Ontology highlight
ABSTRACT:
PROVIDER: PRJNA932457 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23364825.fastq.gz | Fastqsanger.gz | |||
| SRR23364826.fastq.gz | Fastqsanger.gz | |||
| SRR23364827.fastq.gz | Fastqsanger.gz | |||
| SRR23364828.fastq.gz | Fastqsanger.gz | |||
| SRR23364829.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Acetic acid bacteria are obligately aerobic alphaproteobacteria that have a unique ability to incompletely oxidize various alcohols and sugars to organic acids. The ability of these bacteria to incompletely oxidize ethanol to acetate has been historically utilized for vinegar production. The mechanism of switching between incomplete oxidation and assimilatory oxidation and the control of energy and carbon metabolism in acetic acid bacteria are not fully understood. To understand the physiology and molecular biology of acetic acid bacteria better, we determined the draft genome sequence of Acetobacter aceti NBRC 14818, which is the type strain of the genus. Based on this draft genome sequence, the transcriptome profiles in A. aceti cells grown on ethanol, acetate, glucose, or mix of ethanol and glucose was determined by using NimbleGen Prokaryotic Expression array (4x72K).
2011-01-17 | GSE24361 | GEO
Project description:Acetic acid bacteria are obligately aerobic alphaproteobacteria that have a unique ability to incompletely oxidize various alcohols and sugars to organic acids. The ability of these bacteria to incompletely oxidize ethanol to acetate has been historically utilized for vinegar production. The mechanism of switching between incomplete oxidation and assimilatory oxidation and the control of energy and carbon metabolism in acetic acid bacteria are not fully understood. To understand the physiology and molecular biology of acetic acid bacteria better, we determined the draft genome sequence of Acetobacter aceti NBRC 14818, which is the type strain of the genus. Based on this draft genome sequence, the transcriptome profiles in A. aceti cells grown on ethanol, acetate, glucose, or mix of ethanol and glucose was determined by using NimbleGen Prokaryotic Expression array (4x72K). Acetobacter aceti NBRC14818 was cultivated in the medium containing ethanol, acetate, glucose, or mix of ethanol and glucose as carbon sources in Erlenmeyer flask with rotary shaking. Total RNA was extracted when optical density at 600 nm was 0.3-0.4. The experiment was performed in duplicate independent cultures.
2011-01-17 | E-GEOD-24361 | biostudies-arrayexpress
Project description:Subjects with different allergic phenotypes showed distinct gut microbial patterns and functions. AD+FA subjects showed the mixtures of gut microbial patterns of FA and AD, while gut microbial pattern of FA seems to dominate in subjects with AD+FA
2021-08-04 | PXD027692 | JPOST Repository
Project description:This is an SBML version of the reaction network used in the article:
Metabolic pathway analysis of yeast strengthens the bridge between transcriptomics and metabolic networks
Tunahan Çakir, Betül Kirdar, Kutlu Ö. Ülgen. Biotechnol Bioeng 2004 86:251-60;
PubmedID: 15083505
; DOI: 10.1002/bit.20020
Abstract:
Central carbon metabolism of the yeast Saccharomyces cerevisiae was analyzed using metabolic pathway analysis tools. Elementary flux modes for three substrates (glucose, galactose, and ethanol) were determined using the catabolic reactions occurring in yeast. Resultant elementary modes were used for gene deletion phenotype analysis and for the analysis of robustness of the central metabolism and network functionality. Control-effective fluxes, determined by calculating the efficiency of each mode, were used for the prediction of transcript ratios of metabolic genes in different growth media (glucose-ethanol and galactose-ethanol). A high correlation was obtained between the theoretical and experimental expression levels of 38 genes when ethanol and glucose media were considered. Such analysis was shown to be a bridge between transcriptomics and fluxomics. Control-effective flux distribution was found to be promising in in silico predictions by incorporating functionality and regulation into the metabolic network structure.
Some typographical errors in the paper have been corrected:
Reaction (49) has substrate NADcyt (rather than NADmit)
Reaction (53) is missing products 90 NADPcyt
CO2 and O2 are also set as external metabolites
This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team.
For more information see the terms of use
.
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
2005-01-01 | MODEL1008240001 | BioModels
Project description:Recent advances in (meta)genomic methods have provided new opportunities to examine host-microbe-environment interactions in the human gut. While opportunities exist to extract DNA from freshly sourced colonic tissue there are potentially valuable sources of DNA from historical studies that might also be examined. We examined how four different tissue DNA extraction methods employed in past clinical trials might impact the recovery of microbial DNA from a colonic tissue sample as assessed using a custom designed phylogenetic microarray for human gut bacteria and archaebacteria. While all methods of DNA extraction produced similar phylogenetic profiles some extraction specific biases were also observed. Real time PCR analysis targeting several bacterial groups substantiated this observation. These data suggest that while the efficacy of different DNA extraction methods differs somewhat all the methods tested produce an accurate representation of microbial diversity. This suggests that DNA samples archived in biobanks should be suitable for retrospective analyses. Three technical replicates per sample (extraction method) were analysed
2010-05-16 | E-GEOD-18420 | biostudies-arrayexpress
Project description:This study investigates the role of carbon-to-phosphorus (C/P) ratios in shaping microbial community dynamics and polyhydroxyalkanoates (PHA) production in sequencing batch reactors (SBR) fed with volatile fatty acids. Three conditions, characterized by fixed organic loading rates but varying C/P ratios (Run 1 = 170 Cmol Pmol-1; Run 2 = 235 Cmol Pmol-1; Run 3 = 400 Cmol Pmol-1;), were tested to explore their impact on PHA accumulation, biomass growth, and reactor stability. Results indicate that the moderate phosphorus limitation of Run 2 achieves the best overall performance, with a PHA volumetric productivity of 2.02 g PHA L⁻¹ d⁻¹ and process stability. Under these conditions, PHA-accumulating bacteria, primarily Sphaerotilus and Leadbetterella, dominated the microbial community, with a notable contribution from eukaryotic organisms, particularly Rhogostoma, Vorticella and Tokophrya, which appeared to regulate bacterial populations through selective predation. Conversely, higher C/P ratio increased the storage yield but lowered the productivity (1.55 gPHA L-1 h-1), compromising sludge settleability and reactor stability, indicating impaired microbial functionality. Transmission electron microscopy further confirmed the presence of intracellular PHA granules and polyphosphate reserves, reinforcing the connection between nutrient limitation and adaptive microbial strategies. Overall, these findings highlight the critical role of the C/P ratio in shaping the performance of mixed microbial cultures, demonstrating that a well-balanced nutrient supply can enhance PHA production while maintaining microbial community stability. The results contribute to optimizing the selection process for mixed microbial cultures, offering valuable insights into the impact of carbon-to-nutrient ratios in the feeding strategy.
2025-07-14 | GSE302519 | GEO