Bacteria
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA622382 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11476065_1.fastq.gz | Fastqsanger.gz | |||
| SRR11476065_2.fastq.gz | Fastqsanger.gz | |||
| SRR11476066_1.fastq.gz | Fastqsanger.gz | |||
| SRR11476066_2.fastq.gz | Fastqsanger.gz | |||
| SRR11476067_1.fastq.gz | Fastqsanger.gz |
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Project description:Predator-prey dynamics are fundamental drivers of ecosystem stability, having evolved over millions of years through complex co-evolutionary processes. Despite the critical role these dynamics play, the molecular mechanisms underpinning such interactions, particularly the communication and defense strategies between predator and prey, remain largely elusive. Nematode-trapping fungi (NTFs), including Arthrobotrys oligospora, have evolved specialized trapping structures to capture nematodes, yet how these fungi engage in molecular crosstalk with their prey has been insufficiently explored.Here, we demonstrate that A. oligospora releases extracellular vesicles (EVs) containing odorants, such as phenylethyl alcohol, which function as olfactory cues to attract nematodes. Additionally, we show that fungal microRNAs (miRNAs), specifically Ao-miR263 and Ao-miR384, are encapsulated within these EVs and delivered into the nematode hosts. Once internalized, these miRNAs target key regulatory genes involved in nematode physiology, thereby enhancing fungal predation efficiency. In a sophisticated counter-defensive maneuver, nematodes respond by releasing their own EVs containing miRNA let-7, which is capable of suppressing fungal virulence-related genes, neutralizing the predatory advantage. Our findings uncover a previously unknown dimension of predator-prey dynamics, wherein extracellular vesicles act as vehicles for molecular warfare, mediating a tit-for-tat exchange of miRNAs between fungi and nematodes. This study not only broadens our understanding of the molecular underpinnings of these interactions but also sheds light on the broader ecological implications of EV-mediated communication in predator-prey systems.
2026-10-01 | GSE280052 | GEO
Project description:Bdellovibrio bacteriovorus is a Gram-negative bacterium that is a pathogen of other Gram-negative bacteria, including many bacteria which are pathogens of humans, animals and plants. As such Bdellovibrio has potential as a biocontrol agent, or living antibiotic. B. bacteriovorus HD100 has a large genome and it is not yet known which of it encodes the molecular machinery and genetic control of predatory processes. We have tried to fill this knowledge-gap using mixtures of predator and prey mRNAs to monitor changes in Bdellovibrio gene expression at a timepoint of early-stage prey infection and prey killing in comparison to control cultures of predator and prey alone and also in comparison to Bdellovibrio growing axenically (in a prey-or host independent “HI” manner) on artificial media containing peptone and tryptone. From this we have highlighted genes of the early predatosome with predicted roles in prey killing and digestion and have gained insights into possible regulatory mechanisms as Bdellovibrio enter and establish within the prey bdelloplast. Approximately seven percent of all Bdellovibrio genes were significantly up-regulated at 30 minutes of infection- but not in HI growth- implicating the role of these genes in prey digestion. Five percent were down-regulated significantly, implicating their role in free-swimming, attack-phase physiology. This study gives the first post- genomic insight into the predatory process and reveals some of the important genes that Bdellovibrio expresses inside the prey bacterium during the initial attack. Keywords: Transcriptional analysis
2009-12-09 | GSE9269 | GEO
Project description:Bdellovibrio bacteriovorus is a Gram-negative bacterium that is a pathogen of other Gram-negative bacteria, including many bacteria which are pathogens of humans, animals and plants. As such Bdellovibrio has potential as a biocontrol agent, or living antibiotic. B. bacteriovorus HD100 has a large genome and it is not yet known which of it encodes the molecular machinery and genetic control of predatory processes. We have tried to fill this knowledge-gap using mixtures of predator and prey mRNAs to monitor changes in Bdellovibrio gene expression at a timepoint of early-stage prey infection and prey killing in comparison to control cultures of predator and prey alone and also in comparison to Bdellovibrio growing axenically (in a prey-or host independent âHIâ manner) on artificial media containing peptone and tryptone. From this we have highlighted genes of the early predatosome with predicted roles in prey killing and digestion and have gained insights into possible regulatory mechanisms as Bdellovibrio enter and establish within the prey bdelloplast. Approximately seven percent of all Bdellovibrio genes were significantly up-regulated at 30 minutes of infection- but not in HI growth- implicating the role of these genes in prey digestion. Five percent were down-regulated significantly, implicating their role in free-swimming, attack-phase physiology. This study gives the first post- genomic insight into the predatory process and reveals some of the important genes that Bdellovibrio expresses inside the prey bacterium during the initial attack. Keywords: Transcriptional analysis 3 replicates of attack phase cells and 3 replicates of 30 minutes post-infection cells were analysed on individual arrays. Replicate 3 was normalized separately.
