Table 2.
Hypothetical genes with a logFC ≥ 5 in transcription levels in a single condition compared to LB 1
| Gene tag | Product | Ref’s | gene active in | LB | LB-pH9 | LB-pH4 | LB-15°C | LB-nitrite | LB-antibiotics | LB-solid | minimal medium | spinach juice | radish sprouts | feces |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Z0840 | hypothetical protein | LB-pH4 | 1 (2) | 1.4 (3) | 5.5 (18) | 2.0 (8) | −1.4 (0) | −1.4 (0) | −1.4 (0) | −1.4 (0) | 2.9 (10) | −1.4 (0) | 4.4 (9) | |
| Z1576 | hypothetical protein | LB-pH4 | 1 (0) | 0.0 (0) | 5.3 (3) | 3.4 (4) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 3.0 (2) | 0.0 (0) | |
| Z1850 | hypothetical protein | LB-pH4 | 1 (0) | 0.0 (0) | 5.3 (3) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 0.0 (0) | |
| Z4062 | hypothetical protein | LB-15°C | 1 (9) | 2.7 (36) | −4.4 (0) | 5.1 (275) | 1.5 (26) | −4.4 (0) | 1.3 (8) | −4.4 (0) | 0.4 (7) | 0.1 (5) | −4.4 (0) | |
| Z4925 | hypothetical protein | LB-15°C | 1 (114) | 2.4 (388) | 0.2 (23) | 5.0 (3365) | 3.3 (1157) | −9.0 (0) | −1.1 (18) | 2.7 (482) | 4.1 (1163) | 1.6 (210) | −0.1 (18) | |
| Z5688 | hypothetical protein | LB-15°C | 1 (2) | 1.7 (5) | −3.6 (0) | 5.5 (90) | 2.2 (10) | −3.6 (0) | −3.6 (0) | 0.0 (1) | 1.2 (3) | 2.2 (6) | −3.6 (0) | |
| Z1924 | hypothetical protein | LB-nitrite | 1 (9) | 5.3 (250) | 3.7 (23) | 4.3 (182) | 6.0 (659) | −3.9 (0) | 4.7 (90) | 3.2 (59) | 1.6 (18) | 4.1 (101) | 4.7 (47) | |
| Z0314 | prophage CP-933H, tail fiber | LB-antibiotics | 1 (5) | −0.3 (2) | 0.4 (1) | 0.4 (6) | −0.7 (3) | 6.0 (92) | −0.7 (1) | −0.3 (3) | −0.6 (2) | −4.9 (0) | −4.9 (0) | |
| Z0316 | prophage CP-933H, tail fiber | LB-antibiotics | 1 (12) | −0.6 (4) | −0.5 (1) | −0.1 (9) | 0.6 (17) | 5.3 (123) | 0.4 (5) | −1.2 (3) | −0.6 (5) | −2.8 (1) | 0.1 (2) | |
| Z0344 | hypothetical protein | LB-antibiotics | 1 (1) | 1.3 (2) | 3.9 (3) | 1.1 (2) | 2.2 (5) | 5.2 (12) | −1.4 (0) | −1.4 (0) | 2.8 (5) | 1.6 (2) | −1.4 (0) | |
| Z0392 | hypothetical protein | LB-antibiotics | 1 (0) | 2.8 (1) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 5.6 (3) | 0.0 (0) | 3.6 (2) | 0.0 (0) | 0.0 (0) | 0.0 (0) | |
| Z0949 | prophage CP-933K | [37] | LB-antibiotics | 1 (17) | 0.5 (14) | 2.4 (15) | 0.2 (17) | −0.7 (10) | 5.0 (143) | −4.9 (0) | 0.3 (13) | −1.5 (3) | 0.3 (12) | 2.6 (17) |
| Z1098 | hypothetical protein | LB-antibiotics | 1 (1) | −2.1 (0) | −2.1 (0) | 1.8 (3) | 1.5 (3) | 5.1 (11) | −2.1 (0) | 1.5 (2) | −2.1 (0) | 0.9 (1) | −2.1 (0) | |
| Z1433 | prophage BP-933W | [37] | LB-antibiotics | 1 (15) | 0.5 (13) | −5.1 (0) | 0.8 (22) | 1.0 (29) | 5.9 (231) | −5.1 (0) | 0.0 (10) | −0.8 (5) | 0.3 (11) | 0.8 (4) |
| Z1434 | prophage BP-933W | [37, 38] | LB-antibiotics | 1 (5) | 2.2 (14) | 2.4 (4) | 2.3 (21) | 2.2 (21) | 7.2 (203) | 1.3 (4) | 2.6 (19) | 0.4 (3) | 1.6 (8) | −3.0 (0) |
