be of high copy number, such as the pUC ori (500-700 copies per cell), pGEM ori (300-400 copies per cell), pTZ ori (>1000 copies per cell), or pBluescript ori (300-500 copies per cell).

[0052] In one embodiment, the bacterial origin of replication is ColE1, pMB1 and variants (such as pBR322, pET, pUC), p15a, ColA, ColE2, pOSAK, pSC101, R6K, IncW (such as pSa), IncFII, pT181, P1, F IncP, IncC, IncJ, IncN, IncP1, IncP4, IncQ, IncH11, RSF1010, CloDF13, NTP16, R1, f5, pPS10, pC194, pE194, BBR1, pBC1, pEP2, pWVO1, pLF1311, pAP1, pWKS1, pLS1, pLS11, pUB6060, pJD4, pIJ101, pSN22, pAMbeta1, pIP5 01, pIP407, ZM6100(Sa), pCU1, RA3, pMOL98, RK2 / RP4 / RP1 / R68, pB10, R300B, pRO1614, pRO1600, pECB2, pCM1, pFA3, RepFIA, RepFIB, RepFIC, pYVE439-80, R387, phasyl, RA1, TF-FC2, pMV158 and pUB113.

[0053] More preferably, the bacterial origin of replication is an E. coli origin of replication selected from the group consisting of ColE1, pMB1 and variants (such as pBR322, pET, pUC), p15a, ColA, ColE2, pOSAK, pSC101, R6K, IncW (such as pSa), IncFII, pT181, P1, F IncP, IncC, IncJ, IncN, IncP1, IncP4, IncQ, IncH11, RSF1010, CloDF13, NTP16, R1, f5, and pPS10.

[0054] More preferably, the bacterial origin of replication is selected from the group consisting of pC194, pE194, BBR1, pBC1, pEP2, pWVO1, pLF1311, pAP1, pWKS1, pLS1, pLS11, pUB6060, pJD4, pIJ101, pSN22, pAMbeta1, pIP501, pIP407, ZM6100(Sa), pCU1, RA3, pMOL98, RK2 / RP4 / RP1 / R68, pB10, R300B, pRO1614, pRO1600, pECB2, pCM1, pFA3, RepFIA, RepFIB, RepFIC, pYVE439-80, R387, phasyl, RA1, TF-FC2, pMV158 and pUB113.

[0055] Even more preferably, the bacterial origin of replication is ColE1.

[0056] The delivered nucleic acid sequence according to the present disclosure may comprise a phage origin of replication that, upon complementation of the complete phage genome, can initiate replication of the delivered nucleic acid sequence for subsequent encapsulation into a different capsid.

[0057] The phage origin of replication included in the delivered nucleic acid sequences of the present disclosure can be any origin of replication found in a phage.

[0058] Preferably, the phage origin of replication can be the wild-type or non-wild-type sequence of M13, f1, φX174, P4, lambda, P2, lambda-like, HK022, mEP237, HK97, HK629, HK630, mEP043, mEP213, mEP234, mEP390, mEP460, mEPx1, mEPx2, phi80, mEP234, T2, T4, T5, T7, RB49, phiX174, R17, PRD1 P1-like, P2-like, P22, P22-like, N15, and N15-like bacteriophages.

[0059] More preferably, the phage origin of replication is selected in the group consisting of M13, f1, φX174, P4, and lambda phage origins of replication.

[0060] In certain embodiments, the phage origin of replication is a lambda or P4 origin of replication.

[0061] The nucleic acid of interest to be delivered comprises a nucleic acid sequence under the control of a promoter. In certain embodiments of the present invention, the nucleic acid of interest is selected from the group consisting of a Cas nuclease gene, a Cas9 nuclease gene, a guide RNA, a CRISPR locus, a toxin gene, a gene expressing an enzyme such as a nuclease or kinase, a TALEN, a ZFN, a meganuclease, a recombinase, a bacterial receptor, a membrane protein, a structural protein, a secreted protein, a gene expressing resistance to antibiotics or drugs in general, a gene expressing a toxin protein or a toxin factor, and a gene expressing a virulence protein or a virulence factor, or any combination thereof. In embodiments of the present invention, the nucleic acid payload encodes a therapeutic protein. In other embodiments, the nucleic acid payload encodes an antisense nucleic acid molecule. In some embodiments, the nucleic acid payload encodes two nucleic acids of interest, one a nuclease gene, e.g., a Cas nuclease gene, and one any other nucleic acid of interest.

[0062] In one embodiment, the sequence of interest is delivered to a target bacterium via a programmable nuclease circuit. This programmable nuclease circuit can mediate in vivo sequence-specific removal of bacteria containing a target gene of interest (e.g., a gene harmful to humans). Some embodiments of the present disclosure relate to engineered variants of the Type II CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR-associated) system of Streptococcus pyogenes. Other programmable nucleases that can be used include other CRISPR-Cas systems, engineered TALEN (Transcription Activator-Like Effector Nuclease) variants, engineered zinc finger nuclease (ZFN) variants, naturally occurring, evolved, or engineered meganuclease or recombinase variants, and any combination or hybrid of programmable nucleases. Thus, the engineered decentralized nuclease circuits provided herein can be used to selectively cleave DNA encoding genes of interest, such as toxin genes, virulence factor genes, antibiotic resistance genes, remodeling genes, or regulatory genes (see WO2014124226).

[0063] Other sequences of interest, preferably programmable, can be added to the nucleic acid sequence to be delivered to the target bacterium. Preferably, the sequence of interest added to the nucleic acid sequence to be delivered results in cell death of the target bacterium. For example, the nucleic acid sequence of interest added to the plasmid can encode a holin or a toxin.

[0064] Alternatively, the sequence of interest added to the delivered nucleic acid sequence does not result in bacterial death. For example, the sequence of interest may encode a reporter gene that produces a luminescent or fluorescent signal. Alternatively, the sequence of interest may include proteins and enzymes that perform useful functions, such as modifying the metabolism of the bacteria or the composition of its environment.

[0065] In certain embodiments, the nucleic acid sequence of interest is selected from the group consisting of Cas9, a single guide RNA (sgRNA), a CRISPR locus, a gene expressing an enzyme such as a nuclease or a kinase, a TALEN, a ZFN, a meganuclease, a recombinase, a bacterial receptor, a membrane protein, a structural protein, a secreted protein, a gene expressing resistance to antibiotics or drugs in general, a gene expressing a toxin protein or toxin factor, and a gene expressing a virulence protein or virulence factor.

[0066] In certain embodiments, the nucleic acid sequence delivered according to the present disclosure comprises a nucleic acid sequence of interest encoding a bacteriocin, which can be a proteinaceous toxin produced by bacteria that kills or inhibits the growth of other bacteria. Bacteriocins are categorized in several ways, including by the strain that produces them, their common resistance mechanism, and their mechanism of death. Such bacteriocins have been described from Gram-negative bacteria (e.g., microcins, colicin-like bacteriocins, and tylosins) and from Gram-positive bacteria (e.g., Class I, Class II, Class III, or Class IV bacteriocins).

[0067] In one embodiment, the nucleic acid sequence delivered according to the present disclosure further comprises a sequence of interest encoding a toxin selected from the group consisting of a microcin, a colicin-like bacteriocin, a tylosin, a class I, a class II, a class III, and a class IV bacteriocin.

[0068] In certain embodiments, the corresponding immunity polypeptides (i.e., antitoxins) may be used to protect bacterial cells for delivery nucleic acid sequence production and encapsidation purposes (Cotter et al., Nature Reviews Microbiology 11: 95, 2013), but are not included in the pharmaceutical compositions and within the target bacteria to which the delivery nucleic acid sequences of the present disclosure are delivered.

[0069] In one embodiment of the present disclosure, a CRISPR system is included in the delivered nucleic acid sequence. CRISPR systems contain two distinct elements: i) an endonuclease, in this case a CRISPR-associated nuclease (Cas or "CRISPR-associated protein"), and ii) a guide RNA. The guide RNA is a form of chimeric RNA consisting of a combination of a bacterial CRISPR (RNAcr) RNA and a trans-activating RNA CRISPR (RNAtracr) (Jinek et al., Science 2012). The guide RNA combines the targeting specificity of the RNAcr, which corresponds to a "spacing sequence" that serves as a guide for the Cas protein, with the structural characteristics of the RNAtracr in a single transcript. When the guide RNA and Cas protein are simultaneously expressed in a cell, the target genome sequence can be permanently modified or disrupted. The modification is advantageously guided by a repair matrix. Generally, CRISPR systems comprise two major classes depending on the nuclease mechanism of action. Class 1 consists of multi-subunit effector complexes and includes types I, III, and IV. Class 2, like Cas9 nuclease, consists of a single-unit effector module and includes types II (II-A, II-B, II-C, II-C variant), V (VA, VB, VC, VD, VE, V-U1, V-U2, V-U3, V-U4, V-U5), and VI (VI-A, VI-B1, VI-B2, VI-C, VI-D).

[0070] The sequence of interest according to the present disclosure includes a nucleic acid sequence encoding a Cas protein. Various CRISPR enzymes are available for use as the sequence of interest in a plasmid. In some embodiments, the CRISPR enzyme is a type II CRISPR enzyme. In some embodiments, the CRISPR enzyme catalyzes DNA cleavage. In some other embodiments, the CRISPR enzyme catalyzes RNA cleavage. In one embodiment, the CRISPR enzyme can be bound to an sgRNA. In certain embodiments, the sgRNA targets a gene selected from the group consisting of antibiotic resistance genes, virulence proteins or virulence factor genes, toxin proteins or virulence factor genes, bacterial receptor genes, membrane protein genes, structural protein genes, secreted protein genes, and genes that generally express resistance to drugs.

[0071] Non-limiting examples of Cas proteins, either as part of a multi-subunit effector or as a single unit effector, include Cas1, Cas1B, Cas2, Cas3, Cas4, Cas5, Cas6, Cas7, Cas8, Cas9 (also known as Csn1 and Csx12), Cas10, Cas11 (SS), Cas12a (Cpf1), Cas12b (C2c1), Cas12c (C2c3), Cas12d (CasY), Cas12e (CasX), C2c4, C2c8, C2c5, C2c10, C2c9, Cas13a (C2c2), Cas13b (C2c6), Cas13c (C2c7), Cas13d, Csa5, Csc 1, Csc2, Cse1, Cse2, Csy1, Csy2, Csy3, Csf1, Csf2, Csf3, Csf4, Csm2, Csm3, Csm4, Csm5, Csm6, Cmr1, Cmr3, Cmr4, Cmr5, Cmr6, Csn2, Csb1, Csb2, Csb3, Csx17, Csx14, Csx10, Csx1 In some embodiments, the CRISPR enzyme cleaves both strands of the target nucleic acid at a protospacer adjacent motif (PAM) site.

[0072] In certain embodiments, the CRISPR enzyme is any Cas9 protein, such as any naturally occurring bacterial Cas9, as well as any variant, homolog, or ortholog thereof.

[0073] By "Cas9" is meant the protein Cas9 (also called Csn1 or Csx12) or a functional protein, peptide, or polypeptide fragment thereof, i.e., capable of interacting with a guide RNA and exerting an enzymatic activity (nuclease) that allows it to make a double-stranded break in the DNA of the target genome. Thus, "Cas9" refers, for example, to a modified protein in which domains of the protein that are not essential for the protein's predefined function have been truncated to remove them, in particular domains that are not required for interaction with the gRNA.

[0074] As used in the context of the present disclosure, a sequence encoding Cas9 (whole protein or a fragment thereof) can be obtained from any known Cas9 protein (Fonfara et al., Nucleic Acids Res 42 (4), 2014; Koonin et al., Nat Rev Microbiol 15(3), 2017). Examples of Cas9 proteins useful in the present disclosure include, but are not limited to, the Cas9 proteins of Streptococcus pyogenes (SpCas9), Streptococcus thermophiles (St1Cas9, St3Cas9), Streptococcus mutans, Staphylococcus aureus (SaCas9), Campylobacter jejuni (CjCas9), Francisella novicida (FnCas9), and Neisseria meningitides (NmCas9).

[0075] As used in the context of the present disclosure, a sequence encoding Cpf1 (Cas12a) (whole protein or a fragment thereof) can be obtained from any known Cpf1 (Cas12a) protein (Koonin et al., 2017). Examples of Cpf1 (Cas12a) proteins useful in the present disclosure include, but are not limited to, the Cpf1 (Cas12a) proteins of Acidaminococcus sp., Lachnospiraceae bacteriu, and Francisella novicida.

[0076] The sequence encoding Cas13a (whole protein or a fragment thereof) can be obtained from any known Cas13a (C2c2) protein (Abudayyeh et al., 2017). Examples of Cas13a (C2c2) proteins useful in the present disclosure include, but are not limited to, the Cas13a (C2c2) protein of Leptotrichia wadei (LwaCas13a).

[0077] The sequence encoding Cas13d (whole protein or a fragment thereof) can be obtained from any known Cas13d protein (Yan et al., 2018). Examples of Cas13d proteins useful in the present disclosure include, but are not limited to, the Cas13d proteins of Eubacterium siraeum and Ruminococcus sp.

[0078] In certain embodiments, the nucleic acid sequence of interest is a CRISPR / Cas9 system for the reduction of gene expression or inactivation of a gene selected in the group consisting of antibiotic resistance genes, virulence factor or protein genes, toxin factor or protein genes, bacterial receptors, membrane proteins, structural proteins, genes expressing secreted proteins, and generally genes expressing resistance to drugs.

[0079] In one embodiment, the CRISPR system is used to target and inactivate virulence factors. Virulence factors can be any substance produced by a pathogen that alters host-pathogen interactions by increasing the degree of damage inflicted on the host. Virulence factors are used by pathogens in many ways, including, for example, cell adhesion or colonization of a niche in the host, avoiding the host's immune response, promoting invasion and release from host cells, obtaining nutrients from the host, or inhibiting other physiological processes in the host. Virulence factors can include enzymes, endotoxins, adhesion factors, motility factors, factors involved in complement evasion, and factors that promote biofilm formation. For example, such targeted virulence factor genes include, but are not limited to, E. coli virulence factor genes, such as EHEC-HlyA, Stx1 (VT1), Stx2 (VT2), Stx2a (VT2a), Stx2b (VT2b), Stx2c (VT2c), Stx2d (VT2d), Stx2e (VT2e), and Stx2f (VT2f), Stx2h (VT2h), fimA, fimF, fimH, neuC, kpsE, sfa, foc, iroN, aer, iha, papC, papGI, papGII, papGIII, hlyC, cnf1, hra, sat, ireA, usp The targeted virulence factor gene may be ompT, ibeA, malX, fyuA, irp2, traT, afaD, ipaH, eltB, estA, bfpA, eaeA, espA, aaiC, aatA, TEM, CTX, SHV, csgA, csgB, csgC, ​​csgD, csgE, csgF, csgG, csgH, T1SS, T2SS, T3SS, T4SS, T5SS, or T6SS (secretion system). For example, such a targeted virulence factor gene may be a Shigella dysenteriae virulence factor gene, such as, but not limited to, stx1 and stx2. For example, such a targeted virulence factor gene may be a Yersinia pestis virulence factor gene, such as, but not limited to, yscF (plasmid-borne (pCD1) T3SS outer needle subunit).For example, such a targeted virulence factor gene can be a Francisella tularensis virulence factor gene, such as, but not limited to, fslA. For example, such a targeted virulence factor gene can be a Bacillus anthracis virulence factor gene, such as, but not limited to, pag (anthrax toxin, cell-associated protective antigen). For example, such a targeted virulence factor gene can be a Vibrio cholera virulence factor gene, such as, but not limited to, ctxA and ctxB (cholera toxin), tcpA (toxin coregulator pilus), and toxT (master virulence regulator). For example, such targeted virulence factor genes can be Pseudomonas aeruginosa virulence factor genes, such as, but not limited to, pyoverdin (e.g., sigma factor pvdS, biosynthetic control genes pvdL, pvdl, pvdJ, pvdH, pvdA, pvdF, pvdQ, pvdN, pvdM, pvdO, pvdP, transporter genes pvdE, pvdR, pvdT, opmQ), siderophore pyochelin (e.g., pchD, pchC, pchB, pchA, pchE, pchF, and pchG), and toxins (e.g., exoU, exoS, and exoT). For example, such targeted virulence factor genes can be Klebsiella pneumoniae virulence factor genes, such as, but not limited to, fimA (adhesion, type 1 pilus major subunit) and cps (capsular polysaccharide). For example, such targeted virulence factor genes can be Acinetobacter baumannii virulence factor genes, such as, but not limited to, ptk (capsule polymerization) and epsA (assembly). For example, such targeted virulence factor genes can be Salmonella enterica Typhi virulence factor genes, such as, but not limited to, MIA (invasion, SPI-1 regulator), ssrB (SPI-2 regulator), and those associated with bile resistance, including the efflux pump genes acrA, acrB, and tolC.For example, such a targeted virulence factor gene can be a Fusobacterium nucleatum virulence factor gene, such as, but not limited to, FadA and TIGIT. For example, such a targeted virulence factor gene can be a Bacteroides fragilis virulence factor gene, such as, but not limited to, bft.

[0080] In another embodiment, the CRISPR / Cas9 system is used to encode an antibiotic resistance gene, such as, but not limited to, GyrB, ParE, ParY, AAC(1), AAC(2'), AAC(3), AAC(6'), ANT(2"), ANT(3"), ANT(4'), ANT(6), ANT(9), APH(2"), APH(3"), APH(3'), APH(4), APH(6), APH(7"), APH(9), ArmA, RmtA, RmtB, RmtC, Sgm, AER, BLA1, CTX-M, KPC, SHV, TEM, BlaB, CcrA, IMP, NDM, VIM, ACT, AmpC, CMY, LAT, PDC, OXA β-lactamase, mecA, Omp36, OmpF, PIB, bla (blaI, blaR1) and mec (mecI, mecR1) operons, chloramphenicol acetyltransferase (CAT), chloramphenicol phosphotransferase, ethambutol-resistant arabinosyltransferase (EmbB), MupA, MupB, integral membrane protein MprF, Cfr 23S rRNA methyltransferase, rifampin ADP-ribosyltransferase (Arr), rifampin glycosyltransferase, rifampin monooxygenase, rifampin phosphotransferase, DnaA, RbpA, rifampin-resistant beta-subunit of RNA polymerase (RpoB), Erm 23SrRNA methyltransferase, Lsa, MsrA, Vga, VgaB, streptogramin Vgb lyase, Vat acetyltransferase, fluoroquinolone acetyltransferase, fluoroquinolone resistance DNA topoisomerase, fluoroquinolone resistance GyrA, GyrB, ParC, quinolone resistance protein (Qnr), FomA, FomB, FosC, FosA, FosB, FosX, VanA, VanB, VanD, VanR, VanS, lincosamide nucleotidyltransferase (Lin), EreA, EreB, GimA, Mgt, Ole, macrolide phosphotransferase (MPH) , MefA, MefE, Mel, streptothricin acetyltransferase (sat), Sul1, Sul2, Sul3, sulfonamide resistance FolP, tetracycline inactivation enzymes TetX, TetA, TetB, TetC, Tet30, Tet31, TetM, TetO, TetQ, Tet32, Tet36, MacAB-TolC, MsbA, MsrA, VgaB, EmrD, EmrAB-TolC, NorB, GepA, MepA, AdeABC, AcrD, MexAB-OprM, mtrCDE, EmrE, adeR, acrR, baeSR, mexR, phoPQ, mtrR, or any antibiotic resistance gene listed in the Comprehensive Antibiotic Resistance Database (CARD https: / / card.mcmaster.ca / ).

