Mechanism of bacterial predation via ixotrophy
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB75513 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR13063108.fastq.gz | Fastqsanger.gz | |||
| ERR13063109.fastq.gz | Fastqsanger.gz | |||
| ERR13063110.fastq.gz | Fastqsanger.gz | |||
| ERR13063111.fastq.gz | Fastqsanger.gz |
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Project description:We have recently shown that the coprophilous model mushroom Coprinopsis cinerea transcribes a broad array of genes encoding defense proteins in the vegetative mycelium and fruiting bodies that target bacterial competitors and animal predators challenging the respective tissues of this fungus. In addition, we have demonstrated in previous work that two nematotoxic defense proteins from Coprinopsis, CGL1 and CGL2, were induced in vegetative mycelium challenged with the predatory nematode Aphelenchus avenae; however, the specificity and broadness of this response remained unclear. In order to resolve these issues, we sequenced the poly(A)-positive transcriptome of vegetative mycelium of C. cinerea confronted with nematode predation, hyphal mechanical damage or bacterial co-culture.
2015-09-01 | E-MTAB-2763 | biostudies-arrayexpress
Project description:Phage therapy is a promising adjunct therapeutic approach against bacterial multidrug-resistant infections, including Pseudomonas aeruginosa-derived infections. Nevertheless, the current knowledge about the phage-bacteria interaction within a human environment is limited. In this work, we performed a transcriptome analysis of phage-infected P. aeruginosa adhered to a human epithelium (Nuli-1 ATCC® CRL-4011™). To this end, we performed RNA-sequencing from a complex mixture comprising phage–bacteria–human cells at early, middle, and late infection and compared it to uninfected adhered bacteria. Overall, we demonstrated that phage genome transcription is unaltered by bacterial growth and phage employs a core strategy of predation through upregulation of prophage-associated genes, a shutdown of bacterial surface receptors, and motility inhibition. In addition, specific responses were captured under lung-simulating conditions, with the expression of genes related to spermidine syntheses, sulfate acquisition, spermidine syntheses, biofilm formation (both alginate and polysaccharide syntheses), lipopolysaccharide (LPS) modification, pyochelin expression, and downregulation of virulence regulators. These responses should be carefully studied in detail to better discern phage-induced changes from bacterial responses against phage. Our results establish the relevance of using complex settings that mimics in vivo conditions to study phage-bacteria interplay, being obvious the phage versatility on bacterial cell invasion.
2023-05-31 | GSE213159 | GEO
Project description:Purpose: Protozoan predators affect the structure of bacterial communities, but investigations into how predation influences bacterial evolution and antagonistic behaviours are scarce. We performed a 20-day predator-prey evolution experiment on solid media to investigate the adaptive traits that arise in bacterial prey under continuous protozoan predation. Methods: Pseudomonas fluorescens SBW25 and a wild Acanthamoeba sp. isolate as a predator prey pair co-evolved for 20 days yielded both previously described (Wrinkly Spreader; WS) and novel colony morphotype (Wrinkly Fried Egg; WFE) isolates with conferred grazing resistance. These isolates were subjected to RNAseq profiling with and without predation to determine transcriptional changes contributing to grazing resistance. Results: For differential gene expression the WT SBW25 without predation was used as a baseline. For the WS condition, a total of 881 differentially expressed genes (DEGs) were identified, of which 424 were upregulated and 457 were downregulated. In the WFE condition, a total of 908 DEGs were identified, of which 475 were upregulated and 434 were downregulated. Among all DEGs, 335 upregulated and 313 downregulated genes were shared between the WS1 and WFE conditions Conclusions: Our findings suggest that protozoan predation can profoundly influence the course of genetic and phenotypic evolution in a short period of time. Together, the differential expression results suggest expression of features that would be expected to increase biofilm formation in WFE according to previous studies. However, increased expression of these traits may not lead to a stronger biofilm, but may still provide predation resistance. For example, fibrils may increase the effective profile size of a bacterial cell. Increased Fap-mediated biofilm formation also induces increased alginate synthesis in P. aeruginosa PA01, an exopolysaccharide that protects mucoid P. aeruginosa against macrophage killing. Interestingly, we found increased expression of alginate biosynthesis genes in both WFE and WS1 (algA, algF), suggesting alternate mechanisms leading to increased alginate production in these two strains.
