TY - JOUR
T1 - Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits
AU - Seif, Yara
AU - Kavvas, Erol
AU - Lachance, Jean Christophe
AU - Yurkovich, James T.
AU - Nuccio, Sean Paul
AU - Fang, Xin
AU - Catoiu, Edward
AU - Raffatellu, Manuela
AU - Palsson, Bernhard O.
AU - Monk, Jonathan M.
N1 - Funding Information:
This research was supported by the Novo Nordisk Foundation through the Center for Biosustainability at the Technical University of Denmark (NNF10CC1016517), and the NIH NIAID grant (1-U01-AI124316-01).
Publisher Copyright:
© 2018, The Author(s).
PY - 2018/12/1
Y1 - 2018/12/1
N2 - Salmonella strains are traditionally classified into serovars based on their surface antigens. While increasing availability of whole-genome sequences has allowed for more detailed subtyping of strains, links between genotype, serovar, and host remain elusive. Here we reconstruct genome-scale metabolic models for 410 Salmonella strains spanning 64 serovars. Model-predicted growth capabilities in over 530 different environments demonstrate that: (1) the Salmonella accessory metabolic network includes alternative carbon metabolism, and cell wall biosynthesis; (2) metabolic capabilities correspond to each strain’s serovar and isolation host; (3) growth predictions agree with 83.1% of experimental outcomes for 12 strains (690 out of 858); (4) 27 strains are auxotrophic for at least one compound, including l-tryptophan, niacin, l-histidine, l-cysteine, and p-aminobenzoate; and (5) the catabolic pathways that are important for fitness in the gastrointestinal environment are lost amongst extraintestinal serovars. Our results reveal growth differences that may reflect adaptation to particular colonization sites.
AB - Salmonella strains are traditionally classified into serovars based on their surface antigens. While increasing availability of whole-genome sequences has allowed for more detailed subtyping of strains, links between genotype, serovar, and host remain elusive. Here we reconstruct genome-scale metabolic models for 410 Salmonella strains spanning 64 serovars. Model-predicted growth capabilities in over 530 different environments demonstrate that: (1) the Salmonella accessory metabolic network includes alternative carbon metabolism, and cell wall biosynthesis; (2) metabolic capabilities correspond to each strain’s serovar and isolation host; (3) growth predictions agree with 83.1% of experimental outcomes for 12 strains (690 out of 858); (4) 27 strains are auxotrophic for at least one compound, including l-tryptophan, niacin, l-histidine, l-cysteine, and p-aminobenzoate; and (5) the catabolic pathways that are important for fitness in the gastrointestinal environment are lost amongst extraintestinal serovars. Our results reveal growth differences that may reflect adaptation to particular colonization sites.
UR - http://www.scopus.com/inward/record.url?scp=85053335363&partnerID=8YFLogxK
U2 - 10.1038/s41467-018-06112-5
DO - 10.1038/s41467-018-06112-5
M3 - Article
C2 - 30218022
AN - SCOPUS:85053335363
SN - 2041-1723
VL - 9
JO - Nature Communications
JF - Nature Communications
IS - 1
M1 - 3771
ER -