| Z1441 | prophage BP-933W | [37] | LB-antibiotics | 1 (274) | 0.0 (167) | −0.3 (35) | 1.4 (607) | 0.9 (464) | 5.5 (3123) | −0.8 (52) | 1.3 (424) | 0.0 (160) | 1.6 (482) | −2.5 (8) |
| Z1501 | hypothetical protein | LB-antibiotics | 1 (27) | −0.1 (15) | −0.3 (4) | 0.0 (23) | −0.1 (24) | 5.1 (235) | −0.1 (8) | 0.1 (18) | −0.7 (10) | 1.3 (38) | −0.7 (3) | |
| Z1656 | hypothetical protein | LB-antibiotics | 1 (0) | −1.4 (0) | −1.4 (0) | −1.4 (0) | −1.4 (0) | 5.2 (7) | −1.4 (0) | −1.4 (0) | −1.4 (0) | 1.6 (1) | −1.4 (0) | |
| Z1840 | hypothetical protein | LB-antibiotics | 1 (0) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 2.7 (4) | 5.6 (9) | 0.0 (0) | 0.0 (0) | 3.3 (4) | 0.0 (0) | 0.0 (0) | |
| Z3353 | hypothetical protein | LB-antibiotics | 1 (0) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 7.9 (29) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 3.0 (2) | 0.0 (0) | |
| Z3369 | prophage CP-933V | [37] | LB-antibiotics | 1 (7) | −0.3 (3) | −3.9 (0) | 0.4 (7) | −1.2 (2) | 5.7 (92) | −3.9 (0) | −0.3 (3) | −3.9 (0) | 1.9 (15) | −3.9 (0) |
| Z3370 | prophage CP-933V | [37] | LB-antibiotics | 1 (32) | −2.6 (3) | −2.4 (1) | −0.3 (21) | −1.7 (9) | 5.4 (312) | −1.3 (4) | −2.2 (4) | −4.4 (1) | 0.7 (30) | −7.8 (0) |
| Z3371 | prophage CP-933V | [37] | LB-antibiotics | 1 (6) | 2.0 (16) | −4.2 (0) | 2.9 (42) | 1.3 (15) | 7.6 (337) | 1.0 (4) | −4.2 (0) | −0.9 (2) | 1.2 (9) | −4.2 (0) |
| Z3372 | prophage CP-933V | LB-antibiotics | 1 (14) | 1.4 (22) | −5.3 (0) | 0.6 (18) | 0.0 (13) | 5.1 (126) | −5.3 (0) | −0.8 (5) | 0.9 (15) | 0.7 (13) | 0.5 (3) | |
| Z3609 | restricted to Escherichia | LB-antibiotics | 1 (3) | 1.2 (4) | −4.7 (0) | 1.1 (6) | 0.2 (3) | 5.4 (35) | −4.7 (0) | −4.7 (0) | 0.1 (2) | −4.7 (0) | 3.1 (5) | |
| Z4174 | hypothetical protein | LB-antibiotics | 1 (2) | 2.1 (6) | −2.1 (0) | 4.2 (37) | 3.8 (31) | 5.5 (30) | 3.1 (7) | 1.5 (4) | 2.7 (9) | 0.9 (2) | −2.1 (0) | |
| Z4183 | hypothetical protein | LB-antibiotics | 1 (0) | 0.0 (0) | 0.0 (0) | 3.4 (12) | 0.0 (0) | 5.6 (19) | 0.0 (0) | 3.6 (11) | 0.0 (0) | 0.0 (0) | 0.0 (0) | |
| Z4201 | hypothetical protein | LB-antibiotics | 1 (0) | 2.8 (1) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 5.6 (3) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 3.0 (1) | 0.0 (0) | |
| Z5018 | restricted to Escherichia and Salmonella | LB-antibiotics | 1 (1) | 1.5 (2) | 3.2 (2) | 0.4 (1) | 1.5 (3) | 5.1 (11) | −2.1 (0) | 2.4 (4) | 2.1 (3) | −2.1 (0) | −2.1 (0) | |
| Z5071 | inner membrane protein | LB-antibiotics | 1 (4) | −0.7 (1) | 1.9 (2) | 0.5 (5) | −0.7 (2) | 5.7 (51) | 2.4 (7) | −4.4 (0) | 1.2 (5) | 0.5 (3) | −4.4 (0) | |