[0081] In another embodiment, the CRISPR / Cas9 system is used to target and inactivate bacterial toxin genes. Bacterial toxins can be classified as either exotoxins or endotoxins. Exotoxins are produced and actively secreted; endotoxins remain part of the bacterium. Responses to bacterial toxins can include severe inflammation and can lead to suppuration. Such toxins can be, for example, botulinum neurotoxin, tetanus toxin, staphylococcal toxin, diphtheria toxin, anthrax toxin, alpha toxin, pertussis toxin, Shiga toxin, heat-stable enterotoxin (Escherichia coli ST), colibactin, BFT (Bacteroides fragilis toxin), or any of the toxins described in Henkel et al. (Toxins from Bacteria in EXS. 2010; 100: 1-29).

[0082] The bacteria targeted by the bacterial delivery vehicles disclosed herein can be any bacteria present in a mammalian organism. In certain embodiments, the bacteria is targeted via interaction of the chimeric RBP expressed by the delivery vehicle with the bacterial cell. It can be any commensal, symbiotic, or pathogenic bacteria of the microbiota or microbiome.

[0083] The microbiome contains a variety of endogenous bacterial species, any of which may be targeted in accordance with the present disclosure. In some embodiments, the genus and / or species of the targeted endogenous bacterial cells may depend on the type of bacteriophage used to prepare the bacterial delivery vehicle. For example, some bacteriophages exhibit tropism or preferentially target specific host species of bacteria. Other bacteriophages do not exhibit such tropism and may be used to target many different genera and / or species of endogenous bacterial cells.

[0084] Examples of bacterial cells include, but are not limited to, Yersinia spp., Escherichia spp., Klebsiella spp., Acinetobacter spp., Bordetella spp., Neisseria spp., Aeromonas spp., Francisella spp., Corynebacterium spp., Citrobacter spp., Chlamydia spp., Haemophilus spp., Brucella spp., spp.), Mycobacterium spp., Legionella spp., Rhodococcus spp., Pseudomonas spp., Helicobacter spp., Vibrio spp., Bacillus spp., Erysipelothrix spp., Salmonella spp., Streptomyces spp., Streptococcus spp., Staphylococcus spp., Bacteroides spp. spp.), Prevotella spp., Clostridium spp., Bifidobacterium spp., Clostridium spp., Brevibacterium spp., Lactococcus spp., Leuconostoc spp., Actinobacillus spp., Selenomonas spp.), Shigella spp., Zymonas spp., Mycoplasma spp., Treponema spp., Leuconostoc spp., Corynebacterium spp., Enterococcus spp., Enterobacter spp., Pyrococcus spp., Serratia spp., Morganella spp., Parvimonas spp., Fusobacterium spp., Actinomyces spp. spp.), Porphyromonas spp., Micrococcus spp., Bartonella spp., Borrelia spp., Brucelia spp., Campylobacter spp., Chlamydophilia spp., Cutibacterium spp., Propionibacterium spp., Gardnerella spp., Ehrlichia spp., Haemophilus spp., Leptospira spp. Examples of suitable bacterial cells include cells derived from bacteria of the genera Listeria spp., Mycoplasma spp., Nocardia spp., Rickettsia spp., Ureaplasma spp., and Lactobacillus spp., as well as mixtures thereof.

[0085] Thus, a bacterial delivery vehicle may target (e.g., specifically target) bacterial cells from any one or more of the aforementioned genera of bacteria and specifically deliver a payload of interest in accordance with the present disclosure.

[0086] Preferably, the targeted bacteria may be selected from the group consisting of Yersinia spp., Escherichia spp., Klebsiella spp., Acinetobacter spp., Pseudomonas spp., Helicobacter spp., Vibrio spp., Salmonella spp., Streptococcus spp., Staphylococcus spp., Bacteroides spp., Clostridium spp., Shigella spp., Enterococcus spp., Enterobacter spp., Listeria spp., Cutibacterium spp., Propionibacterium spp., Fusobacterium spp., Porphyromonas spp., and Gardnerella spp.

[0087] In some embodiments, the bacterial cells of the present disclosure are anaerobic bacterial cells (e.g., cells that do not require oxygen for growth). Anaerobic bacterial cells include facultative anaerobic cells, such as, but not limited to, Escherichia coli, Shewanella oneidensis, Gardnerella vaginalis, and Listeria. Anaerobic bacterial cells also include obligate anaerobic cells, such as Bacteroides, Clostridium, Cutibacterium, Propionibacterium, Fusobacterium, and Purphyromonas species. In humans, anaerobic bacteria are most commonly found in the gastrointestinal tract. Thus, in some specific embodiments, the target bacteria are bacteria most commonly found in the gastrointestinal tract. The bacteriophages used to prepare bacterial viral particles, which in turn can target (e.g., specifically target) anaerobic bacterial cells and specifically deliver plasmids according to their specific spectrum known to those skilled in the art.

[0088] In some embodiments, the target bacterial cell is selected from the group consisting of, but not limited to, Bacteroides thetaiotaomicron, Bacteroides fragilis, Bacteroides distasonis, Bacteroides vulgatus, Clostridium leptum, Clostridium coccoides, Staphylococcus aureus, Bacillus subtilis, Clostridium butyricum, Brevibacterium lactofermentum, Streptococcus agalactiae, Lactococcus lactis, and the like. lactis, Leuconostoc lactis, Actinobacillus actinobycetemcomitans, cyanobacteria, Escherichia coli, Helicobacter pylori, Selnomonas ruminatium, Shigella sonnei, Zymomonas mobilis, Mycoplasma mycoides, Treponema denticola, Bacillus thuringiensis, Staphylococcus lugdunensis lugdunensis, Leuconostoc oenos, Corynebacterium xerosis, Lactobacillus plantarum, Lactobacillus rhamnosusrhamnosus, Lactobacillus casei, Lactobacillus acidophilus, Enterococcus faecalis, Bacillus coagulans, Bacillus cereus, Bacillus popillae, Synechocystis strain PCC6803, Bacillus liquefaciens, Pyrococcus abyssi, Selenomonas nominantium, Lactobacillus hilgardii hilgardii, Streptococcus ferus, Lactobacillus pentosus, Bacteroides fragilis, Staphylococcus epidermidis, Streptomyces phaechromogenes, Streptomyces ghanaenis, Klebsiella pneumoniae, Enterobacter cloacae, Enterobacter aerogenes, Serratia marcescens, Morganella morganii, Citrobacter freundii freundii, Propionibacterium freudenreichii, Pseudomonas aerigunosa, Parvimonas micramicra, Prevotella intermedia, Fusobacterium nucleatum, Prevotella nigrescens, Actinomyces israelii, Porphyromonas endodontalis, Porphyromonas gingivalis, Micrococcus luteus, Bacillus megaterium, Aeromonas hydrophila, Aeromonas caviae, Bacillus anthracis, Bartonella henselae henselae, Bartonella Quintana, Bordetella pertussis, Borrelia burgdorferi, Borrelia garinii, Borrelia afzelii, Borrelia recurrentis, Brucella abortus, Brucella canis, Brucella melitensis, Brucella suis, Campylobacter jejuni, Campylobacter coli, Campylobacter fetus, Chlamydia pneumoniae pneumoniae, Chlamydia trachomatis, Chlamydophila psittaci, Clostridium botulinumbotulinum, Clostridium difficile, Clostridium perfringens, Clostridium tetani, Corynebacterium diphtheria, Cutibacterium acnes (formerly Propionibacterium acnes), Ehrlichia canis, Ehrlichia chaffeensis, Enterococcus faecium, Francisella tularensis, Haemophilus influenzae, Legionella pneumophila pneumophila, Leptospira interrogans, Leptospira santarosai, Leptospira weilii, Leptospira noguchii, Listeria monocytogenes, Mycobacterium leprae, Mycobacterium tuberculosis, Mycobacterium ulcerans, Mycoplasma pneumonia, Neisseria gonorrhoeae, Neisseria meningitides, Nocardia asteroids), Rickettsia rickettsia, Salmonella enteritidis, Salmonella typhityphi, Salmonella paratyphi, Salmonella typhimurium, Shigella flexnerii, Shigella dysenteriae, Staphylococcus saprophyticus, Streptococcus pneumoniae, Streptococcus pyogenes, Gardnerella vaginalis, Streptococcus viridans, Treponema pallidum, Ureaplasma urealyticum, Vibrio cholerae, Vibrio parahaemolyticus, Yersinia pestis pestis, Yersinia enterocolitica, Yersinia pseudotuberculosis, Actinobacter baumannii, Pseudomonas aerignosa, and mixtures thereof, and preferably, the target bacterium is Escherichia coli, Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter cloacae, and Enterobacter aerogenes, and mixtures thereof.

[0089] In one embodiment, the target bacterium is Escherichia coli.

[0090] Thus, the bacteriophage used to prepare the bacterial delivery vehicle, and then the bacterial delivery vehicle, can target (e.g., specifically target) and specifically deliver plasmids to bacterial cells from any one or more of the aforementioned bacterial genera and / or species.

[0091] In one embodiment, the target bacteria is a pathogenic bacterium. The target bacteria can be a pathogenic bacterium.

[0092] The target bacteria are antibacterial-resistant bacteria, and may be preferably selected from the group consisting of extended-spectrum beta-lactamase-producing (ESBL) Escherichia coli, ESBL Klebsiella pneumoniae, vancomycin-resistant Enterococcus (VRE), methicillin-resistant Staphylococcus aureus (MRSA), multidrug-resistant (MDR) Acinetobacter baumannii, MDR Enterobacter species, and combinations thereof. Preferably, the target bacteria may be selected from the group consisting of extended-spectrum beta-lactamase-producing (ESBL) Escherichia coli strains.

[0093] Alternatively, the target bacteria may be bacteria of the microbiome of a given species, preferably bacteria of the human microbiota.

[0094] The present disclosure is directed to a bacterial delivery vehicle containing a payload described herein. The bacterial delivery vehicle is prepared from a bacterial virus. The bacterial delivery vehicle is selected so as to be capable of introducing the payload into the target bacterium.

[0095] The bacterial virus from which the bacterial delivery vehicle having the chimeric receptor-binding protein can be derived is preferably a bacteriophage. Optionally, the bacteriophage is selected from the Order Caudovirales, based on the taxonomy of Krupovic et al., Arch Virol, 2015.

[0096] Bacteriophages include those of the Myoviridae family (e.g., but not limited to, the genus Cp220virus, genus Cp8virus, genus Ea214virus, genus Felixo1virus, genus Mooglevirus, genus Suspvirus, genus Hp1virus, genus P2virus, genus Kayvirus, genus P100virus, genus Silviavirus, genus Spo1virus, genus Tsarbombavirus, genus Twortvirus, genus Cc31virus, genus Jd18virus, genus Js98virus, genus Kp15virus, genus Moonvirus, genus Rb49virus, genus Rb69virus, genus S16virus, genus Schizot4virus, genus Sp18virus, genus T4virus, genus Cr3virus, genus Se1virus, genus V5virus, genus Abouovirus, genus Agatevirus, genus Agrican357virus, genus Ap22virus, genus Arv1virus, and B4virus). The virus may be selected from the genera Bastillevirus, Bastillevirus, Bc431virus, Bcep78virus, Bcepmuvirus, Biquartavirus, Bxz1virus, Cd119virus, Cp51virus, Cvm10virus, Eah2virus, Elvirus, Hapunavirus, Jimmervirus, Kpp10virus, M12virus, Machinavirus, Marthavirus, Msw3virus, Muvirus, Myohalovirus, Nit1virus, P1virus, Pakpunavirus, Pbunavirus, Phikzvirus, Rheph4virus, Rsl2virus, Rslunavirus, Secunda5virus, Sep1virus, Spn3virus, Svunavirus, Tg1virus, Vhmlvirus and Wphvirus.

[0097] Bacteriophages include those of the family Podoviridae (e.g., but not limited to, the genus Fri1virus, Kp32virus, Kp34virus, Phikmvvirus, Pradovirus, Sp6virus, T7virus, Cp1virus, P68virus, Phi29virus, Nona33virus, Pocjvirus, Tl2011virus, Bcep22virus, Bpp1virus, Cba41virus, Dfl12virus, and the like). The virus may be selected from the genera: B1, B2, B3, B4, B5, B6, B7, B8, B9, B10, B11, B12, B13, B14, B15, B16, B17, B18, B19, B20, B21, B22, B23, B24, B25, B26, B27, B28, B29, B30, B31, B32, B33, B34, B35, B36, B37, B38, B39, B40, B41, B42, B43, B44, B45, B46, B47, B48, B49, B49, B49, B40, B41, B42, B43, B44, B45, B46, B47, B48, B49, B49, B49, B40, B41, B42, B43, B44, B45, B45, B46, B47, B48, B49 ...0, B41, B42, B43, B44, B4

[0098] Bacteriophages include those of the family Siphoviridae (e.g., but not limited to, the genera Camvirus, Likavirus, R4virus, Acadianvirus, Coopervirus, Pg1virus, Pipefishvirus, Rosebushvirus, Brujitavirus, Che9cvirus, Hawkeyevirus, Plotvirus, Jerseyvirus, K1gvirus, Sp31virus, Lmd1virus, Una4virus, Bongovirus, Revirus, and the like). y virus genus, Butters virus genus, Charlie virus genus, Redi virus genus, Baxter virus genus, Nymphadora virus genus, Bignus virus genus, Fishburne virus genus, Phayonce virus genus, Kp36 virus genus, Rogue1 virus genus, Rtp virus genus, T1 virus genus, Tls virus genus, Ab18 virus genus, Amigo virus genus, Anatole virus genus, Andromeda virus genus, Attis virus genus, Barnyard virus genus, Bernal13 virus genus, Biseptima virus genus, Bron virus genus, C2 virus genus, C5 virus genus, Cba181 virus genus, Cbast virus genus, Ceci virus genus, Che8 virus genus, Chi virus genus, Cjw1 virus genus, Corndog virus genus, Cronus virus genus, D3112 virus genus, D3 virus genus, Decurro virus genus, Demosthenes virus genus, Doucette virus genus, E125 virus genus, Eiau virus genus, Ff47 virus genus, Gaia virus genus, Giles virus genus, Gordon virus genus Virus genera, Gordtnk virus genus, Harrison virus genus, Hk578 virus genus, Hk97 virus genus, Jenst virus genus, Jwx virus genus, Kellezio virus genus, Korra virus genus, L5 virus genus, lambda virus genus, Laroye virus genus, Liefie virus genus, Marvin virus genus, Mudcat virus genus, N15 virus genus, Nonag virus genus, Np1 virus genus, Omega virus genus, P12002 virus genus, P12024 virus genus, P23 virus genus, P70 virus genus,Pa6 virus genus, Pamx74 virus genus, Patience virus genus, Pbi1 virus genus, Pepy6 virus genus, Pfr1 virus genus, Phic31 virus genus, Phicbk virus genus, Phieta virus genus, Phifel virus genus, Phijl1 virus genus, Pis4a virus genus, Psa virus genus, Psimuna virus genus, Rdjl virus genus, Rer2 virus genus, Sap6 virus genus, Send513 virus genus, Septima3 virus genus, Seurat virus genus, Sextaec virus genus, Sfi11 virus genus, Sfi21dt1 virus genus, Sitara virus The virus may be selected from the genera: Sarcovirus, Sk1virus, Slashvirus, Smoothievirus, Soupsvirus, Spbetavirus, Ssp2virus, T5virus, Tankvirus, Tin2virus, Titanvirus, Tm4virus, Tp21virus, Tp84virus, Triavirus, Trigintaduovirus, Vegasvirus, Vendettavirus, Wbetavirus, Wildcatvirus, Wizardvirus, Woesvirus, Xp10virus, Ydn12virus, and Yuavirus.

[0099] The bacteriophage may be selected from the family Ackermannviridae (for example, but not limited to, the genera Ag3, Limestone, Cba120, and Vi1).

[0100] In some cases, the bacteriophage is not part of the Caudovirales order, but belongs to a family with an unclassified order, such as, but not limited to, the family Tectiviridae (e.g., genera Alphatectiviridae, Betatectiviridae), the family Corticoviridae (e.g., genus Corticovirus), the family Inoviridae (e.g., genus Fibrovirus, genus Habenivirus, genus Inovirus, genus Lineavirus, genus Plectrovirus, genus Saevirus, genus tivirus, Vespertiliovirus), Cystoviridae (e.g., Cystovirus), Leviviridae (e.g., Allolevivirus, Levivirus), Microviridae (e.g., Alpha3microvirus, G4microvirus, Phix174microvirus, Bdellomicrovirus, Chlamydiamicrovirus, Spiromicrovirus), and Plasmaviridae (e.g., Plasmavirus).

[0101] In some cases, the bacteriophage targets archaea that are not part of the Caudovirales but are from a family with an unclassified order, such as, but not limited to, Ampullaviridae, Fuselloviridae, Globuloviridae, Guttaviridae, Liposthrixviridae, Pleolipoviridae, Rudiviridae, Salterprovirus, and Bicaudaviridae.

[0102] A non-exhaustive list of bacterial genera and their known host-specific bacterial viruses is provided in the following paragraphs. The chimeric RBPs and bacterial delivery vehicles disclosed herein can be engineered from the following phages, as non-limiting examples: Synonyms and orthographic variations are indicated in parentheses. Homophones are repeated the various times they occur (e.g., D, D, d). Unnamed phages are indicated by "NN" next to their genus and their number in parentheses.

[0103] Bacteria of the genus Actinomyces can be infected by the following phages: Av-I, Av-2, Av-3, BF307, CT1, CT2, CT3, CT4, CT6, CT7, CT8 and 1281.

[0104] Bacteria of the genus Aeromonas can be infected by the following phages: AA-I, Aeh2, N, PMl, TP446, 3, 4, 11, 13, 29, 31, 32, 37, 43, 43-10T, 51, 54, 55R.1, 56, 56RR2, 57, 58, 59.1, 60, 63, Aehl, F, PM2, 1, 25, 31, 40RR2.8t, (syn= 44R), (syn= 44RR2.8t), 65, PM3, PM4, PM5, and PM6.

