Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Microbiome remodeling through bacterial competition and host behavior enables rapid adaptation to environmental toxins

ABSTRACT: Microbiome remodeling through bacterial competition and host behavior enables rapid adaptation to environmental toxins

PROVIDER: PRJNA1036219 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR26682944_1.fastq.gz	Fastqsanger.gz
	SRR26682944_2.fastq.gz	Fastqsanger.gz
	SRR26682945_1.fastq.gz	Fastqsanger.gz
	SRR26682945_2.fastq.gz	Fastqsanger.gz
	SRR26682946_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 24

Similar Datasets

Microbiome remodeling through bacterial competition and host behavior enables rapid adaptation to environmental toxins

Project description:Human activity is altering the environment at a rapid pace, challenging the adaptive capacities of genetic variation within animal populations. Animals also harbor extensive gut microbiomes, which play diverse roles in host health and fitness and may help expanding host capabilities. The unprecedented scale of human usage of xenobiotics and contamination with environmental toxins describes one challenge against which bacteria with their immense biochemical diversity are particularly suited to offer solutions. To explore the paths leading to bacteria-assisted rapid adaptation, we used Caenorhabditis elegans harboring a defined microbiome, and the antibiotic neomycin as a model toxin, harmful for the worm host and neutralized to different extents by microbiome members. Worms exposed to neomycin showed delayed development and decreased survival but were protected when colonized by neomycin-resistant members of the microbiome. Through a combination of 16S gene sequencing, counting of live bacteria and behavioral assays we identified two distinct mechanisms that facilitated adaptation: gut enrichment for a neomycin-modifying strain driven by altered bacterial competition; and host avoidance behavior, which depended on the stress-activated KGB-1/JNK and enabled preference of neomycin-protective bacteria. The straightforwardness of these mechanisms suggests that bacteria-assisted host adaptation may be more common than currently appreciated, protecting animals from novel stressors. However, gut remodeling may also cause dysbiosis, and additional experiments identified fitness trade-offs including increased susceptibility to infection as well as metabolic remodeling. Extending these results to other toxins suggests yet unaccounted-for microbiome-dependent long-term consequences of toxin exposure.

2023-11-09 | GSE246966 | GEO

Microbiome remodeling through bacterial competition and host behavior enables rapid adaptation to environmental toxins.

Project description:Human activity is altering the environment in a rapid pace, challenging the adaptive capacities of genetic variation within animal populations. Animals also harbor extensive gut microbiomes, which play diverse roles in host health and fitness and may help expanding host capabilities. The unprecedented scale of human usage of xenobiotics and contamination with environmental toxins describes one challenge against which bacteria with their immense biochemical diversity would be useful, by increasing detoxification capacities. To explore the potential of bacteria-assisted rapid adaptation, we used Caenorhabditis elegans worms harboring a defined microbiome, and neomycin as a model toxin, harmful for the worm host and neutralized to different extents by some microbiome members. Worms raised in the presence of neomycin showed delayed development and decreased survival but were protected when colonized by neomycin-resistant members of the microbiome. Two distinct mechanisms facilitated this protection: gut enrichment driven by altered bacterial competition for the strain best capable of modifying neomycin; and host avoidance behavior, which depended on the conserved JNK homolog KGB-1, enabling preference and acquisition of neomycin-protective bacteria. We further tested the consequences of adaptation, considering that enrichment for protective strains may represent dysbiosis. We found that neomycin-adapted gut microbiomes caused increased susceptibility to infection as well as an increase in gut lipid storage, suggesting metabolic remodeling. Our proof-of-concept experiments support the feasibility of bacteria-assisted host adaptation and suggest that it may be prevalent. The results also highlight trade-offs between toxin adaptation and other traits of fitness.

| S-EPMC10462140 | biostudies-literature

Stenotrophomonas rhizophila strain:BIGb262

Project description:Microbiome remodeling through bacterial competition and host behavior enables rapid adaptation to environmental toxins

| PRJNA986126 | ENA

Prenatal exposure to environmental toxins induces sexually dimorphic transcriptome changes in neonatal offspring

