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.

1 - 28 . (canceled) 
     
     
         29 . A method for treating or reducing the risk of a disease or condition in a subject comprising a mixed population of bacteria, wherein the mixed population of bacteria comprises a first bacterial subpopulation and a second bacterial sub-population, wherein the first bacterial sub-population comprises a first bacterial species and the second bacterial sub-population comprises a population of host cells of a second bacterial species, wherein the second bacterial species is a different species than the first bacterial species, wherein the disease or condition is caused by the hosts cells, and wherein the first bacterial species is probiotic, commensal or symbiotic with the subject, the method comprising:
 (a) contacting the mixed population of bacteria with an engineered nucleic acid for producing a host modifying crRNA (HM-crRNA), and   (b) producing the HM-crRNA in the host cells;   wherein:   (i) the HM-crRNA is operable with a Type II Cas in the host cells, wherein the engineered nucleic acid and the Type II Cas are comprised by a Type II HM-CRISPR/Cas system in the   host cells;   and   (ii) the HM-crRNA comprises a nucleotide sequence that is capable of hybridizing to a target sequence in the host cells to guide the Type II Cas to modify the target sequence in the host cells;   wherein the first bacterial species does not comprise the target sequence, wherein the host cells are killed or growth of the host cells is inhibited in the subject, and wherein growth of the first bacterial species is not inhibited.   
     
     
         30 . A method for treating an industrial or medical fluid, a surface, an apparatus, a container, a waterway, water, a beverage, a foodstuff, or a cosmetic, wherein the industrial or medical fluid, surface, apparatus, container, waterway, water, beverage, foodstuff or cosmetic comprises a mixed population of bacteria, wherein the mixed population of bacteria comprises a first bacterial sub-population and a second bacterial sub-population, wherein the first bacterial sub-population comprises a first bacterial species and the second bacterial sub-population comprises a population of host cells of a second bacterial species, wherein the second bacterial species is a different species than the first bacterial species, the method comprising:
 (a) contacting the mixed population of bacteria with an engineered nucleic acid for producing a host modifying crRNA (HM-crRNA), and   (b) producing the HM-crRNA in the host cells;   
       wherein:
 (i) the HM-crRNA is operable with a Type II Cas in the host cells, wherein the engineered nucleic acid and the Type II Cas are comprised by a Type II HM-CRISPR/Cas system in the host cells; 
 and 
 (ii) the HM-crRNA comprises a nucleotide sequence that is capable of hybridizing to a target sequence in the host cells to guide the Type II Cas to modify the target sequence in the host cells; 
 
       wherein the host cells are killed or growth of the host cells is inhibited. 
     
     
         31 . The method of  claim 29 , wherein step (b) comprises producing a plurality of different HM-crRNAs in the host cells, wherein the plurality of different HM-crRNAs comprises a first nucleotide sequence that hybridizes to a first target sequence in the host cells; and a second nucleotide sequence that hybridizes to a second-target sequence in the host cells, wherein the second target sequence is different from the first target sequence; and wherein:
 (i) the first target sequence is comprised by a first antibiotic resistance gene or RNA thereof and the second target sequence is comprised by a second antibiotic resistance gene or RNA thereof;   (ii) the first target sequence is comprised by an antibiotic resistance gene or RNA thereof and the second target sequence is comprised by an essential gene or a virulence gene or RNA thereof;   (iii) the first target sequence is comprised by a first essential gene or RNA thereof and the second target sequence is comprised by a second essential gene or a virulence gene or RNA thereof; or   (iv) the first target sequence is comprised by a first virulence gene or RNA thereof and the second target sequence is comprised by an essential gene or a second virulence gene or RNA thereof.   
     
     
         32 . The method of  claim 29 , wherein the Type II Cas is a Cas9. 
     
     
         33 . The method of  claim 29 , wherein the Type II Cas is encoded by an engineered nucleic acid. 
     
     
         34 . The method of  claim 29 , wherein the Type II Cas is an endogenous Cas of the host cells. 
     
     
         35 . The method of  claim 29 , wherein the engineered nucleic acid for producing the HM-crRNA is present in a phage, phagemid or plasmid. 
     
     
         36 . The method of  claim 33 , wherein the engineered nucleic acid encoding the Type II Cas is present in a phage, phagemid or plasmid. 
     
     
         37 . The method of  claim 29 , wherein the mixed population of bacteria is present in a human microbiota. 
     
     
         38 . The method of  claim 29 , wherein the host cells are gram positive cells. 
     
     
         39 . The method of  claim 38 , wherein the target sequence is a host target sequence. 
     
     
         40 . The method of  claim 29 , wherein the Type II Cas is a  Streptococcus  Cas9. 
     
     
         41 . The method of  claim 29 , wherein the Type II HM-CRISPR/Cas system comprises an endogenous tracrRNA of the host cells. 
     
     
         42 . The method of  claim 29 , wherein the Type II HM-CRISPR/Cas system comprises a tracrRNA, and wherein the tracrRNA is encoded by an engineered nucleic acid. 
     
     
         43 . The method of  claim 42 , wherein the engineered nucleic acid for producing the HM-crRNA encodes a single guide RNA comprising the tracrRNA and the HM-crRNA. 
     
     
         44 . The method of  claim 29 , wherein the host cells are  C. difficile, E. coli  or  Salmonella  cells. 
     
     
         45 . The method of  claim 29 , wherein the mixed population of bacteria comprises  E. coli  and a bacterial species selected from the group consisting of  Lactobacillus  and  Streptococcus.    
     
     
         46 . The method of  claim 29 , wherein the method inhibits growth of the host cells on a surface. 
     
     
         47 . The method of  claim 29 , wherein the first bacterial species has a 16s ribosomal RNA-encoding DNA sequence that is at least about 80% identical to a 16s ribosomal RNA-encoding DNA sequence of the second bacterial species, and wherein the growth of the first bacterial species in the mixed population is not inhibited. 
     
     
         48 . The method of  claim 29 , wherein the first bacterial species is a  Firmicutes  and the second bacterial species is a  Firmicutes.    
     
     
         49 . The method of  claim 29 , wherein the first bacterial species is a gram positive species and the second bacterial species is a gram positive species. 
     
     
         50 . The method of  claim 29 , wherein the mixed population of bacteria comprises a third bacterial species. 
     
     
         51 . The method of  claim 50 , wherein (i) the first bacterial species is a  Firmicutes , the second bacterial species is a  Firmicutes  and the third bacterial species is a human gut commensal species or a human gut probiotic species; or (ii) wherein the first bacterial species is a gram positive species, the second bacterial species is a gram positive species and the third bacterial species is a human gut commensal species or a human gut probiotic species. 
     
     
         52 . The method of  claim 29 , wherein the host cells are wild-type cells. 
     
     
         53 . The method of  claim 29 , wherein the method reduces the growth of the host cells by at least 5-fold.