Comparative integrated omics

Identification of key functionalities in microbial community-wide metabolic networks

Hugo Roume, Anna Heintz-Buschart, Emilie E.L. Muller, Patrick May, Venkata P. Satagopam, Cédric C. Laczny, Shaman Narayanasamy, Laura A. Lebrun, Michael R. Hoopmann, James M. Schupp, John D. Gillece, Nathan D. Hicks, David M. Engelthaler, Thomas Sauter, Paul S Keim, Robert L. Moritz, Paul Wilmes

Research output: Contribution to journalArticle

27 Citations (Scopus)

Abstract

BACKGROUND: Mixed microbial communities underpin important biotechnological processes such as biological wastewater treatment (BWWT). A detailed knowledge of community structure and function relationships is essential for ultimately driving these systems towards desired outcomes, e.g., the enrichment in organisms capable of accumulating valuable resources during BWWT. METHODS: A comparative integrated omic analysis including metagenomics, metatranscriptomics and metaproteomics was carried out to elucidate functional differences between seasonally distinct oleaginous mixed microbial communities (OMMCs) sampled from an anoxic BWWT tank. A computational framework for the reconstruction of community-wide metabolic networks from multi-omic data was developed. These provide an overview of the functional capabilities by incorporating gene copy, transcript and protein abundances. To identify functional genes, which have a disproportionately important role in community function, we define a high relative gene expression and a high betweenness centrality relative to node degree as gene-centric and network topological features, respectively. RESULTS: Genes exhibiting high expression relative to gene copy abundance include genes involved in glycerolipid metabolism, particularly triacylglycerol lipase, encoded by known lipid accumulating populations, e.g., Candidatus Microthrix parvicella. Genes with a high relative gene expression and topologically important positions in the network include genes involved in nitrogen metabolism and fatty acid biosynthesis, encoded by Nitrosomonas spp. and Rhodococcus spp. Such genes may be regarded as 'keystone genes' as they are likely to be encoded by keystone species. CONCLUSION: The linking of key functionalities to community members through integrated omics opens up exciting possibilities for devising prediction and control strategies for microbial communities in the future.

Original languageEnglish (US)
Article number15007
Journalnpj Biofilms and Microbiomes
Volume1
DOIs
StatePublished - Jun 17 2015
Externally publishedYes

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Metabolic Networks and Pathways
Genes
Waste Water
Gene Regulatory Networks
Nitrosomonas
Rhodococcus
Gene Expression
Metagenomics
Lipase
Nitrogen
Fatty Acids
Lipids
Population

ASJC Scopus subject areas

  • Biotechnology
  • Microbiology
  • Applied Microbiology and Biotechnology

Cite this

Roume, H., Heintz-Buschart, A., Muller, E. E. L., May, P., Satagopam, V. P., Laczny, C. C., ... Wilmes, P. (2015). Comparative integrated omics: Identification of key functionalities in microbial community-wide metabolic networks. npj Biofilms and Microbiomes, 1, [15007]. https://doi.org/10.1038/npjbiofilms.2015.7

Comparative integrated omics : Identification of key functionalities in microbial community-wide metabolic networks. / Roume, Hugo; Heintz-Buschart, Anna; Muller, Emilie E.L.; May, Patrick; Satagopam, Venkata P.; Laczny, Cédric C.; Narayanasamy, Shaman; Lebrun, Laura A.; Hoopmann, Michael R.; Schupp, James M.; Gillece, John D.; Hicks, Nathan D.; Engelthaler, David M.; Sauter, Thomas; Keim, Paul S; Moritz, Robert L.; Wilmes, Paul.

In: npj Biofilms and Microbiomes, Vol. 1, 15007, 17.06.2015.

Research output: Contribution to journalArticle

Roume, H, Heintz-Buschart, A, Muller, EEL, May, P, Satagopam, VP, Laczny, CC, Narayanasamy, S, Lebrun, LA, Hoopmann, MR, Schupp, JM, Gillece, JD, Hicks, ND, Engelthaler, DM, Sauter, T, Keim, PS, Moritz, RL & Wilmes, P 2015, 'Comparative integrated omics: Identification of key functionalities in microbial community-wide metabolic networks', npj Biofilms and Microbiomes, vol. 1, 15007. https://doi.org/10.1038/npjbiofilms.2015.7
Roume, Hugo ; Heintz-Buschart, Anna ; Muller, Emilie E.L. ; May, Patrick ; Satagopam, Venkata P. ; Laczny, Cédric C. ; Narayanasamy, Shaman ; Lebrun, Laura A. ; Hoopmann, Michael R. ; Schupp, James M. ; Gillece, John D. ; Hicks, Nathan D. ; Engelthaler, David M. ; Sauter, Thomas ; Keim, Paul S ; Moritz, Robert L. ; Wilmes, Paul. / Comparative integrated omics : Identification of key functionalities in microbial community-wide metabolic networks. In: npj Biofilms and Microbiomes. 2015 ; Vol. 1.
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AU - Satagopam, Venkata P.

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AU - Hoopmann, Michael R.

AU - Schupp, James M.

AU - Gillece, John D.

AU - Hicks, Nathan D.

AU - Engelthaler, David M.

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N2 - BACKGROUND: Mixed microbial communities underpin important biotechnological processes such as biological wastewater treatment (BWWT). A detailed knowledge of community structure and function relationships is essential for ultimately driving these systems towards desired outcomes, e.g., the enrichment in organisms capable of accumulating valuable resources during BWWT. METHODS: A comparative integrated omic analysis including metagenomics, metatranscriptomics and metaproteomics was carried out to elucidate functional differences between seasonally distinct oleaginous mixed microbial communities (OMMCs) sampled from an anoxic BWWT tank. A computational framework for the reconstruction of community-wide metabolic networks from multi-omic data was developed. These provide an overview of the functional capabilities by incorporating gene copy, transcript and protein abundances. To identify functional genes, which have a disproportionately important role in community function, we define a high relative gene expression and a high betweenness centrality relative to node degree as gene-centric and network topological features, respectively. RESULTS: Genes exhibiting high expression relative to gene copy abundance include genes involved in glycerolipid metabolism, particularly triacylglycerol lipase, encoded by known lipid accumulating populations, e.g., Candidatus Microthrix parvicella. Genes with a high relative gene expression and topologically important positions in the network include genes involved in nitrogen metabolism and fatty acid biosynthesis, encoded by Nitrosomonas spp. and Rhodococcus spp. Such genes may be regarded as 'keystone genes' as they are likely to be encoded by keystone species. CONCLUSION: The linking of key functionalities to community members through integrated omics opens up exciting possibilities for devising prediction and control strategies for microbial communities in the future.

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