Multispecies
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA754109 | ENA |
REPOSITORIES: ENA
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Project description: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. 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'.
2016-07-22 | E-GEOD-80267 | biostudies-arrayexpress
Project description: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.
2016-07-22 | GSE80267 | GEO
Project description:The aim of the present study to compare the transcriptomic profile of P.gingivalis when growing within an in vitro multispecies biofilm or in a planktonic state, using microarray technology.
2019-06-05 | GSE132157 | GEO
Project description:Multispecies ZFN analysis Targeted Locus (Loci)
| PRJNA178374 | ENA
Project description:gut metagenome strain:Multispecies Metagenome
| PRJNA698295 | ENA
Project description:Multispecies biofilms are the predominant form of bacterial growth in natural and human-associated environments. Although the pathways involved in monospecies biofilm have been well characterized, less is known about the metabolic pathways and emergent traits of a multispecies biofilm community. Here, we performed a transcriptome survey of the developmental stages of a 3-species biofilm community and combined it with quantitative imaging and growth experiments. We report the remodelling of central metabolism of two of the three species in this community. Specifically, we observed an increase in the expression of genes associated with glycolysis and pentose phosphate pathways in K. pneumoniae. Similarly, a decrease in the expression of the same pathways in P. protegens was observed along with an increase in expression of glyoxalate cycle genes when grown as a mixed species biofilm, suggesting reorganisation of metabolic pathways and metabolite sharing for the community biofilms. To test the possibility of cross-feeding for the community, planktonic growth experiments revealed that both the Pseudomonads grew well in TCA cycle intermediates, while K. pneumoniae grew poorly when given those carbon sources. Despite this poor growth in mono-culture, K. pneumoniae was still the dominant species in mixed species biofilms cultivated in TCA intermediates as the sole source of carbon. The biofilm growth data, combined with the transcriptomics data, suggests there is reorganisation of metabolism for the community members and may allow for cross-feeding that allows K. pneumoniae to dominate the community. We also demonstrated that sdsA1 of P. aeruginosa was induced upon exposure to the surfactant SDS and that this gene was essential in protecting mono and mixed species biofilms from surfactant stress. This also suggests that the community members can share defence mechanisms. Overall, this study describes a comprehensive transcriptomics level investigation of shared resources, metabolites and stress defence that may underpin the emergent properties of mixed species biofilm communities.
2022-10-07 | GSE214543 | GEO
Project description:Application of multispecies probiotics reduces gastro-intestinal discomfort and increases microbial diversity after colonoscopy
| PRJEB56238 | ENA
Project description:S. anginosus, S. aureus LMG 10147 and P. aeruginosa DK2 are often co-isolated in sputum samples from cystic fibrosis patients. We found that S. anginosus LMG 14502 becomes less suceptible towards treatment with several antibiotics when it's grown together with S. aureus LMG 10147 and P. aeruginosa DK2, compared to when it's grown alone. In order to elucidate the molecular mechanisms responsible, we performed RNA-seq of an S. anginosus monospecies biofilm and of a multispecies bioiflm of S. anginosus, S. aureus and P. aeruginosa. First, biofilms of S. anginosus alone or in combination with S. aureus and P. aeruginosa were grown. Next, RNA was isolated. Subsequently, a Truseq stranded RNA library preparation kit (Illumina) was used to create strand specific libraries. After a quality and concentration control, the libraries were equimolarly pooled and sequenced using an Illumina NextSeq 500, generating 75bp unpaired reads.
2017-04-14 | E-MTAB-5426 | biostudies-arrayexpress
Project description:Background Insulinoma is the most common pancreatic neuroendocrine tumour in dogs and humans. The understanding of driving factors and critical survival genes in insulinomas is limited and overall survival is poor for canine and human malignant insulinoma. This study aimed to use single-cell RNA-sequencing to conduct a multispecies analysis of insulinoma cell lines to understand their single-cell transcriptomic landscape. Secondly, the impact of freeze-thawing on the pancreatic beta single-cell transcriptome was investigated, to determine whether cryoarchiving of primary insulinoma samples may be feasible in future studies. Methods Single-cell transcriptomic analysis was performed using fresh and cryopreserved multispecies insulinoma cell lines (canINS, CM, INS-1 and MIN6). R and Seurat were used to perform cell clustering and specific cluster marker genes were identified by the FindMarkers function. Metascape was used to identify statistically enriched pathways for specific cell clusters. Differentially expressed genes between fresh and cryopreserved single-cell transcriptome profiles, were defined as genes with a log2 fold change >0.25 and a Bonferroni-adjusted P<0.05, based on the Wilcoxon rank sum test. Results Based on the specific cell line single-cell transcriptome profiles, five or six cell clusters were constructed per cell line. All cell lines expressed neuroendocrine markers and additionally INS-1 and MIN6 displayed a gene signature indicative of mature/functional pancreatic islet/beta-cells. DEPTOR, BICC1, GHR, CCNB2, CENPA, LMO4, VANGL1, and L1CAM were identified as cross-species conserved insulinoma cluster marker genes. Little effect was found of cryopreservation and thawing on overall gene expression at the single-cell level in insulinoma cell lines: only 6 and 29 genes had a log2 fold change > 1 in cryopreserved versus fresh canINS and CM, respectively. Conclusions canINS, CM, INS-1 and MIN6 are all principally relevant as insulinoma models and the demonstrated differences in their single-cell transcriptomic profiles could aid researchers in selecting the appropriate cell lines for specific study objectives. Cross-species conserved insulinoma cluster marker genes were identified that harbour oncogenes and their involvement in insulinoma tumourigenesis should be investigated in future studies. The good comparability between cryopreserved and fresh insulinoma cells allows for inclusion of cryopreserved insulinoma patient samples in future studies, which allows for reduced assay-based variability.
2025-06-04 | GSE284573 | GEO
Project description:Distinct patterns in global gene expression reflect synergy in a multispecies biofilm
| PRJEB12332 | ENA