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| Status |
Public on Dec 01, 2023 |
| Title |
Effect of supplementation of a minimal culture medium with inulin, corn fiber and pectin, compared with a glucose condition, on the gene expression of a set of bacteria of the intestinal microbiota |
| Organisms |
Bacteroides thetaiotaomicron; Roseburia intestinalis; Subdoligranulum variabile; Bacteroides xylanisolvens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The aim of this RNA-sequencing study is to measure differential gene expression in 4 intestinal bacteria (Bacteroides xylanisolvens, Bacteroides thetaiotaomicron, Subdoligranulum variabile and Roseburia intestinalis). The data highlight the coordinated action of genes within the same locus involved in the degradation of complex carbohydrates. These loci are well characterized in Bacteroidetes species and referred to as polysaccharide utilization loci. In Firmicutes species, these loci are not so clear-cut, athough the GP-PUL concept has already been proposed. Here we compare the differential gene expression in minimal culture medium supplemented with a complex carbohydrate with a minimal culture medium supplemented with glucose. This differential analysis reveals a source-specific genetic response and a coordinated expression of genes involved in carbohydrate transport, carbohydrate degradation and transcriptional activation of these complex enzymatic machineries.
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| Overall design |
To investigate this differential expression, bacterial RNA was extracted after 12h of culture in minimum medium supplemented with one complex carbohydrate or glucose. RNA was extracted using RNAeasy Qiagen kit.
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| Contributor(s) |
Bedu-Ferrari C, Biscarrat P |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Jul 12, 2023 |
| Last update date |
Dec 01, 2023 |
| Contact name |
paul Biscarrat |
| E-mail(s) |
paul.Biscarrat@inrae.Fr
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| Phone |
0681646634
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| Organization name |
INRAE
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| Street address |
4 AVENUE JEAN JAURES-DOMAINE VILVERT
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| City |
JOUY EN JOSAS |
| State/province |
ile de france |
| ZIP/Postal code |
78350 |
| Country |
France |
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| Platforms (4)
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| GPL28094 |
Illumina NextSeq 500 (Bacteroides thetaiotaomicron) |
| GPL33567 |
Illumina NextSeq 500 (Bacteroides xylanisolvens) |
| GPL33568 |
Illumina NextSeq 500 (Roseburia intestinalis) |
| GPL33569 |
Illumina NextSeq 500 (Subdoligranulum variabile) |
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| Samples (36)
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| GSM7595580 |
B.thetaiotaomicron, corn fiber, R1 |
| GSM7595581 |
B.thetaiotaomicron, corn fiber, R2 |
| GSM7595582 |
B.thetaiotaomicron, corn fiber, R3 |
| GSM7595583 |
B.thetaiotaomicron, inulin, R1 |
| GSM7595584 |
B.thetaiotaomicron, inulin, R2 |
| GSM7595585 |
B.thetaiotaomicron, inulin, R3 |
| GSM7595586 |
B.xylanisolvens, glucose, R1 |
| GSM7595587 |
B.xylanisolvens, glucose, R2 |
| GSM7595588 |
B.xylanisolvens, glucose, R3 |
| GSM7595589 |
B.xylanisolvens, corn fiber, R1 |
| GSM7595590 |
B.xylanisolvens, corn fiber, R2 |
| GSM7595591 |
B.xylanisolvens, corn fiber, R3 |
| GSM7595592 |
B.xylanisolvens, inulin, R1 |
| GSM7595593 |
B.xylanisolvens, inulin, R2 |
| GSM7595594 |
B.xylanisolvens, inulin, R3 |
| GSM7595595 |
R.intestinalis, glucose, R1 |
| GSM7595596 |
R.intestinalis, glucose, R2 |
| GSM7595597 |
R.intestinalis, glucose, R3 |
| GSM7595598 |
R.intestinalis, corn fiber, R1 |
| GSM7595599 |
R.intestinalis, corn fiber, R2 |
| GSM7595600 |
R.intestinalis, corn fiber, R3 |
| GSM7595601 |
R.intestinalis, inulin, R1 |
| GSM7595602 |
R.intestinalis, inulin, R2 |
| GSM7595603 |
R.intestinalis, inulin, R3 |
| GSM7595604 |
S.variabile, glucose, R1 |
| GSM7595605 |
S.variabile, glucose, R2 |
| GSM7595606 |
S.variabile, glucose, R3 |
| GSM7595607 |
S.variabile, pectin, R1 |
| GSM7595608 |
S.variabile, pectin, R2 |
| GSM7595609 |
S.variabile, pectin, R3 |
| GSM7595610 |
S.variabile, inulin, R1 |
| GSM7595611 |
S.variabile, inulin, R2 |
| GSM7595612 |
S.variabile, inulin, R3 |
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| Relations |
| BioProject |
PRJNA993982 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE237111_BT_fibre_mais_vs_controle1_DESeq_results.csv.gz |
436.0 Kb |
(ftp)(http) |
CSV |
| GSE237111_BT_inuline_vs_controle1_DESeq_results.csv.gz |
436.8 Kb |
(ftp)(http) |
CSV |
| GSE237111_BX_fibre_mais_vs_controle2_DESeq_results.csv.gz |
454.6 Kb |
(ftp)(http) |
CSV |
| GSE237111_BX_inuline_vs_controle2_DESeq_results.csv.gz |
310.9 Kb |
(ftp)(http) |
CSV |
| GSE237111_RI_fibre_mais_vs_controle3_DESeq_results.csv.gz |
341.3 Kb |
(ftp)(http) |
CSV |
| GSE237111_RI_inuline_vs_controle3_DESeq_results.csv.gz |
342.7 Kb |
(ftp)(http) |
CSV |
| GSE237111_SV_inuline_vs_controle4_DESeq_results.csv.gz |
297.5 Kb |
(ftp)(http) |
CSV |
| GSE237111_SV_pectine_vs_controle4_DESeq_results.csv.gz |
298.6 Kb |
(ftp)(http) |
CSV |
| GSE237111_counts_BT.csv.gz |
310.9 Kb |
(ftp)(http) |
CSV |
| GSE237111_counts_BX.csv.gz |
265.2 Kb |
(ftp)(http) |
CSV |
| GSE237111_counts_RI.csv.gz |
286.1 Kb |
(ftp)(http) |
CSV |
| GSE237111_counts_SV.csv.gz |
243.2 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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