Ontology highlight
ABSTRACT:
PROVIDER: PRJNA623385 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Pelagic marine and freshwater protist diversity in Kimitkeot region (Cambridge Bay, Nunavut, Canada)
| PRJEB24089 | ENA
Project description:Monitoring microbial communities can aid in understanding the state of these habitats. Environmental DNA (eDNA) techniques provide efficient and comprehensive monitoring by capturing broader diversity. Besides structural profiling, eDNA methods allow the study of functional profiles, encompassing the genes within the microbial community. In this study, three methodologies were compared for functional profiling of microbial communities in estuarine and coastal sites in the Bay of Biscay. The methodologies included inference from 16S metabarcoding data using Tax4Fun, GeoChip microarrays, and shotgun metagenomics.
2024-04-14 | E-MTAB-13075 | biostudies-arrayexpress
Project description:To gain improved temporal, spatial and phylogenetic resolution of marine microbial communities, in this study we expanded the original prototype genome proxy array (an oligonucleotide microarray targeting marine microbial genome fragments and genomes), evaluated it against metagenomic sequencing, and applied it to time series samples from the Monterey Bay long term ecological research site. The expanded array targeted 268 microbial genotypes (vs. 14 in the original prototype) across much of the known diversity of cultured and uncultured marine microbes. The target abundances measured by the genome proxy array were highly correlated to pyrosequence-based abundances (linear regression R2 = 0.85-0.91, p<0.0001). Fifty-seven samples from ~4-years in Monterey Bay were examined with the array, spanning the photic zone (0m), the base of the surface mixed layer (30m), and the subphotic zone (200m). A significant portion of the expanded genome proxy array’s targets showed signal (95 out of 268 targets present in ≥ 1 sample). The multi-year community survey showed the consistent presence of a core group of common and abundant targeted taxa at each depth in Monterey Bay, higher variability among shallow than deep samples, and episodic occurrences of more transient marine genotypes. The abundance of the most dominant genotypes peaked after strong episodic upwelling events. The genome-proxy array’s ability to track populations of closely-related genotypes indicated population shifts within several abundant target taxa, with specific populations in some cases clustering by depth or oceanographic season. Although 51 cultivated organisms were targeted (representing 19% of the array) the majority of targets detected and of total target signal (85% and ~92%, respectively) were from uncultivated lineages, often those derived from Monterey Bay. The array provided cost-effective (~$15 per array, for construction and use) insights into the natural history of uncultivated lineages in the wild. To gain improved temporal, spatial and phylogenetic resolution of marine microbial communities, in this study we expanded the original prototype genome proxy array (an oligonucleotide microarray targeting marine microbial genome fragments and genomes), evaluated it against metagenomic sequencing, and applied it to time series samples from the Monterey Bay long term ecological research site. The expanded array targeted 268 microbial genotypes (vs. 14 in the original prototype) across much of the known diversity of cultured and uncultured marine microbes. The target abundances measured by the genome proxy array were highly correlated to pyrosequence-based abundances (linear regression R2 = 0.85-0.91, p<0.0001). Fifty-seven samples from ~4-years in Monterey Bay were examined with the array, spanning the photic zone (0m), the base of the surface mixed layer (30m), and the subphotic zone (200m). A significant portion of the expanded genome proxy array’s targets showed signal (95 out of 268 targets present in ≥ 1 sample). The multi-year community survey showed the consistent presence of a core group of common and abundant targeted taxa at each depth in Monterey Bay, higher variability among shallow than deep samples, and episodic occurrences of more transient marine genotypes. The abundance of the most dominant genotypes peaked after strong episodic upwelling events. The genome-proxy array’s ability to track populations of closely-related genotypes indicated population shifts within several abundant target taxa, with specific populations in some cases clustering by depth or oceanographic season. Although 51 cultivated organisms were targeted (representing 19% of the array) the majority of targets detected and of total target signal (85% and ~92%, respectively) were from uncultivated lineages, often those derived from Monterey Bay. The array provided cost-effective (~$15 per array, for construction and use) insights into the natural history of uncultivated lineages in the wild.