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Project description:Bdellovibrio bacteriovorus HD100 is a predatory bacterium which attacks a wide range of gram negative bacterial pathogens and is proposed to be a potential living antibiotic. In the current study, we evaluated the effects of indole, a bacterial signaling molecule commonly produced within the gut, on the predatory ability of B. bacteriovorus HD100. Indole significantly delayed predation on E. coli MG1655 and S. enterica KACC 11595 at physiological concentrations (0.25 to 1 mM) and completely inhibited predation when present at 2 mM. Microscopic analysis revealed that indole blocked the predator from attacking the prey. Furthermore, indole was not toxic to the predator but slowed down its motility. Microarray and RT-qPCR analyses confirmed this as the gene group showing the greatest down-regulation in the presence of 1 and 2 mM indole was flagellar assembly and motility genes. Aside from this group, indole also caused a wide spectrum changes in gene expression including the general down-regulation of genes involved in ribosome assembly and RNA translation. Furthermore, indole addition to the predatory culture after the entrance of B. bacteriovorus into the prey periplasm slowed down bdelloplast lysis. In conclusion, indole is an important gut-related signaling molecule that can have significant impacts on the predation efficiency and predator behavior. These findings should be taken into consideration especially if B. bacteriovorus is to be applied as a probiotic or living antibiotic.
2013-11-19 | GSE52455 | GEO
Project description:Purpose: The goal of this study was to compare gene expression in whole embryos to identify transcriptomic changes that result from maternal exposure to predation risk. Methods: Whole embryo mRNA profiles of 3 day post-fertilizationstickleback embrosof mothers exposed to simulated predation risk and control embryos were generated by RNA-sequencing of pooled embryos using Illumina Hiseq2000. The sequence reads that passed quality filters were aligned to the stickleback reference genome and analyzed at the gene level (EdgeR) and at the transcript level (Cufflinks/Cuffdiff). Subsets of embryos were also measured for embryo length and eye diameter, and data were analyzed with a general linear model (SPSS). Results: We mapped ~22 million sequence reads per sample to the stickleback reference genome (BROADS1, Ensembl database version 71.1, Feb 2006) and identified 17440 transcripts with the Tophat workflow. Differential expression analysis using both EdgeR and Cufflinks/Cuffdiff identified 455 transcripts were differentially expressed in embryos of mothers exposed to simulated predation risk as compared to control embryos, with an FDR <0.05 (Cuffdiff) or <0.10 (EdgeR). Gene ontology and pathway analysis (DAVID, IPA) of the differentially expressed gene list revealed enrichment of genes involved in growth, metabolism, neurogenesis, and epigenetics. Embryos of mothers exposed to predation risk had elevated expression of growth and metabolism genes and were also larger than control embryos, suggesting at least some of the genes differentially expressed in this study are involved in the transfer of maternal experience to offspring. Conclusions: Our results suggest that early stickleback embryos respond to maternal exposure to predation risk via changes in gene expression, and a general acceleration of the developmental program. Further study is needed to elucidate the myriad molecular interactions between genes that are differentially-regulated as a result of maternal exposure to predation risk and to understand their relationships to previously-observed maternal effects in this system. Whole embryo mRNA profiles of 3dpf stickleback embryos of mothers exposed to simulated predation risk [E] and control mothers [C] were generated by barcoded, multiplexed high-throughput RNA-sequencing on Illumina Hiseq-2000.
