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Nucleic Acids Res. 2015 Nov 16;43(20):9600-12. doi: 10.1093/nar/gkv973. Epub 2015 Sep 29.

The players may change but the game remains: network analyses of ruminal microbiomes suggest taxonomic differences mask functional similarity.

Author information

1
Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA.
2
Department of Civil & Environmental Engineering, University of Missouri, Columbia, MO 65211, USA.
3
Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA Informatics Institute, University of Missouri, Columbia, MO 65211, USA.
4
Informatics Institute, University of Missouri, Columbia, MO 65211, USA Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA.
5
Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA Informatics Institute, University of Missouri, Columbia, MO 65211, USA conantg@missouri.edu.

Abstract

By mapping translated metagenomic reads to a microbial metabolic network, we show that ruminal ecosystems that are rather dissimilar in their taxonomy can be considerably more similar at the metabolic network level. Using a new network bi-partition approach for linking the microbial network to a bovine metabolic network, we observe that these ruminal metabolic networks exhibit properties consistent with distinct metabolic communities producing similar outputs from common inputs. For instance, the closer in network space that a microbial reaction is to a reaction found in the host, the lower will be the variability of its enzyme copy number across hosts. Similarly, these microbial enzymes that are nearby to host nodes are also higher in copy number than are more distant enzymes. Collectively, these results demonstrate a widely expected pattern that, to our knowledge, has not been explicitly demonstrated in microbial communities: namely that there can exist different community metabolic networks that have the same metabolic inputs and outputs but differ in their internal structure.

PMID:
26420832
PMCID:
PMC4787786
DOI:
10.1093/nar/gkv973
[Indexed for MEDLINE]
Free PMC Article

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