2010-04-24 | GSE21502 | GEO
Project description:The human colon contains an extensively diverse microbial ecosystem and one of the most numerous communities of immune cells. Studies have highlighted dynamic crosstalk between immune cells and commensals. While studies have demonstrated increasing diversity of microbiota from stomach to stool, whether and how immune cell heterogeneity and microbiota diversity change across the colon is undefined. Furthermore, whether these changes are co-depended in the healthy colon is unknown. Here, tissue samples are collected from caecum, transverse colon, sigmoid colon and mLN of cadaveric donors by the Cambridge Biorepository of Translational Medicine (CBTM). We use single cell RNA sequencing (10X genomics) to assess the dynamics of immune cell populations across the colon and in matching lymph nodes. Associated microbiome 16S sequencing data is available.
2020-01-01 | E-MTAB-8474 | biostudies-arrayexpress
Project description:The human colon contains an extensively diverse microbial ecosystem and one of the most numerous communities of immune cells. Studies have highlighted dynamic crosstalk between immune cells and commensals. While studies have demonstrated increasing diversity of microbiota from stomach to stool, whether and how immune cell heterogeneity and microbiota diversity change across the colon is undefined. Furthermore, whether these changes are co-depended in the healthy colon is unknown. Here, tissue samples are collected from caecum, transverse colon, sigmoid colon and mLN of cadaveric donors by the Cambridge Biorepository of Translational Medicine (CBTM). We use single cell RNA sequencing (10X genomics) to assess the dynamics of immune cell populations across the colon and in matching lymph nodes. Associated microbiome 16S sequencing data is available.
2020-01-01 | E-MTAB-8007 | biostudies-arrayexpress
Project description:The human colon contains an extensively diverse microbial ecosystem and one of the most numerous communities of immune cells. Studies have highlighted dynamic crosstalk between immune cells and commensals. While studies have demonstrated increasing diversity of microbiota from stomach to stool, whether and how immune cell heterogeneity and microbiota diversity change across the colon is undefined. Furthermore, whether these changes are co-depended in the healthy colon is unknown. Here, tissue samples are collected from caecum, transverse colon, sigmoid colon and mLN of cadaveric donors by the Cambridge Biorepository of Translational Medicine (CBTM). We use single cell RNA sequencing (10X genomics) to assess the dynamics of immune cell populations across the colon and in matching lymph nodes. Associated microbiome 16S sequencing data is available.
2020-01-01 | E-MTAB-8476 | biostudies-arrayexpress
Project description:The human colon contains an extensively diverse microbial ecosystem and one of the most numerous communities of immune cells. Studies have highlighted dynamic crosstalk between immune cells and commensals. While studies have demonstrated increasing diversity of microbiota from stomach to stool, whether and how immune cell heterogeneity and microbiota diversity change across the colon is undefined. Furthermore, whether these changes are co-depended in the healthy colon is unknown. Here, tissue samples are collected from caecum, transverse colon, sigmoid colon and mLN of cadaveric donors by the Cambridge Biorepository of Translational Medicine (CBTM). We use single cell RNA sequencing (10X genomics) to assess the dynamics of immune cell populations across the colon and in matching lymph nodes. Associated microbiome 16S sequencing data is available.
2020-01-01 | E-MTAB-8486 | biostudies-arrayexpress
Project description:The human colon contains an extensively diverse microbial ecosystem and one of the most numerous communities of immune cells. Studies have highlighted dynamic crosstalk between immune cells and commensals. While studies have demonstrated increasing diversity of microbiota from stomach to stool, whether and how immune cell heterogeneity and microbiota diversity change across the colon is undefined. Furthermore, whether these changes are co-depended in the healthy colon is unknown. Here, tissue samples are collected from caecum, transverse colon, sigmoid colon and mLN of cadaveric donors by the Cambridge Biorepository of Translational Medicine (CBTM). We use single cell RNA sequencing (10X genomics) to assess the dynamics of immune cell populations across the colon and in matching lymph nodes. Associated microbiome 16S sequencing data is available.
2020-01-01 | E-MTAB-8484 | biostudies-arrayexpress
Project description:Aquatic microbial communities contain a vast amount of genetic diversity and we have much to learn about how this manifests to functional diversity. Existing long-term time series data includes 16S tags, metagenomes, single amplified genomes (SAGs), and genomes from metagenomes (GFMs). Information about functional diversity and metabolic capabilities is often unavailable. The study sites include three lakes that are the subject of intense study through the North Temperate Lakes Long Term Ecological Research site: Sparkling Lake (oligotrophic), Lake Mendota (eutrophic), and Trout Bog Lake (dystrophic).
The work (proposal:https://doi.org/10.46936/10.25585/60000947) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.
2023-11-02 | MSV000093272 | MassIVE