Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Sponge plasmidome

ABSTRACT: Selectively enrich and characterize plasmids from bacterial isolates and sponge host microbial communities

PROVIDER: PRJNA593396 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other
	SRR11066759_1.fastq.gz	Fastqsanger.gz
	SRR11066759_2.fastq.gz	Fastqsanger.gz
	SRR11066760_1.fastq.gz	Fastqsanger.gz
	SRR11066760_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 17

Similar Datasets

sponge metagenome

Project description:Sponge symbiotic bacterial communities Metagenome

| PRJNA194455 | ENA

sponge metagenome

Project description:Sponge symbiotic bacterial communities Metagenome

| PRJNA297254 | ENA

Sponge-derived Commensal Bacteria MassIVE submission

Project description:This dataset contains several sponge-derived bacteria, along with data from the sponges to enable the assignation of the biosynthetic source of detected metabolite features. Media controls and solvent blanks are also included. Please see metadata for the bacterial source sponge.

2022-10-28 | MSV000090609 | MassIVE

Complete metabolic reconstruction of the microbiome of the model sponge Ianthella basta

Project description:Marine sponges are essential for coral reefs to thrive and harbour a diverse microbiome that is thought to contribute to host health. Although the overall function of sponge symbionts has been increasingly described, in-depth characterisation of each taxa remains challenging, with many sponge species hosting up to 3,000 distinct microbial species. Recently, the sponge Ianthella basta has emerged as a model organism for symbiosis research, hosting only three dominant symbionts: a Thaumarchaeotum, a Gammaproteobacterium, and an Alphaproteobacterium and a range of other minor taxa. Here, we retrieved metagenome assembled genomes (MAGs) for >90% of I. basta’s microbial community which allowed us to make a complete metabolic reconstruction of the sponge’s microbiome, identifying metabolic complementarity between microbes, as well as the importance of symbionts present in low abundance. We also mined the metagenomes for putative viral sequences, highlighting the contribution of viruses to the overall metabolism of the sponge, and complement this data with metaproteomic sequencing to identify active metabolic pathways in both prokaryotes and viruses. This data now allows us to use I. basta as a model organism for studying host-microbe interactions and provides a basis for future (genomic) manipulative experiments.

2023-02-24 | PXD032278 | Pride

Characterization of plasmids mediating carbapenem resistance in Klebsiella pneumoniae in Pretoria, South Africa

Project description:The study aimed to characterize plasmids mediating carbepenem resistance in Klebsiella pneumoniae in Pretoria, South Africa. We analysed 56 K. pneumoniae isolates collected from academic hospital around Pretoria. Based on phenotypic and molecular results of these isolates, 6 representative isolates were chosen for further analysis using long reads sequencing platform. We observed multidrug resistant phenotype in all these isolates, including resistance to aminoglycosides, tetracycline, phenicol, fosfomycin, floroquinolones, and beta-lactams antibiotics. The blaOXA-48/181 and blaNDM-1/7 were manily the plasmid-mediated carbapenemases responsible for carbapenem resistance in the K. pneumoniae isolates in these academic hospitals. These carbapenemase genes were mainly associated with plasmid replicon groups IncF, IncL/M, IncA/C, and IncX3. This study showed plasmid-mediated carbapenemase spread of blaOXA and blaNDM genes mediated by conjugative plasmids in Pretoria hospitals.

2019-10-17 | GSE138949 | GEO

sponge metagenome

Project description:Bacterial community of sponge treated with copper Targeted Locus (Loci)

| PRJNA253082 | ENA

sponge metagenome

Project description:Host-associated microbial community of the marine sponge Aplysina aerophoba from Gulf of Piran - sponge mesohyl, lysed by bead beating metagenome

| PRJNA366444 | ENA

sponge metagenome

Project description:Host-associated microbial community of the marine sponge Aplysina aerophoba from Gulf of Piran - sponge pinacoderm, lysed by bead beating metagenome

| PRJNA366447 | ENA

Trial for Retractor Sponge Evaluation in Laparoscopic Colorectal Surgery

Project description:Laparoscopic surgery of the distal colon and rectum requires surgery with an appropriate field of view. A commonly used technique to create a clear exposure is the steep Trendelenburg position in which the patient is positioned in an angle of 15 to 40 degrees with the head down using the effect of gravity to retract the small intestine. This method is associated with haemostatic changes caused by the cranial shift of abdominal organs and blood. Recently, a cellulose compressed sponge was developed as intraoperative retractor, with the aim to keep the small intestines aside while the patient remains in a horizontal position. The safety of the sponge is secured with CE marking. The retractor sponge ensures a clear surgical field and potentially prevents haemostatic instability by avoiding Trendelenburg position. A pilot study in the St Antonius Hospital Nieuwegein has shown that use of the sponge might be associated with shorter hospital stay.

| 2258291 | ecrin-mdr-crc

sponge metagenome

Project description:Host-associated microbial community of the marine sponge Aplysina aerophoba from Gulf of Piran - sponge mesohyl, lysed by proteinase K digestion metagenome

| PRJNA366446 | ENA

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