[0105] A、aizl、Al-KI、B 、BCJAl、BCl、BC2、BLLl、BLl、BP142、BSLl、BSL2、BS l、BS3、BS8、BS15、BS18、BS22、BS26、BS28、BS31、BS104、BS105、BS106、BTB、B1715V1、C、CK-I、Coll、Co rl, CP-53, CS-I, CSi, D, D, D, D5, entl, FP8, FP9, FSi, FS2, FS3, FS5, FS8, FS9, G, GH8, GT8, GV-I, GV-2, GT-4, g3, gl2, gl3, gl4, gl6, gl7, g21, g23, g24, g29, H2, kenl, KK-88, Kuml, Kyul, J7W-1, LP52, (syn= LP-52)、L7、Mexl、MJ-I、mor2、MP-7、MPlO、MP12、MP14、MP15、Neol、N° 2、N5、N6P、PBCl、PBLA、PBPl、P2、Sa、SF2、SF6、Shal、Sill、SP02、(syn= ΦSPP1)、SPβ、STI、STi、SU-Il、t、TbI、Tb2、Tb5、TbIO、Tb26、Tb51、Tb53、Tb55、 Tb77、Tb97、Tb99、Tb560、Tb595、Td8、Td6、Tdl5、TgI、Tg4、Tg6、Tg7、Tg9、TgIO、 TgIl、Tgl3、Tgl5、Tg21、Tinl、Tin7、Tin8、Tinl3、Tm3、Tocl、Togl、toll、TP-I 、TP-10vir、TP-15c、TP-16c、TP-17c、TP-19、TP35、TP51、TP-84、Tt4、Tt6、type A、type B、type C、type D、type E、Tφ3、VA-9、W、wx23、wx26、Yunl、α、γ、pl l、φmed-2、φT、φμ-4、φ3T、φ75、φlO5、(syn= φlO5)、IA、IB、1-97A、1-97B、2、2、3、3、3、5、12、14、20、30、35、36、37、38、41C、51、6 3、64、138D、I、II、IV、NN-バチルス(13)、alel、ARl、AR2、AR3、AR7、AR9、Bace-11、(syn= 11)、Bastille、BLl、BL2、BL3、BL4、BL5、BL6、BL8、BL9、BP124. BS28, BS80, Ch, CP-51, CP-54, D-5, Darl, Denl, DP-7, Entl, FoSi, FoS2, FS4, FS6, FS7, G, Gall, Gamma, G El, GF-2, GSi, GT-I, GT-2, GT-3, GT-4, GT-5, GT-6, GT-7, GV-6, gl5, 19, 110, ISi, K, MP9, MP13, MP21, MP23 MP24, MP28, MP29, MP30, MP32, MP34, MP36, MP37, MP39, MP40, MP41, MP43, MP44, MP45, MP47, MP50, NLP-I No .l, N17, N19, PBSl, PKl, PMBl, PMB12, PMJl, S, SPOl, SP3, SP5, SP6, SP7, SP8, SP9, SPlO, SP-15, SP50 (syn= SP-50) SP82 SST subl SW Tg8 Tgl2 Tgl3 Tgl4 thul thuΛ thuS Tin4 Tin23 TP-13 TP33 TP50 TSP-I type V type VI, V, Vx, β22, φe, φNR2, φ25, φ63, 1, 1, 2, 2C, 3NT, 4, 5, 6 7, 8, 9, 10, 12, 12, 17, 18, 19, 21, 138, III, 4(B. megateriwn))、4(B.セァリス(B. sphaericus)) AR13 BPP-IO BS32 BS107 Bl B2 GA-I GP-IO GV-3 GV-5 g8 MP20 MP27 MP49N f PP5, PP6, SF5, Tgl8, TP-I, Versailles, φl5, φ29, 1-97, 837 / IV, mι-バチス(1), BatlO, BSLlO, BSLI l, BS6, BSI l, BS16, BS23, BSlOl, BS102, gl8, morl, PBLl, SN45, thu2, thu3, TmI, Tm2, ​​TP-20, TP21, TP52, type F, type G, type IV, HN-BacMus(3), BLE (syn= θc) BS2, BS4, BS5, BS7, BlO, B12, BS20, BS21, F, MJ-4, PBA12. AP50, AP50-04, AP50-11, AP50-23, AP50-26, AP50-27, and Bam3The following Bacillus-specific phages have been deleted: DLP10716, DLP-11946, DPB5, DPB12, DPB21, DPB22, DPB23, GA-2, M, No. IM, PBLB, PBSH, PBSV, PBSW, PBSX, PBSY, PBSZ, phi, SPa, type 1, and μ.

[0106] Bacteria of the genus Bacteriodes can be infected by the following phages: ad I2, Baf-44, Baf-48B, Baf-64, Bf-I, Bf-52, B40-8, F1, β1, φAl, φBrOl, φBrO2, 11, 67.1, 67.3, 68.1, mt-Bacteroides (3), Bf42, Bf71, HN-Bdellovibrio (1), and BF-41.

[0107] Bacteria of the genus Bordetella can be infected by the following phages: 134 and NN-Bordetella (3).

[0108] Bacteria of the genus Borrellia can be infected by the following phages: NN-Borrellia (1) and NN-Borrellia (2).

[0109] Brucella bacteria can be infected by the following phages: A422, Bk, (syn= Berkeley), BM29, FOi, (syn= FOl), (syn= FQl), D, FP2, (syn= FP2), (syn= FD2), Fz, (syn= Fz75 / 13), (syn= Firenze 75 / 13), (syn= Fi), Fi, (syn= Fl), Fim, (syn= FIm), (syn= Fim), FiU, (syn= FlU), (syn= FiU), F2, (syn= F2), F3, (syn= F3), F4, (syn= F4), F5, (syn= F5), F6, F7, (syn= F7), F25, (syn= F25), (syn= £25), F25U, (syn= F25u), (syn= F25U), (syn= F25V), F44, (syn- F44), F45, (syn= F45), F48, (syn= F48), I, Im, M, MC / 75, M51, (syn= M85), P, (syn= D),S708,R,Tb,(syn= TB),(syn= Tbilisi),W,(syn= Wb),(syn= Weybridge),X,3,6,7,10 / 1,(syn= 10),(syn= F8),(syn= F8),12m,24 / 11,(syn= 24),(syn= F9), (syn= F9), 45 / 111, (syn= 45), 75, 84, 212 / XV, (syn= 212), (syn= Fi0), (syn= FlO), 371 / XXIX, (syn= 371), (syn= Fn), (syn= Fl l) and 513.

[0110] Bacteria of the genus Burkholderia can be infected by the following phages: CP75, NN-Burkholderia (1) and 42.

[0111] Bacteria of the Campylobacter genus can be infected by the following phages: C type, NTCC12669, NTCC12670, NTCC12671, NTCC12672, NTCC12673, NTCC12674, NTCC12675, NTCC12676, NTCC12677, NTCC12678, NTCC12679, NTCC12680, NTCC12681, NTCC12682, NTCC12683, NTCC12684, 32f, 111c, 191, NN-Campylobacter (2), Vfi-6, (syn= V19), VfV-3, V2, V3, V8, V16, (syn= Vfi-1), V19, V20 (V45), V46, (syn= Vfi-2), V5, V6, V7, V8, V9, V10, V11, V12, V13, V14, V15, V16, V17, V18, V19, V20 (V45), V19, V21, V22, V23, V24, V25, V26, V27, V28, V29, V30, V31, V32, V33, V34, V35, V36, V37, V38, V39, V46, V47, V48, V49, V49, V49, V50, V51, V52, V53, V54, V55, V56, V57, V58, V59, V59, V59, V60, V61, V62, V63, V64, V65, V66, V67, V68, V69, V69, V69, V-45) and NN-Campylobacter (1).

[0112] Bacteria of the genus Chlamydia can be infected by the following phages: Chpl.

[0113] Clostridium bacteria can be infected by the following phages: CAKl, CA5, Ca7, CEβ, (syn= 1C), CEγ, Cldl, c-n71, c-203 Tox-, DEβ, (syn= ID), (syn= lDt0X+), HM3, KMl, KT, Ms, NAl, (syn= Naltox+), PA135Oe, Pfo, PL73, PL78, PL81, Pl, P50, P5771, P19402, lCt0X+, 2Ct0X\ 2D3 (syn= 2Dt0X+), 3C, (syn= 3Ctox+), 4C, (syn= 4Ct0X+), 56, III-l, NN-Clostridium (61), NBlt0X+, αl, CAl, HMT, HM2, PFl5 P-23, P-46, Q-05, Q-oe, Q-16, Q-21, Q-26, Q-40, Q-46, S111, SA02, WA01, WA03, Wm, W523, 80, C, CA 2, CA3, CPTl, CPT4, cl, c4, c5, HM7, H11 / A1, H18 / Ax, FWS23, Hi58ZA1, K2ZA1, K21ZS23, ML, NA2t0X; Pf2, Pf3, Pf4, S9ZS3, S41ZA1, S44ZS23, α2, 41, 112ZS23, 214 / S23, 233 / Ai, 234 / S23, 235 / S23, II-l, II-2, II-3, NN-Clostridium (12), CAl, Fl, K, S2, 1, 5, and NN-Clostridium (8).

[0114] Bacteria of the genus Corynebacterium can be infected by the following phages: CGKl (deleted), A, A2, A3, AlOl, A128, A133, A137, A139, A155, A182, B, BF, B17, B18, B51, B271, B275, B276, B277, B279, B282, C, capi, CCl, CGl, CG2, CG33, CL31, Cog, (syn= CG5), D, E, F, H, HI, hqi, hq2, 11ZH33, Ii / 31, J, K, K, (syn= Ktox), L, L, (syn= Ktox) Ltox+), M, MC-I, MC-2, MC-3, MC-4, MLMa, N, O, ovi, ov2, ov3, P, P, R, RP6, RS29, S, T, U, UB1, ub2, UH1, UH3, uh3, uh5, uh6, β, (syn= βtox+), βhv64, βvir, γ, (syn= γtoχ-), γl9, δ, (syn= δ'ox+), p, (syn= ptoχ-), Φ9, φ984, ω, IA, 1 / 1180, 2, 2 / 1180, 5 / 1180, 5ad / 9717, 7 / 4465, 8 / 4465, 8ad / 10269, 10 / 9253, 13Z9253, 15 / 3148, 21 / 9253, 28, 29, 55, 2747, 2893, 4498 and 5848.

[0115] Bacteria of the genus Enterococcus are infected by the following phages: DF78, Fl, F2, 1, 2, 4, 14, 41, 867, Dl, SB24, 2BV, 182, 225, C2, C2F, E3, E62, DS96, H24, M35, P3, P9, SBlOl, S2, 2BII, 5, 182a, 705, 873, 881, 940, 1051, 1057, 21096C, NN-Enterococcus (1), PEl, Fl, F3, F4, VD13, 1, 200, 235, and 341.

[0116] Bacteria of the genus Eysipelothrix can be infected by the following phages: NN-Eysipelothrix (1).

[0117] Bacteria of the genus Escherichia can be infected by the following phages: BW73, B278, D6, D108, E, El, E24, E41, FI-2, FI-4, FI-5, HI8A, Ffl8B, i, MM, Mu, (syn= mu), (syn= MuI), (syn= Mu-I), (syn= MU-I), (syn= MuI), (syn= μ), 025, PhI-5, Pk, PSP3, Pl, PlD, P2, P4(deletion), Sl, Wφ, φK13, φR73(deletion), φl, φ2, φ7, φ92, ψ(deletion), 7 A, 8φ, 9φ, 15 (deletion), 18, 28-1, 186, 299, HH-Escherichia (2), AB48, CM, C4, C16, DD-VI, (syn= Dd-Vi), (syn= DDVI), (syn= DDVi), E4, E7, E28, FIl, FI3, H, Hl, H3, H8, K3, M, N, ND-2, ND-3, ND4, ND-5, ND6, ND-7, Ox-I (syn= OXl), (syn= HF), Ox-2 (syn= 0x2), (syn= 0X2), Ox-3, Ox-4, Ox-5, (syn= 0X5), Ox-6, (syn= 66F), (syn= φ66t), (syn= φ66t-)5 0111, PhI-I, RB42, RB43, RB49, RB69, S, SaI-I, Sal-2, Sal-3, Sal-4, Sal-5, Sal-6, TC23, TC45, TuII * -6, (syn= TuII * ), TuIP-24, TuII *46, TuIP-60, T2, (syn= ganuTia), (syn= γ), (syn= PC), (syn= P.C.), (syn= T-2), (syn= T2), (syn= P4), T4, (syn= T-4), (syn= T4), T6, T35, αl, 1, IA, 3, (syn= Ac3), 3A, 3T+, (syn= 3), (syn= Ml), 5φ, (syn= φ5), 9266Q, CFO103, HK620, J, K, KlF, m59, no. A, no. E, no. 3, no. 9, N4, sd, (syn= Sd), (syn= SD), (syn= Sa)3 (syn= sd), (syn= SD), (syn= CD), T3, (syn= T-3), (syn= T3), T7, (syn= T-7), (syn= T7), WPK, W31, ΔH, φC3888, φK3, φK7, φK12, φV-1, Φ04-CF, Φ05, Φ06, Φ07, φl, φl.2, φ20, φ95, φ263, φlO92, φl, φll, (syn= φW), Ω8, 1, 3, 7, 8, 26, 27, 28-2, 29, 30, 31, 32, 38, 39, 42, 933W, NN-Escherichia (1), Esc-7-11, AC30, CVX-5, Cl, DDUP, ECl, EC2, E21, E29, Fl, F26S, F27S, Hi, HK022, HK97, (syn= ΦHK97), HK139, HK253, HK256, K7, ND-I, no.D, PA-2, q, S2, Tl, (syn= α), (syn= P28), (syn= T-I), (syn= Tx), T3C, T5, (syn= T-5), (syn= T5), UC-I, w, β4, γ2, λ(syn= lambda), (syn= Φλ), ΦD326, φγ, Φ06, Φ7, Φ10, φ80, χ, (syn= χi), (syn= φχ), (syn= φχi), 2, 4, 4A, 6, 8A, 102, 150, 168, 174, 3000, AC6, AC7, AC28, AC43, AC50, AC57, AC81, AC95, HK243, KlO, ZG / 3A, 5, 5A, 21EL, H19-J and 933H.

[0118] Bacteria of the genus Fusobacterium are infected by the following phages: NN-Fusobacterium (2), fv83-554 / 3, fv88-531 / 2, 227, fv2377, fv2527, and fv8501.

[0119] Bacteria of the genus Haemophilus are infected by the following phages: HP1, S2 and N3.

[0120] Bacteria of the genus Helicobacter are infected by the following phages: HP1 and ^^-Helicobacter (1).

[0121] Klebsiella bacteria are infected by the following phages: AIO-2, KI4B, Kl6B, Kl9, (syn= K19), Kl14, Kl15, Kl21, Kl28, Kl29, KI32, Kl33, Kl35, Kl106B, Kl171B, Kl181B, Kl832B, AIO-I, AO-I, AO-2, AO-3, FC3-10, K, Kl1, (syn= KI1), Kl2, (syn= K12), Kl3, (syn= K13), (syn= Kl 70 / 11), Kl4, (syn= K14), Kl5, (syn= K15), Kl6, (syn= K16), Kl7, (syn= K17), Kl8, (syn= K18), Kl19, (syn= K19), Kl27, (syn= K127), Kl31, (syn= K131), Kl35, Kl171B, II, VI, IX, CI-I, Kl4B, Kl8, Kl11, Kl12, Kl13, Kl16, Kl17, Kl18, Kl20, Kl22, Kl23, Kl24, Kl26, Kl30, Kl34, Kl106B, KIi65B, Kl328B, KLXI, K328, P5046, 11, 380, III, IV, VII, VIII, FC3-11, Kl2B, (syn= K12B), Kl25, (syn= K125), Kl42B, (syn= K142), (syn= K142B), Kl181B, (syn= KIl 81), (syn= K1181B), Kl765 / !, (syn= K1765 / 1), Kl842B, (syn= K1832B), Kl937B, (syn= K1937B), Ll, φ28, 7, 231, 483, 490, 632 and 864 / 100.

[0122] Bacteria of the genus Lepitospira are infected by the following phages: LEl, LE3, LE4, and NN-leptospira (1).

[0123] Listeria bacteria are infected by the following phages: A511, 01761, 4211, 4286, (syn= BO54), A005, A006, A020, A500, A502, A511, Al 18, A620, A640, B012, B021, B024, B025, B035, B051, B053, B054, B055, B056, BlOl, BI lO, B545, B604, B653, C707, D441, HSO47, HlOG, H8 / 73, H19, H21, H43, H46, H107, H108, HI lO, H163 / 84, H312, H340, H387, H391 / 73, H684 / 74, H924A, PSA, U153, φMLUP5, (syn= P35), 00241, 00611, 02971A, 02971C, 5 / 476, 5 / 911, 5 / 939, 5 / 11302, 5 / 11605, 5 / 11704, 184, 575, 633, 699 / 694, 744, 9 00, 1090, 1317, 1444, 1652, 1806, 1807, 1921 / 959, 1921 / 11367, 1921 / 11500, 1921 / 11566, 1921 / 12460, 1921 / 12582, 1 967, 2389, 2425, 2671, 2685, 3274, 3550, 3551, 3552, 4276, 4277, 4292, 4477, 5337, 5348 / 11363, 5348 / 11646, 5348 / 12430, 5348 / 12434, 10072, 11355C, 11711A, 12029, 12981, 13441, 90666, 90816, 93253, 907515, 910716, and NN-Listeria (15).

[0124] Bacteria of the genus Morganella are infected by the following phages:47

[0125] Bacteria of the genus Mycobacterium are infected by the following phages: 13, AGl, ALi, ATCC 11759, A2, B.C3, BG2, BKl, BK5, butyricum, BI, B5, B7, B30, B35, Clark, Cl, C2, DNAIII, DSP1, D4, D29, GS4E, (syn= GS4E), GS7, (syn= GS-7), (syn= GS7), IPa, lacticola, Legendre, Leo, L5, (syn= ΦL-5), MC-I, MC-3, MC-4, minetti, MTPHI l, Mx4, MyF3P / 59a, phlei, (syn= phlei 1), phlei 4, and Polonus. II, rabinovitschi, smegmatis, TM4, TM9, TMlO, TM20, Y7, YlO, φ630, IB, IF, IH, 1 / 1, 67, 106, 1430, Bl, (syn= Bol), B24, D, D29, FK, FS, HP, Polonus I, Roy, Rl, (syn= Rl-Myb), (syn= Ri), 11, 31, 40, 50, 103a, 103b, 128, 3111-D, 3215-D and NN-Mycobacterium (1).

[0126] Bacteria of the genus Neisseria are infected by the following phages: Group I, group II and NP1.

[0127] Bacteria of the genus Nocardia are infected by the following phages: MNP8, NJ-L, NS-8, N5 and TtiN-Nocardia.

[0128] Bacteria of the genus Proteus are infected by the following phages: Pm5, 13vir, 2 / 44, 4 / 545, 6 / 1004, 13 / 807, 20 / 826, 57, 67b, 78, 107 / 69, 121, 9 / 0, 22 / 608, 30 / 680, PmI, Pm3, Pm4, Pm6, Pm7, Pm9, PmIO, PmI l, Pv2, πl, φm, 7 / 549, 9B / 2, 10A / 31, 12 / 55, 14, 15, 16 / 789, 17 / 971, 19A / 653, 23 / 532, 25 / 909, 26 / 219, 27 / 953, 32A / 909, 33 / 971, 34 / 13, 65, 5006M, 7480b, VI, 13 / 3a, Clichy 12, π2600, φχ7, 1 / 1004, 5 / 742, 9, 12, 14, 22, 24 / 860, 2600 / D52, Pm8 and 24 / 2514.

[0129] Bacteria of the genus Providencia are infected by the following phages: PL25, PL26, PL37, 9211 / 9295, 9213 / 921 Ib, 9248, 7 / R49, 7476 / 322, 7478 / 325, 7479, 7480, 9000 / 9402 and 9213 / 921 Ia.

