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| Status |
Public on Jul 22, 2016 |
| Title |
Distinct gene expression profile of Xanthomonas retroflexus engaged in synergistic multispecies biofilm formation |
| Organisms |
Paenibacillus amylolyticus; Microbacterium oxydans; Stenotrophomonas rhizophila; Xanthomonas retroflexus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
It is well known that bacteria often exist in naturally formed multispecies biofilms. Within these biofilms, interspecies interactions seem to play an important role in ecological processes. Little is known about the effects of interspecies interactions on gene expression in these multispecies biofilms. This study presents a comparative gene expression analysis of the Xanthomonas retroflexus transcriptome when grown in a single-species biofilm and in dual- and four-species consortia with Stenotrophomonas rhizophila, Microbacterium oxydans and Paenibacillus amylolyticus. The results revealed complex interdependent interaction patterns in the multispecies biofilms. Many of the regulated functions are related to interactions with the external environment and suggest a high phenotypic plasticity in response to coexistence with other species. Furthermore, the changed expression of genes involved in aromatic and branched chain amino acid biosynthesis suggests nutrient cross feeding as an contribution factor for the observed synergistic biofilm production when these four species coexists in a biofilm.
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| Overall design |
X. retroflexus was cultivated in three replicates of single-species biofilm and combined with S. rhizophila, M. oxydans and P. amylolyticus in dual-species biofilms with three respective replicates. At last, we combined all four species in a multispecies biofilm with five replicates and conducted a RNA seq based comparative gene expression study utilizing the Illumina sequencing technology.
Please note that the 'prodigal_all_new.txt' contains gene names (which are listed in the matrix_sum.txt) and their position in the genomes, which are included in the file 'all_contigs_500.fasta'.
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| Contributor(s) |
Hansen LB, Ren D, Burmølle M, Sørensen SJ |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Apr 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Lea Benedicte Skov Hansen |
| E-mail(s) |
[email protected]
|
| Organization name |
Technical University of Denmark
|
| Department |
Center for Biological Sequence Analysis
|
| Street address |
Kemitorvet 208
|
| City |
Lyngby |
| ZIP/Postal code |
2800 |
| Country |
Denmark |
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| Platforms (5)
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| GPL21728 |
Illumina HiSeq 2000 (Xanthomonas retroflexus) |
| GPL21729 |
Illumina HiSeq 2000 (Stenotrophomonas rhizophila; Xanthomonas retroflexus) |
| GPL21730 |
Illumina HiSeq 2000 (Microbacterium oxydans; Xanthomonas retroflexus) |
| GPL21731 |
Illumina HiSeq 2000 (Paenibacillus amylolyticus; Xanthomonas retroflexus) |
| GPL21732 |
Illumina HiSeq 2000 (Microbacterium oxydans; Paenibacillus amylolyticus; Stenotrophomonas rhizophila; Xanthomonas retroflexus) |
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| Samples (17)
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| GSM2123130 |
First replicate of X. Retroflexus in single species biofilm |
| GSM2123131 |
Second replicate of X. Retroflexus in single species biofilm |
| GSM2123132 |
Third replicate of X. Retroflexus in single species biofilm |
| GSM2123133 |
First replicate of X. Retroflexus and S. rhizophila in dual species biofilm |
| GSM2123134 |
Second replicate of X. Retroflexus and S. rhizophila in dual species biofilm |
| GSM2123135 |
Third replicate of X. Retroflexus and S. rhizophila in dual species biofilm |
| GSM2123136 |
First replicate of X. Retroflexus and M. oxydansin dual species biofilm |
| GSM2123137 |
Second replicate of X. Retroflexus and M. oxydansin dual species biofilm |
| GSM2123138 |
Third replicate of X. Retroflexus and M. oxydansin dual species biofilm |
| GSM2123139 |
First replicate of X. Retroflexus and P. amylolyticus in dual species biofilm |
| GSM2123140 |
Second replicate of X. Retroflexus and P. amylolyticus in dual species biofilm |
| GSM2123141 |
Third replicate of X. Retroflexus and P. amylolyticus in dual species biofilm |
| GSM2123142 |
First replicate of four species biofilm |
| GSM2123143 |
Second replicate of four species biofilm |
| GSM2123144 |
Third replicate of four species biofilm |
| GSM2123145 |
Fourth replicate of four species biofilm |
| GSM2123146 |
Fifth replicate of four species biofilm |
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| Relations |
| BioProject |
PRJNA318455 |
| SRA |
SRP073295 |
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