TABLE 6.
Transcription of exemplar genes encoding ribosome structural proteins, aminoacyl-tRNA ligases, and regulators of stringent response in S. variabile DSM 15176T and H. hathewayi DSM 13479Ta
| Species and gene name | Product (EC no.) | Pure cultureb
,c
|
Cocultureb
|
|||||
|---|---|---|---|---|---|---|---|---|
| Log2FC SV12 vs SV14 | Log2FC SV12 vs SV16 | FDRd | Log2FC BOSV vs SV24 | Log2FC BOSVHH vs SV24 | FDR | |||
| S. variabile | ||||||||
| SUBVAR_RS01425 | 30S ribosomal protein S9 | – | – | NS | 4.291 | 3.961 | 1.89e-54 | |
| SUBVAR_RS02945 | 30S ribosomal protein S18 | – | – | NS | 3.387 | 3.033 | 1.59e-41 | |
| SUBVAR_RS04660 | 50S ribosomal protein L19 | – | – | NS | 3.291 | 2.966 | 1.57e-42 | |
| SUBVAR_RS05155 | 50S ribosomal protein L31 | – | – | NS | 4.744 | 4.195 | 4.26e-60 | |
| SUBVAR_RS05835 | 50S ribosomal protein L10 | – | – | NS | 4.011 | 3.423 | 2.19e-51 | |
| SUBVAR_RS07650 | 50S ribosomal protein L21 | – | – | NS | 2.640 | 2.428 | 1.73e-30 | |
| SUBVAR_RS04130 | Alanine-tRNA ligase (EC 6.1.1.7) | – | – | NS | 2.332 | 2.945 | 1.13e-31 | |
| SUBVAR_RS04425 | Tyrosine-tRNA ligase (EC 6.1.1.1) | – | – | NS | 2.301 | 2.408 | 3.05e-23 | |
| SUBVAR_RS05990 | Asparagine-tRNA ligase (EC 6.1.1.22) | – | – | NS | 2.185 | 2.207 | 3.84e-23 | |
| SUBVAR_RS06090 | Phenylalanine-tRNA ligase subunit beta (EC 6.1.1.20) | – | – | NS | 1.385 | 1.356 | 3.14e-11 | |
| SUBVAR_RS09185 | Lysine-tRNA ligase (EC 6.1.1.6) | – | – | NS | 2.172 | 1.630 | 1.97e-21 | |
| SUBVAR_RS09715 | Threonine-tRNA ligase (EC 6.1.1.3) | – | – | NS | 1.619 | 2.114 | 5.55e-18 | |
| SUBVAR_RS12040 | Bifunctional (p)ppGpp synthetase/guanosine-3, 5′-bis(diphosphate) 3′-pyrophosphohydrolase (EC 3.1.7.2) | – | – | NS | –1.456 | –11.357 | 1.48e-09 | |
| SUBVAR_RS07640 | GTPase ObgE | – | – | NS | 1.232 | 1.013 | 1.91e-08 | |
| Log2FC HH06 vs HH16 | Log2FC HH06 vs HH18 | Log2FC HH06 vs HH20 | FDR | Log2FC BOHH vs HH24 | Log2FC BOSVHH vs HH24 | FDR | ||
| H. hathewayi | ||||||||
| CLOSTHATH_RS11480 | 50S ribosomal protein L31 | –2.080 | –2.217 | –1.890 | 6.50e-05 | 3.550 | 3.486 | 8.79e-05 |
| CLOSTHATH_RS18880 | 30S ribosomal protein S2 | –1.550 | –1.583 | –1.338 | 5.84e-04 | 2.598 | 2.353 | 2.49e-04 |
| CLOSTHATH_RS18945 | 30S ribosomal protein S21 | –2.511 | –2.503 | –2.416 | 4.68e-04 | 3.912 | 3.597 | 4.24e-05 |
| CLOSTHATH_RS20325 | 50S ribosomal protein L28 | –2.543 | –2.716 | –2.587 | 1.10e-04 | 4.578 | 4.351 | 2.39e-05 |
| CLOSTHATH_RS28340 | 50S ribosomal protein L35 | –1.908 | –1.956 | –1.821 | 1.82e-04 | 2.545 | 2.716 | 2.65e-03 |
| CLOSTHATH_RS30700 | 30S ribosomal protein S20 | –2.869 | –2.588 | –2.106 | 2.44e-05 | 3.198 | 2.701 | 1.23e-04 |
| CLOSTHATH_RS07400 | Glutamine-tRNA ligase/YqeY domain fusion protein (EC 6.1.1.18) | –1.646 | –1.838 | –1.653 | 2.91e-04 | 2.536 | 2.572 | 3.20e-04 |
| CLOSTHATH_RS12900 | Glycine-tRNA ligase (EC 6.1.1.14) | –1.202 | –1.213 | –1.306 | 2.29e-04 | 1.131 | 1.208 | 1.90e-02 |
| CLOSTHATH_RS21545 | Histidine-tRNA ligase (EC 6.1.1.21) | – | –1.031 | – | 2.32e-03 | 1.857 | 2.400 | 6.22e-04 |
| CLOSTHATH_RS27790 | Arginine-tRNA ligase (EC 6.1.1.19) | –1.110 | –1.476 | –1.347 | 2.89e-04 | 1.268 | 1.598 | 3.80e-03 |
| CLOSTHATH_RS28080 | Lysine-tRNA ligase (EC 6.1.1.6) | –1.161 | –1.382 | – | 1.66e-03 | 2.201 | 2.302 | 3.73e-04 |
| CLOSTHATH_RS21480 | Bifunctional (p)ppGpp synthetase/guanosine-3′,5′-bis(diphosphate) 3′-pyrophosphohydrolase (EC 3.1.7.2) | –1.052 | –1.239 | –1.189 | 3.80e-03 | 1.997 | 1.866 | 7.53e-04 |
| CLOSTHATH_RS30045 | GTPase ObgE | – | – | – | NS | – | 1.531 | 3.28e-02 |
Gene name, product, and Log2FC (fold change) of each comparison and FDR (false discovery rate) are reported. Genes showing an FDR of <0.05 and absolute value of Log2FC >1 were considered statistically differentially transcribed.
SV, S. variabile; BO, B. ovatus; BOSV, coculture of B. ovatus and S. variabile; BOSVHH, coculture of B. ovatus, S. variabile, and H. hathewayi; HH, H. hathewayi; BOHH, B. ovatus and H. hathewayi in coculture; BOSVHH, B. ovatus, S. variabile, and H. hathewayi in coculture. Comparisons in S. variabile pure culture are between 12 h and 14 or 16 h of incubation. Comparisons in H. hathewayi pure culture are between transcription at 6 h and 16, 18 or 20 h of incubation. Comparisons in coculture are between pure culture and coculture, both at 24 h of incubation.
–, absolute value Log2FC < 1.
NS, not statistically significant.