Brachybacterium paraconglomeratum LC44
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA70629 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Antibiotic resistance genes expressed in the upper respiratory tract of patients infected with influenza viruses were associated with the microbial community and microbial activities. Interactions between the host systemic responses to influenza infection and ARG expression highlight the importance of antibiotic resistance in viral-bacterial co-infection.
2020-03-19 | GSE126901 | GEO
Project description:Antibiotic resistance genes expressed in the upper respiratory tract of patients infected with influenza viruses were associated with the microbial community and microbial activities. Interactions between the host systemic responses to influenza infection and ARG expression highlight the importance of antibiotic resistance in viral-bacterial co-infection.
2020-03-19 | GSE126900 | GEO
Project description:Antibiotic resistance genes expressed in the upper respiratory tract of patients infected with influenza viruses were associated with the microbial community and microbial activities. Interactions between the host systemic responses to influenza infection and ARG expression highlight the importance of antibiotic resistance in viral-bacterial co-infection.
2020-03-19 | GSE114588 | GEO
Project description:<p>The study of antimicrobial resistance (AMR) in infectious diarrhea has generally been limited to cultivation, antimicrobial susceptibility testing and targeted PCR assays. When individual strains of significance are identified, whole genome shotgun (WGS) sequencing of important clones and clades is performed. Genes that encode resistance to antibiotics have been detected in environmental, insect, human and animal metagenomes and are known as "resistomes". While metagenomic datasets have been mined to characterize the healthy human gut resistome in the Human Microbiome Project and MetaHIT and in a Yanomani Amerindian cohort, directed metagenomic sequencing has not been used to examine the epidemiology of AMR. Especially in developing countries where sanitation is poor, diarrhea and enteric pathogens likely serve to disseminate antibiotic resistance elements of clinical significance. Unregulated use of antibiotics further exacerbates the problem by selection for acquisition of resistance. This is exemplified by recent reports of multiple antibiotic resistance in Shigella strains in India, in Escherichia coli in India and Pakistan, and in nontyphoidal Salmonella (NTS) in South-East Asia. We propose to use deep metagenomic sequencing and genome level assembly to study the epidemiology of AMR in stools of children suffering from diarrhea. Here the epidemiology component will be surveillance and analysis of the microbial composition (to the bacterial species/strain level where possible) and its constituent antimicrobial resistance genetic elements (such as plasmids, integrons, transposons and other mobile genetic elements, or MGEs) in samples from a cohort where diarrhea is prevalent and antibiotic exposure is endemic. The goal will be to assess whether consortia of specific mobile antimicrobial resistance elements associate with species/strains and whether their presence is enhanced or amplified in diarrheal microbiomes and in the presence of antibiotic exposure. This work could potentially identify clonal complexes of organisms and MGEs with enhanced resistance and the potential to transfer this resistance to other enteric pathogens.</p> <p>We have performed WGS, metagenomic assembly and gene/protein mapping to examine and characterize the types of AMR genes and transfer elements (transposons, integrons, bacteriophage, plasmids) and their distribution in bacterial species and strains assembled from DNA isolated from diarrheal and non-diarrheal stools. The samples were acquired from a cohort of pediatric patients and controls from Colombia, South America where antibiotic use is prevalent. As a control, the distribution and abundance of AMR genes can be compared to published studies where resistome gene lists from healthy cohort sequences were compiled. Our approach is more epidemiologic in nature, as we plan to identify and catalogue antimicrobial elements on MGEs capable of spread through a local population and further we will, where possible, link mobile antimicrobial resistance elements with specific strains within the population.</p>
| phs001260 | dbGaP
Project description:In this pioneering study, we present the first comprehensive catalog of 683 small non-coding miRNAs for Astyanax mexicanus. Focusing on an early developmental stage, miRNAs were extracted and sequenced from 24hpf embryos of surface fish and three distinct cavefish morphs (Pachón, Tinaja, and Molino). We utilized in silico analyses to predict putative 3’UTR targets of these miRNAs, revealing a unique and extensive miRNA landscape in cavefish. Small RNA sequencing identified over 100 differentially expressed miRNAs in each cave morph compared to surface fish at 24hpf, suggesting early activation of miRNA-mediated silencing pathways. Notably, a subset of miRNAs was common across all three cave morphs, constituting cave-specific miRNAs potentially instrumental in cave adaptation. To unravel the functional implications of these cave-specific miRNAs, we analyzed their predicted target genes. Gene Ontology (GO) term analysis unveiled pathways which align with known adaptations in cavefish, primarily affecting development and metabolism. Further, cross-validating with a sample mRNAseq data from Pachón and surface fish also strongly suggested impact of these miRNAs on cave adaptation associated pathways. This study establishes a foundation for exploring miRNA-mediated gene regulation in cavefish, shedding light on their potential role in regulating early developmental and metabolic adaptations crucial for troglomorphic features. The comprehensive miRNA catalog provided will also guide future investigations into the intricate world of miRNA-mediated evolution in cave-adapted species.
