PathwayLinks

Network analysis of metabolic pathways across bacterial organisms in a community

Jay Pedersen, Ryan Patch, Lotfollah Najjar, Dhundy Raj Bastola

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

The Human Microbiome Project (HMP) recognizes that several microbiome environments reside within the human body (such as the mouth and the GI tract). HMP is involved in documenting and sequencing bacteria existing in these environments. These environments can be considered to host a community of bacteria, where one bacterium may provide support for the metabolic needs of other bacteria. Publicly available metabolic pathway information exists for many of these organisms, most notably the well-established KEGG database. To predict the metabolic relationships that exist between organisms living in a community, we analyzed publicly available metabolic data and developed a set of procedures whose input is a set of organisms in a community and whose output is a set of predictions of possible metabolic linkages between them. We refer to these procedures collectively as the PathwayLinks procedures, as they find possible links between metabolic pathways. A pilot study was conducted using the well-known Red-Complex of bacteria in the mouth, which is linked to gingivitis. Results indicate that the Citrulline and Protoporphyrin metabolites may link two of the key organisms in the complex. This research shows promise in providing a theoretical basis for predicting metabolic relationships between bacteria living in a community.

Original languageEnglish (US)
Title of host publicationProceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014
EditorsHuiru Zheng, Xiaohua Tony Hu, Yadong Wang, Jin-Kao Hao, David Gilbert, Daniel Berrar, Kwang-Hyun Cho, Werner Dubitzky
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages14-21
Number of pages8
ISBN (Electronic)9781479956692
DOIs
StatePublished - Dec 29 2014
Event2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014 - Belfast, United Kingdom
Duration: Nov 2 2014Nov 5 2014

Publication series

NameProceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014

Conference

Conference2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014
CountryUnited Kingdom
CityBelfast
Period11/2/1411/5/14

Fingerprint

Electric network analysis
Metabolic Networks and Pathways
Bacteria
Microbiota
Mouth
Citrulline
Gingivitis
Metabolites
Human Body
Gastrointestinal Tract
Databases
Research

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics

Cite this

Pedersen, J., Patch, R., Najjar, L., & Bastola, D. R. (2014). PathwayLinks: Network analysis of metabolic pathways across bacterial organisms in a community. In H. Zheng, X. T. Hu, Y. Wang, J-K. Hao, D. Gilbert, D. Berrar, K-H. Cho, ... W. Dubitzky (Eds.), Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014 (pp. 14-21). [6999276] (Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM.2014.6999276

PathwayLinks : Network analysis of metabolic pathways across bacterial organisms in a community. / Pedersen, Jay; Patch, Ryan; Najjar, Lotfollah; Bastola, Dhundy Raj.

Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014. ed. / Huiru Zheng; Xiaohua Tony Hu; Yadong Wang; Jin-Kao Hao; David Gilbert; Daniel Berrar; Kwang-Hyun Cho; Werner Dubitzky. Institute of Electrical and Electronics Engineers Inc., 2014. p. 14-21 6999276 (Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Pedersen, J, Patch, R, Najjar, L & Bastola, DR 2014, PathwayLinks: Network analysis of metabolic pathways across bacterial organisms in a community. in H Zheng, XT Hu, Y Wang, J-K Hao, D Gilbert, D Berrar, K-H Cho & W Dubitzky (eds), Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014., 6999276, Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014, Institute of Electrical and Electronics Engineers Inc., pp. 14-21, 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014, Belfast, United Kingdom, 11/2/14. https://doi.org/10.1109/BIBM.2014.6999276
Pedersen J, Patch R, Najjar L, Bastola DR. PathwayLinks: Network analysis of metabolic pathways across bacterial organisms in a community. In Zheng H, Hu XT, Wang Y, Hao J-K, Gilbert D, Berrar D, Cho K-H, Dubitzky W, editors, Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014. Institute of Electrical and Electronics Engineers Inc. 2014. p. 14-21. 6999276. (Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014). https://doi.org/10.1109/BIBM.2014.6999276
Pedersen, Jay ; Patch, Ryan ; Najjar, Lotfollah ; Bastola, Dhundy Raj. / PathwayLinks : Network analysis of metabolic pathways across bacterial organisms in a community. Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014. editor / Huiru Zheng ; Xiaohua Tony Hu ; Yadong Wang ; Jin-Kao Hao ; David Gilbert ; Daniel Berrar ; Kwang-Hyun Cho ; Werner Dubitzky. Institute of Electrical and Electronics Engineers Inc., 2014. pp. 14-21 (Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014).
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