Freshwater metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA657201 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:In this work we used metaproteomics to study the effect of pH and nitrogen source on cyanobacterial growth of the laboratory cultures. The database for protein identification was obtained from assembled metagenomes.
2021-11-02 | PXD024393 | Pride
Project description:Nitrile-treated enrichment cultures (Metagenomic assembly)
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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 work we used stable isotope probing/proteomics to study uptake of carbon sources by members of the cyanobacterial consortium. The database for protein identification was obtained from assembled metagenomes.
2022-01-21 | PXD028578 | Pride
Project description:A photosynthetic cyanobacterial/microbial consortium was incubated in the dark for 12 days. During the course of this dark incubation, samples were taken every two days from the biomass portion and the liquid (supernatant) portion of the bioreactor. Metaproteomics analysis was conducted on these time series samples and binned and assembled metagenomes from the same samples were used as the database for protein identification.
2023-11-01 | PXD023504 | Pride
Project description:Eutrophication can lead to an uncontrollable increase in algal biomass, which has repercussions for the entire microbial and pelagic community. Studies have shown how nutrient enrichment affects microbial species succession, however details regarding the impact on community functionality are rare. Here, we applied a metaproteomic approach to investigate the functional changes to algal and bacterial communities, over time, in oligotrophic and eutrophic conditions, in freshwater microcosms. Samples were taken early during algal and cyanobacterial dominance and later under bacterial dominance. 1048 proteins, from the two treatments and two timepoints, were identified and quantified by their exponentially modified protein abundance index. In oligotrophic conditions, Bacteroidetes express extracellular hydrolases and Ton-B dependent receptors to degrade and transport high molecular weight compounds captured while attached to the phycosphere. Alpha- and Beta-proteobacteria were found to capture different substrates from algal exudate (carbohydrates and amino acids, respectively) suggesting resource partitioning to avoid direct competition. In eutrophic conditions, environmental adaptation proteins from cyanobacteria suggested better resilience compared to algae in a low carbon nutrient enriched environment. This study provides insight into differences in functional microbial processes between oligo- and eutrophic conditions at different timepoints and highlights how primary producers control bacterial resources in freshwater environments.
2016-08-01 | PXD004592 | Pride
Project description:Metagenomic Sequencing Enrichment Cultures of Strep Pneumoniae
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Project description:Metaproteome of cyanobacterial crusts exposed to stratosphere. To explore changes in community structure and function. The changes in function involve overall metabolic response, interactions between species and function, and content related to life history strategies. The article mainly focuses on metagenomic and metatranscriptome data, while metaproteomic data is mainly used to assist in confirming the conclusions drawn.
2024-02-19 | PXD049715 | iProX
Project description:Water column metagenomes from two Canadian Boreal Shield lakes
| PRJNA518727 | ENA