Table 4.
Genes compared to LB with high logFCs in feces 1
| Gene tag | Product | LB | LB-pH9 | LB-pH4 | LB-15°C | LB-nitrite | LB-antibiotics | LB-solid | minimal medium | spinach juice | radish sprouts | feces |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Z0014 | molecular chaperone DnaK | 1 (185) | −1.0 (55) | 0.1 (33) | 1.6 (470) | 1.6 (520) | 0.5 (70) | 0.8 (109) | 0.0 (120) | 3.6 (1290) | 1.2 (248) | 3.7 (398) |
| Z0015 | chaperone protein DnaJ | 1 (74) | −1.4 (16) | −1.4 (4) | 1.3 (150) | 0.8 (120) | −0.9 (10) | 0.0 (23) | −0.5 (31) | 0.9 (78) | 1.2 (99) | 4.2 (220) |
| Z0045 | crotonobetainyl-CoA dehydrogenase | 1 (7) | 1.3 (10) | 0.4 (1) | −0.1 (5) | 0.9 (12) | 0.7 (3) | 2.7 (14) | 1.2 (9) | 2.5 (23) | −1.5 (1) | 5.8 (63) |
| Z2477 | thiosulfate:cyanide sulfurtransferase | 1 (558) | 0.4 (470) | −0.1 (94) | 0.9 (963) | 0.1 (603) | −2.3 (31) | −0.7 (121) | −2.2 (83) | −1.6 (113) | −0.4 (252) | 2.4 (537) |
| Z2478 | peripheral inner membrane phage-shock protein | 1 (17) | 1.4 (28) | −4.9 (0) | 2.0 (60) | 1.2 (37) | −4.9 (0) | 1.6 (17) | 0.6 (16) | 0.6 (15) | 4.3 (198) | 7.7 (598) |
| Z2479 | DNA-binding transcriptional activator PspC | 1 (17) | 1.5 (31) | −0.4 (2) | 1.9 (57) | 1.4 (46) | −0.1 (5) | −5.7 (0) | 0.8 (20) | −0.9 (6) | 4.1 (182) | 7.2 (470) |
| Z2480 | phage shock protein B | 1 (25) | 1.4 (39) | −0.2 (4) | 1.9 (80) | 1.2 (55) | −5.5 (0) | −0.3 (7) | −0.9 (8) | 0.0 (15) | 3.9 (228) | 6.8 (482) |
| Z2482 | phage shock protein PspA | 1 (64) | 0.8 (63) | 0.8 (18) | 2.0 (206) | 0.5 (81) | −0.4 (12) | 0.6 (31) | 0.6 (59) | 0.6 (56) | 4.8 (1077) | 6.5 (970) |
| Z2611 | DNA replication terminus site-binding protein Tus | 1 (9) | −0.4 (4) | 1.3 (4) | 1.8 (26) | 0.8 (15) | −6.0 (0) | 0.2 (3) | −1.4 (2) | −1.2 (2) | 0.7 (9) | 5.0 (47) |
| Z2876 | heat shock protein HtpX | 1 (93) | 1.4 (154) | 0.2 (19) | 1.8 (284) | 1.0 (187) | −0.2 (22) | 3.0 (262) | 0.0 (60) | −0.3 (46) | 0.1 (59) | 3.9 (246) |
| Z2900 | DNA damage-inducible protein YebG | 1 (112) | −0.1 (61) | 1.3 (42) | −0.1 (83) | 0.3 (123) | 2.8 (196) | 0.8 (59) | 0.6 (99) | 0.0 (60) | 0.8 (113) | 3.7 (226) |
| Z3886 | protein disaggregation chaperone ClpB | 1 (239) | −1.6 (44) | 2.4 (194) | 0.5 (267) | 0.3 (265) | −0.1 (56) | 0.9 (140) | −0.4 (106) | 2.7 (827) | 1.1 (292) | 2.5 (216) |
| Z4227 | isopentenyl-diphosphate delta-isomerase | 1 (22) | 1.9 (52) | 0.3 (5) | 1.2 (43) | 2.0 (89) | −6.6 (0) | 1.2 (18) | 0.2 (16) | 1.6 (40) | 1.5 (38) | 5.6 (180) |
| Z4291 | 16S ribosomal RNA methyltransferase RsmE | 1 (57) | −1.0 (17) | 1.0 (18) | −0.9 (26) | −0.8 (30) | 0.9 (27) | −1.4 (7) | −0.1 (33) | 1.1 (70) | 0.0 (34) | 4.1 (165) |
| Z4401 | glycogen synthesis protein GlgS | 1 (240) | 0.4 (182) | −0.2 (32) | −0.4 (141) | 1.2 (480) | −0.3 (47) | 4.0 (1226) | 0.5 (196) | −0.3 (104) | 2.6 (838) | 6.6 (3617) |
| Z5182 | heat shock chaperone IbpB | 1 (26) | −0.2 (13) | −0.1 (4) | 0.4 (29) | 0.3 (29) | 1.5 (19) | 2.5 (47) | −0.3 (13) | 1.0 (30) | 2.4 (80) | 5.7 (224) |
| Z5183 | heat shock protein IbpA | 1 (26) | 0.5 (22) | 1.7 (14) | 2.1 (96) | 1.2 (55) | 1.5 (20) | 2.6 (54) | 0.1 (17) | 3.0 (125) | 2.2 (72) | 6.9 (509) |
| Z5458 | periplasmic repressor CpxP | 1 (25) | 3.2 (127) | 1.7 (13) | 0.0 (20) | 1.1 (47) | 2.9 (45) | 4.6 (191) | −0.2 (13) | −2.3 (3) | 2.5 (84) | 6.0 (260) |
1For each gene, the first number indicates the logFC of a certain condition compared to LB; RPKM values are shown in parentheses. Significantly differentially expressed genes are in bold (i.e., p values ≤ 0.05 in edgeR). For a graphic version, indicating the magnitude of the absolute value of logFC in shades of grey, see Additional file 4.