2025-01-03 | GSE254598 | GEO
Project description:Bacteria are recognized for their diverse metabolic capabilities, yet the impact of microbe-microbe interactions on multispecies community structure and dynamics is poorly understood. Cell-to-cell signaling in the form of quorum sensing (QS) often regulates secondary metabolite production and microbial interactions. Here we examine how acylhomoserine lactone (AHL) mediated QS impacts microbial community structure in a 10-member synthetic community of isolates from Populus deltoides. To explore the role of QS in microbial community structure and dynamics, we disrupted AHL signaling using purified AiiA-lactonase, an enzyme that cleaves the lactone ring. Microbial community structure resulting from signal inactivation, as measured by 16S amplicon sequencing and secondary metabolite production, was assessed after successive passaging of the community. Further, we investigated the impact of quorum quenching on microbe-microbe interactions using pairwise inhibition assays. Our results indicate that AHL inactivation alters the relative abundance of dominant community members at later passages but does not impact the overall membership in the community. Quorum quenching significantly alters the metabolic profile in AiiA-lactonase treated communities. This metabolic alteration impacts microbe-microbe interactions through decreased inhibition of other community members. Together, these results indicate that QS impacts microbial community structure through the regulation of secondary metabolites in dominant members and that membership of microbial communities can be relatively stable despite changes in metabolic profiles
2024-11-08 | MSV000096353 | MassIVE
Project description:Isolated from poultry deep litter
| PRJNA17026 | ENA
Project description:Organisms adapt to and survive in environments with varying nutrient availability. Cis-regulatory changes play important roles in adaptation and phenotypic evolution. To what extent cis-regulatory elements contribute to metabolic adaptation is less understood. Here we have utilized a unique vertebrate model, Astyanax mexicanus, that survives in nutrient rich surface and nutrient deprived cave water to uncover gene regulatory networks in metabolic adaptation. We performed genome-wide analysis of accessible chromatin and histone modifications in the liver tissue of one surface and two independently derived cave populations, providing the first genome-wide epigenetic landscape in this organism. We find that many cis-regulatory elements differ between surface and the cavefish, while the two independently derived cave populations have evolved remarkably similar regulatory signatures. Changes in gene regulatory networks between the surface and cave morphotypes point to global changes in key metabolic pathways.
2021-09-07 | GSE153049 | GEO
Project description:Organisms adapt to and survive in environments with varying nutrient availability. Cis-regulatory changes play important roles in adaptation and phenotypic evolution. To what extent cis-regulatory elements contribute to metabolic adaptation is less understood. Here we have utilized a unique vertebrate model, Astyanax mexicanus, that survives in nutrient rich surface and nutrient deprived cave water to uncover gene regulatory networks in metabolic adaptation. We performed genome-wide analysis of accessible chromatin and histone modifications in the liver tissue of one surface and two independently derived cave populations, providing the first genome-wide epigenetic landscape in this organism. We find that many cis-regulatory elements differ between surface and the cavefish, while the two independently derived cave populations have evolved remarkably similar regulatory signatures. Changes in gene regulatory networks between the surface and cave morphotypes point to global changes in key metabolic pathways.
2021-09-07 | GSE153048 | GEO
Project description:Microbe-microbe interactions are critical for gut microbiome function. A challenging task to understand health and disease-related microbiome signatures is to move beyond descriptive community-level profiling towards disentangling microbial interaction networks. Here, we aimed to determine members taking on a keystone role in shaping the community ecology of a widely used synthetic bacterial community (OMM12).
2022-11-14 | MSV000090704 | MassIVE