SELECTIVELY ALTERING MICROBIOTA FOR IMMUNE MODULATION
The invention relates to methods of modulating immune cells in a patient by altering microbiota of the patient. The invention also relates to methods of modulating treatments or therapies in a subject organism by altering microbiota of the subject. The invention also relates to cell populations, systems, arrays, cells, RNA, kits and other means for effecting this. In an example, advantageously selective targeting of a particular species in a human gut microbiota using guided nucleic acid modification is carried out to effect the alteration.
1 - 20 . (canceled)
21 . A method of treating a liver disease or liver condition in a human or animal subject, the method comprising altering the relative proportion of a sub-population of host bacterial cells in a microbiota of the subject, wherein the host bacterial cells are Enterococcus cells.
22 . The method of claim 21 , wherein the host bacterial cells are Enterococcus faecalis cells.
23 . The method of claim 21 , wherein the microbiota is a liver microbiota.
24 . The method of claim 21 , wherein the liver disease or liver condition is liver fibrosis.
25 . The method of claim 21 , wherein the liver disease or liver condition is hepatitis.
26 . The method of claim 25 , wherein the liver disease or liver condition is autoimmune hepatitis.
27 . The method of claim 21 , wherein the liver disease or liver condition is primary biliary cirrhosis or primary sclerosing cholangitis.
28 . The method of claim 21 , wherein the liver disease or liver condition is liver cancer.
29 . The method of claim 21 , wherein the method comprises administering a bacterial transplant to the subject, wherein the bacterial transplant comprises cells of a bacterial species that is different from Enterococcus cells, thereby reducing relative proportion of the sub-population of host bacterial cells in the microbiota of the subject.
30 . The method of claim 21 , wherein the method comprises selective targeting of the host bacterial cells of the microbiota using a guided nuclease, thereby reducing relative proportion of the sub-population of host bacterial cells in the microbiota of the subject.
31 . The method of claim 30 , wherein the guide nuclease is a Cas, TALEN, meganuclease or zinc finger nuclease.
32 . The method of claim 30 , wherein the guided nuclease is a Cas nuclease.
33 . The method of claim 32 , wherein the Cas is a Cas3, Cas9 or Cpf1.
34 . The method of claim 32 , wherein the method comprises:
a. contacting the microbiota with an engineered nucleic acid sequence for producing a host modifying (HM) crRNA, and
b. producing the HM-crRNA in a host bacterial cell,
wherein the HM-crRNA is operable with a Cas nuclease in the host bacterial cell to form a HM-CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas system, and
wherein the HM-crRNA comprises a sequence that is capable of hybridizing to a target sequence of the host bacterial cell to guide the Cas nuclease to the target sequence in the host bacterial cell, whereby the target sequence is modified by the HM-CRISPR/Cas system and the host bacterial cell is killed or growth of host bacterial cells is reduced, thereby reducing the relative proportion of host bacterial cells in the microbiota.
35 . The method of claim 34 , wherein the HM-crRNA is comprised by a single guide RNA (sgRNA).
36 . The method of claim 35 , wherein the nucleic acid sequence encoding the sgRNA is under a constitutive promoter.
37 . The method of claim 34 , wherein the nucleic acid sequence encoding the HM-crRNA is under a constitutive promoter.
38 . The method of claim 34 , wherein the Cas is a wild-type endogenous host cell Cas nuclease.
39 . The method of claim 38 , wherein the Cas is a wild-type host cell endogenous Type II Cas.
40 . The method of claim 30 , wherein the microbiota comprises a mixed population of liver microbiota bacteria of different species, and wherein the method comprises selectively killing or inhibiting growth of Enterococcus cells and sparing cells of the other species.
41 . The method of claim 40 , wherein the Enterococcus cells are Enterococcus faecalis cells.