An integrative framework for functional analysis of cattle rumen microbiomes

Jyotsna Talreja Wassan, Huiru Zheng, Fiona Browne, J M Bowen, Paul Walsh, R Roehe, RJ Dewhurst, Cintia Palu, Brian Kelly, Haiying Wang

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

Abstract

Metagenomics is the study of environmental microbial communities and has various applications and implications in biological research. This paper aims to study the role of microbial communities in cattle rumen and their relation to probiotic diet supplement usage as part of the EU H2020 MetaPIat project l1 MetaPlat, http://www.metaplat.eu. In this research, we proposed and evaluated a computational framework to classify 16S rRNA samples from Bos taurus (cattle) rumen microbiome into a diet phenotype. We performed analysis by benchmarking various phylogeny-driven methods based on integration of biological domain knowledge of relationships and non-phylogenetic methods based on the raw abundances. The integrative approach incorporating phylogenetic tree structure into machine learning (ML) modelling achieved a high predictive performance with Accuracy of 0.925 and Kappa of 0.900 for classifying cattle microbiomes into diets supplemented with oil, nitrate, a combination and controls.
Original languageEnglish
Title of host publicationProceedings of 2018 IEEE International Conference on Bioinformatics and Biomedicine
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages1854
Number of pages1860
ISBN (Electronic)978-1-5386-5488-0
DOIs
Publication statusPrint publication - 12 Mar 2018

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Functional analysis
Nutrition
Benchmarking
Learning systems
Nitrates

Cite this

Wassan, J. T., Zheng, H., Browne, F., Bowen, J. M., Walsh, P., Roehe, R., ... Wang, H. (2018). An integrative framework for functional analysis of cattle rumen microbiomes. In Proceedings of 2018 IEEE International Conference on Bioinformatics and Biomedicine (pp. 1854). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM.2018.8621104
Wassan, Jyotsna Talreja ; Zheng, Huiru ; Browne, Fiona ; Bowen, J M ; Walsh, Paul ; Roehe, R ; Dewhurst, RJ ; Palu, Cintia ; Kelly, Brian ; Wang, Haiying. / An integrative framework for functional analysis of cattle rumen microbiomes. Proceedings of 2018 IEEE International Conference on Bioinformatics and Biomedicine. Institute of Electrical and Electronics Engineers Inc., 2018. pp. 1854
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Wassan, JT, Zheng, H, Browne, F, Bowen, JM, Walsh, P, Roehe, R, Dewhurst, RJ, Palu, C, Kelly, B & Wang, H 2018, An integrative framework for functional analysis of cattle rumen microbiomes. in Proceedings of 2018 IEEE International Conference on Bioinformatics and Biomedicine. Institute of Electrical and Electronics Engineers Inc., pp. 1854. https://doi.org/10.1109/BIBM.2018.8621104

An integrative framework for functional analysis of cattle rumen microbiomes. / Wassan, Jyotsna Talreja; Zheng, Huiru; Browne, Fiona; Bowen, J M; Walsh, Paul; Roehe, R; Dewhurst, RJ; Palu, Cintia; Kelly, Brian; Wang, Haiying.

Proceedings of 2018 IEEE International Conference on Bioinformatics and Biomedicine. Institute of Electrical and Electronics Engineers Inc., 2018. p. 1854.

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

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AB - Metagenomics is the study of environmental microbial communities and has various applications and implications in biological research. This paper aims to study the role of microbial communities in cattle rumen and their relation to probiotic diet supplement usage as part of the EU H2020 MetaPIat project l1 MetaPlat, http://www.metaplat.eu. In this research, we proposed and evaluated a computational framework to classify 16S rRNA samples from Bos taurus (cattle) rumen microbiome into a diet phenotype. We performed analysis by benchmarking various phylogeny-driven methods based on integration of biological domain knowledge of relationships and non-phylogenetic methods based on the raw abundances. The integrative approach incorporating phylogenetic tree structure into machine learning (ML) modelling achieved a high predictive performance with Accuracy of 0.925 and Kappa of 0.900 for classifying cattle microbiomes into diets supplemented with oil, nitrate, a combination and controls.

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Wassan JT, Zheng H, Browne F, Bowen JM, Walsh P, Roehe R et al. An integrative framework for functional analysis of cattle rumen microbiomes. In Proceedings of 2018 IEEE International Conference on Bioinformatics and Biomedicine. Institute of Electrical and Electronics Engineers Inc. 2018. p. 1854 https://doi.org/10.1109/BIBM.2018.8621104