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MetabolomicsStreamlined identification of strain engineering targets for bioprocess improvement using metabolic pathway enrichment analysis
Metabolomics is a powerful tool for the identification of genetic targets for bioprocess optimisation. However, in most cases, only the biosynthetic pathway directed to product formation is analysed, limiting the identification of these targets. Some studies have used untargeted metabolomics, allowi...
2023-08-31 | MTBLS6667 | MetaboLights
MetabolomicsMulti-Omics Unveils Strain-Specific Neuroactive Metabolite Production Linked to Inflammation Modulation by Bacteroides and Their Vesicles

18 Bacteroidetes isoaltes were analyzed for their neuroactive potentail using un-targeted and targeted metabolomics. The bacteria were grown to stationary phase, the supernatant was separated and purified using 0.22 um filter. The metabolome from the supernatant was extracted using standard Metha...

2025-08-12 | MTBLS10526 | MetaboLights
ProteomicsAn Isoprenol Biosensor for Combinatorial High Throughput Strain Engineering in Pseudomonas putida
Our group has evaluated the productivity of the alcohol isoprenol (3-methyl-3-buten-1-ol), platform commodity chemical with attractive properties specifically as a diesel fuel blendstock and precursor for the bio-jetfuel DMCO, across a number of microbial hosts. While there are strengths and drawbac...
ORGANISM(S): Pseudomonas putida KT2440 
2025-09-12 | PXD061547 | Pride
Biomanufacturing Biosensors Strain engineering High-throughput Jbei Biofuels Isoprenol P. putida 
TranscriptomicsGene expression level during L-threonine production
The comparative transcriptome profiling of L-threonine producing strain (TH07 strain harboring pBRThrABC) and control W3110 (lacI-deleted) strain harboring pKK223-3 has been analyzed using oligo nucleotide microarray. Keywords: comparative transcriptome analysis (between L-threonine producing strai...
ORGANISM(S): Escherichia coli 
2010-05-25 | E-GEOD-9434 | biostudies-arrayexpress
TranscriptomicsComparison of the metabolic response to over-production of p-coumaric acid in two yeast strains
We aimed to study how production of p-coumaric acid, a precursor of multiple secondary aromatic metabolites, influences the cellular metabolism of Saccharomyces cerevisiae. We evaluated the growth and p-coumaric acid production in batch and chemostat cultivations and analyzed the transcriptome and i...
ORGANISM(S): Saccharomyces cerevisiae 
2017-11-21 | E-MTAB-6208 | biostudies-arrayexpress
MetabolomicsLinking genetic, metabolic and phenotypic diversity 1 among S. cerevisiae strains using multi-omics associations
The selection of bioengineering platform strains and engineering strategies to improve the stress resistance of Saccharomyces cerevisiae remains a pressing need in bio-based chemical production. Thus, a systematic effort to exploit the genotypic and phenotypic diversity to boost yeast’s industrial v...
2019-01-16 | MTBLS780 | MetaboLights
ProteomicsEngineering cell-free systems by chemoproteomic-assisted phenotypic screening.
Phenotypic screening is a valuable tool to both understand and engineer complex biological systems. We demonstrate the functionality of this approach in the development of cell-free protein synthesis (CFPS) technology. Phenotypic screening identified numerous compounds that enhanced protein produc...
ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast) 
2024-07-22 | PXD047986 | JPOST Repository
TranscriptomicsComparative genomics reveals new molecular targets for accelerated strain improvement of rifamycin B-producing strains
In the present study, we have used a genomic approach to understand how the classical mutate-and-screen method actually generated an improved rifamycin B producer. Compared with the reference strains Amycolatopsis mediterranei S699 (rifamycin B producer) and U32 (rifamycin SV producer), a total of 2...
ORGANISM(S): Amycolatopsis mediterranei S699 
2014-08-26 | E-GEOD-51015 | biostudies-arrayexpress
ProteomicsMetabonomics analyses of pgds engineering strain in Bacillus licheniformis CGMCC 2876
In order to study the changes of metabolic pathways in recombinant strain Bl/pP2967-pgdS, non-targeted metabolomics was used for omics analysis of metabolites in the original and pgds engineering strains..
ORGANISM(S): Bacillus Licheniformis 
2023-05-06 | PXD042048 |
TranscriptomicsTranscriptome- and fluxome-guided metabolic engineering of 3-hydroxypropionic acid production in Saccharomyces cerevisiae
In this study, we analyse a high 3HP producing strain of Saccharomyces cerevisiae through 13C metabolic flux and transcriptomic analyses. The engineered strain saw upregulation across glycolysis and the pentose phosphate pathway compared to the reference strain. Our analysis of the transcriptomic da...
ORGANISM(S): Saccharomyces cerevisiae 
2022-08-30 | E-MTAB-7819 | biostudies-arrayexpress
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