 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 08, 2024 |
| Title |
Transcriptomic analysis of polysaccharide utilization loci reveals substrate preferences in two ruminal generalists Segatella bryantii TF1-3 and Xylanibacter ruminicola KHP1 |
| Organisms |
Xylanibacter ruminicola; Segatella bryantii |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Bacteria of the genera Xylanibacter and Segatella are one of the most dominant groups in the rumen microbiota. They are characterized by the ability to utilize different hemicelluloses and pectin of plant cell-wall as well as plant energy storage polysaccharides. The degradation is possible with the use of cell envelope bound multiprotein apparatuses coded in polysaccharide utilization loci (PULs), which have been shown to be substrate specific. The knowledge of PUL presence in rumen Xylanibacter and Segatella based on bioinformatic analyses is already established and transcriptomic and genetic approaches confirmed predicted PULs for a limited number of substrates. In this study, we transcriptomically identified additional different PULs in Xylanibacter ruminicola KHP1 and Segatella bryantii TF1-3. We also identified substrate preferences and found that specific growth rate and extent of growth impacted the choice of substrates preferentially used for degradation. These preferred substrates were used by both strains simultaneously as judged by their PUL upregulation. Lastly, β-glucan and xyloglucan were used by these strains in the absence of bioinformatically and transcriptomically identifiable PUL systems.
|
| |
|
| Overall design |
We were growing each bacteria in 11 different polysaccharides and glucose as reference. And performed RNAseq analysis for each polysaccharide (22 experiments) + 2 glucose. We also did the RNAseq in minimal medium with glucose and beta-glucan for S. bryantii TF1-3.
|
| |
|
| Contributor(s) |
Murovec U, Accetto T |
| Citation(s) |
38769483 |
| |
| Submission date |
Mar 28, 2024 |
| Last update date |
Jun 05, 2024 |
| Contact name |
Urška Murovec |
| E-mail(s) |
Urska.Murovec@bf.uni-lj.si
|
| Organization name |
Biotechnical Faculty
|
| Street address |
Jamnikarjeva 101
|
| City |
Ljubljana |
| ZIP/Postal code |
1000 |
| Country |
Slovenia |
| |
|
| Platforms (3) |
| GPL34343 |
NextSeq 550 (Xylanibacter ruminicola) |
| GPL34344 |
Illumina NovaSeq 6000 (Xylanibacter ruminicola) |
| GPL34345 |
Illumina NovaSeq 6000 (Segatella bryantii) |
|
| Samples (78)
|
| GSM8174397 |
Pullulan, KHP1, biol rep 1 |
| GSM8174398 |
Pullulan, KHP1, biol rep 2 |
| GSM8174399 |
Pullulan, KHP1, biol rep 3 |
| GSM8174400 |
Beta-glucan, KHP1, biol rep 1 |
| GSM8174401 |
Beta-glucan, KHP1,biol rep 2 |
| GSM8174402 |
Beta-glucan, KHP1, biol rep 3 |
| GSM8174403 |
Galactomannan, KHP1, biol rep 1 |
| GSM8174404 |
Galactomannan, KHP1, biol rep 2 |
| GSM8174405 |
Galactomannan, KHP1, biol rep 3 |
| GSM8174406 |
Glucomannan, KHP1, biol rep 1 |
| GSM8174407 |
Glucomannan, KHP1, biol rep 2 |
| GSM8174408 |
Glucomannan, KHP1, biol rep 3 |
| GSM8174409 |
Xylogluclan, KHP1, biol rep 1 |
| GSM8174410 |
Xylogluclan, KHP1, biol rep 2 |