[0130] (syn=) Pf-I)、Pf2、Pf3、PP7、PRRl、7s、im-シュードモナス(1)、AI-I、AI-2、B 17、B89、CB3、Col 2、Col 11、Col 18、Col (syn= PBl)、pfl6、PMN17、PPl、PP8、Psal、PsPl、PsP2、PsP3、PsP4、PsP5、PS3、PS17、PTB80、PX4、PX 7、PYOl、PYO2、PYO5、PYO6、PYO9、PYOlO、PYO13、PYO14、PYO16、PYO18、PYO19、PYO20、PYO29、 PYO32, PYO33, PYO35, PYO36, PYO37, PYO38, PYO39, PYO41, PYO42, PYO45, PYO47, PYO48, PYO64, PYO69, PYO103, PlK, SLPl, SL2, S2, UNL-I, wy, Yai, Ya4, Yan, φBE, φCTX, φC17, φKZ, (syn= ΦKZ)、φ-LT、Φmu78、φNZ、φPLS-1、φST-1、φW-14、φ-2、1 / 72、2 / 79、3、3 / DO、4 / 237、5 / 406、6C、6 / 6660、7、7v、7 / 184、8 / 280、9 / 95、10 / 502、11 / DE、12 / 100、12S、16、21、24、25F、27、31、44、68、71、95、109、188、33 7、352、1214、HN-シュードモナス(23)、A856、B26、CI-I、CI-2、C5、D、gh-1、Fl 16、HF、H90、K5、K6、Kl 04、K109、K166、K267、N4、N5、O6N-25P、PE69、Pf、PPN25、PPN3 5、PPN89、PPN91、PP2、PP3、PP4、PP6、PP7、PP8、PP56、PP87、PPl 14、PP206、PP207、PP306、PP651、Psp231a、Pssy401、Pssy9220、psi、PTB2、PTB20、PTB42、PXl、PX 3,P 7, φPLS743, φS-1, 1, 2, 2, 3, 4, 5, 6, 7, 7, 8, 9, 10, 11, 12, 12B, 13, 14 15, 14, 15, 16, 17, 18, 19, 20, 20, 21, 21, 22, 23, 23, 24, 25, 31, 119x, 145, 147, 170, 267, 284, 308, 525, NN-Current (5) of A7, B3 B33, B39, BI-I, C22, D3, D37, D40, D62, D3112, F7, FlO, g, gd, ge, gξ Hwl2, Jb 19. KFl, L°, OXN-32P, O6N-52P, PCH-I, PC13-1, PC35-1, PH2, PH51 PH93, PH132, PMW, PM13, PM57, PM61, PM62, PM63, PM69, PM105, PMl 13 PM681, PM682, PO4, PPl, PP4, PP5, PP64, PP65, PP66, PP71, PP86, PP88, PP92, PP401, PP711, PP891 Pssy41, Pssy42, Pssy403, Pssy404, Pssy420, Pssy923, PS4, PS-IO, Pz, SDl, SLl, SL3, SL5, SM, φC5, φCl l, φCl l-1, φC13, φC15, φMO, φX, φO4, φl l φ240, 2, 2F, 5, 7m, 11, 13, 13 / 441, 14, 20, 24, 40, 45, 49, 61, 73, 148, 160, 198, 218, 222, 236, 242, 246, 249, 258, 269, 295, 297, 309, 318, 342, 350, 351, 357-1, 400-1, HN- GlOl, M6, M6a, Ll, PB2, Pssyl5, Pssy4210, Pssy4220, PYO12, PYO34, PYO4 9. PYO50, PYO51, PYO52, PYO53, PYO57, PYO59, PYO200, PX2, PX5, SL4, φO3, φO6, and 31214.

[0131] The diagram of the rhinoceros is in the form of NN-Rickettsia.

[0132] Bacteria of the genus Salmonella are infected by the following phages: b, Beccles, CT, d, Dundee, f, FeIs 2, GI, GUI, GVI, GVIII, k, K, i, j, L, 01, (syn = 0-1), (syn = O1), (syn = O-I), (syn = 7), 02, 03, P3, P9a, PlO, Sab3, Sab5, SanlS, Sanl7, SI, Taunton, ViI, (syn = ViI), 9, im Salmonella(1), N-I, N-5, N-IO, N-17, N-22, 11, 12, 16-19, 20.2, 36, 449C / C178, 966A / C259, a, B.A.O.R., e, G4, GUI, L, LP7, M, MG40, N-18, PSA68, P4, P9c, P22, (syn = P22), (syn = PLT22), (syn = PLT22), P22al, P22-4, P22-7, P22-11, SNT-I, SNT-2, SP6, Villi, ViIV, ViV, ViVI, ViVII, Worksop, Sj5, ε34, 1,37, 1(40), (syn = φl

[40] ), 1,422, 2, 2.5, 3b, 4, 5, 6,14(18), 8, 14(6,7), 10, 27, 28B, 30, 31, 32, 33, 34, 36, 37, 39, 1412, SNT-3, 7-11, 40.3, c, C236, C557, C625, C966N, g, GV, G5, Gl 73, h, IRA, Jersey, MB78, P22-1, P22-3, P22-12, Sabl, Sab2, Sab2, Sab4, Sanl, San2, San3, San4, San6, San7, San8, San9, Sanl3, Sanl4, Sanl6, Sanl8, Sanl9, San20, San21, San22, San23, San24, San25, San26, SasLl, SasL2, SasL3, SasL4, SasL5, SlBL, SII, ViII, φl, 1, 2, 3a, 3al, 1010, Ym-Salmonella(1), N-4, SasL6 and 27.

[0133] Serratia bacteria are infected by the following phages: A2P, PS20, SMB3, SMP, SMP5, SM2, V40, V56, ic, ΦCP-3, ΦCP-6, 3M, 10 / la, 20A, 34CC, 34H, 38T, 345G, 345P, 501B, SMB2, SMP2, BC, BT, CW2, CW3, CW4, CW5, Lt232, L2232, L34, L.228, SLP, SMPA, V .43, σ, φCWl, ΦCP6-1, ΦCP6-2, ΦCP6-5, 3T, 5, 8, 9F, 10 / 1, 2OE, 32 / 6, 34B, 34CT, 34P, 37, 41, 56, 56D, 56P, 6OP, 6 1 / 6, 74 / 6, 76 / 4, 101 / 8900, 226, 227, 228, 229F, 286, 289, 290F, 512, 764a, 2847 / 10, 2847 / 1Oa, L.359 and SMBl.

[0134] You can also use the following expression: Fsa(syn= a)(syn=d=(FSD=2d)2d). W2d). HVIII)、SKγ66、(syn= gamma 66)、(syn= yββ)、(syn= γ66b)、SKm、(syn= SIIIb)5 (syn= UI)、SKw、(syn= Siva)、(S=(syn=IC)、、(Syn=IC IV). SIVA.) (syn= IVA)、(syn= KVI)、(syn= Svi)、(syn= VI)、SKvm、(syn= Svm)、(syn= VIII)、SKVΠIA、(syn= SvmA=)、(syn= SvmA=)、 VIIIA). K29)、FlO、(syn= FSlO)、(syn= K31)、I1、(syn= alpha)、(syn= FSa)、(syn= Kl 8)、(syn= α)、I2、(syn= a)、、、= K19)、、= K19 G35). K2)、(syn= KII)、(syn= Sn)、(syn= II)、(syn= Sm)、(syn= SsIV)、(syn= IV)、SK1Va、(syn= Swab)(sIVa=syn=) IVa)、SKV、(syn= K4)、(syn= KV)、(syn= SV)、(syn= SsV)、(syn= V)、SKx、(syn= K9)、(syn= KX)、(syn= SX)、(X=)、= SsX T35)、(syn= 35-50-R)、STvm、(syn=T8345)、(syn= 8345-SO-SR)、W1、(syn= D8)、(syn= FSD8)、W2a、(syn= D2A)、(syn= FS2a)、DD-2、Sf6、FSi=6、(syn=F F6). 1881-SO-R)、γ66、(syn= gamma 66a)、(syn= Ssγ66)、φ2、BIl、DDVII、(syn= DD7)、FSD2b、(syn= W2B)、=Fsyn2= F2)、FS4、(syn= F4)、(syn= F4)、FS5、(syn= F5)、(syn= F5)、FS9、(syn= F9)、(syn= F9)、FI l、P2-S0-S、(syn=G6)-SO、(syn=G36)、 G36). HXn)、SKI、KI、(syn= S1)、(syn= SsI)、(syn= Svπ)、(syn= SsVII)、(syn= KIX)、(syn= S1x) SsIX)、SKXII、(syn= KXII)、(syn= Sxn)、(syn= SsXII)、STi、STffl、STrv、STVi、STvπ、S70、S206、U2-S0-S、3 210-SO-S、3859-SO-S、4020-SO-S、φ3、φ5、φ7、φ8、ϕ9、φlO、φl l、ϕl3、ϕl4、ϕl8、SHm、(syn= Hπi)、SHχi、(syn= HXt) or SKxI、(syn= KXI)、(syn= Sχi)、=X= Ss(XπI)

[0135] A、EW、K、Ph5、Ph9:A、EW、K、Ph5、Ph9 (syn= Sb-I)、S3K、Twort、ΦSK311、φ812、06、40、58、119、130、131、200、1623、STCl、(syn= stcl)、STC2、(syn= stc2)、44AHJD、68、ACl、AC2、A6"C"、A9"C"、b581、CA-I、CA-2、CA-3、CA-4、CA-5、DI l, L39x35, L54a, M42, Nl, N2, N3, N4, N5, N7, N8, NlO, Ni l, N12, N13, N14, N16, Ph6, Phl2, Phl4, UC-18, U4, U15, Sl, S2, S3, S4, S5, X2, Z1, φB5-2, φD, ω, 11, (syn= φl l), (syn= P11-M15)、15、28、28A、29、31、31B、37、42D、(syn= P42D)、44A、48、51、52、52A、(syn= P52A)、52B、53、55、69、71、(syn= P71)、71A、72、75、76、77、79、80、80α、82、82A、83 A、84、85、86、88、88A、89、90、92、95、96、102、107、1 08、111、129-26、130、130A、155、157、157A、165、187 、275、275A、275B、356、456、459、471、471A、489、58 1、676、898、1139、1154A、1259、1314、1380、1405、15 63、2148、2638A、2638B、2638C、2731、2792A、2792B、2818、2835、2848A、3619、5841、12100、AC3、A8、AlO A13, b594n, D, HK2, N9, N15, P52, P87, Sl, S6, Z4, φRE, 3A, 3B, 3C, 6, 7, 16, 21, 42B, 42C, 42E, 44, 47, 47A5 47C、51、54、54x1、70、73、75、78、81、82、88、93、94、1 01、105、110、115、129 / 16、174、594n、1363 / 14、2460 and mS-スタフィロコッカス(1)。

[0136] Bacteria of the genus Streptococcus are infected by the following phages: EJ-I, NN-Streptococcus (1), a, Cl, FL0Ths, H39, Cp-I, Cp-5, Cp-7, Cp-9, Cp-IO, AT298, A5, alO / Jl, alO / J2, alO / J5, alO / J9, A25, BTIl, b6, CAl, c20-l, c20-2, DP-I, Dp-4, DTl, ET42, elO, FA101, FEThs, Fκ, FKKIOI, FKLIO, FKP74, FKH, FLOThs, FyIOl, fl, F10, F20140 / 76, g, GT-234, HB3, (syn= HB-3), HB-623, HB-746, M102, O1205, φO1205, PST, PO, Pl, P2, P3, P5, P6, P8, P9, P9, P12, P13, P14, P49, P50, P5 1, P52, P53, P54, P55, P56, P57, P58, P59, P64, P67, P69, P71, P73, P75, P76, P77, P82, P83, P88, sc, sch, sf, SfIl 1, (syn= SFiI l), (syn= φSFill), (syn= ΦSfil l), (syn= φSfil l), sfil9, (syn= SFil9), (syn= φSFil9), (syn= φSfil9), Sfi21, (syn= SFi21), (syn= φSFi21), (syn= φSfi21), ST0, STX, st2, ST2, ST4, S3, (syn= φS3), s265, φ17, φ42, φ57, φ80, φ81, φ82, φ83, φ84, φ85, φ86, φ87, φ88, φ89, φ90, φ91, φ92, φ93, φ94, φ95, φ96, φ97, φ98, φ99, φlOO, φlOl, φlO2, φ227, φ7201, ωl, ω2, ω3, ω4, ω5, ω6, ω8, ωlO, 1, 6, 9, 1OF, 12 / 12, 14, 1 7SR, 19S, 24, 50 / 33, 50 / 34, 55 / 14, 55 / 15, 70 / 35, 70 / 36, 71 / ST15, 71 / 45, 71 / 46, 74F, 79 / 37, 79 / 38, 80 / J4, 80 / J9, 80 / ST16, 80 / 15, 80 / 47, 80 / 48, 101, 103 / 39, 103 / 40, 121 / 41, 121 / 42, 123 / 43, 123 / 44, 124 / 44 , 337 / ST17, and mStreptococcus ( 34 ).

[0137] Bacteria of the genus Treponema are infected by the following phages: NN-Treponema (1).

[0138] The structure of the solvent is as follows: CTXΦ and fs (syn= si) fs2, Ivpf5, Vfl2, Vf33, VPIΦ, VSK, v6, 493, CP-Tl, ET25, kappa, K13 9. Labol) XN-69P, OXN-86, O6N-21P, PB-I, P147, rp-1, SE3, VA-I (syn= VcA-I), VcA-2, VPl, VP2, VP4, VP7, VP8, VP9, ​​VPlO, VP17, VP18, VP19, X29 (syn= 29). d'Herelle)、t、ΦHAWI-1、ΦHAWI-2、ΦHAWI-3、ΦHAWI-4、ΦHAWI-5、ΦHAWI-6、ΦHAWI-7、 SHOW-8, ΦSHOW-9, ΦSHOW-10, ΦHCl-1, ΦHC1-2, ΦHC1-3, ΦHC1-4, ΦHC2-1,>HC2-2, ΦH C2-3, ΦHC2-4, ΦHC3-1, ΦHC3-2, ΦHC3-3, ΦHD1S-1, ΦHD1S-2, ΦHD2S-1, ΦHD2S-2, ΦHD2 S-3, ΦHD2S-4, ΦHD2S-5, ΦHDO-1, ΦHDO-2, ΦHDO-3, ΦHDO-4, ΦHDO-5, ΦHDO-6, ΦKL-33, Φ KL-34, ΦKL-35, ΦKL-36, ΦKWH-2, ΦKWH-3, ΦKWH-4, ΦMARQ-1, ΦMARQ-2, ΦMARQ-3, ΦMOA T-1, ΦO139, ΦPEL1A-1, ΦPEL1A-2, ΦPEL8A-1, ΦPEL8A-2, ΦPEL8A-3, ΦPEL8C-1, ΦPEL8C -2, ΦPEL13A-1, ΦPEL13B-1, ΦPEL13B-2, ΦPEL13B-3, ΦPEL13B-4, ΦPEL13B-5, ΦPEL1 B-6, ΦPEL13B-7, ΦPEL13B-8, ΦPEL13B-9, ΦPEL13B-10, φVP143, φVP253, Φ16, φl38, 1- II, 5, 13, 14, 16, 24, 32, 493, 6214, 7050, 7227 II (syn= group II) (syn= φ2), V, VIII, ~m-ビリオ(13), KVP20, KVP40, nt-1, O6N-22P, P68, el, e2, e3, e4, e5, FK, G, I K, Nt-6, Nl, N2, N3, N4, N5, O6N-34P, OXN-72P, OXN-85P, OXN-100P, P, Ph-I, PL163 / 10, Q. S, T, φ92, 1-9, 37, 51, 57, 70A-8, 72A-4, 72A-10, 110A-4, 333, 4996, I (syn= group I), III (syn= group III), VI, (syn= A-Saratov), ​​VII, IX, lOA-1, 110A-5, 110A-7, hv-1, OXN-52P, P13, P38, P53, P65, P108, Pill, TPl3 VP3, VP6, VP12, VP13, 70A-3, 70A-4, 70A-10, 72A-1, 108A-3, 109-B1, 110A-2, 149, (syn = φl49), IV, (syn = group IV), NN-Vibrio (22), VP5, VP11, VP15, VP16, αl, α2, α3a, α3b, 353B, and HN-Vibrio (7).

[0139] Bacteria of the genus Yersinia are infected by the following phages: H, HI, H-2, H-3, H-4, Lucas 110, Lucas 303, Lucas 404, YerA3, YerA7, YerA20, YerA41, 3 / M64-76, 5 / G394-76, 6 / C753-76, 8 / C239-76, 9 / F18167, 1701, 1710, PST, 1 / F2852-76, D'Herelle, EV, H, Kotljarova, PTB, R, Y, YerA41, φYerO3-12, 3, 4 / C1324-76, 7 / F783-76, 903, 1 / M6176, and Yer2AT.

