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FROG analysis ensures the reproducibility of genome scale metabolic models
Raman, Karthik; Kratochvil, Miroslav; Olivier, Brett G.; Konig, Matthias; Sengupta, Pratyay; Baskaran, Dinesh Kumar Kuppa; Nguyen, Tung V NGenome scale metabolic models (GEMs) and other constraint-based models (CBMs) play a pivotal role in understanding biological phenotypes and advancing research in areas like metabolic engineering, human disease modelling, drug discovery, and personalized medicine. Despite their growing application, a significant challenge remains in ensuring the reproducibility of GEMs, primarily due to inconsistent reporting a...
MEMOTE for standardized genome-scale metabolic model testing
Lieven, Christian; Beber, Moritz E.; Olivier, Brett G.; Bergmann, Frank T.; Ataman, Meric; Babaei, Parizad; Bartell, Jennifer A.; Blank, Lars M.Reconstructing metabolic reaction networks enables the development of testable hypotheses of an organisms metabolism under different conditions1. State-of-the-art genome-scale metabolic models (GEMs) can include thousands of metabolites and reactions that are assigned to subcellular locations. Geneproteinreaction (GPR) rules and annotations using database information can add meta-information to GEMs. GEMs with ...
Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing
Lieven, Christian; Beber, Moritz E.; Olivier, Brett G.; Bergmann, Frank T.; Ataman, Meric; Babaei, Parizad; Bartell, Jennifer A.; Blank, Lars M.An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Organohalide-respiring Desulfoluna species isolated from marine environments
Peng, Peng; Goris, Tobias; Lu, Yue; Nijsse, Bart; Burrichter, Anna; Schleheck, David; Koehorst, Jasper J.; Liu, Jie; Sipkema, DetmerThe genus Desulfoluna comprises two anaerobic sulfate-reducing strains, D. spongiiphila AA1T and D. butyratoxydans MSL71T, of which only the former was shown to perform organohalide respiration (OHR). Here we isolated a third strain, designated D. spongiiphila strain DBB, from marine intertidal sediment using 1,4-dibromobenzene and sulfate as the electron acceptors and lactate as the electron donor. Each strain...
Metabolic shift induced by synthetic co-cultivation promotes high yield of chai...
Diender, Martijn; Parera Olm, Ivette; Gelderloos, Marten; Koehorst, Jasper J.; Schaap, Peter J.; Stams, Alfons Johannes Maria; Sousa, Diana Zita MachadoBio-catalytic processes for sustainable production of chemicals and fuels receive increased attention within the concept of circular economy. Strategies to improve these production processes include genetic engineering of bio-catalysts or process technological optimization. Alternatively, synthetic microbial co-cultures can be used to enhance production of chemicals of interest. It remains often unclear however...
Genome and proteome analysis of Pseudomonas chloritidismutans AW-1T that grows ...
Mehboob, Farrakh; Oosterkamp, Margreet J.; Koehorst, Jasper J.; Farrakh, Sumaira; Veuskens, Teun; Plugge, Caroline M.; Boeren, Sjef; Vos, Willem M. deGrowth of Pseudomonas chloritidismutans AW-1T on C7 to C12 n-alkanes with oxygen or chlorate as electron acceptor was studied by genome and proteome analysis. Whole genome shotgun sequencing resulted in a 5 Mbp assembled sequence with a G+C content of 62.5% The automatic annotation identified 4767 protein-encoding genes and a putative function could be assigned to almost 80% of the predicted proteins. The disti...
A genomic view on syntrophic versus non-syntrophic lifestyle of anaerobic fatty...
Worm, Petra; Koehorst, Jasper J.; Visser, Michael; Sedano-Núñez, Vicente T.; Schaap, Peter J.; Plugge, Caroline M.; Sousa, D. Z.In sulfate-reducing and methanogenic environments complex biopolymers are degraded by fermentative micro-organisms that produce hydrogen, carbon dioxide and short chain fatty acids. Degradation of short chain fatty acids can be coupled to methanogenesis or to sulfate reduction. We applied a genomic approach to understand why some bacteria are able to grow in syntrophy with methanogens and others are not. Bacter...
A genomic view on syntrophic versus non-syntrophic lifestyle in anaerobic fatty...
Worm, Petra; Koehorst, Jasper J.; Visser, Michael; Sedano-Núñez, Vicente T.; Schaap, Peter J.; Plugge, Caroline M.; Sousa, D. Z.In sulfate-reducing and methanogenic environments complex biopolymers are hydrolyzed and degraded by fermentative micro-organisms that produce hydrogen, carbon dioxide and short chain fatty acids. Degradation of short chain fatty acids can be coupled to methanogenesis or to sulfate-reduction. Here we study from a genome perspective why some of these micro-organisms are able to grow in syntrophy with methanogens...
Genome analyses of the carboxydotrophic sulfate-reducers Desulfotomaculum nigri...
Visser, Michael; Parshina, Sofiya N.; Alves, Joana I.; Sousa, D. Z.; Pereira, Inês A. C.; Muyzer, Gerard; Kuever, Jan; Lebedinsky, Alexander V.Desulfotomaculum nigrificans and D. carboxydivorans are moderately thermophilic members of the polyphyletic spore-forming genus Desulfotomaculum in the family Peptococcaceae. They are phylogenetically very closely related and belong to 'subgroup a' of the Desulfotomaculum cluster 1. D. nigrificans and D. carboxydivorans have a similar growth substrate spectrum; they can grow with glucose and fructose as electro...