| GSM8174411 |
Xylogluclan, KHP1, biol rep 3 |
| GSM8174412 |
Arabinan, KHP1, biol rep 1 |
| GSM8174413 |
Arabinan, KHP1, biol rep 2 |
| GSM8174414 |
Arabinan, KHP1, biol rep 3 |
| GSM8174415 |
Rhamnogalactuornan, KHP1, biol rep 1 |
| GSM8174416 |
Rhamnogalactuornan, KHP1, biol rep 2 |
| GSM8174417 |
Rhamnogalactuornan, KHP1, biol rep 3 |
| GSM8174418 |
Arabinogalactan, KHP1, biol rep 1 |
| GSM8174419 |
Arabinogalactan, KHP1, biol rep 2 |
| GSM8174420 |
Arabinogalactan, KHP1, biol rep 3 |
| GSM8174421 |
Pectic galactan, KHP1, biol rep 1 |
| GSM8174422 |
Pectic galactan, KHP1, biol rep 2 |
| GSM8174423 |
Pectic galactan, KHP1, biol rep 3 |
| GSM8174424 |
Starch, KHP1, biol rep 1 |
| GSM8174425 |
Starch, KHP1, biol rep 2 |
| GSM8174426 |
Starch, KHP1, biol rep 3 |
| GSM8174427 |
Homogalacturonan, KHP1, biol rep 1 |
| GSM8174428 |
Homogalacturonan, KHP1, biol rep 2 |
| GSM8174429 |
Homogalacturonan, KHP1, biol rep 3 |
| GSM8174430 |
Arabinogalactan, TF13, biol rep 1 |
| GSM8174431 |
Arabinogalactan, TF13, biol rep 2 |
| GSM8174432 |
Arabinogalactan, TF13, biol rep 3 |
| GSM8174433 |
Arabinan, TF13, biol rep 1 |
| GSM8174434 |
Arabinan, TF13, biol rep 2 |
| GSM8174435 |
Arabinan, TF13, biol rep 3 |
| GSM8174436 |
Beta-glucan, TF13, min, biol rep 1 |
| GSM8174437 |
Beta-glucan, TF13, min, biol rep 2 |
| GSM8174438 |
Beta-glucan, TF13, min, biol rep 3 |
| GSM8174439 |
Beta-glucan, TF13, biol rep 1 |
| GSM8174440 |
Beta-glucan, TF13, biol rep 2 |
| GSM8174441 |
Beta-glucan, TF13, biol rep 3 |
| GSM8174442 |
Galactomannan, TF13, biol rep 1 |
| GSM8174443 |
Galactomannan, TF13, biol rep 2 |
| GSM8174444 |
Galactomannan, TF13, biol rep 3 |
| GSM8174445 |
Glucose, TF13, min, biol rep 1 |
| GSM8174446 |
Glucose, TF13, min, biol rep 2 |
| GSM8174447 |
Glucose, TF13, min, biol rep 3 |
| GSM8174448 |
Glucose, TF13, biol rep 1 |
| GSM8174449 |
Glucose, TF13, biol rep 2 |
| GSM8174450 |
Glucose, TF13, biol rep 3 |
| GSM8174451 |
Glucomannan, TF13, biol rep 1 |
| GSM8174452 |
Glucomannan, TF13, biol rep 2 |
| GSM8174453 |
Glucomannan, TF13, biol rep 3 |
| GSM8174454 |
Homogalactuornan, TF13, biol rep 1 |
| GSM8174455 |
Homogalactuornan, TF13, biol rep 2 |
| GSM8174456 |
Homogalactuornan, TF13, biol rep 3 |
| GSM8174457 |
Pectic galactan, TF13, biol rep 1 |
| GSM8174458 |
Pectic galactan, TF13, biol rep 2 |
| GSM8174459 |
Pectic galactan, TF13, biol rep 3 |
| GSM8174460 |
Pullulan, TF13, biol rep 1 |
| GSM8174461 |
Pullulan, TF13, biol rep 2 |
| GSM8174462 |
Pullulan, TF13, biol rep 3 |
| GSM8174463 |
Rhamnogalacturonan, TF13, biol rep 1 |
| GSM8174464 |
Rhamnogalacturonan, TF13, biol rep 2 |
| GSM8174465 |
Rhamnogalacturonan, TF13, biol rep 3 |
| GSM8174466 |
Starch, TF13, biol rep 1 |
| GSM8174467 |
Starch, TF13, biol rep 2 |
| GSM8174468 |
Starch, TF13, biol rep 3 |
| GSM8174469 |
Xyloglucan, TF13, biol rep 1 |
| GSM8174470 |
Xyloglucan, TF13, biol rep 2 |
| GSM8174471 |
Xyloglucan, TF13, biol rep 3 |
|
| Relations |
| BioProject |
PRJNA1093057 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE262719_RAW.tar |
3.2 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
Less...
More...