[0140] More preferably, the bacteriophage is Salmonella virus SKML39, Shigella virus AG3, Dickeya virus Limestone, Dickeya virus RC2014, Escherichia virus CBA120, Escherichia virus PhaxI, Salmonella virus 38, Salmonella virus Det7, Salmonella virus GG32, Salmonella virus PM10, Salmonella virus SFP10, Salmonella virus SH19, Salmonella virus SJ3, Escherichia virus ECML4, Salmonella virus Marshall, Salmonella virus Irsu Maynard, Salmonella virus SJ2, Salmonella virus STML131, Salmonella virus ViI, Erwinia virus Ea2809, Klebsiella virus 0507KN21, Serratia virus IME250, Serratia virus MAM1, Campylobacter virus CP21, Campylobacter virus CP220, Campylobacter virus CPt10, Campylobacter virus IBB35, Campylobacter virus CP81, Campylobacter virus CP30A, Campylobacter virus CPX, Campylobacter virus Rus NCTC12673, Erwinia virus Ea214, Erwinia virus M7, Escherichia virus AYO145A, Escherichia virus EC6, Escherichia virus HY02, Escherichia virus JH2, Escherichia virus TP1, Escherichia virus VpaE1, Escherichia virus wV8, Salmonella virus FelixO1, Salmonella virus HB2014, Salmonella virus Mushroom, Salmonella virus UAB87, Citrobacter virus Moogle, Citrobacter virus Mordin, Escherichia virus Escherichia virus SUSP1, Escherichia virus SUSP2, Aeromonas virus phiO18P, Haemophilus virus HP1, Haemophilus virus HP2, Pasteurella virus F108, Vibrio virus K139, Vibrio virus Kappa, Burkholderia virus phi52237, Burkholderia virus phiE122, Burkholderia virus phiE202, Escherichia virus 186, Escherichia virus P4, Escherichia virus P2, Escherichia virus Wphi, Mannheimia virus PHL101,Pseudomonas virus phiCTX, Ralstonia virus RSA1, Salmonella virus Fels2, Salmonella virus PsP3, Salmonella virus SopEphi, Yersinia virus L413C, Staphylococcus virus G1, Staphylococcus virus G15, Staphylococcus virus JD7, Staphylococcus virus K, Staphylococcus virus MCE2014, Staphylococcus virus P108, Staphylococcus virus Rodi, Staphylococcus virus S253, Staphylococcus virus S25 -4, Staphylococcal virus SA12, Listeria virus A511, Listeria virus P100, Staphylococcal virus Remus, Staphylococcal virus SA11, Staphylococcal virus Stau2, Bacillus virus Camphawk, Bacillus virus SPO1, Bacillus virus BCP78, Bacillus virus TsarBomba, Staphylococcal virus Twort, Enterococcal virus phiEC24C, Lactobacillus virus Lb338-1, Lactobacillus virus LP65, Enterobacter Virus PG7, Escherichia virus CC31, Klebsiella virus JD18, Klebsiella virus PKO111, Escherichia virus Bp7, Escherichia virus IME08, Escherichia virus JS10, Escherichia virus JS98, Escherichia virus QL01, Escherichia virus VR5, Enterobacter virus Eap3, Klebsiella virus KP15, Klebsiella virus KP27, Klebsiella virus Matisse, Klebsiella virus Miro, Citrobacter virus Merlin, Citrobacter virus Irus Moon, Escherichia virus JSE, Escherichia virus phi1, Escherichia virus RB49, Escherichia virus HX01, Escherichia virus JS09, Escherichia virus RB69, Shigella virus UTAM, Salmonella virus S16, Salmonella virus STML198, Vibrio virus KVP40, Vibrio virus nt1, Vibrio virus ValKK3, Escherichia virus VR7, Escherichia virus VR20, Escherichia virus VR25, Escherichia virus VR26, Shigella virus SP18,Escherichia virus AR1, Escherichia virus C40, Escherichia virus E112, Escherichia virus ECML134, Escherichia virus HY01, Escherichia virus Ime09, Escherichia virus RB3, Escherichia virus RB14, Escherichia virus T4, Shigella virus Pss1, Shigella virus Shfl2, Yersinia virus D1, Yersinia virus PST, Acinetobacter virus 133, Aeromonas virus 65, Aeromonas virus Aeh1, Escherichia virus RB16, Escherichia Virus RB32, Escherichia virus RB43, Pseudomonas virus 42, Cronobacter virus CR3, Cronobacter virus CR8, Cronobacter virus CR9, Cronobacter virus PBES02, Pectobacterium virus phiTE, Cronobacter virus GAP31, Escherichia virus 4MG, Salmonella virus SE1, Salmonella virus SSE121, Escherichia virus FFH2, Escherichia virus FV3, Escherichia virus JES2013, Escherichia virus V5, Brevibacillus virus Abouo, Brevibacillus virus Davies, Bacillus virus Agate, Bacillus virus Bobb, Bacillus virus Bp8pC, Erwinia virus Deimos, Erwinia virus Ea35-70, Erwinia virus RAY, Erwinia virus Simmy50, Erwinia virus Special G, Acinetobacter virus AB1, Acinetobacter virus AB2, Acinetobacter virus AbC62, Acinetobacter virus AP22, Arthrobacter virus ArV1, Arthrobacter virus T rina, Bacillus virus AvesoBmore, Bacillus virus B4, Bacillus virus Bigbertha, Bacillus virus Riley, Bacillus virus Spock, Bacillus virus Troll, Bacillus virus Bastille, Bacillus virus CAM003, Bacillus virus Bc431, Bacillus virus Bcp1, Bacillus virus BCP82, Bacillus virus BM15, Bacillus virus Deepblue, Bacillus virus JBP901, Burkholderia virus Bcep1, Burkholderia virus Bcep43,Burkholderia virus Bcep781, Burkholderia virus BcepNY3, Xanthomonas virus OP2, Burkholderia virus BcepMu, Burkholderia virus phiE255, Aeromonas virus 44RR2, Mycobacterium virus Alice, Mycobacterium virus Bxz1, Mycobacterium virus Dandelion, Mycobacterium virus HyRo, Mycobacterium virus I3, Mycobacterium virus Nappy, Mycobacterium virus Sebata, Clostridium Clostridial virus phiC2, Clostridial virus phiCD27, Clostridial virus phiCD119, Bacillus virus CP51, Bacillus virus JL, Bacillus virus Shanette, Escherichia virus CVM10, Escherichia virus ep3, Erwinia virus Asesino, Erwinia virus EaH2, Pseudomonas virus EL, Halomonas virus HAP1, Vibrio virus VP882, Brevibacillus virus Jimmer, Brevibacillus virus Osiris, Pseudomonas virus Ab 03, Pseudomonas virus KPP10, Pseudomonas virus PAKP3, Sinorhizobium virus M7, Sinorhizobium virus M12, Sinorhizobium virus N3, Erwinia virus Machina, Arthrobacter virus Brent, Arthrobacter virus Jawnski, Arthrobacter virus Martha, Arthrobacter virus Sonny, Edwardsiella virus MSW3, Edwardsiella virus PEi21, Escherichia virus Mu, Shigella virus SfMu, Halobacterium virus phiH, Bacillus virus Grass, Bacillus virus NIT1, Bacillus virus SPG24, Aeromonas virus 43, Escherichia virus P1, Pseudomonas virus CAb1, Pseudomonas virus CAb02, Pseudomonas virus JG004, Pseudomonas virus PAKP1, Pseudomonas virus PAKP4, Pseudomonas virus PaP1, Burkholderia virus BcepF1, Pseudomonas virus 141, Pseudomonas virus Ab28, Pseudomonas virus DL60, Pseudomonas virus DL68,Pseudomonas virus F8, Pseudomonas virus JG024, Pseudomonas virus KPP12, Pseudomonas virus LBL3, Pseudomonas virus LMA2, Pseudomonas virus PB1, Pseudomonas virus SN, Pseudomonas virus PA7, Pseudomonas virus phiKZ, Rhizobium virus RHEph4, Ralstonia virus RSF1, Ralstonia virus RSL2, Ralstonia virus RSL1, Aeromonas virus 25, Aeromonas virus 31, Aeromonas virus Aes12, Aeromonas virus Solanum virus Aes508, Aeromonas virus AS4, Stenotrophomonas virus IME13, Staphylococcus virus IPLAC1C, Staphylococcus virus SEP1, Salmonella virus SPN3US, Bacillus virus 1, Geobacillus virus GBSV1, Yersinia virus R1RT, Yersinia virus TG1, Bacillus virus G, Bacillus virus PBS1, Microcystis virus Ma-LMM01, Vibrio virus MAR, Vibrio virus VHML, Vibrio virus VP585, Bacillus virus BPS 13, Bacillus virus Hakuna, Bacillus virus Megatron, Bacillus virus WPh, Acinetobacter virus AB3, Acinetobacter virus Abp1, Acinetobacter virus Fri1, Acinetobacter virus IME200, Acinetobacter virus PD6A3, Acinetobacter virus PDAB9, Acinetobacter virus phiAB1, Escherichia virus K30, Klebsiella virus K5, Klebsiella virus K11, Klebsiella virus Kp1, Klebsiella virus KP32, Klebsiella virus K30 Klebsiella virus KpV289, Klebsiella virus F19, Klebsiella virus K244, Klebsiella virus Kp2, Klebsiella virus KP34, Klebsiella virus KpV41, Klebsiella virus KpV71, Klebsiella virus KpV475, Klebsiella virus SU503, Klebsiella virus SU552A, Pantoea virus Limelight, Pantoea virus Limezero, Pseudomonas virus LKA1, Pseudomonas virus phiKMV, Xanthomonas virus f20, Xanthomonas virus f30,Xylella virus Prado, Erwinia virus Era103, Escherichia virus K5, Escherichia virus K1-5, Escherichia virus K1E, Salmonella virus SP6, Escherichia virus T7, Kluyvera virus Kvp1, Pseudomonas virus gh1, Prochlorococcus virus PSSP7, Synechococcus virus P60, Synechococcus virus Syn5, Streptococcus virus Cp1, Streptococcus Coccal virus Cp7, Staphylococcal virus 44AHJD, Streptococcal virus C1, Bacillus virus B103, Bacillus virus GA1, Bacillus virus phi29, Kurthia virus 6, Actinomyces virus Av1, Mycoplasma virus P1, Escherichia virus 24B, Escherichia virus 933W, Escherichia virus Min27, Escherichia virus PA28, Escherichia virus Stx2 II, Shigellavirus 7502Stx, Shigellavirus POCJ13, Escherichiavirus 191, Escherichiavirus PA2, Escherichiavirus TL2011, Shigellavirus VASD, Burkholderiavirus Bcep22, Burkholderiavirus Bcepil02, Burkholderiavirus Bcepmigl, Burkholderiavirus DC1, Bordetellavirus BPP1, Burkholderiavirus BcepC6B, Cernophagavirus Cba41, Cernophagavirus Cba172, Dinorceobactervirus DFL12, Erwiniavirus Ea9-2, Erwiniavirus Frozen, Escherichiavirus ph iV10, Salmonella virus Epsilon15, Salmonella virus SPN1S, Pseudomonas virus F116, Pseudomonas virus H66, Escherichia virus APEC5, Escherichia virus APEC7, Escherichia virus Bp4, Escherichia virus EC1UPM, Escherichia virus ECBP1, Escherichia virus G7C, Escherichia virus IME11, Shigella virus Sb1, Achromobacter virus Axp3, Achromobacter virus JWAlpha, Edwardsiella virus KF1, Pseudomonas virus KPP25, Pseudomonas virus R18, Pseudomonas virus Ab09, Pseudomonas virus,Lus LIT1, Pseudomonas virus PA26, Pseudomonas virus Ab22, Pseudomonas virus CHU, Pseudomonas virus LUZ24, Pseudomonas virus PAA2, Pseudomonas virus PaP3, Pseudomonas virus PaP4, Pseudomonas virus TL, Pseudomonas virus KPP21, Pseudomonas virus LUZ7, Escherichia virus N4, Salmonella virus 9NA, Salmonella virus SP069, Salmonella virus BTP1, Salmonella virus HK620, Salmonella virus P22, Salmonella virus ST64T, Shigella virus Sf6, Bacillus virus Page, Bacillus virus Palmer, Bacillus virus Pascal, Bacillus virus Pony, Bacillus virus Pookie, Escherichia virus 172-1, Escherichia virus ECB2, Escherichia virus NJ01, Escherichia virus phiEco32, Escherichia virus Septima11, Escherichia virus SU10, Brucella virus Pr, Brucella virus Tb, Escherichia virus Pollock, Salmonella virus FSL SP-058, Salmonella virus FSL SP-076, Helicobacter virus 1961P, Helicobacter virus KHP30, Helicobacter virus KHP40, Hamiltonella virus APSE1, Lactococcus virus KSY1, Phormidium virus WMP3, Phormidium virus WMP4, Pseudomonas virus 119X, Roseobacter virus SIO1, Vibrio virus VpV262, Vibrio virus VC8, Vibrio virus VP2, Vibrio virus VP5, Streptomyces virus Amela, Streptomyces Streptomyces virus phiCAM, Streptomyces virus Aaronocolus, Streptomyces virus Caliburn, Streptomyces virus Danzina, Streptomyces virus Hydra, Streptomyces virus Izzy, Streptomyces virus Lannister, Streptomyces virus Lika, Streptomyces virus Sujidade, Streptomyces virus Zemlya, Streptomyces virus ELB20, Streptomyces virus R4,Streptomyces virus phiHau3, Mycobacterium virus Acadian, Mycobacterium virus Baee, Mycobacterium virus Reprobate, Mycobacterium virus Adawi, Mycobacterium virus Bane1, Mycobacterium virus BrownCNA, Mycobacterium virus Chrisnmich, Mycobacterium virus Cooper, Mycobacterium virus JAMaL, Mycobacterium virus Nigel, Mycobacterium virus Stinger, My Mycobacterium virus Vincenzo, Mycobacterium virus Zemanar, Mycobacterium virus Apizium, Mycobacterium virus Manad, Mycobacterium virus Oline, Mycobacterium virus Osmaximus, Mycobacterium virus Pg1, Mycobacterium virus Soto, Mycobacterium virus Suffolk, Mycobacterium virus Athena, Mycobacterium virus Bernardo, Mycobacterium virus Gadjet, Mycobacterium Mycobacterium virus Pipefish, Mycobacterium virus Godines, Mycobacterium virus Rosebush, Mycobacterium virus Babsiella, Mycobacterium virus Brujita, Mycobacterium virus Che9c, Mycobacterium virus Sbash, Mycobacterium virus Hawkeye, Mycobacterium virus Plot, Salmonella virus AG11, Salmonella virus Ent1, Salmonella virus f18SE, Salmonella virus Jersey, Salmonella virus L13 , Salmonella virus LSPA1, Salmonella virus SE2, Salmonella virus SETP3, Salmonella virus SETP7, Salmonella virus SETP13, Salmonella virus SP101, Salmonella virus SS3e, Salmonella virus wksl3, Escherichia virus K1G, Escherichia virus K1H, Escherichia virus K1ind1, Escherichia virus K1ind2, Salmonella virus SP31, Leuconostoc virus Lmd1, Leuconostoc virus LN03, Leuconostoc virus LN04,Leuconostoc virus LN12, Leuconostoc virus LN6B, Leuconostoc virus P793, Leuconostoc virus 1A4, Leuconostoc virus Ln8, Leuconostoc virus Ln9, Leuconostoc virus LN25, Leuconostoc virus LN34, Leuconostoc virus LNTR3, Mycobacterium virus Bongo, Mycobacterium virus Rey, Mycobacterium virus Butters, Mycobacterium virus Michelle, Mycobacterium virus Virus Charlie, Mycobacterium virus Pipsqueaks, Mycobacterium virus Xeno, Mycobacterium virus Panchino, Mycobacterium virus Phrann, Mycobacterium virus Redi, Mycobacterium virus Skinnyp, Gordonia virus BaxterFox, Gordonia virus Yeezy, Gordonia virus Kita, Gordonia virus Zirinka, Gordonia virus Nymphadora, Mycobacterium virus Bignus, Mycobacterium virus Brusacoram, Mycobacterium virus Donovan, Mycobacterium virus Fishburne, Mycobacterium virus Jebeks, Mycobacterium virus Malithi, Mycobacterium virus Phayonce, Enterobacter virus F20, Klebsiella virus 1513, Klebsiella virus KLPN1, Klebsiella virus KP36, Klebsiella virus PKP126, Klebsiella virus Sushi, Escherichia virus AHP42, Escherichia virus Rus AHS24, Escherichia virus AKS96, Escherichia virus C119, Escherichia virus E41c, Escherichia virus Eb49, Escherichia virus Jk06, Escherichia virus KP26, Escherichia virus Rogue1, Escherichia virus ACGM12, Escherichia virus Rtp, Escherichia virus ADB2, Escherichia virus JMPW1, Escherichia virus JMPW2, Escherichia virus T1, Shigella virus PSf2, Shigella virus Shfl1, Citrobacter virus Stevie,Escherichia virus TLS, Salmonella virus SP126, Cronobacter virus Esp2949-1, Pseudomonas virus Ab18, Pseudomonas virus Ab19, Pseudomonas virus PaMx11, Arthrobacter virus Amigo, Propionibacterium virus Anatole, Propionibacterium virus B3, Bacillus virus Andromeda, Bacillus virus Blastoid, Bacillus virus Curly, Bacillus virus Eoghan, Bacillus virus Finn, Bacillus virus Glit tering, Bacillus virus Riggi, Bacillus virus Taylor, Gordonia virus Attis, Mycobacterium virus Barnyard, Mycobacterium virus Konstantine, Mycobacterium virus Predator, Mycobacterium virus Bernal13, Staphylococcus virus 13, Staphylococcus virus 77, Staphylococcus virus 108PVL, Mycobacterium virus Bron, Mycobacterium virus Faith1, Mycobacterium virus Joe dirt, Mycobacterium virus Rumpelstiltskin, Lactococcus virus bIL67, Lactococcus virus c2, Lactobacillus virus c5, Lactobacillus virus Ld3, Lactobacillus virus Ld17, Lactobacillus virus Ld25A, Lactobacillus virus LLKu, Lactobacillus virus phiLdb, Cellulophaga virus Cba121, Cellulophaga virus Cba171, Cellulophaga virus Cba181, Cellulophaga virus ST, Bacillus virus 250, Bacillus virus IEBH, Mycobacterium virus Ardmore, Mycobacterium virus Avani, Mycobacterium virus Boomer, Mycobacterium virus Che8, Mycobacterium virus Che9d, Mycobacterium virus Deadp, Mycobacterium virus Dlane, Mycobacterium virus Dorothy, Mycobacterium virus Dotproduct, Mycobacterium virus Drago, Mycobacterium virus Fruitloop, Mycobacterium virus Gumbie,Mycobacterium virus Ibhubesi, Mycobacterium virus Llij, Mycobacterium virus Mozy, Mycobacterium virus Mutaforma13, Mycobacterium virus Pacc40, Mycobacterium virus PMC, Mycobacterium virus Ramsey, Mycobacterium virus Rockyhorror, Mycobacterium virus SG4, Mycobacterium virus Shauna1, Mycobacterium virus Shilan, Mycobacterium virus Spartacus, Mycobacterium Mycobacterium virus Taj, Mycobacterium virus Tweety, Mycobacterium virus Wee, Mycobacterium virus Yoshi, Salmonella virus Chi, Salmonella virus FSLSP030, Salmonella virus FSLSP088, Salmonella virus iEPS5, Salmonella virus SPN19, Mycobacterium virus 244, Mycobacterium virus Bask21, Mycobacterium virus CJW1, Mycobacterium virus Eureka, Mycobacterium virus Kostya, Mycobacterium Umvirus Porky, Mycobacterium virus Pumpkin, Mycobacterium virus Sirduracell, Mycobacterium virus Toto, Mycobacterium virus Corndog, Mycobacterium virus Firecracker, Rhodobacter virus RcCronus, Pseudomonas virus D3112, Pseudomonas virus DMS3, Pseudomonas virus FHA0480, Pseudomonas virus LPB1, Pseudomonas virus MP22, Pseudomonas virus MP29, Pseudomonas virus Rus MP38, Pseudomonas virus PA1KOR, Pseudomonas virus D3, Pseudomonas virus PMG1, Arthrobacter virus Decurro, Gordonia virus Demosthenes, Gordonia virus Katyusha, Gordonia virus Kvothe, Propionibacterium virus B22, Propionibacterium virus Doucette, Propionibacterium virus E6, Propionibacterium virus G4, Burkholderia virus phi6442, Burkholderia virus phi1026b,Burkholderia virus phiE125, Edwardsiella virus eiAU, Mycobacterium virus Ff47, Mycobacterium virus Muddy, Mycobacterium virus Gaia, Mycobacterium virus Giles, Arthrobacter virus Captnmurica, Arthrobacter virus Gordon, Gordonia virus GordTnk2, Paenibacillus virus Harrison, Escherichia virus EK99P1, Escherichia virus HK578, Escherichia virus JL1, Escherichia virus SSL2009a, Escherichia virus YD2008s, Shigella virus EP23, Sodalis virusSO1, Escherichia virus HK022, Escherichia virus HK75, Escherichia virus HK97, Escherichia virus HK106, Escherichia virus HK446, Escherichia virus HK542, Escherichia virus HK544, Escherichia virus HK633, Escherichia virus mEp234, Escherichia virus mEp235, Escherichia virus mEpX1, Escherichia virus mEpX2, Escherichia virus mEp043, Escherichia virus mEp213, Escherichia virus mEp237, Escherichia virus mEp390, Escherichia virus mEp460, Escherichia virus mEp505, Escherichia virus mEp506, Brevibacillus virus Jenst, Achromobacter virus S83-24, Achromobactervirus JWX, Arthrobactervirus Kellezzio, Arthrobactervirus Kitkat, Arthrobactervirus Bennie, Arthrobactervirus DrRobert, Arthrobactervirus Glenn, Arthrobactervirus HunterDalle, Arthrobactervirus Joann, Arthrobactervirus Korra, Arthrobactervirus Preamble, Arthrobactervirus Pumancara, Arthrobactervirus Wayne, Mycobacteriumvirus Alma, Mycobacteriumvirus Arturo, Mycobacteriumvirus Astro, Mycobacteriumvirus Backyardigan, Mycobacteriumvirus BBPiebs31,Mycobacterium virus Benedict, Mycobacterium virus Bethlehem, Mycobacterium virus Billknuckles, Mycobacterium virus Bruns, Mycobacterium virus Bxb1, Myco, Mycobacterium virus Bxz2, Mycobacterium virus Che12, Mycobacterium virus Cuco, Mycobacterium virus D29, Mycobacterium virus Doom, Mycobacterium virus Ericb, Mycobacterium virus Euphoria, Mycobacterium virus George, Mycobacterium virus Gladiator, Mycobacterium virus Goose, Mycobacterium virus Hammer, Mycobacterium virus Heldan, Mycobacterium virus Jasper , Mycobacterium virus JC27, Mycobacterium virus Jeffabunny, Mycobacterium virus JHC117, Mycobacterium virus KBG, Mycobacterium virus Kssjeb, Mycobacterium virus Kugel, Mycobacterium virus L5, Mycobacterium virus Lesedi, Mycobacterium virus LHTSCC, Mycobacterium virus lockley, Mycobacterium virus Marcell, Mycobacterium virus Microwolf, Mycobacterium Virus Mrgordo, Mycobacterium Virus Museum, Mycobacterium Virus Nepal, Mycobacterium Virus Packman, Mycobacterium Virus Peaches, Mycobacterium Virus Perseus, Mycobacterium Virus Pukovnik, Mycobacterium Virus Rebeuca, Mycobacterium Virus Redrock, Mycobacterium Virus Ridgecb, Mycobacterium Virus Rockstar, Mycobacterium Virus Saintus, Mycobacterium Mycobacterium virus Skipole, Mycobacterium virus Solon, Mycobacterium virus Switzer, Mycobacterium virus SWU1, Mycobacterium virus Ta17a, Mycobacterium virus Tiger, Mycobacterium virus Timshel, Mycobacterium virus Trixie, Mycobacterium virus Turbido, Mycobacterium virus Twister, Mycobacterium virus U2, Mycobacterium virus Violet, Mycobacterium virus Wonder,Escherichia virus DE3, Escherichia virus HK629, Escherichia virus HK630, Escherichia virus lambda, Arthrobacter virus Laroye, Mycobacterium virus Halo, Mycobacterium virus Liefie, Mycobacterium virus Marvin, Mycobacterium virus Mosmoris, Arthrobacter virus Circum, Arthrobacter virus Mudcat, Escherichia virus N15, Escherichia virus 9g, Escherichia virus JenK1, Escherichia virus Virus JenP1, Escherichia virus JenP2, Pseudomonas virus NP1, Pseudomonas virus PaMx25, Mycobacterium virus Baka, Mycobacterium virus Courthouse, Mycobacterium virus Littlee, Mycobacterium virus Omega, Mycobacterium virus Optimus, Mycobacterium virus Thibault, Polaribacter virus P12002L, Polaribacter virus P12002S, Non-Lavens virus P12024L, Non-Lavens virus P 12024S, Thermus virus P23-45, Thermus virus P74-26, Listeria virus LP26, Listeria virus LP37, Listeria virus LP110, Listeria virus LP114, Listeria virus P70, Propionibacterium virus ATCC29399BC, Propionibacterium virus ATCC29399BT, Propionibacterium virus Attacne, Propionibacterium virus Keiki, Propionibacterium virus Kubed, Propionibacterium virus Lauchell y, Propionibacterium virus MrAK, Propionibacterium virus Ouroboros, Propionibacterium virus P91, Propionibacterium virus P105, Propionibacterium virus P144, Propionibacterium virus P1001, Propionibacterium virus P1.1, Propionibacterium virus P100A, Propionibacterium virus P100D, Propionibacterium virus P101A, Propionibacterium virus P104A, Propionibacterium virus PA6,Propionibacterium virus Pacnes201215, Propionibacterium virus PAD20, Propionibacterium virus PAS50, Propionibacterium virus PHL009M11, Propionibacterium virus PHL025M00, Propionibacterium virus PHL037M02, Propionibacterium virus PHL041M10, Propionibacterium virus PHL060L00, Propionibacterium virus PHL067M01, Propionibacterium virus PHL070N0 ...0L00, Propionibacterium virus PHL067M01, Propionibacterium virus PHL070N00, Propionibacterium virus PHL060L00, Propionibacterium virus PHL060L00, Propionibacterium virus PHL067M01, Propionibacterium virus PHL070N00, Propionibacterium virus PHL060L00, Propionibacterium virus PHL060L00, Propionibacterium virus PHL067M01, Propionibacterium virus Pionibacterium virus PHL071N05, Propionibacterium virus PHL082M03, Propionibacterium virus PHL092M00, Propionibacterium virus PHL095N00, Propionibacterium virus PHL111M01, Propionibacterium virus PHL112N00, Propionibacterium virus PHL113M01, Propionibacterium virus PHL114L00, Propionibacterium virus PHL116M00, Propionibacterium virus PHL117M00, Propionibacterium virus PHL117M01, Propionibacterium virus PHL132N00, Propionibacterium virus PHL141N00, Propionibacterium virus PHL151M00, Propionibacterium virus PHL151N00, Propionibacterium virus PHL152M00, Propionibacterium virus PHL163M00, Propionibacterium virus PHL171M01, Propionibacterium virus PHL179M0, Propionibacterium virus PHL194M 00, Propionibacterium virus PHL199M00, Propionibacterium virus PHL301M00, Propionibacterium virus PHL308M00, Propionibacterium virus Pirate, Propionibacterium virus Procrass1, Propionibacterium virus SKKY, Propionibacterium virus Solid, Propionibacterium virus Stormborn, Propionibacterium virus Wizzo, Pseudomonas virus PaMx28, Pseudomonas virus PaMx74,Mycobacterium virus Patience, Mycobacterium virus PBI1, Rhodococcus virus Pepy6, Rhodococcus virus Poco6, Propionibacterium virus PFR1, Streptomyces virus phiBT1, Streptomyces virus phiC31, Streptomyces virus TG1, Caulobacter virus Karma, Caulobacter virus Magneto, Caulobacter virus phiCbK, Caulobacter virus Rogue, Caulobacter virus Swift, Staphylococcus virus Staphylococcal virus 11, Staphylococcal virus 29, Staphylococcal virus 37, Staphylococcal virus 53, Staphylococcal virus 55, Staphylococcal virus 69, Staphylococcal virus 71, Staphylococcal virus 80, Staphylococcal virus 85, Staphylococcal virus 88, Staphylococcal virus 92, Staphylococcal virus 96, Staphylococcal virus 187, Staphylococcal virus 52a, Staphylococcal virus 80alpha, Staphylococcal virus CNPH82, Staphylococcal virus EW, Staphylococcal virus IPLA5, Staphylococcal virus IPLA7, Staphylococcal virus IPLA88, Staphylococcal virus PH15, Staphylococcal virus phiETA, Staphylococcal virus phiETA2, Staphylococcal virus phiETA3, Staphylococcal virus phiMR11, Staphylococcal virus phiMR25, Staphylococcal virus phiNM1, Staphylococcal virus phiNM2, Staphylococcal Lactobacillus virus phiNM4, Staphylococcus virus SAP26, Staphylococcus virus X2, Enterococcus virus FL1, Enterococcus virus FL2, Enterococcus virus FL3, Lactobacillus virus ATCC8014, Lactobacillus virus phiJL1, Pediococcus virus cIP1, Aeromonas virus pIS4A, Listeria virus LP302, Listeria virus PSA, Methanobacterium virus psiM1, Roseobacter virus RDJL1, Roseobacter virus RDJL2,Rhodococcus virus RER2, Enterococcus virus BC611, Enterococcus virus IMEEF1, Enterococcus virus SAP6, Enterococcus virus VD13, Streptococcus virus SPQS1, Mycobacterium virus Papyrus, Mycobacterium virus Send513, Burkholderia virus KL1, Pseudomonas virus 73, Pseudomonas virus Ab26, Pseudomonas virus Kakheti25, Escherichia virus Cajan, Escherichia virus Seurat, Staphylococcus aureus Staphylococcus virus SEP9, Staphylococcus virus Sextaec, Streptococcus virus 858, Streptococcus virus 2972, Streptococcus virus ALQ132, Streptococcus virus O1205, Streptococcus virus Sfi11, Streptococcus virus 7201, Streptococcus virus DT1, Streptococcus virus phiAbc2, Streptococcus virus Sfi19, Streptococcus virus Sfi21, Paenibacillus virus Diva, Paenibacillus virus Hb10c2, Paenibacillus virus Rani, Paenibacillus virus Shelly, Paenibacillus virus Sitara, Paenibacillus virus Willow, Lactococcus virus 712, Lactococcus virus ASCC191, Lactococcus virus ASCC273, Lactococcus virus ASCC281, Lactococcus virus ASCC465, Lactococcus virus ASCC532, Lactococcus virus Bibb29, Lactococcus virus bIL170, Lactococcus virus CB13, Lactococcus virus CB14, Lactococcus virus CB19, Lactococcus virus CB20, Lactococcus virus jj50, Lactococcus virus P2, Lactococcus virus P008, Lactococcus virus sk1, Lactococcus virus Sl4, Bacillus virus Slash, Bacillus virus Stahl, Bacillus virus Staley, Bacillus virus Stills, Gordonia virus Bachita, Gordonia virus ClubL, Gordonia virus OneUp, Gordonia virus Smoothie, Gordonia virus Soups,Bacillus virus SPbeta, Vibriovirus MAR10, Vibriovirus SSP002, Escherichia virus AKFV33, Escherichia virus BF23, Escherichia virus DT57C, Escherichia virus EPS7, Escherichia virus FFH1, Escherichia virus H8, Escherichia virus slur09, Escherichia virus T5, Salmonella virus 118970sal2, Salmonella virus Shivani, Salmonella virus SPC35, Salmonella virus Stitch, Arthrobacter virus Tan k, Tsukamurella virus TIN2, Tsukamurella virus TIN3, Tsukamurella virus TIN4, Rhodobacter virus RcSpartan, Rhodobacter virus RcTitan, Mycobacterium virus Anaya, Mycobacterium virus Angelica, Mycobacterium virus Crimd, Mycobacterium virus Fionnbarth, Mycobacterium virus Jaws, Mycobacterium virus Larva, Mycobacterium virus Macncheese, Mycobacterium virus Pixie, My Cobacterium virus TM4, Bacillus virus BMBtp2, Bacillus virus TP21, Geobacillus virus Tp84, Staphylococcus virus 47, Staphylococcus virus 3a, Staphylococcus virus 42e, Staphylococcus virus IPLA35, Staphylococcus virus phi12, Staphylococcus virus phiSLT, Mycobacterium virus 32HC, Rhodococcus virus RGL3, Paenibacillus virus Vegas, Gordonia virus Vendetta, Bacillus virus Wbeta, Mycobacterial virus Wildcat, Gordonia virus Twister6, Gordonia virus Wizard, Gordonia virus Hotorobo, Gordonia virus Monty, Gordonia virus Woes, Xanthomonas virus CP1, Xanthomonas virus OP1, Xanthomonas virus phil7, Xanthomonas virus Xop411, Xanthomonas virus Xp10, Streptomyces virus TP1604, Streptomyces virus YDN12, Alphaproteobacterial virus phiJl001,Pseudomonas virus LKO4, Pseudomonas virus M6, Pseudomonas virus MP14, 12, Pseudomonas virus PAE1, Pseudomonas virus Yua, Pseudoalteromonas virus PM2, Pseudomonas virus phi6, Pseudomonas virus phi8, Pseudomonas virus phi12, Pseudomonas virus phi13, Pseudomonas virus phi2954, Pseudomonas virus phiNN, Pseudomonas virus phiYY, Vibrio virus fs1, Vibrio virus VGJ, Ralstonia virus RS603, Ralstonia virus RSM1, Ralstonia virus RSM3, Escherichia coli Avirus M13, Escherichia virus I22, Salmonella virus IKe, Acholeplasma virus L51, Vibrio virus fs2, Vibrio virus VFJ, Escherichia virus If1, Propionibacterium virus B5, Pseudomonas virus Pf1, Pseudomonas virus Pf3, Ralstonia virus PE226, Ralstonia virus RSS1, Spiroplasma virus SVTS2, Stenotrophomonas virus PSH1, Stenotrophomonas virus SMA6, Stenotrophomonas virus SMA7, Stenotrophomonas virus Vibriovirus SMA9, Vibriovirus CTXphi, Vibriovirus KSF1, Vibriovirus VCY, Vibriovirus Vf33, Vibriovirus VfO3K6, Xanthomonas virus Cf1c, Spiroplasma virus C74, Spiroplasma virus R8A2B, Spiroplasma virus SkV1CR23x, Escherichia virus FI, Escherichia virus Qbeta, Escherichia virus BZ13, Escherichia virus MS2, Escherichia virus alpha3, Escherichia virus ID21, Escherichia virus ID32, Escherichia virus ID62, Escherichia virus NC28, Escherichia virus NC29, Escherichia virus NC35, Escherichia virus phiK, Escherichia virus St1, Escherichia virus WA45, Escherichia virus G4, Escherichia virus ID52, Escherichia virus Talmos, Escherichia virus phiX174, Bdellovibriovirus MAC1, Bdellovibriovirus MH2K, Chlamydia virus Chp1, Chlamydia virus Chp2, Chlamydia virus CPAR39,Chlamydia virus CPG1, Spiroplasma virus SpV4, Acholeplasma virus L2, Pseudomonas virus PR4, Pseudomonas virus PRD1, Bacillus virus AP50, Bacillus virus Bam35, Bacillus virus GIL16, Bacillus virus Wip1, Escherichia virus phi80, Escherichia virus RB42, Escherichia virus T2, Escherichia virus T3, Escherichia virus T6, Escherichia virus VT2-Sa, Escherichia virus VT1-Sakai, Escherichia virus VT2-Sakai, Escherichia virus CP-933V, Escherichia virus P27, Escherichia virus Stx2phi-I, Escherichia virus Stx1phi, Selected from the group consisting of Escherichia virus Stx2phi-II, Escherichia virus CP-1639, and based on Escherichia virus BP-4795, Escherichia virus 86, Escherichia virus Min27, Escherichia virus 2851, Escherichia virus 1717, Escherichia virus YYZ-2008, Escherichia virus EC026_P06, Escherichia virus ECO103_P15, Escherichia virus ECO103_P12, Escherichia virus ECO111_P16, Escherichia virus ECO111_P11, Escherichia virus VT2phi_272, Escherichia virus TL-2011c, Escherichia virus P13374, Escherichia virus Sp5,

