Sponge metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA260847 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1582372.fastq.gz | Fastqsanger.gz | |||
| SRR1582373.fastq.gz | Fastqsanger.gz | |||
| SRR1582374.fastq.gz | Fastqsanger.gz | |||
| SRR1582375.fastq.gz | Fastqsanger.gz | |||
| SRR1582376.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 8 |
Similar Datasets
Project description:Coral reef sponge microbiome Targeted Locus (Loci)
| PRJNA253216 | ENA
Project description:Sponges are efficient filter feeders, removing significant portions of particulate and dissolved organic matter (POM, DOM) from the water column. While the assimilation and respiration of POM and DOM by sponges and their abundant microbial symbiont communities have received much attention, there is virtually no information on the impact of sponge holobiont metabolism on the composition of DOM at a molecular-level. We applied untargeted and targeted metabolomics techniques to characterize DOM in seawater samples prior to entering the sponge (inhalant reef water), in samples exiting the sponge (exhalent seawater), and in samples collected just outside the reef area (off reef seawater). Samples were collected from two sponge species, Ircinia campana and Spheciospongia vesparium, on a near-shore hard bottom reef in the Florida Keys. Metabolic profiles generated from untargeted metabolomics analysis indicated that many more compounds were enhanced in the exhalent samples than in the inhalant samples. Targeted metabolomics analysis revealed differences in diversity and concentration of metabolites between exhalent and off reef seawater. For example, most of the nucleosides were enriched in the exhalent seawater, while the aromatic amino acids, caffeine and the nucleoside xanthosine were elevated in the off reef water samples. Although the metabolic profile of the exhalent seawater was unique, the impact of sponge metabolism on the overall reef DOM profile was spatially limited in our study. There were also no significant differences in the metabolic profiles of exhalent water between the two sponge species, potentially indicating that there is a characteristic DOM profile in the exhalent seawater of Caribbean sponges. Additional work is needed to determine whether the impact of sponge DOM is greater in habitats with higher sponge cover and diversity. This work provides the first insight into the molecular-level impact of sponge holobiont metabolism on reef DOM and establishes a foundation for future experimental studies addressing the influence of sponge-derived DOM on chemical and ecological processes in coral reef ecosystems.
2016-02-01 | MTBLS281 | MetaboLights
Project description:Twelve inshore and six offshore colonies were reciprocally transplanted during 1 year (July 2017- July 2018) at Florida Keys (location). After this period samples were collected from the field and brought to the Experimental Reef Laboratory facilities (RSMAS, Miami) to be acclimated to 30C during 7 days in six aquaria. Three aquaria were keep under initial conditions for the duration of the experiment (30C) and three aquaria had the temperature increased everyday during 7 days to a final temperature of 32C. A total of 56 samples were collected for RNAseq after 6 days of the temperature treatment and stored at -80C.
2024-05-01 | GSE233773 | GEO
Project description:Marine sponge-associated bacteria are known as bio-active compound produce. We have constructed metagenome libraries of the bacteria and developed a metagenomic screening approach. Activity-based screening successfully identified novel genes and novel enzymes; however, the efficiency was only in 1 out of 104 clones. Therefore, in this study, we thought that bioinformatics could help to reduce screening efforts, and combined activity-based screening with database search. Neutrophils play an important role for the immune system to recognize excreted bacterial by-products as chemotactic factors and are recruited to infection sites to kill pathogens via phagocytosis. These excreted by-products are considered critical triggers that engage the immune system to mount a defense against infection, and identifying these factors may guide developments in medicine and diagnostics. We focused on genes encoding amino acid ligase and peptide synthetase and selected from an in-house sponge metagenome database. Cell-free culture medium of each was used in a neutrophil chemiluminescence assay in luminol reaction. The clone showing maximum activity had a genomic sequence expected to produce a molecule like a phospho-N-acetylmuramyl pentapeptide by the metagenome fragment analysis.
| S-EPMC8402132 | biostudies-literature
Project description:Survey of microbial diversity from coral reef habitat in Goa and Malvan using 16S rRNA amplicon sequencing
| PRJNA594178 | ENA
Project description:Microbial survey of coral reef seawater microbial communities from Cuba and the Florida Keys
| PRJNA517146 | ENA
Project description:We report data associated with the identification of three polyhydroxyalkanoate synthase genes (phaC) isolated from the marine bacteria metagenome of Aaptos aaptos marine sponge in the waters of Bidong Island, Terengganu, Malaysia. Our data describe the extraction of bacterial metagenome from sponge tissue, measurement of purity and concentration of extracted metagenome, polymerase chain reaction (PCR)-mediated amplification using degenerate primers targeting Class I and II phaC genes, sequencing at First BASE Laboratories Sdn Bhd, and phylogenetic analysis of identified and known phaC genes. The partial nucleotide sequences were aligned, refined, compared with the Basic Local Alignment Search Tool (BLAST) databases, and released online in GenBank. The data include the identified partial putative phaC and their GenBank accession numbers, which are Rhodocista sp. phaC (MF457754), Pseudomonas sp. phaC (MF437016), and an uncultured bacterium AR5-9d_16 phaC (MF457753).
| S-EPMC5694960 | biostudies-literature
Project description:Three indole derivatives, a novel benzoxazine-indole hybrid (1) and two known indole trimers (2, 3), were isolated from the metagenomic library of the marine sponge Discodermia calyx based on functional screening. Their structures were elucidated by extensive spectroscopic analysis and comparison of their NMR data to that of known compounds. The antibacterial assay indicated that only compound 2 displayed significant antibacterial activity against Bacillus cereus, with approximately 20 mm diameter growth inhibition at 10 µg/paper. HPLC analyses revealed that compound 2 is a newly induced metabolite, and the concentration of 3 was obviously enhanced in contrast to negative control, while 1 was not detected, allowing us to predict that the formation of 2 might be induced by exogenous genes derived from the sponge metagenome, whereas compound 1 could be formed through a non-enzymatic process during the isolation procedure.
| S-EPMC6154727 | biostudies-literature