SRA STUDY
SRA Study Id ERP010550  (Link to NCBI )
Study Title Integrated microbiome and host profiling in a mouse model of colitis suggests host immune activity drives changes in the gut micro-environment that influence both microbial community structure and gene expression
SRA Experiments
SRA Experiment Id ERX978690  (Link to NCBI )
Experiment Title Illumina HiSeq 2500 paired end sequencing; Integrated microbiome and host profiling in a mouse model of colitis suggests host immune activity drives changes in the gut micro-environment that influence both microbial community structure and gene expression
Exp Library Strategy RNA_SEQ
Library Source METATRANSCRIPTOMIC
Library Selection RANDOM
Library Name rna_stool-ss-R3
Library Layout PAIRED
Library Instrument ILLUMINA_HI_SEQ_2500
   
SRA Experiment Id ERX978691  (Link to NCBI )
Experiment Title Illumina HiSeq 2500 paired end sequencing; Integrated microbiome and host profiling in a mouse model of colitis suggests host immune activity drives changes in the gut micro-environment that influence both microbial community structure and gene expression
Exp Library Strategy RNA_SEQ
Library Source METATRANSCRIPTOMIC
Library Selection RANDOM
Library Name rna_stool-HhaIL10R-R1
Library Layout PAIRED
Library Instrument ILLUMINA_HI_SEQ_2500
   
SRA Experiment Id ERX978704  (Link to NCBI )
Experiment Title Illumina HiSeq 2500 paired end sequencing; Integrated microbiome and host profiling in a mouse model of colitis suggests host immune activity drives changes in the gut micro-environment that influence both microbial community structure and gene expression
Exp Library Strategy RNA_SEQ
Library Source METATRANSCRIPTOMIC
Library Selection RANDOM
Library Name rna_stool-HhaIL10R-R2
Library Layout PAIRED
Library Instrument ILLUMINA_HI_SEQ_2500
   
SRA Experiment Id ERX978700  (Link to NCBI )
Experiment Title Illumina HiSeq 2500 paired end sequencing; Integrated microbiome and host profiling in a mouse model of colitis suggests host immune activity drives changes in the gut micro-environment that influence both microbial community structure and gene expression
Exp Library Strategy RNA_SEQ
Library Source METATRANSCRIPTOMIC
Library Selection RANDOM
Library Name rna_stool-aIL10R-R2
Library Layout PAIRED
Library Instrument ILLUMINA_HI_SEQ_2500
   
SRA Experiment Id ERX978678  (Link to NCBI )
Experiment Title Illumina HiSeq 2500 paired end sequencing; Integrated microbiome and host profiling in a mouse model of colitis suggests host immune activity drives changes in the gut micro-environment that influence both microbial community structure and gene expression
Exp Library Strategy RNA_SEQ
Library Source METATRANSCRIPTOMIC
Library Selection RANDOM
Library Name rna_stool-Hh-R2
Library Layout PAIRED
Library Instrument ILLUMINA_HI_SEQ_2500
   
SRA Experiment Id ERX978679  (Link to NCBI )
Experiment Title Illumina HiSeq 2500 paired end sequencing; Integrated microbiome and host profiling in a mouse model of colitis suggests host immune activity drives changes in the gut micro-environment that influence both microbial community structure and gene expression
Exp Library Strategy RNA_SEQ
Library Source METATRANSCRIPTOMIC
Library Selection RANDOM
Library Name rna_stool-ss-R2
Library Layout PAIRED
Library Instrument ILLUMINA_HI_SEQ_2500
   
SRA Experiment Id ERX978702  (Link to NCBI )
Experiment Title Illumina HiSeq 2500 paired end sequencing; Integrated microbiome and host profiling in a mouse model of colitis suggests host immune activity drives changes in the gut micro-environment that influence both microbial community structure and gene expression
Exp Library Strategy RNA_SEQ
Library Source METATRANSCRIPTOMIC
Library Selection RANDOM
Library Name rna_stool-Hh-R4
Library Layout PAIRED
Library Instrument ILLUMINA_HI_SEQ_2500
   
SRA Experiment Id ERX978703  (Link to NCBI )
Experiment Title Illumina HiSeq 2500 paired end sequencing; Integrated microbiome and host profiling in a mouse model of colitis suggests host immune activity drives changes in the gut micro-environment that influence both microbial community structure and gene expression
Exp Library Strategy RNA_SEQ
Library Source METATRANSCRIPTOMIC
Library Selection RANDOM
Library Name rna_stool-aIL10R-R4
Library Layout PAIRED
Library Instrument ILLUMINA_HI_SEQ_2500
   
SRA Experiment Id ERX978674  (Link to NCBI )
Experiment Title Illumina HiSeq 2500 paired end sequencing; Integrated microbiome and host profiling in a mouse model of colitis suggests host immune activity drives changes in the gut micro-environment that influence both microbial community structure and gene expression
Exp Library Strategy RNA_SEQ
Library Source METATRANSCRIPTOMIC
Library Selection RANDOM
Library Name rna_stool-ss-R4
Library Layout PAIRED
Library Instrument ILLUMINA_HI_SEQ_2500
   
