b Covers SGO_0054, 0056, 0057, 0327, 0393, 0515, 0586, 0631, 0671, 0672, 0763, 0804, 0886, 0948, 0969, 0975, 1009, 1010, 1011, 1013, 1020, 1025, 1026, 1400, 1446, 1447, 1623, 1624, 1638, 1676, 1717, 1768, 1854, 2010, 2104, 2037. Table 5 Protein ratios for rhamnose synthesis and attachment Protein SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg this website vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg SGO_1009 2.1 1.5 1.1 −0.6 −0.9 −0.4

SGO_1010 0.8 0.9 0.9 0.1 0.1 0 SGO_1011 2.4 1.2 0.6 −1.2 −1.7 −0.5 SGO_1020 1.1 0.7 0.5 −0.5 −0.6 −0.1 SGO_1026 −1.9 −2.2 −3.2 −0.2 −1.3 −1.0 Bold: statistically significant difference, all ratios are log2. Transport and ARS-1620 clinical trial export As mentioned above, PTS sugar transport systems are almost all reduced in the mixed organism samples.

The other transport and export proteins are also generally reduced in the mixed samples as shown in Table 6. Some exceptions show increases PX-478 mouse compared to Sg alone and are shown in detail in Table 7. Two, SGO_0006 and SGO_2100, are ABC transporter proteins with unknown substrates. SGO_1059 is a phosphate transport protein showing significantly lower levels in SgFn vs Sg but higher levels with SgPg or SgPgFn. Interestingly, the phosphate transport system regulatory protein, SGO_1060, is significantly down in SgFn and SgPgFn implying another level of regulation for SGO_1059. In contrast PAK6 to the phosphate transporter, the predicted Trk potassium uptake system protein, SGO_1666, is up in SgFn but significantly reduced in SgPgFn. Table 6 Export and non-PTS transport proteins a   SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Total 61 58 45 58 45 44 Unchanged 18 15 6 26 19 38 Increased 3 5 4 24 18 1 Decreased 40 38 35 8 8 5 a Proteins covered SGO_0006, 0015, 0104, 0255, 0291, 0352, 0353, 0398, 0415, 0457, 0458, 0460, 0488, 0505, 0538, 0548, 0579, 0750, 0751, 0767, 0798, 0805, 0808, 0851, 0856, 0955, 0982, 1024,

1036, 1037, 1059, 1060, 1118, 1123, 1216, 1338, 1342, 1458,1465,1572, 1580, 1605, 1619, 1626, 1630, 1634, 1666, 1708, 1709, 1711, 1712, 1713, 1715, 1716, 1727, 1728, 1744, 1763, 1802, 1936, 2100. Table 7 Protein ratios of selected export and transport proteins Protein SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg SGO_0006 0.2 0.5 0.1 0.3 −0.1 −0.4 SGO_0255 −1.9 −1.6 −2.2 0.3 −0.2 −0.1 SGO_0415 −1.1 −1.0 −1.2 0.1 −0.1 −0.1 SGO_1059 −1.6 0.5 0.8 2.1 2.4 0.3 SGO_1060 −1.6 −0.2 −1.3 1.4 0.4 −1.0 SGO_1123 1.0 1.2 1.0 0.3 0.0 −0.2 SGO_1216 1.4 1.8 1.2 0.4 −0.2 −0.6 SGO_1338 −0.7 −3.0 nd −2.3 nd nd SGO_1666 0.8 −1.0 −2.5 −1.8 −3.3 −1.5 SGO_2100 −0.9 2.6 2.7 3.5 3.6 0.1 Bold: statistically significant difference, all ratios are log2. nd: not detected in one or more of the compared samples.