| Z5212 | hypothetical protein | LB-antibiotics | 1 (0) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 5.6 (2) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 0.0 (0) | |
| Z5214 | espY5′, orphan, secreted protein | [39–41] | LB-antibiotics | 1 (2) | −1.5 (0) | 2.1 (1) | −0.6 (1) | −0.6 (1) | 6.0 (31) | 1.6 (2) | −5.2 (0) | −1.8 (0) | −1.2 (0) | 2.7 (2) |
| Z5339 | hypothetical protein | LB-antibiotics | 1 (3) | 1.3 (4) | 2.4 (3) | 1.4 (7) | 1.7 (9) | 5.1 (26) | −2.9 (0) | −2.9 (0) | 1.9 (6) | 1.1 (3) | 3.9 (8) | |
| Z2783 | hypothetical protein | LB-solid | 1 (1) | 0.7 (1) | −2.1 (0) | 0.4 (1) | 0.6 (1) | −2.1 (0) | 5.2 (8) | −2.1 (0) | 2.7 (2) | 3.1 (3) | −2.1 (0) | |
| Z4570 | hypothetical protein | LB-solid | 1 (11) | 2.4 (34) | 0.6 (3) | 2.7 (61) | 1.4 (26) | −0.1 (3) | 5.6 (176) | 4.2 (123) | 4.3 (120) | 2.1 (28) | 4.7 (48) | |
| Z0359 | hypothetical protein | minimal medium | 1 (0) | −1.4 (0) | −1.4 (0) | −1.4 (0) | −1.4 (0) | −1.4 (0) | 2.8 (1) | 5.4 (13) | −1.4 (0) | 1.6 (1) | −1.4 (0) | |
| Z0360 | hypothetical protein | minimal medium | 1 (2) | 0.1 (2) | −3.5 (0) | −3.5 (0) | 1.6 (7) | 2.1 (3) | −3.5 (0) | 5.2 (60) | −3.5 (0) | 2.4 (8) | 2.3 (2) | |
| Z0726 | hypothetical protein | minimal medium | 1 (3) | 2.0 (8) | −2.6 (0) | 2.2 (14) | 3.6 (41) | −2.6 (0) | 1.6 (3) | 7.5 (400) | −2.6 (0) | −2.6 (0) | 4.8 (17) | |
| Z1519 | hypothetical protein | minimal medium | 1 (10) | 2.1 (26) | 2.6 (10) | 0.8 (15) | 1.6 (29) | 0.6 (4) | −0.3 (3) | 5.0 (204) | −0.8 (3) | 3.0 (45) | −0.2 (1) | |
| Z1521 | hypothetical protein | minimal medium | 1 (11) | 1.7 (24) | 2.4 (10) | 0.2 (12) | 1.6 (33) | −6.9 (0) | 0.2 (5) | 5.6 (356) | −0.4 (5) | 1.9 (25) | −6.9 (0) | |
| Z1966 | hypothetical protein | minimal medium | 1 (1) | 1.0 (1) | −2.6 (0) | −2.6 (0) | 2.3 (3) | −2.6 (0) | −2.6 (0) | 5.8 (26) | −2.6 (0) | −2.6 (0) | 3.2 (1) | |
| Z2005 | hypothetical protein | minimal medium | 1 (0) | 3.7 (2) | 0.0 (0) | 2.5 (1) | 3.6 (2) | 0.0 (0) | 0.0 (0) | 5.5 (6) | 3.3 (1) | 0.0 (0) | 0.0 (0) | |
| Z2511 | hypothetical protein | minimal medium | 1 (0) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 3.6 (4) | 0.0 (0) | 0.0 (0) | 5.1 (7) | 0.0 (0) | 3.0 (1) | 0.0 (0) | |
| Z3065 | hypothetical protein | minimal medium | 1 (19) | 0.1 (13) | −6.7 (0) | −1.4 (6) | 4.0 (297) | 1.5 (15) | 1.6 (21) | 8.9 (6063) | 2.1 (49) | 0.6 (17) | 4.6 (80) | |
| Z3066 | hypothetical protein | minimal medium | 1 (1) | −1.4 (0) | −1.4 (0) | −1.4 (0) | 4.1 (37) | −1.4 (0) | −1.4 (0) | 7.9 (337) | −1.4 (0) | −1.4 (0) | −1.4 (0) | |
| Z4912 | hypothetical protein | minimal medium | 1 (5) | 1.5 (8) | 2.9 (6) | 0.9 (7) | 3.5 (51) | −3.4 (0) | 0.8 (3) | 7.4 (532) | 1.4 (7) | 2.6 (17) | −3.4 (0) | |
| Z4915 | hypothetical protein | minimal medium | 1 (2) | −0.5 (1) | −3.2 (0) | 0.1 (2) | 2.3 (11) | −3.2 (0) | 1.0 (2) | 6.9 (181) | 1.0 (3) | 1.7 (4) | −3.2 (0) | |
