Altering microbial populations & modifying microbiota

Patent metadata

Field	Value
Publication number	US-2018084785-A1
Application number	US-201715817142-A
Country	US
Kind code	A1
Filing date	Nov 17, 2017
Priority date	May 6, 2015
Publication date	Mar 29, 2018
Grant date	—

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

1 . A method for modifying a target sequence in a bacterial or archaeal host cell, the method comprising:
(a) contacting the host cell with an engineered nucleic acid for producing a host modifying crRNA (HM-crRNA), and (b) producing the HM-crRNA in the host cell;
wherein
(i) the HM-crRNA is operable with a Type II Cas in the host cell, wherein the engineered nucleic acid and the Type II Cas are comprised by a Type II HM-CRISPR/Cas system in the host cell;
(ii) the HM-crRNA comprises a nucleotide sequence that is capable of hybridizing to the target sequence in the host cell to guide the Type II Cas to modify the target sequence in the host cell;
(iii) wherein the Type II Cas is an endogenous Cas of the host cell;

wherein the target sequence is modified by the Type II HM-CRISPR/Cas system.

2 . The method of claim 1 , wherein the host cell is killed or growth of the host cell is inhibited.

3 . The method of claim 1 , wherein the Type II Cas is a Cas9.

4 . The method of claim 3 , wherein the Type II Cas is a Streptococcus Cas9.

5 . The method of claim 1 , wherein the engineered nucleic acid for producing the HM-crRNA is present in a phage, phagemid or plasmid.

6 . The method of claim 1 , wherein the target sequence is a host target sequence.

7 . The method of claim 1 , wherein the Type II HM-CRISPR/Cas system comprises an endogenous tracrRNA of the host cell.

8 . The method of claim 1 , wherein the Type II HM-CRISPR/Cas system comprises a tracrRNA, and wherein the tracrRNA is encoded by an engineered nucleic acid.

9 . The method of claim 8 , wherein the engineered nucleic acid for producing the HM-crRNA encodes a single guide RNA comprising the tracrRNA and the HM-crRNA.

10 . The method of claim 1 , wherein the host cell is a C. dificile, E. coli or Salmonella cell.

11 . A method for treating an infection in an organism or limiting spread of the infection in the organism, the method comprising subjecting the host cells in the organism to the method of claim 1 , wherein the host cells are modified and the infection is treated or the spread of the infection is limited.

12 . The method of claim 11 , wherein the host cells are killed or growth of the host cells is inhibited.

13 . The method of claim 11 , wherein the method is for medical, dental or ophthalmic use.

14 . The method of claim 11 , wherein the organism is a plant.

15 . The method of claim 14 , wherein the organism is a crop.

16 . The method of claim 11 , wherein the organism is an animal.

17 . The method of claim 16 , wherein the organism is a human.

18 . The method of claim 1 , wherein the host cell is of a strain or species found in a human microbiota.

19 . The method of claim 11 , wherein the method is for medical, dental or ophthalmic use, and wherein the organism is an animal or a human.

20 . The method of claim 11 , wherein the method is for environmental or agricultural use, and wherein the organism is a plant.

21 . The method of claim 11 , wherein the Type II Cas is a Cas9.

22 . The method of claim 11 , wherein the target sequence is a host target sequence.

23 . The method of claim 11 , wherein the host cells are C. dificile, E. coli or Salmonella cells.

24 . The method of claim 19 , wherein the host cells are C. dificile, E. coli or Salmonella cells.

25 . A method for modifying a target sequence comprised by a bacterial or archaeal host cell, the method comprising:
(a) contacting the host cell with an engineered nucleic acid for producing a host modifying crRNA (HM-crRNA), and (b) producing the HM-crRNA in the host cell;
wherein
(i) the HM-crRNA is operable with a Type II Cas and a tracrRNA in the host cell, wherein the engineered nucleic acid, the tracrRNA and the Type II Cas are comprised by a Type II HM-CRISPR/Cas system in the host cell;
(ii) the HM-crRNA comprises a nucleotide sequence that is capable of hybridizing to the target sequence in the host cell to guide the Type II Cas to modify the target sequence in the host cell; and
(iii) the tracrRNA is an endogenous tracrRNA of the host cell;
wherein the target sequence is modified by the Type II HM-CRISPR/Cas system.

26 . The method of claim 25 , wherein the host cell is killed or growth of the host cell is inhibited.

27 . The method of claim 25 , wherein the Type II Cas is a Cas9.

28 . The method of claim 25 , wherein the host cell is a C. dificile, E. coli or Salmonella cell.

Assignees

• Snipr Tech Ltd

Inventors

• Clube Jasper

Classifications

• A61K31/711

  Natural deoxyribonucleic acids, i.e. containing only 2'-deoxyriboses attached to adenine, guanine, cytosine or thymine and having 3'-5' phosphodiester links · CPC title

• C12N2310/20

  involving clustered regularly interspaced short palindromic repeats [CRISPR] · CPC title

• A61K45/06

  Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca · CPC title

• C12N15/746

  for lactic acid bacteria (Streptococcus; Lactococcus; Lactobacillus; Pediococcus; Enterococcus; Leuconostoc; Propionibacterium; Bifidobacterium; Sporolactobacillus) · CPC title

• C12N15/70

  Vectors or expression systems specially adapted for E. coli · CPC title