Project description:Purpose: Gestational exposure to environmental toxins and socioeconomic stressors are epidemiologically linked to neurodevelopmental disorders with strong male-bias, such as autism. We modeled these prenatal risk factors in mice, by co-exposing pregnant dams to an environmental pollutant and limited-resource stress, which robustly activated the maternal immune system. Only male offspring displayed long-lasting behavioral abnormalities and alterations in the activity of brain networks encoding social interactions. Cellularly, prenatal stressors diminished microglial function within the anterior cingulate cortex, a central node of the social coding network, in males during early postnatal development. Genetic ablation of microglia during the same critical period mimicked the impact of prenatal stressors on a male-specific behavior, indicating that environmental stressors alter neural circuit formation in males via impairing microglia function during development.

2020-10-29 | GSE160344 | GEO

Comparative chemical-genomic profiling of plant-based hydrolysate toxins enables predictive assessment of responses to complex mixtures

Project description:Many toxins and stressors found in hydrolysates inhibit microbial metabolism and product formation, requiring mitigation strategies including strain engineering. To identify mechanisms of toxicity and targets for genetic engineering, we used a chemical genomics approach with a library of S. cerevisiae deletion mutants cultured anaerobically in dozens of individual compounds found in different types of hydrolysates, to explore shared and divergent gene requirements across inhibitors. Relationships in chemical-genomic profiles identified classes of toxins that provoked similar cellular responses, spanning inhibitor relationships that were not expected from chemical classification. Our results also revealed widespread antagonistic effects across inhibitors, such that the same gene deletions are beneficial for surviving some toxins but detrimental for others. As a proof of principle, we used the gene-deletion responses to single inhibitors to successfully predict strains whose fitness was improved in complex inhibitor mixes found in synthetic hydrolysates. We discuss the implications for strain engineering and the potential of this rich dataset for identifying engineering targets.

2021-11-01 | GSE186866 | GEO

Marine toxins spectral database for dereplication purpose

Project description:We present an open access marine toxins spectral database for dereplication purpose using the new tool GNPS MASST.This interface enables you to search a single MS/MS spectrum against public GNPS spectral libraries including MetaboLights and all public MS/MS datasets.The database will be incremented with toxins MS/MS data throughout the project Alertox-Net (https://www.alertox-net.eu/).

2020-01-14 | MTBLS599 | MetaboLights

Expression of E. coli RNase toxins

Project description:The purpose of this experiment was to identify cleavage sites of E. coli RNase toxins within the E. coli genome.

2020-06-11 | GSE144029 | GEO

Comparative chemical-genomic profiling of plant-based hydrolysate toxins enables predictive assessment of responses to complex mixtures

Project description:Comparative chemical-genomic profiling of plant-based hydrolysate toxins enables predictive assessment of responses to complex mixtures

| PRJNA776529 | ENA

Clostridioides difficile toxins deregulate tight junction proteins.

Project description:The Clostridioides difficile toxins TcdA and TcdB are responsible for diarrhea and colitis. The aim of this project was to explore the effects of the toxins on epithelial barrier function and the molecular mechanisms for diarrhea and inflammation. RNA-seq of toxin-treated intestinal cell monolayers was performed to describe the C. difficile-mediated effects. mRNA profiles from intestinale epithelial cells were generated by deep sequencing using Illumina NovaSeq 6000. This data provide the basis for subsequent upstream regulator analysis.

2023-11-29 | GSE232704 | GEO

Mechanism of translation inhibition by type II GNAT toxins: AtaT, TacT, and ItaT

Project description:Type II toxin-antitoxin (TA) systems are two-gene modules widely distributed among prokaryotes. GNAT toxins associated with the DUF1778 antitoxins represent a large family of type II TAs. GNAT toxins inhibit cell growth by disrupting translation via acetylation of aminoacyl-tRNAs. Using ribosome profiling, we investigated the in vivo substrate specificity of three GNAT toxins: AtaT2, TacT3, and ItaT.

2020-06-17 | GSE148424 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data