| Z4917 | hypothetical protein | minimal medium | 1 (3) | 1.7 (6) | 1.3 (1) | −1.5 (1) | 2.9 (23) | −4.0 (0) | 2.2 (5) | 6.7 (207) | −0.7 (1) | 0.5 (3) | 2.9 (4) | |
| Z5122 | hypothetical protein | minimal medium | 1 (175) | −1.7 (35) | −3.5 (3) | −5.4 (3) | 0.5 (245) | 3.9 (743) | −0.3 (52) | 5.6 (5816) | −1.3 (45) | −4.8 (4) | −2.0 (8) | |
| Z2156 | hypothetical protein | spinach | 1 (17) | −1.1 (4) | −4.7 (0) | −4.7 (0) | −0.6 (10) | 0.9 (8) | −4.7 (0) | 4.4 (221) | 5.5 (448) | 1.2 (23) | −4.7 (0) | |
| Z3271 | hypothetical protein | spinach | 1 (9) | −0.5 (4) | −4.6 (0) | −0.3 (6) | 0.7 (14) | −4.6 (0) | 4.7 (79) | 2.9 (41) | 5.2 (191) | 0.8 (9) | 2.8 (10) | |
| Z3560 | hypothetical protein | spinach | 1 (1) | 1.7 (2) | −3.4 (0) | −0.1 (1) | 0.7 (1) | −3.4 (0) | 3.7 (4) | 2.7 (4) | 5.5 (25) | 1.1 (1) | −3.4 (0) | |
| Z4375 | hypothetical protein | spinach | 1 (4) | 1.1 (6) | −4.1 (0) | −1.6 (1) | 1.4 (11) | −4.1 (0) | 1.7 (5) | 1.8 (9) | 5.0 (85) | 0.4 (3) | 2.8 (5) | |
| Z4376 | hypothetical protein | spinach | 1 (7) | 0.2 (5) | 1.0 (2) | 0.7 (9) | 2.8 (44) | 1.3 (4) | 1.4 (6) | 2.2 (18) | 6.4 (320) | 2.0 (15) | 1.5 (3) | |
| Z4601 | hypothetical protein | spinach | 1 (0) | 2.8 (2) | 0.0 (0) | 2.5 (3) | 0.0 (0) | 0.0 (0) | 4.2 (4) | 4.6 (9) | 6.6 (36) | 3.9 (5) | 0.0 (0) | |
| Z4890 | hypothetical protein | spinach | 1 (17) | 2.1 (45) | −0.4 (2) | 3.9 (230) | 4.9 (500) | −0.7 (3) | −2.1 (1) | 4.7 (286) | 5.6 (485) | 2.1 (42) | 0.8 (5) | |
| Z4909 | hypothetical protein | spinach | 1 (15) | 0.7 (14) | −5.9 (0) | 2.7 (80) | 2.5 (77) | −5.9 (0) | −5.9 (0) | 2.6 (54) | 5.2 (301) | 0.8 (14) | −5.9 (0) | |
| Z5730 | hypothetical protein | spinach | 1 (4) | −3.3 (0) | −3.3 (0) | 1.0 (7) | 1.9 (14) | −3.3 (0) | −3.3 (0) | 1.3 (6) | 5.1 (81) | 1.6 (7) | −3.3 (0) | |
| Z0351 | hypothetical protein | radish | 1 (0) | 4.2 (1) | 0.0 (0) | 0.0 (0) | 4.6 (3) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 3.3 (1) | 5.7 (4) | 0.0 (0) | |
| Z1023 | ybiJ, biofilm formation | [42, 43] | radish | 1 (17) | −0.2 (8) | 0.2 (3) | −2.6 (2) | 1.5 (45) | 2.5 (25) | −0.9 (3) | 1.7 (35) | 1.7 (31) | 6.6 (945) | 3.3 (28) |
| Z1027 | ybiM, biofilm formation | [44] | radish | 1 (17) | −0.3 (8) | −5.6 (0) | −3.1 (1) | −0.3 (12) | 0.0 (4) | −5.6 (0) | −5.6 (0) | −2.3 (2) | 7.5 (1751) | −5.6 (0) |
| Z1511 | hypothetical protein | radish | 1 (0) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 6.2 (5) | 0.0 (0) | |
| Z4396 | ygiD, biofilm formation | [45] | radish | 1 (11) | 0.8 (13) | −6.3 (0) | 1.7 (33) | 1.0 (24) | 0.9 (6) | −6.3 (0) | 1.3 (19) | 1.0 (14) | 5.6 (337) | 1.5 (6) |
| Z4455 | hypothetical protein | radish | 1 (4) | 1.0 (5) | −3.9 (0) | 4.2 (58) | 2.0 (14) | −3.9 (0) | −3.9 (0) | −3.9 (0) | 2.3 (11) | 5.1 (79) | 3.0 (5) | |
