Bioreactor metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA934175 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23436963.fastq.gz | Fastqsanger.gz | |||
| SRR23436964.fastq.gz | Fastqsanger.gz |
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Project description:Glycerol is an attractive feedstock for biofuels since it accumulates as a byproduct during biodiesel operations; hence, it is interesting to consider converting glycerol to hydrogen using the formate hydrogen lyase system of Escherichia coli which converts pyruvate to hydrogen. Starting with Escherichia coli BW25113 frdC that lacks fumarate reductase to eliminate the negative effect of accumulated hydrogen on glycerol fermentation and by using both adaptive evolution and chemical mutagenesis combined with a selection method based on increased growth on glycerol, we obtained an improved strain, HW2, that produces 20-fold more hydrogen in glycerol medium (0.68 mmol/L/h) compared to that of frdC mutant. HW2 also grows 5-fold faster (0.25 1/h) than BW25113 frdC on glycerol, so it achieves a reasonable growth rate. Corroborating the increase in hydrogen production, glycerol dehydrogenase activity in HW2 increased 4-fold compared to BW25113 frdC. In addition, a whole-transcriptome study revealed that several pathways that would decrease hydrogen yields were repressed in HW2 (fbp, focA, and gatYZ) while a beneficial pathway, eno which encodes enolase was induced.
2010-10-31 | GSE18972 | GEO
Project description:Abstract. Microbial gas fermentation remains a promising biotechnology for the production of a variety of industrially relevant chemicals under relatively benign conditions using ubiquitous feedstocks, such as carbon dioxide. Implementation of these gas fermentation processes requires an understanding of the microbial response to different ratios of the gaseous feedstocks (carbon dioxide, oxygen, and hydrogen) supplied to the reactor. Here, we used Cupriavidus necator (strain ATCC 17699 / DSM 428 / KCTC 22496 / NCIMB 10442 / H16 / Stanier 337) as a microbial biocatalyst due to its metabolic diversity, genetic tractability, and ability to grow to high cell densities during aerobic fermentation in bioreactors. Specifically, we investigate whether the supply of different proportions of hydrogen and carbon dioxide in the gas stream (1:1, 3:1, and 8:1 H2:CO2) affects the physiology of C. necator, with a focus on the accumulation of single cell protein (SCP) and poly-3-hydroxybutyrate (PHB) within the microbial biomass. We found that an 8:1 ratio of H2:CO2 led to both the highest overall biomass production and PHB content within the biomass after a seven-day incubation. Intracellular SCP content varied as a function of both length of incubation and gas ratio supplied. We conducted a proteomic analysis to determine whether differences in productivity could be correlated with changes in protein expression over time and across treatment groups. This study highlights the importance of considering gaseous substrate composition and its potential effects on microbial physiology and metabolism during fermentation.
2026-05-15 | PXD064900 | Pride
Project description:The goal of the study is to use Next generation sequencing (RNA-seq) and 13C based flux analysis to study the underlying regulation of citric acid metabolism in mixed culture fermentation (glucose and glycerl) of Yarrowia lipolytica. We sequenced the RNA from 4 different samples in the mixed culture (glucose and glycerol) under oxygen excess and limited conditions with 2 replicates each . Transcriptional profiles showed that under oxygen limited conditions, due to deficient mitochondrial activity, citric acid is being consumed back after glycerol exhaustion eventhough glucose is present in excess. Transcriptome and fluxome profiles showed that glucose is mainly directed towards the Pentose phosphate pathway in the dual substrate fermentations.
2017-05-08 | GSE83109 | GEO
Project description:The goal of the study is to use Next generation sequencing (RNA-seq) to study the underlying regulation of glycerol metabolism in mixed culture fermentation (glucose and glycerol) of Rhodosporidium toruloides. We sequenced the RNA from 4 different samples in the mixed culture (glucose and glycerol) with 2 replicates each. Transcriptional profiles showed that glycerol might be produced intracellularly and glycerol kinase (GUT1) and glycerol 3–phosphate dehydrogenase (GUT2) enzymes were not down-regulated in the presence of glucose at the transcriptional level. It also showed that this yeast has a different regulation compared to S.cerevisiae. Certain insights into lipid biosynthesis on these mixed cultures are provided at systems level. This analysis provides interesting targets for metabolic engineering in this organism growing on glucose and glycerol.
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Project description:Biotechnology suggests that microorganisms can be used as chemical factories that transform renewable feedstock into value-added chemicals. Conversion of glycerol, using direct transformation or fermentation, into valuable products such as polymers, surfactants, solvents, and chemical intermediates has attained growing interest in recent years due to the dramatic growth of the biodiesel industry. However, the use of cell factories could be limited by low growth and uptake rates under certain environmental conditions, thus understanding microbial nutritional requirements is a critical point to use them as cell factories. Here, we compared E. coli ATCC 8739 transcriptomic responses to glycerol under aerobic conditions in an optimized culture medium (Condition 3) and one evolved strain in glycerol using as a reference a glycerol-based medium (Condition 11). Our analyses revealed 478 and 431 differentially expressed genes (DEGs) with log2 fold change (FC) > |2| and p Adjusted value < 0.05, for the bacteria growing in the optimized culture medium and the evolved strain, respectively. Among the DEGs, glp operon was found to be up-regulated as a response to glycerol uptake. Interestingly, between them, it was found genes that requires the use of phosphorous to ovoid the toxicity during glycerol consumption. Previously, we identified using a computational approach that phosphorous and nitrogen are essential compound that support high glycerol consumption in E. coli.
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