2010-05-18 | E-GEOD-9269 | biostudies-arrayexpress
Project description:Indole is an intercellular and interkingdom signaling molecule, which is widespread in diverse ecological niches. Caenorhabditis elegans is a bacterivorous nematode living in soil and compost environments and a useful model host for the study of host-microbe interactions. While various bacteria and some plants produce a large quantity of extracellular indole, little is known about the effects of indole, its derivatives, and indole-producing bacteria on behaviors in C. elegans and animals. Here, we show that C. elegans senses and moves toward indole and indole-producing bacteria, such as Escherichia coli, Shigella boydii, Providencia stuartii, and Klebsiella oxytoca, while avoids non-indole producing pathogenic bacteria. It was also found that indole-producing bacteria and non-indole-producing bacteria exert divergent effects on egg-laying behavior of C. elegans via indole. In addition, various indole derivatives also modulate chemotaxis, egg-laying behavior, and survival of C. elegans. In contrast, indole at a high concentration to kill C. elegans that has the ability to detoxify indole via oxidation and glucosylation, indicating predator-prey interactions via a double-edged molecule indole. Transcriptional analysis showed that indole markedly up-regulated gene expression of cytochrome P450 family, UDP-glucuronosyltransferase, glutathione S-transferase, which explained well the modification of indole in C. elegans, while down-regulated expression of collagen genes and F-box genes. Our findings suggest that indole and its derivatives are important interkingdom signaling molecules in bacteria-nematode interactions.
2019-08-31 | GSE86312 | GEO
Project description:Predatory bacterium Bdellovibrio bacteriovorus is ubiquitous and has a broad bacterial prey range including many antimicrobial resistant pathogens. However, it is currently unclear whether prey bacteria can evolve genetically-determined resistance against predation by B. bacteriovorus. In this project we found that the model bacterium Escherichia coli K-12 MG1655 consistently evolves resistance against B. bacteriovorus HD100 during experimental evolution. From one E. coli K-12 MG1655 ancestor eight different E. coli prey cultures were evolved each under no, low and high predatory pressure by B. bacteriovorus (for 15 evolution cycles). The ancestor (AN) as well as the eight E. coli prey lineages that evolved under high predatory pressure (H1-H8) were analysed by shot-gun proteomics. This proteomics data revealed a strong downregulation of OmpF and other structures on the prey surface. This study showed on the proteomic level what can cause resistance to predation. This will contribute to understand this ecologically important predator-prey interactions in more detail, and can advance the development of predatory bacteria as ‘living antibiotics’ to combat pathogenic bacteria.
2026-09-20 | PXD080500 | Pride
Project description:Long-term predator-prey coevolution effect on prey
| PRJEB85532 | ENA
Project description:Predator-prey interactions between bacteria and the nematode Caenorhabditis elegans via interkingdom signaling molecule indole
| PRJNA341683 | ENA
Project description:This is the reduced model described in the article:
A synthetic Escherichia coli predator–prey ecosystem
Balagaddé FK, Song H, Ozaki J, Collins CH, Barnet M, Arnold FH, Quake SR, You L.Mol Syst Biol. 2008;4:187. Epub 2008 Apr 15. PMID: 18414488; DOI:10.1038/msb.2008.24
Abstract:
We have constructed a synthetic ecosystem consisting of two Escherichia coli populations, which communicate bi-directionally through quorum sensing and regulate each other's gene expression and survival via engineered gene circuits. Our synthetic ecosystem resembles canonical predator–prey systems in terms of logic and dynamics. The predator cells kill the prey by inducing expression of a killer protein in the prey, while the prey rescue the predators by eliciting expression of an antidote protein in the predator. Extinction, coexistence and oscillatory dynamics of the predator and prey populations are possible depending on the operating conditions as experimentally validated by long-term culturing of the system in microchemostats. A simple mathematical model is developed to capture these system dynamics. Coherent interplay between experiments and mathematical analysis enables exploration of the dynamics of interacting populations in a predictable manner.
In the article the cell density is given in per 103 cells per microlitre. To evade a conversion factor in the SBML implementation, the unit for the cell densities was just left the same as for the AHLs A and A2 (nM).
This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2012 The BioModels.net Team.
For more information see the terms of use.
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
2024-09-02 | BIOMD0000000296 | BioModels