Altering microbial populations and modifying microbiota

Patent metadata

Field	Value
Publication number	US-12226430-B2
Application number	US-202318501825-A
Country	US
Kind code	B2
Filing date	Nov 3, 2023
Priority date	May 6, 2015
Publication date	Feb 18, 2025
Grant date	Feb 18, 2025

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.

First claim

What is claimed is:

1. A method of modifying a mixed population of bacteria, wherein the mixed population comprises a first bacterial sub-population and a second bacterial sub-population, wherein the first bacterial sub-population comprises target host cells of a first bacterial species and the second bacterial sub-population comprises second cells of a second bacterial species, wherein the first bacterial species is different from the second bacterial species, wherein the second cells comprise a conjugative plasmid comprising an origin of transfer (oriT) and a nucleic acid sequence for producing a CRISPR RNA (crRNA), and wherein the method comprises:
a. transferring the conjugative plasmid from second cells of the second bacterial sub-population to the target host cells, and
b. producing the crRNA in the target host cells,
wherein the host cells comprise an exogenous nucleotide sequence for producing a desired protein in the host cell,
wherein the nucleic acid sequence for producing the crRNA is under control of an inducible promoter in the host cell, and
wherein the crRNA comprises a nucleic acid sequence that is capable of hybridizing to a target nucleotide sequence in the target host cells to guide a Cas to modify the target nucleotide sequence in the target host cells, wherein the modification of the target sequence inhibits expression of the desired protein in the host cell.

2. The method of claim 1 , wherein the target nucleotide sequence is a host cell plasmid sequence.

3. The method of claim 1 , wherein the desired protein is an antibiotic.

4. The method of claim 1 , wherein the crRNA and Cas are comprised by a Type I, II or III CRISPR/Cas system.

5. The method of claim 1 , wherein the crRNA and Cas are comprised by a Type I CRISPR/Cas system.

6. The method of claim 1 , wherein the crRNA and Cas are comprised by a Type II CRISPR/Cas system.

7. The method of claim 1 , wherein the crRNA and Cas are comprised by a Type III CRISPR/Cas system.

8. The method of claim 1 , wherein the Cas is a Cas9.

9. The method of claim 1 , wherein the Cas is a Cas nuclease.

10. The method of claim 9 , wherein the crRNA guides the Cas to modify the target nucleotide sequence by cutting the target nucleotide sequence to inactivate a gene comprising the target sequence.

11. The method of claim 1 , wherein the Cas is a dead Cas.

12. The method of claim 1 , wherein the exogenous nucleotide sequence for producing the desired protein comprises the target nucleotide sequence.

13. The method of claim 1 , wherein the Cas is an endogenous Cas of the host cell.

14. The method of claim 1 , wherein the Cas is an exogenous Cas.

15. A modified bacterial population produced by a method of modifying a mixed population of bacteria, wherein the mixed population comprises a first bacterial sub-population and a second bacterial sub-population, wherein the first bacterial sub-population comprises target host cells of a first bacterial species and the second bacterial sub-population comprises second cells of a second bacterial species, wherein the second cells comprise a conjugative plasmid comprising an origin of transfer (oriT) and a nucleic acid sequence for producing a crRNA, and wherein the method comprises:
a. transferring the conjugative plasmid from second cells of the second bacterial sub-population to the target host cells, and
b. producing the crRNA in the target host cells,
wherein the host cells comprise an exogenous nucleotide sequence for producing a desired protein in the host cell,
wherein the nucleic acid sequence for producing the crRNA is under the control of an inducible promoter in the host cells, and
wherein the crRNA comprises a nucleic acid sequence that is capable of hybridizing to a target nucleotide sequence in the target host cells to guide a Cas to modify the target nucleotide sequence in the target host cells, wherein the modification of the target sequence inhibits expression of the desired protein in the host cells.

16. The modified bacterial population of claim 15 , wherein the target nucleotide sequence is a host cell plasmid sequence.

Assignees

• Snipr Tech Ltd

Inventors

• Clube Jasper
• Sommer Morten
• Grøndahl Christian
• Van Der Helm Eric
• Vazquez-Uribe Ruben

Classifications

• A61K2300/00

  Mixtures or combinations of active ingredients, wherein at least one active ingredient is fully defined in groups A61K31/00 - A61K41/00 · CPC title

• C12N2795/00032

  Use of virus as therapeutic agent, other than vaccine, e.g. as cytolytic agent · CPC title

• C12N7/00

  Viruses; Bacteriophages; Compositions thereof; Preparation or purification thereof (preparing medicinal viral antigen or antibody compositions, e.g. virus vaccines, A61K39/00) · CPC title

• C12N1/20

  Bacteria; Culture media therefor · CPC title

• A61K48/005

  characterised by an aspect of the 'active' part of the composition delivered, i.e. the nucleic acid delivered · CPC title