[0141] One of the main entrances is BW73 and B278. D6, D108, E, El, E24, E41, FI-2, FI-4, FI-5, H I8A, Ffl8B, i, MM, Mu, 025, PhI-5, Pk, PSP3, P l, PlD, P2, P4, Sl, Wφ, φK13, φl, φ2, φ7, φ92, 7 A, 8φ, 9φ, 18, 28-1, 186, 299, HH-Carlich (2), AB48, CM, C4, C16, DD-VI E4, E7, E28, FIl, FI3, H, Hl, H3, H8, K3, M, N, ND-2, ND-3, ND4, ND-5, ND 6, ND-7, Ox-I, Ox-2, Ox-3, Ox-4, Ox-5, Ox-6, PhI-I, RB42, RB43, RB49 RB69, S, SaI-I, Sal-2, Sal-3, Sal-4, Sal-5, Sal-6, TC23, TC45, TuII * -6, TuIP-24, TuII*46, TuIP-60, T2, T4, T6, T35, αl, 1, IA 3A, 3T+, 5φ, 9266Q, CFO103, HK620, J, K, KlF, m59, no. A、no. Yes, no. 3、No. 9, N4, sd, T3, T7, WPK, W31, ΔH, φC3888, φK3, φK7, φK12, φV-1, Φ04-CF, Φ 05, Φ06, Φ07, φl, φl.2, φ20, φ95, φ263, φlO92, φl, φll, Ω8, 1, 3, 7, 8, 27. 28-2. 29. 30. 31. 32. 38. 39. 42. 933W C30, CVX-5, Cl, DDUP, ECl, EC2, E21, E29, Fl, F26S, F27S, Hi, HK022, HK 97, HK139, HK253, HK256, K7, ND-I, PA-2, q, S2, Tl,) T3C, T5, UC-I, w. β4, γ2, λ, ΦD326, φγ, Φ06, Φ7, Φ10, φ80, χ, 2, 4, 4A, 6, 8A, 102, 150, 168; 174, 3000, AC6, AC7, AC28, AC43, AC50, AC57, AC81, AC95, HK243, KlO, Z G / 3A, 5, 5A, 21EL, H19-J and 933H It's a great way to get your hands on.

[0142] Prebiotics include, but are not limited to, amino acids, biotin, fructo-oligosaccharides, galacto-oligosaccharides, hemicelluloses (e.g., arabinoxylan, xylan, xyloglucan, and glucomannan), inulin, chitin, lactulose, mannan oligosaccharides, oligofructose-enriched inulin, gums (e.g., guar gum, gum arabic, and carrageenan), oligofructose, oligodextrose, tagatose, resistant maltodextrins (e.g., resistant starch), trans-galacto-oligosaccharides, pectins (e.g., xylogalacturonan, citrus pectin, apple pectin, and rhamnogalacturonan-I), dietary fiber (e.g., soy fiber, sugar beet fiber, pea fiber, corn bran, and oat fiber), and xylo-oligosaccharides.

[0143] Probiotics include, but are not limited to, lactobacilli, bifidobacteria, streptococci, enterococci, propionibacteria, yeasts (saccaromycetes), lactobacilli, bifidobacteria, or proteobacteria.

[0144] Antibiotics include penicillins, e.g., penicillin G, penicillin K, penicillin N, penicillin O, penicillin V, methicillin, benzylpenicillin, nafcillin, oxacillin, cloxacillin, dicloxacillin, ampicillin, amoxicillin, pivampicillin, hetacillin, bacampicillin, methampicillin, talampicillin, epicillin, carbenicillin, ticarcillin, temocillin, mezlocillin, and piperacillin; cephalosporins, e.g., cefacetrile, cefazolin, Adroxil, cephalexin, cephaloglycin, cephalonium, cephaloridine, cephalothin, cephapirin, cefatrizine, cefazaflur, cefazedone, cefazolin, cephradine, cefroxadine, ceftezole, cefaclor, cefonicid, cefprozil, cefuroxime, cefuzonam, cefmetazole, cefotetan, cefoxitin, loracarbef, cefbuperazone, cefminox, cefotetan, cefoxitin, cefotiam, cefcapene, cefdaroxacin Sim, cefdinir, cefditoren, cefetamet, cefixime, cefmenoxime, cefodizime, cefotaxime, cefovecin, cefpimizole, cefpodoxime, cefteram, ceftamele, ceftibuten, ceftiofur, ceftiolene, ceftizoxime, ceftriaxone, cefoperazone, ceftazidime, latamoxef, cefclidine, cefepime, cefluprenam, cefoselis, cefozopran, cefpirome, cefquinome, flomoxef, ceftobiprole, ceftaroline ceftolozane, cephaloram, cefaparol, cefcanel, cefedrolol, cefempidone, cefetrizole, cefibitril, cefmatilen, cefmepidium, cefoxazole, cefrotil, cefsumide, ceftioxide, cefuracetime, and nitrocefin; polymyxins, such as Polysporin, Neosporin, Polymyxin B, and Polymyxin E; rifampicins, such as rifampicin, rifapentine, and rifaximin; fidaxomicin;Quinolones, such as cinoxacin, nalidixic acid, oxolinic acid, piromidic acid, pipemidic acid, losoxacin, ciprofloxacin, enoxacin, fleroxacin, lomefloxacin, nadifloxacin, norfloxacin, ofloxacin, pefloxacin, rufloxacin, balofloxacin, grepafloxacin, levofloxacin, pazufloxacin, temafloxacin, tosufloxacin, clinafloxacin, gatifloxacin, gemifloxacin, moxifloxacin, sitafloxacin, trovafloxacin, prulifloxacin, de lafloxacin, nemonoxacin, and zavofloxacin; sulfonamides such as sulfafurazole, sulfacetamide, sulfadiazine, sulfadimidine, sulfafurazole, sulfisomidine, sulfadoxine, sulfamethoxazole, sulfamoxole, sulfanitran, sulfadimethoxine, sulfamethoxypyridazine, sulfamethoxydiazine, sulfadoxine, sulfamethopyrazine, and terephthyl; macrolides such as azithromycin, clarithromycin, erythromycin, fidaxomicin, Telithromycin, carbomycin A, josamycin, kitasamycin, midecamycin, oleandomycin, solithromycin, spiramycin, troleandomycin, tylosin, and roxithromycin; ketolides such as telithromycin and cethromycin; luoloketolides such as solithromycin; lincosamides such as lincomycin, clindamycin, and pirlimycin; tetracyclines such as demeclocycline, doxycycline, minocycline, oxytetracycline, and tetracycline; Aminoglycosides such as amikacin, dibekacin, gentamicin, kanamycin, neomycin, netilmicin, sisomicin, tobramycin, paromomycin, and streptomycin; ansamycins such as geldanamycin, herbimycin, and rifaximin; carbacephems such as loracarbef; carbapenems such as ertapenem, doripenem, imipenem (or cilastatin), and meropenem; glycopeptides such as teicoplanin, vancomycin, telavancin, dalbavancin, and oritavancin;The anti-inflammatory drug may be selected from the group consisting of lincosamides, such as clindamycin and lincomycin; lipopeptides, such as daptomycin; monobactams, such as aztreonam; nitrofurans, such as furazolidone and nitrofurantoin; oxazolidinones, such as linezolid, pozizolid, radezolid, and torezolid; teixobactin, clofazimine, dapsone, capreomycin, cycloserine, ethambutol, ethionamide, isoniazid, pyrazinamide, rifabutin, arsphenamine, chloramphenicol, fosfomycin, fusidic acid, metronidazole, mupirocin, platensimycin, quinupristin (or dalfopristin), thiamphenicol, tigecycline, tinidazole, trimethoprim, alatrofloxacin, fidaxomicin, nalidixic acid, rifampin, derivatives and combinations thereof;

[0145] The present invention provides pharmaceutical or veterinary compositions comprising one or more of the bacterial delivery vehicles disclosed herein and a pharmaceutically acceptable carrier. Generally, for pharmaceutical use, the bacterial delivery vehicle can be formulated as a pharmaceutical or composition comprising at least one bacterial delivery vehicle and at least one pharmaceutically acceptable carrier, diluent, or excipient, and optionally one or more additional pharmaceutically active compounds. Such formulations can be in a form suitable for oral administration, parenteral administration (e.g., by intravenous, intramuscular, or subcutaneous injection, or intravenous infusion), topical administration, inhalation, skin patch, implant, suppository, etc. Such dosage forms can be solid, semisolid, or liquid, depending on the method and route of administration. For example, formulations for oral administration can be provided with an enteric coating to enable the synthetic bacterial delivery vehicle in the formulation to withstand the stomach environment and pass into the intestine. More generally, synthetic bacterial delivery vehicle formulations for oral administration can be formulated to be suitable for delivery to any desired portion of the gastrointestinal tract. Additionally, suitable suppositories may be used for delivery to the gastrointestinal tract. A variety of pharmaceutically acceptable carriers, diluents, and excipients useful in bacterial delivery vehicle compositions are known to those skilled in the art.

