COMPOSITIONS AND METHODS FOR SUPPRESSING PATHOGENIC ORGANISMS

1 - 109 . (canceled)

110 . A method for suppressing colonization by a pathogenic organism in a subject, the method comprising administering to the subject a therapeutically effective amount of a composition comprising one or more of:

(i) a bacterial strain comprising a 16S rDNA sequence having at least 97% sequence identity to the nucleotide sequence of SEQ ID NO: 48;

(ii) a bacterial strain comprising a 16S rDNA sequence having at least 97% sequence identity to the nucleotide sequence of SEQ ID NO: 49;

(iii) a bacterial strain comprising a 16S rDNA sequence having at least 97% sequence identity to the nucleotide sequence of SEQ ID NO: 50;

(iv) a bacterial strain comprising a 16S rDNA sequence having at least 97% sequence identity to the nucleotide sequence of SEQ ID NO: 51;

(v) a bacterial strain comprising a 16S rDNA sequence having at least 97% sequence identity to the nucleotide sequence of SEQ ID NO: 60;

(vi) a bacterial strain comprising a 16S rDNA sequence having at least 97% sequence identity to the nucleotide sequence of SEQ ID NO: 64;

(vii) a bacterial strain comprising a 16S rDNA sequence having at least 97% sequence identity to the nucleotide sequence of SEQ ID NO: 71;

(viii) a bacterial strain comprising a 16S rDNA sequence having at least 97% sequence identity to the nucleotide sequence of SEQ ID NO: 75; and

(ix) a bacterial strain comprising a 16S rDNA sequence having at least 97% sequence identity to the nucleotide sequence of SEQ ID NO: 77.

111 . The method of claim 110 , wherein:

the bacterial strain of (i) comprises a 16S rDNA sequence having at least 99% sequence identity to the nucleotide sequence of SEQ ID NO: 48;

the bacterial strain of (ii) comprises a 16S rDNA sequence having at least 99% sequence identity to the nucleotide sequence of SEQ ID NO: 49;

the bacterial strain of (iii) comprises a 16S rDNA sequence having at least 99% sequence identity to the nucleotide sequence of SEQ ID NO: 50;

the bacterial strain of (iv) comprises a 16S rDNA sequence having at least 99% sequence identity to the nucleotide sequence of SEQ ID NO: 51;

the bacterial strain of (v) comprises a 16S rDNA sequence having at least 99% sequence identity to the nucleotide sequence of SEQ ID NO: 60;

the bacterial strain of (vi) comprises a 16S rDNA sequence having at least 99% sequence identity to the nucleotide sequence of SEQ ID NO: 64;

the bacterial strain of (vii) comprises a 16S rDNA sequence having at least 99% sequence identity to the nucleotide sequence of SEQ ID NO: 71;

the bacterial strain of (viii) comprises a 16S rDNA sequence having at least 99% sequence identity to the nucleotide sequence of SEQ ID NO: 75; and

the bacterial strain of (ix) comprises a 16S rDNA sequence having at least 99% sequence identity to the nucleotide sequence of SEQ ID NO: 77.

112 . The method of claim 111 , wherein the composition further comprises one or more bacterial strains comprising 16S rDNA sequences having at least 99% sequence identity to any one of SEQ ID NOs: 42-46, 52-59, 61-63, 65-70, 72-74, and 76.

113 . The method of claim 111 , wherein the composition comprises:

the bacterial strain comprising a 16S rDNA sequence having at least 99% sequence identity to SEQ ID NO: 48;

the bacterial strain comprising a 16S rDNA sequence having at least 99% sequence identity to SEQ ID NO: 75; and

the bacterial strain comprising a 16S rDNA sequence having at least 99% sequence identity to SEQ ID NO: 77.

