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Peer-reviewedCC BYGenomics & informatics

Genome-scale metabolic model analysis of Korean Campylobacter jejuni isolates reveals lineage-level metabolic structure.

  • Myeong-Won Jo1,2
  • Seung-Hyun Jung1,3,4
  • Jeong-Ih Shin5,6
  • Yeun-Jun Chung7,8,9
9 affiliations
  1. 1Department of Medical Sciences, Graduate School of the Catholic University of Korea, Seoul, 06591, Republic of Korea.
  2. 2Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea.
  3. 3Catholic Research Institute for Human Genome Polymorphism, Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea.
  4. 4Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea.
  5. 5Department of Medical Sciences, Graduate School of the Catholic University of Korea, Seoul, 06591, Republic of Korea. [email protected].
  6. 6Catholic Research Institute for Human Genome Polymorphism, Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea. [email protected].
  7. 7Department of Medical Sciences, Graduate School of the Catholic University of Korea, Seoul, 06591, Republic of Korea. [email protected].
  8. 8Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea. [email protected].
  9. 9Catholic Research Institute for Human Genome Polymorphism, Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea. [email protected].
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Abstract

Genome-scale metabolic models (GSMMs) of Campylobacter jejuni (C. jejuni) have been studied mainly for reference strains, and their characteristics at the lineage level remain poorly understood. We reconstructed GSMMs for 86 C. jejuni isolates collected in Korea using gapseq and analyzed them together with in vitro substrate utilization data for seven substrates measured on the same isolates. Strain-specific GSMMs clustered by clonal complex (CC): in all nine CCs with ≥ 2 isolates the mean within-CC Jaccard distance was smaller than the mean between-CC distance; across all strain pairs the median distance was 0.082 within CCs and 0.130 between CCs (P < 0.001). In the in vitro phenotypes, only five of the nine CCs showed smaller within- than between-CC distances, and the GSMM and in vitro distances were only weakly correlated (Mantel r = 0.13, P = 0.03). In an exploratory comparison of two lineages with contrasting profiles, CC-443 (n = 7) showed negative mean z-scores for all seven substrates, whereas CC-658 (n = 4) showed positive mean z-scores for all seven, the highest being sulfite (z = + 0.95). In GSMMs, CC-443 lacked reactions for the monoamine/polyamine oxidase family and pantothenate/CoA biosynthesis, whereas CC-658 was enriched in fatty acid/phospholipid biosynthesis, sialic acid metabolism, and anaerobic sulfur respiration. Anaerobic sulfur respiration-related reactions were more prevalent in CC-658 (75%) than in the other CCs (11%), consistent with its high in vitro sulfite utilization; this difference was retained when the comparison was restricted to chicken isolates (0% in CC-443 vs. 100% in CC-658). In silico growth simulations under two gut-mimicking diets (Western and high-fiber) showed consistently lower predicted growth for CC-443 than for CC-658 under both conditions (exact permutation test, P = 0.048), although the eleven models yielded only four distinct predicted values under each diet, which limits the strength of this comparison. These results indicate that metabolic modeling of C. jejuni benefits from considering lineage-level diversity rather than relying on a single reference-strain GSMM.

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Cite

BibTeXRIS
BibTeX
@article{jo2026genomescale,
  title = {{Genome-scale metabolic model analysis of Korean Campylobacter jejuni isolates reveals lineage-level metabolic structure.}},
  author = {Myeong-Won Jo and Seung-Hyun Jung and Jeong-Ih Shin and Yeun-Jun Chung},
  journal = {Genomics \& informatics},
  year = {2026},
  month = nov,
  doi = {10.1186/s44342-026-00086-3},
  url = {https://europepmc.org/article/MED/42972461},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - Genome-scale metabolic model analysis of Korean Campylobacter jejuni isolates reveals lineage-level metabolic structure.
AU  - Myeong-Won Jo
AU  - Seung-Hyun Jung
AU  - Jeong-Ih Shin
AU  - Yeun-Jun Chung
PY  - 2026
DA  - 2026/11/02
JO  - Genomics & informatics
DO  - 10.1186/s44342-026-00086-3
UR  - https://europepmc.org/article/MED/42972461
AB  - Genome-scale metabolic models (GSMMs) of Campylobacter jejuni (C. jejuni) have been studied mainly for reference strains, and their characteristics at the lineage level remain poorly understood. We reconstructed GSMMs for 86 C. jejuni isolates collected in Korea using gapseq and analyzed them together with in vitro substrate utilization data for seven substrates measured on the same isolates. Strain-specific GSMMs clustered by clonal complex (CC): in all nine CCs with ≥ 2 isolates the mean within-CC Jaccard distance was smaller than the mean between-CC distance; across all strain pairs the median distance was 0.082 within CCs and 0.130 between CCs (P < 0.001). In the in vitro phenotypes, only five of the nine CCs showed smaller within- than between-CC distances, and the GSMM and in vitro distances were only weakly correlated (Mantel r = 0.13, P = 0.03). In an exploratory comparison of two lineages with contrasting profiles, CC-443 (n = 7) showed negative mean z-scores for all seven substrates, whereas CC-658 (n = 4) showed positive mean z-scores for all seven, the highest being sulfite (z = + 0.95). In GSMMs, CC-443 lacked reactions for the monoamine/polyamine oxidase family and pantothenate/CoA biosynthesis, whereas CC-658 was enriched in fatty acid/phospholipid biosynthesis, sialic acid metabolism, and anaerobic sulfur respiration. Anaerobic sulfur respiration-related reactions were more prevalent in CC-658 (75%) than in the other CCs (11%), consistent with its high in vitro sulfite utilization; this difference was retained when the comparison was restricted to chicken isolates (0% in CC-443 vs. 100% in CC-658). In silico growth simulations under two gut-mimicking diets (Western and high-fiber) showed consistently lower predicted growth for CC-443 than for CC-658 under both conditions (exact permutation test, P = 0.048), although the eleven models yielded only four distinct predicted values under each diet, which limits the strength of this comparison. These results indicate that metabolic modeling of C. jejuni benefits from considering lineage-level diversity rather than relying on a single reference-strain GSMM.
SN  - 1598-866X
SN  - 2234-0742
ER  -