| Z4460 | hypothetical protein | radish | 1 (5) | −2.1 (1) | −4.8 (0) | −1.5 (1) | −0.3 (4) | 1.8 (5) | −0.6 (1) | −4.8 (0) | 0.9 (6) | 5.9 (197) | 3.6 (10) | |
| Z4807 | yhhW, quercetin detoxification | [46] | radish | 1 (13) | 0.0 (8) | 0.7 (4) | 2.1 (47) | 0.4 (17) | 1.0 (7) | −6.2 (0) | 0.9 (16) | 1.7 (25) | 5.8 (430) | −0.3 (2) |
| Z5808 | yjfY, biofilm formation | [47–49] | radish | 1 (13) | 2.7 (50) | 1.5 (6) | 0.4 (15) | 3.0 (99) | 1.8 (12) | 2.1 (19) | −0.3 (7) | 1.8 (27) | 7.5 (1365) | 4.5 (49) |
| Z0245 | hypothetical protein | feces | 1 (0) | 3.7 (2) | 0.0 (0) | 3.4 (2) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 3.3 (1) | 3.0 (1) | 5.8 (3) | |
| Z0387 | annotated as “dubious” | feces | 1 (3) | 0.1 (2) | 4.2 (12) | −2.6 (0) | 0.1 (3) | 3.0 (8) | 2.5 (7) | 1.0 (4) | −2.6 (0) | −2.6 (0) | 6.0 (40) | |
| Z0706 | hypothetical protein | feces | 1 (0) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 5.8 (3) | |
| Z0742 | methionine biosynthesis | [50–52] | feces | 1 (4) | 0.1 (2) | −5.1 (0) | 0.5 (5) | 0.9 (7) | −5.1 (0) | −5.1 (0) | 4.8 (68) | 1.7 (7) | 1.6 (7) | 5.1 (23) |
| Z1197 | hypothetical protein | feces | 1 (0) | 0.0 (0) | 0.0 (0) | 2.5 (3) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 4.6 (9) | 3.3 (3) | 0.0 (0) | 5.8 (6) | |
| Z1517 | hypothetical protein | feces | 1 (0) | 0.0 (0) | 0.0 (0) | 3.4 (7) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 5.8 (8) | |
| Z1527 | switches between biofilm and planctonic life style, ycdT | [53–55] | feces | 1 (7) | −0.6 (3) | −6.4 (0) | −0.7 (4) | 0.5 (10) | 1.2 (5) | 0.8 (4) | 2.5 (28) | 0.9 (8) | −1.0 (2) | 5.4 (56) |
| Z2119 | hypothetical protein | feces | 1 (0) | 0.0 (0) | 0.0 (0) | 2.5 (3) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 5.8 (8) | |
| Z2199 | hypothetical protein | feces | 1 (0) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 2.7 (3) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 0.0 (0) | 5.8 (6) | |
| Z2368 | encoded within prophage CP-933R | feces | 1 (5) | 0.2 (3) | −2.6 (0) | 0.8 (7) | 1.0 (10) | −2.6 (0) | 4.4 (37) | −2.6 (0) | −2.6 (0) | 1.9 (11) | 6.8 (104) | |
| Z2560 | hypothetical protein | feces | 1 (6) | −0.4 (3) | 0.7 (2) | 0.2 (6) | −0.1 (5) | 1.0 (3) | 1.9 (7) | −1.0 (2) | 2.0 (14) | −4.6 (0) | 5.0 (33) | |
| Z2619 | membrane protein, glucuronate metabol. | [38, 56] | feces | 1 (0) | −1.4 (0) | −1.4 (0) | 3.2 (2) | 2.2 (1) | −1.4 (0) | −1.4 (0) | 3.1 (2) | −1.4 (0) | 2.5 (1) | 6.0 (4) |
| Z3722 | contains functional domain | feces | 1 (21) | 0.7 (21) | 1.8 (12) | −1.0 (9) | 0.8 (35) | −7.4 (0) | 1.0 (14) | 1.3 (33) | −1.4 (5) | 2.5 (70) | 5.2 (129) |
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.