SRA Experiment Id ERX978675  (Link to NCBI )
Experiment Title Illumina HiSeq 2500 paired end sequencing; Integrated microbiome and host profiling in a mouse model of colitis suggests host immune activity drives changes in the gut micro-environment that influence both microbial community structure and gene expression
Exp Library Strategy RNA_SEQ
Library Source METATRANSCRIPTOMIC
Library Selection RANDOM
Library Name rna_stool-aIL10R-R3
Library Layout PAIRED
Library Instrument ILLUMINA_HI_SEQ_2500
   
SRA Experiment Id ERX978686  (Link to NCBI )
Experiment Title Illumina HiSeq 2500 paired end sequencing; Integrated microbiome and host profiling in a mouse model of colitis suggests host immune activity drives changes in the gut micro-environment that influence both microbial community structure and gene expression
Exp Library Strategy RNA_SEQ
Library Source METATRANSCRIPTOMIC
Library Selection RANDOM
Library Name rna_stool-ss-R1
Library Layout PAIRED
Library Instrument ILLUMINA_HI_SEQ_2500
   
SRA Experiment Id ERX978676  (Link to NCBI )
Experiment Title Illumina HiSeq 2500 paired end sequencing; Integrated microbiome and host profiling in a mouse model of colitis suggests host immune activity drives changes in the gut micro-environment that influence both microbial community structure and gene expression
Exp Library Strategy RNA_SEQ
Library Source METATRANSCRIPTOMIC
Library Selection RANDOM
Library Name rna_stool-HhaIL10R-R3
Library Layout PAIRED
Library Instrument ILLUMINA_HI_SEQ_2500
   
SRA Experiment Id ERX978698  (Link to NCBI )
Experiment Title Illumina HiSeq 2500 paired end sequencing; Integrated microbiome and host profiling in a mouse model of colitis suggests host immune activity drives changes in the gut micro-environment that influence both microbial community structure and gene expression
Exp Library Strategy RNA_SEQ
Library Source METATRANSCRIPTOMIC
Library Selection RANDOM
Library Name rna_stool-HhaIL10R-R4
Library Layout PAIRED
Library Instrument ILLUMINA_HI_SEQ_2500
   
SRA Experiment Id ERX978692  (Link to NCBI )
Experiment Title Illumina HiSeq 2500 paired end sequencing; Integrated microbiome and host profiling in a mouse model of colitis suggests host immune activity drives changes in the gut micro-environment that influence both microbial community structure and gene expression
Exp Library Strategy RNA_SEQ
Library Source METATRANSCRIPTOMIC
Library Selection RANDOM
Library Name rna_stool-Hh-R1
Library Layout PAIRED
Library Instrument ILLUMINA_HI_SEQ_2500
   
SRA Experiment Id ERX978683  (Link to NCBI )
Experiment Title Illumina HiSeq 2500 paired end sequencing; Integrated microbiome and host profiling in a mouse model of colitis suggests host immune activity drives changes in the gut micro-environment that influence both microbial community structure and gene expression
Exp Library Strategy RNA_SEQ
Library Source METATRANSCRIPTOMIC
Library Selection RANDOM
Library Name rna_stool-Hh-R3
Library Layout PAIRED
Library Instrument ILLUMINA_HI_SEQ_2500
   
SRA Experiment Id ERX978695  (Link to NCBI )
Experiment Title Illumina HiSeq 2500 paired end sequencing; Integrated microbiome and host profiling in a mouse model of colitis suggests host immune activity drives changes in the gut micro-environment that influence both microbial community structure and gene expression
Exp Library Strategy RNA_SEQ
Library Source METATRANSCRIPTOMIC
Library Selection RANDOM
Library Name rna_stool-aIL10R-R1
Library Layout PAIRED
Library Instrument ILLUMINA_HI_SEQ_2500
Study Abstract The gut microbiome is significantly altered in inflammatory bowel diseases, but the basis of these changes is not well understood. We have combined metagenomic and metatranscriptomic profiling of the gut microbiome to assess changes to both bacterial community structure and transcriptional activity in a mouse model of colitis. Gene families involved in microbial resistance to oxidative stress, including Dps/ferritin, Fe-dependent peroxidase and glutathione S-transferase, were transcriptionally up-regulated in colitis, implicating a role for increased oxygen tension in gut microbiota modulation. Transcriptional profiling of the host gut tissue and host RNA in the gut lumen revealed a marked increase in the transcription of genes with an activated macrophage and granulocyte signature, suggesting the involvement of these cell types in influencing microbial gene expression. Down-regulation of host glycosylation genes further supports a role for inflammation-driven changes to the gut niche that may impact the microbiome. We propose that members of the bacterial community react to inflammation-associated increased oxygen tension by inducing genes involved in oxidative stress resistance. Furthermore, correlated transcriptional responses between host glycosylation and bacterial glycan utilisation support a role for altered usage of host-derived carbohydrates in colitis.
Alias E-MTAB-3562
External Id BioProject=PRJEB9443