Ontology highlight
ABSTRACT:
PROVIDER: PRJNA780079 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Understanding natural defence mechanisms against parasites can be a valuable tool for the development of innovative therapies. In this study, we investigated the interplay between the gill mucus metabolome and microbiome of Chaetodon lunulatus, a butterflyfish known to avoid gill monogeneans whilst living amongst closely related parasitized species. In an attempt to identify metabolites and OTUs potentially involved in parasite defence mechanisms, we studied the metabolome (LC-MS/MS) and microbiome of several sympatric butterflyfish species, including the only non-parasitized species C. lunulatus. After observing significant differences between the metabolome and microbiome of parasitized versus non-parasitized fish (PCoA, ANOSIM), we obtained the discriminant metabolites and OTUs using a supervised analysis. Some of the most important discriminant metabolites were identified as peptides, and three new β-subunit haemoblogin-derived peptides from C. lunulatus (CLHbβ-1, CLHbβ-2 and CLHbβ-3) were purified, characterised and synthesised. We also identified specific bacterial families and OTUs typical from low-oxygen habitats in C. lunulatus gill mucus. By using a correlation network between the two datasets, we found a Fusobacteriaceae strain exclusively present in C. lunulatus highly correlated to the peptides. Finally, we discuss the possible involvement of these peptides and Fusobacteriaceae in monogenean avoidance by this fish species.
2020-11-25 | PXD018867 | Pride
Project description:This study investigated the microbial community of rock varnish Based on consensus sequences for 16S OTUs
2013-04-26 | E-GEOD-46347 | biostudies-arrayexpress
Project description:Circadian clocks are important for gut health. This experiment aimed to determine the role of core clock gene Bmal1 in regulating microbial rhythmicity in health and dextran sulphate sodium induced colitis. Mice were generated with Bmal1 selectively deleted in Villin-expressing cells (predominantly IECs).Microbial DNA was extracted from fecal pellets collected from IEC-Bmal1-/- and Bmal1flox mice (aged 8-19 weeks) at zeitgeber time 0, 4, 8, 12, 16, 20 across the 24h day with the DNeasy PowerSoil Pro Kit (Qiagen), as per manufacturer’s instructions. Pre-amplification of the V4 region of 16S rRNA was performed using forward primer 5'-ACACTCTTTCCCTACACGACGCTCTTCCGAT-CTNNNNNGTGCCAGCMGCCGCGGTAA-3' (annealing sites in bold) and reverse primer 5'-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGGACTACHVGGGTWTCTAAT-3'. Sequencing was performed by the University of Liverpool Centre for genomics Research, using the Illumina MiSeq v2 platform (Illumina), generating 250bp paired-end reads. PhiX control v3 library (PhiX) was spiked into samples to balance low base diversity often found in microbiome samples. Quality control was performed and OTU tables were generated using a pipeline provided by the University of Manchester Bioinformatics Core Facility local Galaxy service. Briefly, VSEARCH clustered OTUs and removed chimeras. The OTU database was mapped to the SILVA (v138) reference database with >97% homology threshold. All samples passed quality checks and had sequence depth >45,000. The OTU table was analysed using R packages phyloseq, vegan, limma and ALDEx2. JTK_CYCLE 93 was used to identify rhythmic OTUs with a period of 24 h and an adjusted P value < 0.05.
2025-07-04 | E-MTAB-15306 | biostudies-arrayexpress