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Abstract
Metagenomics is proliferating for studying environmental microbial communities and their role in animal functions. This paper aims to study the role of functions of microbial communities present in cattle (Bos taurus) and their relation to dietary supplement usage. The functional study was conducted as part of the EU H2020 MetaPlat project11MetaPlat, http://www.metaplat.eu. In this research, we proposed a novel phylogeny-driven approach to classify 16S rRNA samples from cattle rumen microbiome and relate them to the functional phenotype of diet (referred to as functional analysis). Phylogeny covers biological relationships from different taxonomical levels combined with their respective evolutionary measures. We performed this analysis by proposing a novel method based on phylogeny-adjusted distance-based indices. These indices are used in ranking microbial feature space derived from the topology of the phylogenetic tree. The integrative approach incorporating phylogeny into feature engineering as part of machine learning (ML) modeling, achieved high predictive performance with Accuracy of 0.962 and Kappa of 0.950 for classifying cattle microbiome into the phenotype of a diet supplemented with oil, nitrate, combined (with oil and nitrate) and controls.
Original language | English |
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Title of host publication | Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019 |
Editors | Illhoi Yoo, Jinbo Bi, Xiaohua Tony Hu |
Publisher | Institute of Electrical and Electronics Engineers Inc. |
Pages | 1900-1906 |
Number of pages | 7 |
ISBN (Electronic) | 9781728118673 |
DOIs | |
Publication status | Print publication - Nov 2019 |
Event | 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019 - San Diego, United States Duration: 18 Nov 2019 → 21 Nov 2019 |
Publication series
Name | Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019 |
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Conference
Conference | 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019 |
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Country/Territory | United States |
City | San Diego |
Period | 18/11/19 → 21/11/19 |
Keywords
- Classification
- Machine Learning
- Metagenomics
- Phylogenetic INteraction-Adjusted index (PINA)
- Phylogeny
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Dive into the research topics of 'A Phylogeny-aware Feature Ranking for Classification of Cattle Rumen Microbiome'. Together they form a unique fingerprint.Projects
- 1 Finished
Research output
- 1 Article
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A heat diffusion multilayer network approach for the identification of functional biomarkers in rumen methane emissions
Wang, M., Wang, H., Zheng, H., Dewhurst, R. & Roehe, R., Aug 2021, In: Methods. 192, p. 57-66 10 p., 2020.09.014 .Research output: Contribution to journal › Article › peer-review
Open AccessFile7 Citations (Scopus)17 Downloads (Pure)