114 . The method of claim 113 , wherein the composition further comprises:

a bacterial strain comprising a 16S rDNA sequence having at least 99% sequence identity to the nucleotide sequence of SEQ ID NO: 52;

a bacterial strain comprising a 16S rDNA sequence having at least 99% sequence identity to the nucleotide sequence of SEQ ID NO: 55;

a bacterial strain comprising a 16S rDNA sequence having at least 99% sequence identity to the nucleotide sequence of SEQ ID NO: 62;

a bacterial strain comprising a 16S rDNA sequence having at least 99% sequence identity to the nucleotide sequence of SEQ ID NO: 67; and

a bacterial strain comprising a 16S rDNA sequence having at least 99% sequence identity to the nucleotide sequence of SEQ ID NO: 72.

115 . The method of claim 114 , wherein the composition further comprises:

a bacterial strain comprising a 16S rDNA sequence having at least 99% sequence identity to SEQ ID NO: 23; and

a bacterial strain comprising a 16S rDNA sequence having at least 99% sequence identity to SEQ ID NO: 26.

116 . The method of claim 110 , wherein the pathogenic organism is a pathobiont.

117 . The method of claim 116 , wherein the pathobiont induces a Th1 response in a subject.

118 . The method of claim 110 , wherein the pathogenic organism belongs to the family Enterobacteriace.

119 . The method of claim 110 , wherein the pathogenic organism belongs to the genus Enterococcus.

120 . The method of claim 110 , wherein the pathogenic organism belongs to the genus Shigella.

121 . The method of claim 110 , wherein the pathogenic organism belongs to the species Klebsiella pneumoniae.

122 . The method of claim 110 , wherein the pathogenic organism belongs to the species Escherichia coli.

123 . The method of claim 110 , wherein the administration suppresses replication and/or survival of the pathogenic organism.

124 . The method of claim 110 , wherein the composition is a pharmaceutical composition comprising a pharmaceutically acceptable excipient.

125 . The method of claim 124 , wherein the pharmaceutical composition is formulated for delivery to the intestine.

126 . The method of claim 124 , wherein the pharmaceutical composition comprises a pH-sensitive composition comprising one or more enteric polymers.

127 . A composition comprising a purified bacterial mixture, the purified bacterial mixture comprising:

(i) a bacterial strain comprising a 16S rDNA sequence having at least 97% sequence identity to the nucleotide sequence of SEQ ID NO: 48;

(ii) a bacterial strain comprising a 16S rDNA sequence having at least 97% sequence identity to the nucleotide sequence of SEQ ID NO: 49;

(iii) a bacterial strain comprising a 16S rDNA sequence having at least 97% sequence identity to the nucleotide sequence of SEQ ID NO: 50;

(iv) a bacterial strain comprising a 16S rDNA sequence having at least 97% sequence identity to the nucleotide sequence of SEQ ID NO: 51;

(v) a bacterial strain comprising a 16S rDNA sequence having at least 97% sequence identity to the nucleotide sequence of SEQ ID NO: 60;

(vi) a bacterial strain comprising a 16S rDNA sequence having at least 97% sequence identity to the nucleotide sequence of SEQ ID NO: 64;

(vii) a bacterial strain comprising a 16S rDNA sequence having at least 97% sequence identity to the nucleotide sequence of SEQ ID NO: 71;

(viii) a bacterial strain comprising a 16S rDNA sequence having at least 97% sequence identity to the nucleotide sequence of SEQ ID NO: 75; and/or

(ix) a bacterial strain comprising a 16S rDNA sequence having at least 97% sequence identity to the nucleotide sequence of SEQ ID NO: 77.

128 . A method of treating a disease or disorder associated with bacterial colonization in a subject, the method comprising administering to the subject a therapeutically effective amount of the composition of claim 127 .

129 . The method of claim 128 , wherein the disease or disorder is:

(a) associated with a Th1 immune response;

(b) associated with use of a proton pump inhibitor;

(c) an autoimmune disease or an inflammatory bowel disease; and/or

(d) non-alcoholic steatohepatitis (NASH), primary sclerosing cholangitis (PSC), non-alcoholic fatty liver disease (NAFLD), gastroesophageal reflux disease (GERD), or alcoholism.

130 . A method of suppressing colonization of an intestine of a subject with oral microbiome bacteria, the method comprising administering to the subject a therapeutically effective amount of the composition of claim 127 .