Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome.

Rubino, Francesco, Carberry, Ciara, M Waters, Sinéad, Kenny, David, McCabe, Matthew S and Creevey, Christopher J (2017) Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome.. The ISME journal, 11 4: 932-944. doi:10.1038/ismej.2016.172


Author Rubino, Francesco
Carberry, Ciara
M Waters, Sinéad
Kenny, David
McCabe, Matthew S
Creevey, Christopher J
Title Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome.
Journal name The ISME journal   Check publisher's open access policy
ISSN 1751-7370
Publication date 2017-04-01
Sub-type Article (original research)
DOI 10.1038/ismej.2016.172
Open Access Status Not yet assessed
Volume 11
Issue 4
Start page 932
End page 944
Total pages 13
Abstract Many microbes in complex competitive environments share genes for acquiring and utilising nutrients, questioning whether niche specialisation exists and if so, how it is maintained. We investigated the genomic signatures of niche specialisation in the rumen microbiome, a highly competitive, anaerobic environment, with limited nutrient availability determined by the biomass consumed by the host. We generated individual metagenomic libraries from 14 cows fed an ad libitum diet of grass silage and calculated functional isoform diversity for each microbial gene identified. The animal replicates were used to calculate confidence intervals to test for differences in diversity of functional isoforms between microbes that may drive niche specialisation. We identified 153 genes with significant differences in functional isoform diversity between the two most abundant bacterial genera in the rumen (Prevotella and Clostridium). We found Prevotella possesses a more diverse range of isoforms capable of degrading hemicellulose, whereas Clostridium for cellulose. Furthermore, significant differences were observed in key metabolic processes indicating that isoform diversity plays an important role in maintaining their niche specialisation. The methods presented represent a novel approach for untangling complex interactions between microorganisms in natural environments and have resulted in an expanded catalogue of gene targets central to rumen cellulosic biomass degradation.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Unknown

Document type: Journal Article
Sub-type: Article (original research)
Collection: Pubmed Import
 
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Created: Wed, 15 Nov 2017, 13:50:50 EST