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 inter alia to methods of controlling microbiologically influenced corrosion (MIC) or biofouling of a substrate or fluid in an industrial or domestic system.

What is claimed is: 
     
         1 . An engineered nucleic acid vector comprising a host modifying (HM) CRISPR array the array comprising a spacer sequence (HM-spacer) and repeats encoding a HM-crRNA, the HM-crRNA comprising a sequence that is capable of hybridizing to a host cell target sequence to guide a Cas to the target in the host cell to modify the target sequence,
 wherein the host cell is a bacterial or archaeal cell,   and wherein vector comprises a HM-DNA, and the HM-DNA in the vector is flanked by site-specific recombination sites which can be cut by the action of a site specific recombinase.   
     
     
         2 . The vector of  claim 1 , wherein the HM-crRNA is operable with a Type I Cas. 
     
     
         3 . The vector of  claim 1 , wherein the HM-crRNA is operable with a Type II Cas. 
     
     
         4 . The vector of  claim 1 , wherein the HM-crRNA is operable with a Type III Cas. 
     
     
         5 . The vector of  claim 1 , wherein the Cas is a dead Cas, and the vector comprises a nucleotide sequence encoding the dead Cas. 
     
     
         6 . The vector of  claim 1 , wherein the vector does not comprise a Cas endonuclease-encoding sequence 
     
     
         7 . The vector of  claim 1 , wherein the vector is a phagemid. 
     
     
         8 . The vector of  claim 1 , wherein the vector is a plasmid. 
     
     
         9 . The vector of  claim 1 , wherein the vector comprises a nucleotide sequence encoding the site specific recombinase. 
     
     
         10 . A method of modifying a target nucleotide sequence of a host cell, comprising transforming the host cell with the vector of  claim 1 , wherein the site specific recombinase is encoded by the vector or by the host cell, wherein the modifying comprises inserting the HM-DNA at the target nucleotide sequence.