Metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA17779 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We developed a method that allows measuring the stable carbon isotope composition of individual species in microbial communities using metaproteomics. We call this methods “Direct Protein-SIF”. We validated and tested the method extensively using pure cultures (PXD006762) and mock communities (PXD006118, https://www.ebi.ac.uk/pride/archive/projects/PXD006118). As a case study we applied Direct Protein-SIF to the Olavius algarvensis symbiosis. Olavius algarvensis is a marine worm that lives in shallow-water sediments off the coast of Elba, Italy. The worm has no digestive and excretory system, instead it harbors five bacterial symbionts that fulfill its nutritional and waste recycling needs (http://www.pnas.org/content/109/19/E1173.short). For this project we generated metaproteomes of 14 O. algarvensis individuals. A total of 18 LC-MS/MS runs were generated. For Direct Protein-SIF the data from all runs was combined. In this submission we are including the Direct Protein-SIF specific isotope pattern file as well as the .mzML files and PSM file required as input for the Direct Protein-SIF software (Calis-p). In addition to the Olavius algarvensis samples a protein reference material (MKH files) was measured. The respective .raw files and isotopic pattern files are available through project PXD006762 (see publication for details on how the reference material is used to calibrate the method).
2018-05-21 | PXD007510 | Pride
Project description:Worm MetaG Olavius vacuus BAHAMAS.1 metagenome
| PRJNA410297 | ENA
Project description:When studying gene expression in microbe-animals symbioses collected in the field it is essential to quickly and efficiently preserve in situ symbiont and host gene expression patterns. One of the most commonly used sample preservation methods for samples targeted for proteomic analyses is flash freezing, however, liquid nitrogen or dry ice needed for flash freezing are often not available at remote field sites. We tested if RNAlater allows to preserve proteins in animal-microbe symbioses as efficiently as flash freezing and without introducing issues with downstream processing. We used the marine gutless oligochaete Olavius algarvensis as a model for testing. Olavius algarvensis lives in shallow water sediments off the coast of Elba, Italy. It has no digestive and excretory system and harbors five bacterial symbionts that fulfill its nutritional and waste recycling needs (Kleiner et al., 2012, PNAS 109(19):1173-82). We compared five RNAlater preserved and five flash frozen samples in terms of the number of identified proteins, abundances of individual proteins and potential biases against specific protein or taxonomic groups. Five worms were incubated in RNAlater for 24 hours. After incubation, RNAlater was removed and samples were stored at -80°C. The remaining five worms were preserved with liquid nitrogen and stored at -80 °C immediately after preservation.
2021-11-03 | PXD014591 | Pride
Project description:When studying gene expression in microbe-animals symbioses collected in the field it is essential to quickly and efficiently preserve in situ symbiont and host protein abundance patterns. One of the most commonly used sample preservation methods for samples targeted for proteomic analyses is flash freezing, however, liquid nitrogen or dry ice needed for flash freezing are often not available at remote field sites. We replicated our experiment from PXD014591 to test if RNAlater allows preserving proteins in animal-microbe symbioses as efficiently as flash freezing and without introducing issues with downstream processing. We used the marine gutless oligochaete Olavius algarvensis as a model for testing. Olavius algarvensis lives in shallow water sediments off the coast of Elba, Italy. It has no digestive and excretory system and harbors five bacterial symbionts that fulfill its nutritional and waste recycling needs (Kleiner et al., 2012, PNAS 109(19):1173-82). We compared six RNAlater preserved and eight flash frozen samples in terms of the number of identified proteins, abundances of individual proteins and potential biases against specific protein or taxonomic groups. Six worms were incubated in RNAlater for 24 hours. After incubation, RNAlater was removed and samples were stored at -80°C. Eight worms were directly flash frozen in liquid nitrogen and stored at -80 °C immediately after preservation.
2021-11-03 | PXD026631 | Pride
Project description:Bacterial symbionts of the pinewood nematode Metagenome
| PRJNA78843 | ENA
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
Project description:high throughput sequencing of the metagenome of mexican children
2020-03-16 | GSE143207 | GEO
Project description:Phylogenetic linkage between host and symbionts in the marine gutless annelid Olavius algarvensis
| PRJEB42310 | ENA
Project description:The goal of this study was to use heterologous microarray hybridization to determine genomic content shared among different vesicomyid symbionts. These symbionts are closely related and can be thought of as different strains of bacteria, facilitating the use of heterologous microarray hybridization to determine genomic content. Keywords: comparative genomic hybridization Microarrays were built off the Ruthia magnifica genome and two replicate hybridizations to this organism were used as a baseline for comparisons. Genomic DNA from two other vesicomyid symbionts (Calyptogena kilmeri and C. pacifica symbionts) was also hybridized to the array with three biological replicates for each sample.
2010-05-15 | E-GEOD-13447 | biostudies-arrayexpress
Project description:The goal of this study was to use heterologous microarray hybridization to determine genomic content shared among different vesicomyid symbionts. These symbionts are closely related and can be thought of as different strains of bacteria, facilitating the use of heterologous microarray hybridization to determine genomic content. Keywords: comparative genomic hybridization
2008-11-28 | GSE13447 | GEO