Altering microbial populations & modifying microbiota

Abstract

The invention relates to methods, uses, systems, arrays, engineered nucleotide sequences and vectors for inhibiting bacterial population growth or for altering the relative ratio of sub-populations of first and second bacteria in a mixed population of bacteria. The invention is particularly useful, for example, for treatment of microbes such as for environmental, medical, food and beverage use The invention relates infer alio to methods of controlling microbiologically influenced corrosion (MIC) or biofouling of a substrate or fluid in an industrial or domestic system.

1 . An engineered virus that is capable of transforming a host cell, the engineered virus
 (a) comprising a nucleic acid sequence for producing a crRNA; and   (b) lacking a nucleic acid sequence encoding a Cas nuclease that is operable with the crRNA;   
       wherein the crRNA is operable with a Cas nuclease in a host cell to guide Cas nuclease modification of a target sequence in the host cell. 
     
     
         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 virus comprises a host-modifying array (HM-array) for producing the crRNA, wherein the HM-array comprises a constitutive promoter. 
     
     
         5 . The virus of  claim 1 , wherein the virus comprises an HM-array for producing the crRNA, wherein the HM-array comprises a Cas nuclease promoter. 
     
     
         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. 
     
     
         10 . The virus of  claim 1 , wherein the virus comprises a component for producing an endolysin. 
     
     
         11 . The virus of  claim 1 , wherein the virus is a Corticoviridae, Cystoviridae, Inoviridae, Leviviridae, Microviridae, Myoviridae, Podoviridae, Siphoviridae or Tectivirdae virus. 
     
     
         12 . The virus of  claim 1 , wherein the virus comprises an HM-array for producing the crRNA, wherein the HM-array does not comprise a protospacer adjacent motif (PAM) recognized by the Cas nuclease. 
     
     
         13 . The virus of  claim 1 , wherein the virus comprises an 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 identical to repeat sequence of said system. 
     
     
         14 . The virus of  claim 1 , wherein the virus does not comprise a tracrRNA-encoding sequence. 
     
     
         15 . The virus of  claim 1 , wherein the virus comprises a first HM-array comprising a spacer sequence (HM-spacer) and repeats encoding the crRNA. 
     
     
         16 . The virus of  claim 15 , wherein the virus comprises a second HM-array that encodes a second crRNA, wherein the second crRNA comprises a nucleotide 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 nucleotide sequence encoding a non-host Cas that is functional in the host cell. 
     
     
         18 . The virus of  claim 16 , wherein the virus comprises a nucleotide sequence encoding a non-host Cas that is functional in the host cell, wherein the second crRNA is operable with the non-host Cas in the host cell to guide Cas modification of the second target sequence in the host cell. 
     
     
         19 . The virus of  claim 17 , wherein
 (i) the non-host Cas is a Type I Cas and the host Cas is a Type II or III Cas;   (ii) the non-host Cas is a Type II Cas and the host Cas is a Type I or III Cas;   (iii) the non-host Cas is a Type III Cas and the host Cas is a Type I or II Cas; or   (iv) the host cell does not express a Type of Cas that is the same as the Type of the non-host Cas.   
     
     
         20 . The virus of  claim 18 , wherein
 (i) the non-host Cas is a Type I Cas and the host Cas is a Type II or III Cas;   (ii) the non-host Cas is a Type II Cas and the host Cas is a Type I or III Cas;   (iii) the non-host Cas is a Type III Cas and the host Cas is a Type I or II Cas;   (iv) the host cell does not express a Type of Cas that is the same as the Type of the non-host Cas.   
     
     
         21 . The virus of  claim 1 , wherein the virus comprises an HM-array for producing the crRNA, wherein the HM-array does not comprise a PAM recognized by Cas9. 
     
     
         22 . The virus of  claim 16 , wherein the first HM-array is an array of a first CRISPR/Cas Type and the second HM-array is an array of a second CRISPR/Cas Type. 
     
     
         23 . The virus of  claim 22 , wherein
 (a) the first HM-array is a Type II array and the second HM-array is a Type I or III array;   (b) the first HM-array is a Type II-A array and the second HM-array is a Type II-B array;   (c) the second HM-array is a Type II array and the first HM-array is a Type I or III array; or   (d) the second HM-array is a Type II-A array and the first HM-array is a Type II-B array.   
     
     
         24 . The virus of  claim 16 , wherein the first HM-array is operable with the host Cas nuclease and the second HM-array 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 second HM-array repeats. 
     
     
         26 . An engineered virus that is capable of transforming a host cell, the engineered virus
 (a) comprising a nucleic acid sequence for producing a crRNA; and   (b) lacking a nucleic acid sequence encoding a Type I 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. 
     
     
         27 . An engineered virus that is capable of transforming a host cell, the engineered virus
 (a) comprising a nucleic acid sequence for producing a crRNA; and   (b) lacking 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. 
     
     
         28 . An engineered virus that is capable of transforming a host cell, the engineered virus
 (a) comprising a nucleic acid sequence for producing a crRNA; and   (b) lacking 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.