[0146] Also provided are methods for treating bacterial infections using the synthetic bacterial delivery vehicles disclosed herein. The methods include administering a synthetic bacterial delivery vehicle or composition disclosed herein to a subject having a bacterial infection in need of treatment. In some embodiments, the subject is a mammal. In some embodiments, the subject is a human.

[0147] Pharmaceutical or veterinary compositions according to the present disclosure may further comprise a pharmaceutically acceptable vehicle. Solid pharmaceutically acceptable vehicles may include one or more substances which may also act as flavoring agents, lubricants, solubilizers, suspending agents, dyes, fillers, glidants, compression aids, inert binders, sweeteners, preservatives, pigments, coating agents, or tablet disintegrating agents. Suitable solid vehicles include, for example, calcium phosphate, magnesium stearate, talc, sugars, lactose, dextrin, starch, gelatin, cellulose, polyvinylpyrrolidine, low melting point waxes, and ion exchange resins.

[0148] Pharmaceutical or veterinary compositions may be prepared as sterile solid compositions that can be suspended at the time of administration using sterile water, saline, or other appropriate sterile injectable medium. Pharmaceutical or veterinary compositions of the present disclosure may be orally administered in the form of a sterile solution or suspension containing other solutes or suspending agents (e.g., sufficient saline or glucose to make the solution isotonic), bile salts, acacia, gelatin, sorbitan monoleate, polysorbate 80 (oleic acid esters of sorbitol and its anhydrides copolymerized with ethylene oxide), or the like. Particles according to the present disclosure may also be orally administered in either liquid or solid composition form. Compositions suitable for oral administration include solid forms such as pills, capsules, granules, tablets, and powders, as well as liquid forms such as solutions, syrups, elixirs, and suspensions. Forms useful for enteral administration include sterile solutions, emulsions, and suspensions.

[0149] The bacterial delivery vehicle according to the present disclosure can be dissolved or suspended in a pharmaceutically acceptable liquid vehicle, such as water, an organic solvent, a mixture of both, or a pharmaceutically acceptable oil or lipid. The liquid vehicle may contain other suitable pharmaceutical additives, such as solubilizers, emulsifiers, buffers, preservatives, sweeteners, flavorings, suspending agents, thickeners, colorants, viscosity adjusters, stabilizers, or osmolality adjusters. Suitable examples of liquid vehicles for oral and enteral administration include water (partially containing additives such as those described above, such as cellulose derivatives, preferably carboxymethylcellulose sodium solution), alcohols (including monohydric and polyhydric alcohols, such as glycols) and their derivatives, and oils (e.g., coconut oil and peanut oil). For parenteral administration, the vehicle can also be an oily ester, such as ethyl oleate and isopropyl myristate. Sterile liquid vehicles are useful in sterile liquid form compositions for enteral administration. The liquid vehicle for pressurized compositions can be halogenated hydrocarbon or other pharmaceutically acceptable propellant.

[0150] For transdermal administration, the pharmaceutical or veterinary compositions may be formulated in the form of an ointment, cream, or gel, and penetration may be enhanced using suitable penetrants or surfactants, such as, for example, dimethyl sulfoxide, dimethylacetamide, and dimethylformamide.

[0151] For transmucosal administration, nasal sprays, rectal or vaginal suppositories can be used.The active compound can be incorporated into any known suppository base by methods known in the art.Examples of such bases include cocoa butter, polyethylene glycol (carbowax), polyethylene monostearate sorbitan, and mixtures thereof with other compatible materials that modify the melting point or dissolution rate.

[0152] The present invention relates to a method for treating a disease or disorder caused by bacteria, comprising administering a therapeutic amount of a pharmaceutical or veterinary composition disclosed herein, and also to the pharmaceutical or veterinary composition disclosed herein for use in treating a disease or disorder caused by bacteria, and the use of the pharmaceutical or veterinary composition disclosed herein for the manufacture of a medicament in the treatment of a disease or disorder caused by bacteria.

[0153] Diseases or disorders caused by bacteria include abdominal cramps, acne vulgaris, acute epiglottitis, arthritis, bacteremia, bloody diarrhea, botulism, brucellosis, brain abscess, chancroid, chlamydia, Crohn's disease, conjunctivitis, cholecystitis, colorectal cancer, polyposis, intestinal dysbiosis, Lyme disease, diarrhea, diphtheria, duodenal ulcer, endocarditis, erysipelothricosis, enteric fever, fever, glomerulonephritis, gastroenteritis, gastric ulcer, Guillain-Barré syndrome, tetanus, gonorrhea, gingivitis, inflammatory bowel disease, and irritable bowel syndrome. group, leptospirosis, leprosy, listeriosis, tuberculosis, Lady Windermere syndrome, Legionnaires' disease, meningitis, mucopurulent conjunctivitis, multidrug-resistant bacterial infection, multidrug-resistant bacterial carriage, myonecrotizing gas gangrene, Mycobacterium avium complex, neonatal necrotizing enterocolitis, nocardiosis, hospital-acquired infection, otitis, periodontitis, pharyngitis, pneumonia, peritonitis, purpuric fever, Rocky Mountain spotted fever, dysentery, syphilis, sinusitis, sigmoiditis, sepsis, subcutaneous abscess, tularemia, tracheobronchitis, tonsillitis, typhoid fever, ulcerative colitis, urinary infection, and whooping cough.

[0154] The present invention relates to a method for treating an infection caused by a bacterium, comprising administering a therapeutic amount of a pharmaceutical or veterinary composition disclosed herein. It also relates to a pharmaceutical or veterinary composition disclosed herein for use in treating an infection caused by a bacterium, and to the use of a pharmaceutical or veterinary composition disclosed herein for the manufacture of a medicament in the treatment of an infection caused by a bacterium.

[0155] The infection caused by bacteria may be selected from the group consisting of skin infections such as acne, intestinal infections such as esophagitis, gastritis, enteritis, colitis, sigmoiditis, proctitis, and peritonitis, urinary tract infections, vaginal infections, female upper genital tract infections such as salpingitis, endometritis, oophoritis, metritis, parametritis, and pelvic peritoneal infections, respiratory tract infections such as pneumonia, intra-amniotic infections, odontogenic infections, endodontic infections, fibrosis, meningitis, bloodstream infections, hospital-acquired infections such as catheter-associated infections, hospital-acquired pneumonia, postpartum infections, hospital-acquired gastroenteritis, and hospital-acquired urinary tract infections, or combinations thereof. Preferably, the infection according to the present disclosure is caused by bacteria exhibiting antibiotic resistance. In certain embodiments, the infection is caused by a bacterium listed above under the target bacteria.

[0156] The present disclosure relates to pharmaceutical or veterinary compositions for use in the treatment of metabolic disorders, including, for example, obesity and diabetes.

[0157] In certain embodiments, the present disclosure relates to pharmaceutical or veterinary compositions for use in treating pathologies involving bacteria in the human microbiome, such as inflammatory and autoimmune diseases, cancer, infectious diseases, or brain disorders. Indeed, some bacteria in the microbiome may secrete molecules that induce and / or enhance the development of inflammatory or autoimmune diseases or cancer without causing any infectious disease. More specifically, the present disclosure also relates to modifying the composition of the microbiome to improve the efficacy of immunotherapies based on, for example, CAR-T (chimeric antigen receptor T) cells, TILs (tumor-infiltrating lymphocytes), and Tregs (regulatory T cells), also known as suppressor T cells. Modifying the composition of the microbiome to improve the efficacy of immunotherapy may also include the use of immune checkpoint inhibitors known in the art, such as, but not limited to, PD-1 (programmed cell death protein 1) inhibitors, PD-L1 (programmed death ligand 1) inhibitors, and CTLA-4 (cytotoxic T lymphocyte-associated protein 4).

[0158] Some bacteria in the microbiome can also secrete molecules that affect the brain.

[0159] Therefore, a further object of the present disclosure is a method for controlling the microbiome of a subject, comprising administering in said subject an effective amount of a pharmaceutical composition disclosed herein.

[0160] In certain embodiments, the present disclosure also relates to a personalized treatment method for an individual in need of treatment for a bacterial infection, comprising: i) obtaining a biological sample from the individual and determining a group of bacterial DNA sequences from the sample; ii) identifying one or more pathogenic strains or species present in the sample based on the sequence determination; and iii) administering to the individual a pharmaceutical composition according to the present disclosure capable of recognizing or delivering a packaged plasmid for each pathogenic strain or species identified in the sample.

[0161] Preferably, the biological sample contains pathogenic and non-pathogenic species, and after administration of a pharmaceutical or veterinary composition according to the present disclosure to an individual, the amount of pathogenic bacteria on or in the individual is reduced, but the amount of non-pathogenic bacteria is not reduced.

[0162] In another specific embodiment, the present disclosure relates to a pharmaceutical or veterinary composition according to the present disclosure for use in improving the efficacy of a drug. Indeed, some bacteria in the microbiome, while not pathogenic in themselves, are known to be able to metabolize drugs and modify them into ineffective or harmful molecules.

[0163] In another specific embodiment, the present disclosure relates to the in situ bacterial production of any compound of interest, including therapeutic compounds, e.g., mammalian prophylactic and therapeutic vaccines. The compound of interest may be produced within the target bacterium, secreted from the target bacterium, or expressed on the surface of the target bacterium. In a more specific embodiment, an antigen is expressed on the surface of the target bacterium for prophylactic and / or therapeutic vaccination.

[0164] The present disclosure also relates to non-therapeutic uses of the bacterial delivery particles. For example, the non-therapeutic use may be cosmetic use or use to improve the health of a subject, particularly a subject not suffering from a disease. Thus, the present disclosure also relates to cosmetic or non-therapeutic compositions comprising the bacterial delivery particles, in this case. [Example]

[0165] The following examples demonstrate that designated portions of lambda receptor binding proteins (RBPs), such as the stf protein, can be exchanged for portions of different RBPs. More specifically, specific fusion portions of lambda RBPs have been identified that allow for functional chimeric RBPs to be obtained. Specifically, in a non-limiting embodiment, data have demonstrated that in the case of phagemids derived from bacteriophage lambda, modification of the lateral tail fiber protein results in an expanded host range. The addition of a chimeric stf protein to lambdoid phagemids has been demonstrated to be a very powerful approach to modifying and increasing their host range, and in some cases, more efficient than modifying the gpJ gene. Furthermore, modification of the lateral tail fiber protein to encode a depolymerase activity can dramatically increase delivery efficiency. In some cases, the addition of this enzymatic activity allows for 100% delivery efficiency, whereas wild-type lambda phagemids exhibit no invasion at all. These two approaches can be combined to generate phagemid variants with different specificities and delivery efficiencies to many strains of bacterial species.

[0166] Tests were conducted to determine whether modifications to the tail gene (gpJ) would affect the host range of lambda phagemid. The lambda tail was modified to contain the mutations described in

[11] , generating OMPF-lambda. This phagemid now uses OmpF instead of LamB as the primary cell surface receptor. Delivery efficiency was then tested in a collection of E. coli strains spanning various O and K serotypes, as shown in Figure 1.

[0167] As can be seen in Figure 1, the use of phagemids that recognize different cell surface receptors has minimal impact on delivery efficiency and host range. Only three strains show a slight improvement in colony number after treatment with the modified phagemid. This result may be due to the presence of a capsule around most of the cells, which forms a physical barrier to the phagemid and therefore renders this approach unsuccessful. In light of these results, the lambda stf gene was modified to contain enzymatic activity against the bacterial capsule.

[0168] The sequence of lambda stf (SEQ ID NO: 1) is:

[0169] [ka]

[0170] The bold and underlined sequences represent the portion of the protein introduced into T4 phage

[47] . Experiments were performed to determine whether it was possible to exchange the C-terminus of lambda stf with a tail fiber from a different phage, resulting in a chimeric tail fiber with enzymatic activity against encapsulated E. coli. The tail fiber from the K1F phage, which has been extensively studied and whose structure has been elucidated

[19] ,

[20] , was chosen. K1F encodes an enzyme with endosialidase activity active against polymers of sialic acid secreted by K1-encapsulated E. coli. Indeed, K1+ strains are immune to T7 infection because the capsule forms a physical barrier that prevents phage binding. However, if purified K1F enzyme is added to cells prior to infection, T7 is able to lyse them

[21] , confirming that the presence of a bacterial capsule is a powerful mechanism for avoiding recognition by bacteriophages. Therefore, by testing the delivery of the modified lambda-stf-K1 phagemid in a K1+ strain, it is possible to determine whether the lambda-stf chimeric protein retains its enzymatic activity.

[0171] The sequence of the K1F tail fiber is (SEQ ID NO: 121):

[0172] [ka]

[0173] The bolded and underlined sequences represent the portions of the protein that have been crystallized and shown to retain its endosialidase activity. Because there is no identity between the lambda stf protein and the K1F tail fiber, insertion points were made based on conclusions drawn from different sources, including the literature and crystal structures.

[0174] The stf gene was modified to contain the K1F endosialidase at its C-terminus using a Cas9-mediated gene exchange protocol

[22] . The lambda K1F phagemid was produced as in

[23] and titrated against several K1+ strains, particularly E. coli UTI89 and S88. The results were striking: in these strains, there was no delivery when lambda wild-type stf was used, but addition of the K1F variant showed 100% delivery (Figure 2).

[0175] Using the same principles, we subsequently created a different variant of lambda-stf, this time with K5 capsulolytic activity (K5 lyase tail fiber from phage K5A). As with K1F, there is no homology between lambda-stf and K5 lyase, but its crystal structure has been published

[24] . Therefore, we generated stf-K5 chimeric lateral tail fibers using the same approach as for K1F and tested the resulting phagemid against a K5-encapsulated strain of E. coli (ECOR55). However, in this case, the delta-stf lambda producer was generated with the stf fusion gene expressed in trans under the control of an inducible promoter. As shown in Figure 3, there is some residual delivery using wild-type lambda-stf, likely due to the presence of some cells with thinner K5 capsules. However, the addition of the lambda-stf-K5 chimera significantly reduced delivery by 10%. 6 This allows for a more than fold improvement in delivery.

[0176] In some other cases, the lateral tail fiber may be found to have some homology to lambda stf, but no crystal structure is available. In these cases, the insertion point was designed as the final stretch of amino acids with identity to lambda stf. For example, in two phages sequenced in-house, the predicted lateral tail fiber proteins are as follows:

[0177] Phage AG22 stf (SEQ ID NO: 192): MAIYRQGQASMDAQGYVTGYGTKWREQLTLIRPGATIFFLAQPLQAAVITEVISDTSIRAITTGGAVVQKTNYLILLHDSLTVDGLAQDVAETLRYYQGKESEFAGFIEIIKDFDWDKLQKIQEDVKTNADAAAASQQAAKTSENNAKTSATNAANSKKGADTA KAAAESARDAANTAKTGAEAAKSGAESARDAANTAKAGAESARDQAEEYAKQAAEPYKDLLQPLPDVWIPFNDSLDMITGFSPSYKKIVIGDDEITMPGDKIVKFKRASTATYINKSGVLTNAAIDEPRFEKDGLLIEGQRTNLLINSTNPSKWNKSSNMILDRS GVDDFGFQYAKFTLKPEMVGQTSSINIVTVSGSRGFDVTGNEKYVTISCRAQSGTPNLRCRLRFENYDGSAYASLGDAYVNLTDLSIEKTGGAANRITARAVKDEASKWIFFEATIKALDTENMIGAMVQYAPAKDGGGTGADDYIYIATPQVEGGVCASSFIIT EATPVTRASDMVTIPIKNNLYNLPFTVLCEVHKNWYITPNAAPRVFDTGGHQSGAAIILAFGSADGDNDGFPYCDIGKSNRRVNENAKLKKMIIGMRVKSDYNTCCVSNARISSETKTEWRYIVSTATIRIGGQTSTGERHLFGHVRNFRIWHKALTDHQLGEIV

[0178] Its alignment with lambda stf is:

[0179] [ka]

[0180] The sequence of the stf of the second in-house phage is as follows:

[0181] Phage SIEA11 stf (SEQ ID NO: 193) MSTKFKTVITTAGAAKLAAATVPGGKKVTLSAMAVGDGNGKLPVPDAGQTKLVHEVWRHALNKVSVDNKNKNYIVAELVVPPEVGGFWMRELGLYDDAGTLIAVSNMAESYKP ELAEGSGRAQTCRMVIIVSNVASVELSIDASTVMATQDYVDDKIAEHEQSRRHPDATLTEKGFTQLSSATNSTSESLAATPKAVKAANDNANSRLAKNQNGADIQDKSAFLDNV GVTSLTFMKNNGEMPVDADLNTFGSVKAYSGIWSKATSTNATLEKNFPEDNAVGVLEVFTGGNFAGTQRYTTRDGNLYIRKLIGTWNGNDGPWGAWRHVQAVTRALSTTIDLN SLGGAEHLGLWRNSSSAIASFERHYPEQGGDAQGILEIFEGGLYGRTQRYTTRNGTMYIRGLTAKWDAENPQWEDWNQIGYQTSSTFYEDDLDDLMSPGIYSVTGKATHTPIQG QSGFLEVIRRKDGVYVLQRYTTTGTSAATKDRLYERVFLGGSFNAWGEWRQIYNSNSLPLELGIGGAVAKLTSLDWQTYDFVPGSLITVRLDNMTNIPDGMDWGVIDGNLINI SVGPSDDSGSGRSMHVWRSTVSKANYRFFMVRISGNPGSRTITTRRVPIIDEAQTWGAKQTFSAGLSGELSGNAATATKLKTARKINNVSFDGTSDINLTPKNIGAFASGKTGD TVANDKAVGWNWSSGAYNATIGGASTLILHFNIGEGSCPAAQFRVNYKNGGIFYRSARDGYGFEADWSEFYTTTRKPTAGDVGALPLSGGQLNGALGIGTSSALGGNSIVLGDN DTGFKQNGDGNLDVYANSVHVMRFVSGSVQSNKTINITGRVNPSDYGNFDSRYVRDVRLGTRVVQTMQKGVMYEKAGHVITGLGIVGEVDGDDPAVFRPIQKYINGTWYNVAQV

[0182] Its alignment with lambda stf is:

[0183] [ka]

[0184] In these two particular cases, because it was not known which antigens these tail fibers could recognize, lambda-packaged phagemids with chimeric tail fibers were produced and their delivery efficiency was tested in an E. coli collection containing a highly diverse group of O and K serotypes.

