A validated pangenome-scale metabolic model for the <i>Klebsiella pneumoniae</i> species complex.

"strain-specific genome-scale metabolic models (gsmms) used for comparative analyses (deposited in figshare - https://doi org/10 6084/m9 figshare 24871914 ) plus their associated memote reports (indicates completeness and annotation quality) reaction and gene presence-absence matrices across all isolates.; growth phenotype predictions derived from strain-specific gsmms (deposited in figshare - https://doi org/10 6084/m9 figshare 24871914 ).; binarized biolog growth phenotype data (plates pm1 and pm2) for n =37 isolates in aerobic and anaerobic conditions (deposited in figshare - https://doi org/10 6084/m9 figshare 24871914 ).; features of kpsc pan v2 and previously published kpsc metabolic models iyl1228 ikp1289 kpsc pan v1 kpsc pan v2 reactions (excl exchanges) 1973 2178 2017 3190 exchange reactions289 306 303 360 genes1229 1289 1265 2403 memote score* 84 % 61 % 41 % 85 % simulatable carbon sources252 268 266 345 simulatable nitrogen sources149 159 153 192 simulatable phosphorus sources59 59 59 68 simulatable sulphur sources25 25 25 34 *memote scores indicate the level of completeness of the model and its associated annotations (e g nucleotide accessions kegg orthologue ids); full outputs are available on figshare.; aerobic conditions are presented in the first row and anaerobic conditions in the second row (raw values for both conditions are available on figshare)."

"the kpsc pan v2 model is available at https://github com/kelwyres/kpsc-pan-metabolic-model 2024 20 2 2024 20 2 2024 [ comment ] 10 2 001206 21 12 2023 06 2 2024 (c) 2024 the authors2024 https://creativecommons org/licenses/by/4 0/ this is an open-access article distributed under the terms of the creative commons attribution license.; kpsc pan v2 is freely available at https://github com/kelwyres/kpsc-pan-metabolic-model representing a valuable resource for the scientific community both as a source of curated metabolic information and as a reference to derive accurate strain-specific gsmms.; klebsiella pneumoniae species complex (kpsc) pan v2 metabolic model (available at https://github com/kelwyres/kpsc-pan-metabolic-model ).; this model kpsc pan v2 0 1 is available in json and sbml formats at github com/kelwyres/kpsc-pan-metabolic-model along with accompanying nucleotide ( fna) and protein ( faa) sequence files. pmc pmc10926698 pmc10926698 10926698 38376382 38376382 001206 10 1099/mgen 0 001206 bioresources genomic methodologies a validated pangenome-scale metabolic model for the klebsiella pneumoniae species complex http://mgen microbiologyresearch org *correspondence: helena b cooper helena cooper@monash edu *correspondence: kelly l wyres kelly wyres@monash edu all supporting data and protocols have been provided within the article through supplementary data files github or figshare repositories."

"Conflicts of interest The author(s) declare no conflict of interest."

"Funding information This research was supported by an Australian Government Research Training Programme (RTP) Scholarship to H.B.C. and an Australian Research Council Discovery Project award (DP200103364, to K.L.W., K.E.H., S.B. and J.M.M.). K.L.W. is supported by a National Health and Medical Research Council of Australia Investigator Grant (APP1176192). Biolog data generation was supported financially by the French Government’s Investissement d’Avenir programme Laboratoire d’Excellence ‘Integrative Biology of Emerging Infectious Diseases’ (ANR-10-LABX-62-IBEID)."