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 CRISPR nucleic acid vector comprising a mobile genetic element (MGE), wherein the MGE comprises an origin of transfer (oriT) and a CRISPR array for modifying a target sequence in a host bacterial cell,
 (a) wherein the CRISPR array comprises one or more sequences for expression of a crRNA and a promoter for transcription of the sequence(s) in the host bacterial cell;   (b) wherein the crRNA is capable of hybridizing to the target sequence to guide a Cas in the host bacterial cell to modify the target sequence; and   (c) wherein the vector is a phage.   
     
     
         2 . The vector of  claim 1 , wherein the oriT is functional in first and second host bacterial cells, wherein the target sequence is comprised by the first and/or second host bacterial cell. 
     
     
         3 . The vector of  claim 1 , wherein the MGE comprises a transposon. 
     
     
         4 . The vector of  claim 3 , wherein the transposon is a Type I transposon or a Type II transposon. 
     
     
         5 . The vector of  claim 2 , wherein the first host bacterial cell is a  Bacteroidetes  cell, and wherein the target sequence is not comprised by the first host bacterial cell. 
     
     
         6 . The vector of  claim 5 , wherein the second host bacterial cell is a  Firmicutes  cell, and wherein the target sequence is comprised by the second host bacterial cell but not the first host bacterial cell, wherein the crRNA is capable of hybridizing to the target sequence in the second host bacterial cell, thereby directing the Cas in the second cell to cut the target sequence. 
     
     
         7 . The vector of  claim 1 , wherein
 (a) the target sequence is comprised by a first host bacterial cell, wherein the first host bacterial cell is a  Bacteroidetes; Lactobacillus; Bifidobacterium; Streptococcus thermophiles; Enterococcus faecium; Alistipes; Alkaliflexus; Parabacteroides; Tannerella ; or  Xylanibacter  cell; and/or   (b) the target sequence is comprised by a second host bacterial cell, wherein the second host bacterial cell is a cell selected from (i) a  Staphylococcus aureus  cell; (ii) a  Pseudomonas aeuroginosa  cell; (iii) a  Klebsiella  cell; (iv) a  Streptoccocus  cell; (v) a  Salmonella  cell; (vi) a  Shigella  cell; (vii) a  Mycobacterium tuberculosis  cell; (viii) an  Enterococcus  cell; (ix) an  Enterobacteriaceae  cell; (x) an  E. coli  cell; (xi) a  Clostridium  cell; (xii) a  Neisseria gonnorrhoea  cell; (xiii) an  Acinetoebacter baumannii  cell; or (xiv) a  Campylobacter  cell.   
     
     
         8 . An ex vivo composition comprising a plurality of cells, wherein at least one of the plurality of cells comprises a vector according to  claim 1 , wherein the plurality of cells are  Bacteroidetes  cells. 
     
     
         9 . An isolated mixed population of bacterial cells comprising a sub-population of first host bacterial cells and a sub-population of second host bacterial cells, wherein the first host bacterial cells comprise vectors according to  claim 1 , wherein the MGEs of the vectors are capable of horizontal transfer between the first and second host bacterial cell sub-populations. 
     
     
         10 . The mixed population of  claim 9 , wherein one or both of the sub-population of first host bacterial cells and the sub-population of second bacterial species is capable of populating the gut microbiota of a human or non-human animal. 
     
     
         11 . The mixed population of  claim 9 , wherein the sub-population of first host bacterial cells are commensal or symbiotic with humans or animals. 
     
     
         12 . A method of modifying host bacterial cells comprised by a microbiome of a human or non-human animal, comprising administering a pharmaceutical composition comprising the vector of  claim 1  to the human or non-human animal. 
     
     
         13 . A method of modifying host bacterial cells comprised by a microbiome of a human or non-human animal, comprising administering the mixed population of  claim 10  to the human or non-human animal. 
     
     
         14 . A method of modifying a target nucleotide sequence in a host bacterial cell, the method comprising:
 (i) combining the host bacterial cell with a carrier bacterial cell,
 (a) wherein the carrier bacterial cell comprises a CRISPR nucleic acid vector comprising a mobile genetic element (MGE), wherein the MGE comprises an origin of transfer (oriT) and a CRISPR array for modifying a target sequence of a genome of the host bacterial cell or a genome of a virus in the host bacterial cell, 
 (b) wherein the CRISPR array comprises one or more sequences for expression of a crRNA and a promoter for transcription of the sequence(s) in the host bacterial cell; 
 (c) wherein the crRNA is capable of hybridizing to the target sequence to guide a Cas in the host bacterial cell to modify the target sequence, 
 (d) wherein the vector is a phage; and 
   (ii) culturing the host bacterial cell and carrier bacterial cell together to obtain a mixed population of bacteria, wherein the MGE is transferred from the carrier bacterial cell to the host bacterial cell, whereby the crRNA hybridizes to the target sequence to guide the Cas in the host bacterial cell and the target is modified.   
     
     
         15 . The method of  claim 12 , wherein the modifying is cutting, adding, deleting or substituting a nucleic acid sequence at the target sequence. 
     
     
         16 . The method of  claim 13 , wherein the modifying is cutting, adding, deleting or substituting a nucleic acid sequence at the target sequence.