[0185] As shown in Figure 4, the addition of the chimeric stf increased the delivery efficiency of lambda-based phagemids in 25 of 96 strains tested (more than 25% of the collection). In some cases, the increase was modest; in others, it enabled very good delivery efficiency in strains with no or very little penetration by wild-type lambda phagemids. It is also worth noting that AG22, like lambda, belongs to the Siphoviridae family, while SEIA11 is a P2-like phage. This highlights the important observation that stf modules may be interchangeable across bacteriophage genera.

[0186] Other lateral tail fiber genes were analyzed as shown in Figure 4, and as previously shown, several insertion points into the lambda stf gene were identified that resulted in chimeric variants that exhibited different penetration in the E. coli collection. These insertion points were based on results for non-homologous tail fiber variants (e.g., in the case of K1F and K5 above) or on varying degrees of homology between lambda sft and the variants tested. This homology can be short, about 5-10 amino acids, or substantially similar. The insertion points tested are shown below in bold and underlined:

[0187] > Lambda stf (sequence number 1)

[0188] [ka]

[0189] The lambda stf protein consists of 774 amino acids. Insertion points can be found near the N-terminus (amino acid 131, insertion point ADAKKS) or near the C-terminus (amino acid 529, insertion point GAGENS). Figure 5 shows some selected examples of insertion points: ADAKKS, SASAAA, and MDETNR.

[0190] The results described herein demonstrate that it is possible to construct chimeric tail fibers that combine the portion of one tail fiber that binds to the capsid of one phage (usually the N-terminus of the protein) with the portion of another fiber that interacts with bacteria (usually the C-terminus of the protein). Stretched homology between different tail fiber sequences can be considered as favorable recombination points. To identify such points in the phage lambda Stf protein, we performed a scan of the Stf sequence in 50-aa windows and a phmmer search

[25] in each window to identify homologous sequences in a representative proteome 75 database (Figure 6). [Example]

[0191] T4-like phages are a highly diverse family of bacteriophages that share a common long tail fiber structure: a proximal tail fiber that binds the phage particle and a distal tail fiber (DTF) that encodes host specificity, bound by a protein that acts as a "hinge binding factor" (Desplats and Krisch, 2003, Res. Microbiol. 154:259-267; Bartual et al., 2010, Proc. Natl. Acad. Sci. 107:20287-20292). The primary host range determinant of the tail fiber is thought to reside in the distal portion. Therefore, it is very important to understand whether the host range of a given T4-like phage, which is known to be very broad, can be transferred to any other phage or phagemid of interest. The distal tail fibers (C-terminal domains of the T4-like long tail fibers) of several T4-like phages were screened for possible functional insertion sites, and several fusions with the lambda stf gene were generated and screened for their host range.

[0192] We searched for potential insertion sites for DTFs that would generate functional chimeras when fused to a heterologous tail fiber (lambda phage stf). The DTF of phage WW13 was used as a testbed. This phage has a classical T4-like structure, with proximal and distal tail fibers separated by a hinge binding factor, the gp38 chaperone / adhesin that assists in tail fiber folding and host recognition (Trojet et al., 2011, Genome Biol. Evol. 3:674-686), and the gp57A chaperone known to be required for correct tail fiber folding (Matsui et al., 1997, J. Bacteriol. 179:1846-1851). Because the endogenous genome regulation of T4-like phages is complex and may involve unknown regulatory layers (Miller et al., 2003, Microbio. Mol. Biol. Rev. 67:86-156), a synthetic linker encoding an RBS was designed to replace the natural DNA linker between the DTF gene and the adhesin; immediately downstream, another synthetic RBS was added preceding the chaperone pg57A, thus creating a polycistronic mRNA encoding all functions required for correct folding of DTF (Figure 7). This construct was assembled in a plasmid under the control of an inducible promoter and complemented in trans in a strain producing lambda-based phagemids.

[0193] T4-like sequence (underlined is the DTF insertion site used in the above fusion):

[0194] WW13 (sequence number 123)

[0195] [ka]

[0196] Figure 7 shows the structure of engineered lambda stf-T4-like DTF chimeras. Semicircles indicate RBS sites; T marks, transcription terminators; arrows, promoters. Several portions of the C-terminus of DTFs were screened and fused to the lambda stf gene at the GAGENS insertion site. Several variants of the chimeric lambda stf-WW13 are functional, as assessed by production of phagemid particles in a collection of E. coli strains and transduction of a chloramphenicol marker. The functional chimera shown in Figure 8 was obtained by fusion at the IIQLED insertion site of WW13. Additional functional chimeras were obtained by fusion at the lambda stf MDETNR insertion site and the WW13 DTF GNIIDL, VDRAV, and IIQLE insertion sites (Figure 11).

[0197] Other T4-like phages that share sequence homology with WW13, like PP-1, were also tested and found to produce functional chimeras (Fig. 8), which exhibit an IATRV insertion site at the beginning of the PP-1 DTF portion.

[0198] Figure 8 shows the screening of phagemid particles carrying the chimeric lambda stf-T4-like DTF. A collection of 96 different wild-type E. coli strains, covering different serotypes, was transduced with the lambda-based phagemid and plated on Cm LB agar. The left panel represents wild-type lambda stf; the middle panel represents chimeric lambda-stf-WW13; and the right panel represents chimeric lambda-stf-PP-1.

[0199] The insertion site found in WW13 is not always present in a given T4-like DTF, thereby complicating analysis. Another functional insertion site with no homology to WW13 was discovered for a second phage (WW55, Figure 9). The same TPGEL insertion site can be found in a subset of T4-like phages, and at least one of them, WW34, and the MDETNR insertion site in lambda stf, has been shown to give rise to functional chimeras (Figure 9).

[0200] Figure 9 shows the screening of phagemid particles carrying the chimeric lambda stf-T4-like DTF. A collection of 96 different wild-type E. coli strains, covering different serotypes, was transduced with the lambda-based phagemid and plated on Cm LB agar. The left panel represents wild-type lambda stf; the middle panel represents chimeric lambda-stf-WW55; and the right panel represents chimeric lambda-stf-WW34.

[0201] Because T4-like DTF proteins may or may not share a common site for insertion, attempts were made to identify a universal insertion site present in all T4-like DTFs. When aligning several T4-like DTFs, there is no homology along the entire DTF gene present in all sequences, except for the well-conserved N-terminus. The N-terminus of the DTF is thought to interact with the hinge binding factor for binding to the primary phage particle.

[0202] While traditionally, the host range determinant resides in the C-terminal portion of the DTF, recent studies have demonstrated that the N-terminus may also be involved in this process (Chen et al., 2017, Appl. Environ. Microbiol. V1. 83 No. 23). We then scanned the N-terminus of the DTF for insertion sites present in all T4-like phages and capable of generating functional chimeras. We used the phage WW13 DTF and the lambda stf insertion site, MDETNR. While direct fusion of the entire DTF gene (starting at amino acid 2) yielded particles with some activity, we identified a region from amino acids 1 to 90 of the DTF, with a preferred region between amino acids 40 and 50 of the DTF, which recapitulates the behavior of DTF fusions. This region is shown in Figure 10. Importantly, this region was present in all T4-like phages screened and could be used very quickly to generate chimeras with a diverse set of DTFs, including WW55 (Figure 10).

[0203] Thus, the present disclosure is useful for generating phage and phagemid particles with altered host ranges because it provides a particle framework for the construction of chimeras using DTFs from any T4-like phage, highlighting their modularity and translatability. [Example]

[0204] The human microbiome encompasses different regions of the body, including the gastrointestinal tract, skin, vagina, and mouth.

[29] The microbiomes of these regions are composed of different populations of microorganisms, such as bacteria, archaea, and fungi.

[29]

[31] Many studies have attempted to characterize the specific composition of these populations, and it has become clear that although a "core microbiome" may exist, there is much variation in the relative content of each microorganism depending on several factors, such as geographic location, diet, or age.

[32]

[35]

[0205] In particular, in the case of the human gastrointestinal microbiome, it is impossible to know a priori which bacterial species a given individual harbors without performing diagnostic methods. In the case of Escherichia coli, several studies have been performed indicating the prevalence of several serotypes and phylogroups in many individuals, but there are significant variations in the composition of samples depending on the geographic distribution and the time of sampling: for example, samples isolated from Europe, Africa, Asia, and South America in the 1980s show a prevalence of phylogroups A and B1 (55% and 21%, respectively); whereas samples obtained in Europe, North America, Asia, and Australia in the 2000s belonged mainly to group B2 (43%), followed by A (24%), D (21%), and B1 (12%)

[36] . Although phylogroups B2 and D are usually more commonly associated with pathogenic strains than commensal strains

[37] , there are studies showing many human and non-human specific strains belonging to phylogroup B2, which are commensals, and which belong to different serogroups

[38] .

[0206] The inherent variability of the human microbiome, especially that of E. coli subtypes, makes the design of targeted therapeutic approaches challenging. In the case of phage therapy, for example, aimed at killing target bacterial populations, two possible approaches are possible: first, the use of narrow-host-range particles capable of recognizing and targeting specific E. coli serotypes; or second, the use of broad-host-range phages capable of recognizing many different strains, sometimes even from different genera.

[39] This difficulty is exacerbated when considering strategies that do not aim to kill target bacterial populations but seek to add functionality to them (i.e., delivery of factors that have an effect on the host and are expressed by the target microbiota). In this particular case, the use of packaged phagemids is of great interest because they do not kill the host (unless their payload carries genes intended to kill the host), do not replicate or spread, and do not contain any endogenous phage genes. However, in the case of phages, diagnostic research requires identifying the specific serotype / variant of bacteria present in the patient prior to treatment in order to find or design a packaging phagemid that allows delivery of a payload that adds functionality to the target bacteria without killing them.

[0207] Combining these two approaches, we propose using engineered delivery vehicles (i.e., engineered particles with a "broad host range") that can recognize many strains belonging to different serotypes and phylogenetic groups, focusing on E. coli. Contrary to kill-directed approaches, the target bacterial population needs to be reduced in number as close to 100% as possible, and therapeutic delivery approaches do not need to reach a large percentage of bacteria a priori; delivery needs to be high enough to ensure that the therapeutic payload is expressed at precise levels, which can be highly variable depending on the application. Furthermore, the payload can be expressed by different serotypes or phylogenetic groups. This approach increases the chances that the particles will deliver a payload that will be expressed in vivo in the majority of patients.

[0208] To achieve delivery in bacterial populations composed of unknown serotypes / variants of the target strain, delivery vehicles were engineered to contain chimeric lateral tail fibers (stf) selected for their ability to recognize diverse target strains. There are many phages described that have a broad host range in E. coli, many of which belong to the T4 family, but in general, phages against E. coli and related bacteria have a restricted host range.

[0209] However, there is no consensus on how many strains are required to be targeted by a phage to be considered "broad host range" according to

[41] .

[0210] In the case of E. coli, the ECOR collection is a set of strains isolated from different sources that are thought to represent the natural variability of this bacterium

[42] . Some phages have been shown to have a broad host range for this collection (e.g., approximately 53% of ECOR strains can be lysed by phage AR1

[43] and approximately 60% by phage SU16

[44] ). In contrast, a single phage can infect 95% of Staphylococcus aureus strains

[40] .

[0211] Using human strains from this collection, we decided to test engineered delivery vehicles with chimeric stf and evaluate their host range in an attempt to identify variants that can recognize as many hosts as possible, as described in the literature

[45] . The difference is that the present assay measures delivery efficiency relative to lysis.

[0212] Strains from overnight cultures were diluted 1:100 in 600 μL of LB supplemented with 5 mM CaCl2 in 96-deep well plates and grown at 37°C for 2 hours at 900 rpm. 6Ten μL of the packaged phagemids produced at 1 μL / μL were then added to a 90 μL bacterial culture and incubated at 37°C for 30 minutes. Ten μL of the mixture was plated onto LB agar supplemented with 24 μg / mL chloramphenicol and incubated overnight at 37°C. The next day, the density of the dots was scored from 0 to 5, with 0 representing no transductants and 5 representing very dense spots [Figure 11]. The density of the spots corresponds to the number of bacteria that received the payload containing the chloramphenicol acetyltransferase gene, and is therefore directly related to the delivery efficiency of the packaged phagemid.

[0213] Several stf chimeras were tested and screened in 40 human strains from the ECOR collection. As a control, the delivery efficiency of wild-type stf was tested. The packaging phagemid variant used in the delivery experiments was now modified so that its tail-end gpJ recognizes a receptor other than LamB (1A2 variant). In Figure 12, raw dot titrations are shown for 18 stfs, and in Figure 13, a bar-formatted table is shown with delivery efficiency scored by dot density as well as delivery statistics.

[0214] Considering only dots with a density score of 3 or higher (considered to have moderate to high delivery efficiency), some stfs can be considered broad-host-range because their delivery efficiency in selected ECOR strains is significantly higher than when using wild-type stfs. For example, for stf EB6 or stf 68B, approximately 50% of strains show moderate to high delivery efficiency compared to 17.5% of strains with wild-type stfs. These stfs are good candidates for in vivo delivery because they can deliver in different phylogenetic groups and serotypes. At the bottom of the table in Figure 13, a bar-formatted representation of density scores higher than 3 is shown, and the threshold for a broad-host-range stf is set at at least a two-fold increase compared to the baseline for wild-type stfs; this is an stf that can deliver with a score of 3 or higher in at least 35% of strains. Other stfs also showed increased delivery compared to wild-type stfs, setting a less stringent threshold for stfs capable of delivering with a score of 3 or higher, which represents at least a 50% increase compared to the number of strains delivered by wild-type stfs (which delivered with a score of 3 or higher in at least 26.25% of strains). For comparison, data for stf K1 and stf 66D are presented: these stfs appear to be efficiently delivered by a small number of strains (e.g., strains B and AB for stf K1; and strains E and AF for stf 66D), implying that they likely have a narrow host range; in the case of the K1 stf, this is expected since the cognate receptor is the K1 capsule

[46] . Furthermore, data are presented for a chimera with an stf arising in a T4-like phage; as the literature indicates, this chimera does not appear to be the best candidate, but does exhibit a broad host range.

[0215] Taken together, these results suggest that the stf of a delivery vehicle can be engineered to recognize a wide number of target E. coli strains, thus making it "broad host range." This type of particle could be very useful for delivering functional payloads to target bacteria without the need to engineer specific variants that recognize a given bacterial strain.

[0216] List of cited references [References] TIFF0007764247000007.tif73166TIFF0007764247000008.tif207170

[0217] Table 1A

[0218] Table 1B

[0219]

Table 1C

Claims

1. A chimeric receptor-binding protein (RBP), the chimeric RBP comprises a fusion between the N-terminal domain of an RBP from a lambdoid bacteriophage or a lambda bacteriophage and the C-terminal domain of a different RBP from a caudovirus bacteriophage, said N-terminal domain fused to said C-terminal domain within an amino acid region selected from positions 495 to 560 of the N-terminal RBP with respect to the lambda stf sequence (SEQ ID NO: 1); and, the RBP from the lambdoid bacteriophage or lambda bacteriophage is a lateral tail fiber (STF), and the different RBP is a lateral tail fiber (STF), a long tail fiber (LTF), a tail spike, or a distal tail fiber (DTF); Chimeric receptor-binding proteins (RBPs).

2. 2. The chimeric RBP of claim 1, wherein the C-terminal domains of the different RBPs have depolymerase activity against encapsulated bacterial strains.

3. 2. The chimeric RBP of claim 1, wherein the RBP of a lambdoid bacteriophage has an amino acid sequence homology of 35% identity or greater for 45 amino acids, 50% identity or greater for 30 amino acids, or 90% identity or greater for 18 amino acids in the amino acid region ranging from positions 495 to 560 with respect to the lambdoid bacteriophage stf sequence of SEQ ID NO:

1.

4. 2. The chimeric RBP of Claim 1, wherein said N-terminal domain is fused to said C-terminal domain at an insertion site having at least 80% identity to insertion site GAGENS (SEQ ID NO: 182).

5. 2. The chimeric RBP of claim 1, wherein the RBP derived from the different RBP has amino acid sequence homology of 35% identity or more for 45 amino acids, 50% identity or more for 30 amino acids, or 90% identity or more for 18 amino acids in the amino acid region ranging from positions 495 to 560 with respect to the lambda bacteriophage stf sequence of SEQ ID NO:

1.

6. 6. A bacterial delivery vehicle comprising the chimeric RBP of any one of claims 1 to 5.

7. The bacterial delivery vehicle of claim 6 , wherein the bacterial delivery vehicle is a bacteriophage.

8. The bacterial delivery vehicle of claim 6 or 7, wherein the bacterial delivery vehicle is a packaged phagemid.

9. 9. The bacterial delivery vehicle of claim 6, further comprising a nucleic acid payload encoding a protein or nucleic acid of interest.

10. 10. The bacterial delivery vehicle of claim 9, wherein the nucleic acid of interest is selected from the group consisting of a Cas nuclease gene, a Cas9 nuclease gene, a guide RNA, a CRISPR locus, a toxin gene, a gene expressing an enzyme such as a nuclease or a kinase, a TALEN, a ZFN, a meganuclease, a recombinase, a bacterial receptor, a membrane protein, a structural protein, a secreted protein, a gene expressing resistance to antibiotics or drugs in general, a gene expressing a toxin protein or a toxin factor, and a gene expressing a virulence protein or a virulence factor, or any combination thereof.

11. 10. The bacterial delivery vehicle of claim 9, wherein the protein of interest is a nuclease that targets cleavage of the host bacterial cell genome or a host bacterial cell plasmid.

12. The bacterial delivery vehicle of claim 11 , wherein the cleavage occurs in an antibiotic resistance gene.

13. The bacterial delivery vehicle of claim 9, wherein the nucleic acid payload encodes a therapeutic protein.

14. The bacterial delivery vehicle of claim 9, wherein the nucleic acid payload encodes an antisense nucleic acid molecule.

15. 6. A nucleic acid molecule encoding the chimeric RBP of any one of claims 1 to 5.

16. 15. A pharmaceutical or veterinary composition comprising one or more bacterial delivery vehicles according to any one of claims 6 to 14 and a pharmaceutically acceptable carrier, wherein the one or more bacterial delivery vehicles are bacteriophages.

17. 17. A method for treating a bacterial infection, comprising administering to a subject (excluding humans) having a bacterial infection in need of treatment the pharmaceutical or veterinary composition of claim 16.

18. 17. A pharmaceutical or veterinary composition according to claim 16 for use in the treatment of a bacterial infection.

19. 10. An in vitro method for reducing the amount of pathogenic and / or antibiotic-resistant bacteria in a bacterial population, comprising contacting the bacterial population with a bacterial delivery vehicle according to any one of claims 6 to 9.

20. 17. A pharmaceutical or veterinary composition according to claim 16 for use in reducing the amount of pathogenic and / or antibiotic-resistant bacteria in a bacterial population.

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