Similar Datasets
Project description:Analysis of microbial gene expression in response to physical and chemical gradients forming in the Columbia River, estuary, plume and coastal ocean was done in the context of the environmental data base. Gene expression was analyzed for 2,234 individual genes that were selected from fully sequenced genomes of 246 prokaryotic species (bacteria and archaea) as related to the nitrogen metabolism and carbon fixation. Seasonal molecular portraits of differential gene expression in prokaryotic communities during river-to-ocean transition were created using freshwater baseline samples (268, 270, 347, 002, 006, 207, 212). Total RNA was isolated from 64 filtered environmental water samples collected in the Columbia River coastal margin during 4 research cruises (14 from August, 2007; 17 from November, 2007; 18 from April, 2008; and 16 from June, 2008), and analyzed using microarray hybridization with the CombiMatrix 4X2K format. Microarray targets were prepared by reverse transcription of total RNA into fluorescently labeled cDNA. All samples were hybridized in duplicate, except samples 212 and 310 (hybridized in triplicate) and samples 336, 339, 50, 152, 157, and 199 (hybridized once). Sample location codes: number shows distance from the coast in km; CR, Columbia River transect in the plume and coastal ocean; NH, Newport Hydroline transect in the coastal ocean at Newport, Oregon; AST and HAM, Columbia River estuary locations near Astoria (river mile 7-9) and Hammond (river mile 5), respectively; TID, Columbia River estuary locations in the tidal basin (river mile 22-23); BA, river location at Beaver Army Dock (river mile 53) near Quincy, Oregon; UP, river location at mile 74.
2010-09-10 | E-GEOD-18303 | biostudies-arrayexpress
Project description:Analysis of microbial gene expression in response to physical and chemical gradients forming in the Columbia River, estuary, plume and coastal ocean was done in the context of the environmental data base. Gene expression was analyzed for 2,234 individual genes that were selected from fully sequenced genomes of 246 prokaryotic species (bacteria and archaea) as related to the nitrogen metabolism and carbon fixation. Seasonal molecular portraits of differential gene expression in prokaryotic communities during river-to-ocean transition were created using freshwater baseline samples (268, 270, 347, 002, 006, 207, 212).
2010-09-10 | GSE18303 | GEO
Project description:Microbial diversity in Yellow River Estuary
| PRJNA282720 | ENA
Project description:To characterize the taxonomic and functional diversity of biofilms on plastics in marine environments, plastic pellets (PE and PS, ø 3mm) and wooden pellets (as organic control) were incubated at three stations: at the Baltic Sea coast in Heiligendamm (coast), in a dead branch of the river Warnow in Warnemünde (inlet), and in the Warnow estuary (estuary). After two weeks of incubation, all pellets were frozen for subsequent metagenome sequencing and metaproteomic analysis. Biofilm communities in the samples were compared on multiple levels: a) between the two plastic materials, b) between the individual incubation sites, and c) between the plastic materials and the wooden control. Using a semiquantitative approach, we established metaproteome profiles, which reflect the dominant taxonomic groups as well as abundant metabolic functions in the respective samples.
2021-11-01 | PXD012062 | Pride
Project description:<p>Background The gut microbiota plays a significant role in modulating the growth and function of host muscle, and microbiota transplantation experiments provide compelling evidence of its capacity to improve muscle quality. Feeding faba beans improves the muscle quality of Yellow River carp. However, the changes in gut microbiota, along with the specific microorganisms, metabolic pathways, and regulatory mechanisms linked to the enhancement of muscle quality following faba bean consumption remain to be elucidated.</p><p>Results After a 6-week feeding trial with faba beans, growth performance decreased, but muscle texture improved (P < 0.05). Gut microbiota structure also changed, with increased relative abundances of Aeromonas, ZOR0006, Cetobacterium, and Atopobium. Following 8 weeks of whole-intestinal microbiota transplantation (WIMT) from faba bean-fed donors to basal diet-fed recipients of Yellow River carp, growth performance remained unchanged (P > 0.05), while muscle texture improved (P < 0.05). This improvement was mainly due to increased small-diameter muscle fibers, higher collagen levels, and reduced muscle fat content (P < 0.05), which partially replicated the muscle texture of donor fish. Moreover, WIMT promotes intestinal structure and barrier integrity, with significant changes in gut microbiota structure and metabolic profile. WIMT improved the muscle quality of Yellow River carp by regulating mitochondrial autophagy and adipocytokine signaling pathways through the gut-muscle axis. Cetobacterium somerae (C. somerae) and its metabolites, such as acetic acid, played a crucial role in this process. Further feeding experiments demonstrated that C. somerae and acetic acid reduced the crude fat content of muscle while increasing the crude protein and collagen (P < 0.05). C. somerae also mitigated muscle protein degradation under inflammatory and enhanced collagen (P < 0.05), thereby improving muscle texture.</p><p>Conclusion This study establishes that gut microbiota enhance muscle quality in Yellow River carp through WIMT, identifies C. somerae and its metabolite acetic acid as key contributors. The findings provide novel evidence for fish gut-muscle axis research and offer new scientific basis for improving Yellow River carp muscle quality.</p>
2025-10-13 | MTBLS13128 | MetaboLights
Project description:16S_bacterial amplicon of Yellow River estuary
2025-05-22 | OEX00021345 | NODE