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Project description:Bdellovibrio bacteriovorus HD100 is a predatory bacterium which attacks a wide range of gram negative bacterial pathogens and is proposed to be a potential living antibiotic. In the current study, we evaluated the effects of indole, a bacterial signaling molecule commonly produced within the gut, on the predatory ability of B. bacteriovorus HD100. Indole significantly delayed predation on E. coli MG1655 and S. enterica KACC 11595 at physiological concentrations (0.25 to 1 mM) and completely inhibited predation when present at 2 mM. Microscopic analysis revealed that indole blocked the predator from attacking the prey. Furthermore, indole was not toxic to the predator but slowed down its motility. Microarray and RT-qPCR analyses confirmed this as the gene group showing the greatest down-regulation in the presence of 1 and 2 mM indole was flagellar assembly and motility genes. Aside from this group, indole also caused a wide spectrum changes in gene expression including the general down-regulation of genes involved in ribosome assembly and RNA translation. Furthermore, indole addition to the predatory culture after the entrance of B. bacteriovorus into the prey periplasm slowed down bdelloplast lysis. In conclusion, indole is an important gut-related signaling molecule that can have significant impacts on the predation efficiency and predator behavior. These findings should be taken into consideration especially if B. bacteriovorus is to be applied as a probiotic or living antibiotic. Bdellovibrio bacteriovorus HD100 was incubated for 30 min at 30°C in HEPES buffer supplemented with 0,1, and 2 mM indole. RNA was then extracted from each sample and purified. 100 ng of RNA from each sample were used for microarray experiment. For zero and 1 mM indole treatments, three independant samples were tested while for 2 mM indole treatment, two samples were tested. A total of 8 arrays were used.
2013-11-19 | E-GEOD-52455 | biostudies-arrayexpress
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Project description:Small distortions in transcriptional networks might lead to drastic phenotypical changes, especially in cellular developmental programs such as competence for natural transformation. Here, we report a pervasive circuitry rewiring for competence and predation interplay in commensal streptococci. Canonically, in model species of streptococci such as Streptococcus pneumoniae and Streptococcus mutans, the pheromone-based two-component system BlpRH is a central node that orchestrates the production of antimicrobial compounds (bacteriocins) and incorporates signal from the competence activation cascade. However, the human commensal Streptococcus salivarius does not contain a functional BlpRH pair and in this species, the competence signaling system ComRS directly couples bacteriocin production and competence commitment. This network shortcut might account for an optimal reaction against microbial competitors and could explain the high prevalence of S. salivarius in the human digestive tract. Moreover, the broad spectrum of bacteriocin activity against pathogenic bacteria showcases the commensal and genetically tractable S. salivarius species as a user-friendly model for natural transformation and bacterial predation.
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Project description:Purpose: The goal of this study was to compare gene expression in whole embryos to identify transcriptomic changes that result from maternal exposure to predation risk. Methods: Whole embryo mRNA profiles of 3 day post-fertilizationstickleback embrosof mothers exposed to simulated predation risk and control embryos were generated by RNA-sequencing of pooled embryos using Illumina Hiseq2000. The sequence reads that passed quality filters were aligned to the stickleback reference genome and analyzed at the gene level (EdgeR) and at the transcript level (Cufflinks/Cuffdiff). Subsets of embryos were also measured for embryo length and eye diameter, and data were analyzed with a general linear model (SPSS). Results: We mapped ~22 million sequence reads per sample to the stickleback reference genome (BROADS1, Ensembl database version 71.1, Feb 2006) and identified 17440 transcripts with the Tophat workflow. Differential expression analysis using both EdgeR and Cufflinks/Cuffdiff identified 455 transcripts were differentially expressed in embryos of mothers exposed to simulated predation risk as compared to control embryos, with an FDR <0.05 (Cuffdiff) or <0.10 (EdgeR). Gene ontology and pathway analysis (DAVID, IPA) of the differentially expressed gene list revealed enrichment of genes involved in growth, metabolism, neurogenesis, and epigenetics. Embryos of mothers exposed to predation risk had elevated expression of growth and metabolism genes and were also larger than control embryos, suggesting at least some of the genes differentially expressed in this study are involved in the transfer of maternal experience to offspring. Conclusions: Our results suggest that early stickleback embryos respond to maternal exposure to predation risk via changes in gene expression, and a general acceleration of the developmental program. Further study is needed to elucidate the myriad molecular interactions between genes that are differentially-regulated as a result of maternal exposure to predation risk and to understand their relationships to previously-observed maternal effects in this system.
2014-06-07 | GSE56160 | GEO
Project description:Impact of phage predation on bacterial transcriptome under simulated human airway conditions
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