Compositions and methods for modulating growth of a genetically modified gut bacterial cell

Abstract

Compositions and methods are provided for modulating growth of a genetically modified bacterial cell present in a human organ, for modulating growth of a genetically modified bacterial cell in an organ (e.g., gut), for displacing at least a portion of a population of bacterial cells in an organ, and for facilitating gut colonization by a genetically modified bacterial cell. Also provided are genetically modified bacterial cells, e.g., cells that include a heterologous carbohydrate-utilization gene or gene set that provides for the ability to utilize as a carbon source a rare carbohydrate of interest that is utilized as a carbon source by less than 50% of bacterial cells present in a human microbiome.

That which is claimed is: 
     
         1 . A genetically modified  Bacteroides  cell comprising:
 a heterologous carbohydrate-utilization gene or gene set that provides the genetically modified  Bacteroides  cell with an ability to utilize as a carbon source a porphyran,   wherein the heterologous carbohydrate-utilization gene or gene set comprises one or more nucleic acids encoding a porphyranase.   
     
     
         2 . The genetically modified  Bacteroides  cell of  claim 1 , wherein the heterologous carbohydrate-utilization gene or gene set comprises one or more nucleic acids encoding a porphyranase from the  B. plebeius  or  B. ovatus  genome. 
     
     
         3 . The genetically modified  Bacteroides  cell of  claim 1 , wherein one of the nucleic acids encodes a protein having 80% or more sequence identity to SEQ ID NO: 19. 
     
     
         4 . The genetically modified  Bacteroides  cell of  claim 1 , wherein one of the nucleic acids encodes a protein having 80% or more sequence identity to SEQ ID NO: 21. 
     
     
         5 . The genetically modified  Bacteroides  cell of  claim 1 , wherein the  Bacteroides  cell comprises the heterologous carbohydrate-utilization gene set. 
     
     
         6 . The genetically modified  Bacteroides  cell of  claim 5 , wherein the carbohydrate-utilization gene set comprises at least twelve genes. 
     
     
         7 . The genetically modified  Bacteroides  cell of  claim 5 , wherein the carbohydrate-utilization gene set comprises one or more nucleic acids selected from the group consisting of nucleic acids encoding a protein having 80% or more sequence identity to SEQ ID NOs: 14-34. 
     
     
         8 . The genetically modified  Bacteroides  cell of  claim 5 , wherein the carbohydrate-utilization gene set comprises one or more nucleic acids selected from the group consisting of nucleic acids encoding a protein having 90% or more sequence identity to SEQ ID NOs: 14-34. 
     
     
         9 . The genetically modified  Bacteroides  cell of  claim 5 , wherein the carbohydrate-utilization gene set comprises one or more nucleic acids selected from the group consisting of nucleic acids encoding a protein having 95% or more sequence identity to SEQ ID NOs: 14-34. 
     
     
         10 . The genetically modified  Bacteroides  cell of  claim 1 , wherein the carbohydrate utilization gene or gene-set is encoded on a plasmid, encoded on a bacterial artificial chromosome, or genomically integrated. 
     
     
         11 . The genetically modified  Bacteroides  cell of  claim 1 , further comprising one or more therapeutic transgenes. 
     
     
         12 . A genetically modified  Bacteroides  cell comprising:
 a heterologous transgene that encodes a therapeutic peptide; and   a carbohydrate-utilization gene set that provides the genetically modified  Bacteroides  cell with an ability to utilize as a carbon source a porphyran,   wherein the carbohydrate-utilization gene or gene set comprises one or more nucleic acids encoding a porphyranase.   
     
     
         13 . A genetically modified bacterial cell comprising:
 a heterologous carbohydrate-utilization gene set that provides the genetically modified cell with an ability to utilize as a carbon source a porphyran,   wherein the heterologous carbohydrate-utilization gene set comprises one or more nucleic acids that each encode one or more proteins selected from the group consisting of proteins having 90% or more sequence identity to SEQ ID NOs: 1-34.   
     
     
         14 . A genetically modified  Bacteroides  cell comprising:
 a heterologous carbohydrate-utilization gene set that provides the genetically modified  Bacteroides  cell with an ability to utilize as a carbon source a porphyran,   wherein the heterologous carbohydrate-utilization gene or gene set comprises one or more nucleic acids encoding a porphyranase.