Altering microbial populations & modifying microbiota

2:

• The virus of claim 1, wherein the crRNA is comprised by a single guide RNA.

3:

• The virus of claim 1, wherein the Cas nuclease is a dead Cas (dCas).

4:

• The virus of claim 1, wherein the nucleic acid sequence encoding the crRNA comprises a constitutive promoter.

(canceled)

6:

• The virus of claim 1, wherein the virus is a phage.

7:

• The virus of claim 6, wherein the phage is capable of infecting an E coli, Streptocccus, Staphylococcus, Pseudomonas, Vibrio, Neisseria, Bordetella, Haemophilus, Shigella, Brucella, Francisellam Xanthomonas, Agrobacterium, Erwinia, Legionella, Listeria, Campylobacter, Yersinia, Borelia, Helicobacter, Clostridium, Salmonella, Chlamydia, Parachlamydia, Corynebacterium, Klebsiella, Enterococcus or Acinetobacter cell.

8:

• The virus of claim 1, wherein the virus is a virophage.

9:

• The virus of claim 1, wherein the host cell is a bacterial or archaeal host cell.

(canceled)

11:

• The virus of claim 1, wherein the virus is a Corticoviridae, Cystoviridae, Inoviridae, Leviviridae, Microviridae, Myoviridae, Podoviridae, Siphoviridae or Tectivirdae virus.

(canceled)

13:

• The virus of claim 1, wherein the nucleic acid sequence encoding crRNA comprises a host-modifying array (HM-array) for producing the crRNA, wherein the Cas nuclease is a Cas nuclease of a CRISPR/Cas system, wherein the system comprises a CRISPR array comprising a repeat sequence, wherein the HM-array comprises a CRISPR repeat sequence that is at least about 95% identical to repeat sequence of said system.

(canceled)

15:

• The virus of claim 1, wherein the nucleic acid sequence encoding the crRNA comprises an HM-array, wherein the HM-array comprises a spacer sequence (HM-spacer) and repeat sequences, wherein the first HM-spacer and repeat sequences encode the crRNA.

16:

• The virus of claim 15, wherein the virus comprises a second nucleic acid sequence that encodes a second crRNA, wherein the second crRNA is operable with a second Cas in the host cell, and wherein the second crRNA comprises a nucleic acid sequence that is capable of hybridizing to a second host target sequence to guide Cas modification of the second target sequence in the host cell.

17:

• The virus of claim 1, wherein the virus comprises a nucleic acid sequence encoding an exogenous Cas that is functional in the host cell.

18:

• The virus of claim 16, wherein the virus comprises a nucleic acid sequence encoding an exogenous Cas that is functional in the host cell, wherein the second crRNA is operable with the exogenous Cas in the host cell to guide Cas modification of the second target sequence in the host cell.

21:

• The virus of claim 1 wherein the nucleic acid sequence encoding the crRNA does not comprise a PAM recognized by Cas9.

22:

• The virus of claim 16, wherein the nucleic acid sequence encoding the crRNA comprises a first HM-array of a first CRISPR/Cas Type and the second nucleic acid sequence encoding the second crRNA comprises a second HM-array of a second CRISPR/Cas Type.

24:

• The virus of claim 16, wherein the first crRNA is operable with an endogenous Cas nuclease of the host cell and the second crRNA is operable with an exogenous Cas nuclease.

25:

• The virus of claim 16, wherein the virus comprises a Cas nuclease sequence that is not encoded by the host cell and that is cognate to repeat sequences of the second crRNA.

The engineered virus of claim 1, wherein the engineered virus

• lacks a nucleic acid sequence encoding a Type II Cas nuclease;
• wherein the crRNA is operable with a Type I Cas nuclease in a host cell to guide Cas nuclease modification of a target sequence in the host cell, and wherein the nucleic acid sequence does not comprise a PAM recognized by the Type I Cas nuclease.

The engineered virus of claim 1, wherein the engineered virus

• lacks a nucleic acid sequence encoding a Type II Cas nuclease;
• wherein the crRNA is operable with a Type II Cas nuclease in a host cell to guide Cas nuclease modification of a target sequence in the host cell, and wherein the nucleic acid sequence does not comprise a PAM recognized by the Type II Cas nuclease.

The engineered virus of claim 1, wherein the engineered virus

• lacks a nucleic acid sequence encoding a Type III Cas nuclease;
• wherein the crRNA is operable with a Type III Cas nuclease in a host cell to guide Cas nuclease modification of a target sequence in the host cell, and wherein the nucleic acid sequence does not comprise a PAM recognized by the Type III Cas nuclease.

29:

• The engineered virus of claim 26, wherein the host cell comprises an endogenous Type I Cas nuclease and the nucleic acid sequence does not comprise a PAM recognized by the endogenous Type I Cas nuclease.

30:

• The engineered virus of claim 27, wherein the host cell comprises an endogenous Type II Cas nuclease and the nucleic acid sequence does not comprise a PAM recognized by the endogenous Type II Cas nuclease.

31:

• The engineered virus of claim 28, wherein the host cell comprises an endogenous Type III Cas nuclease and the nucleic acid sequence does not comprise a PAM recognized by the endogenous Type III Cas nuclease.

33:

• The engineered virus of claim 32, wherein the first Cas nuclease and the second Cas nuclease are the same.

34:

• The engineered virus of claim 32, wherein the first Cas nuclease and the second Cas nuclease are different.