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

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.

Recovery of gene haplotypes from a metagenome

“…To find isoforms of industrially relevant enzymes we filtered annotations to classes of hydrolase (Enzyme Classification (EC): 3.2, 3.4 and 5.3) known to be found in the rumen [1]. As a proof of concept, a subset of 259 regions were selected by criteria including length and distribution of variants over aligned reads (see Methods).…”

“…It has become clear that population-level genetic variation drives competitiveness and niche specialisation in microbial communities [1]. Novel combinations of variants in individuals (haplotypes) are filtered by natural selection so that those that confer an advantage are retained [2].…”

“…Reads were partitioned with khmer and assembled with Velvet to generate an assembly which served as a pseudo-reference. The previous study annotated the assembly using MGKit[32] with the Uniprot database.To find isoforms of industrially relevant enzymes we filtered annotations to classes of hydrolase (Enzyme Classification (EC): 3.2, 3.4 and 5.3) known to be found in the rumen [1]. As a proof of concept, a subset of 259 regions were selected by criteria including length and distribution of variants over aligned reads (see Methods).…”

Probabilistic recovery of cryptic haplotypes from metagenomic data

“…However many communities (and especially microbial communities) maintain a fine balance between stability and plasticity that is driven both by their genetic breadth and diversity [4,5,6,7]. This necessitates a more holistic approach to allow the simultaneous characterisation of all haplotypes of all organisms in a microbial community (the "metahaplome").…”

“…http://dx.doi.org/10.1101/117838 doi: bioRxiv preprint first posted online Mar. 17, 2017; Genomic research is progressing beyond the use of consensus DNA sequences to represent species, towards the ultimate goal of complete characterisation of the genetic diversity that exists across their populations.So far, research has focused on characterising specific aspects of this diversity, for example: identifying the entire gene-set of all strains of a species (the pangenome) [1]; identifying the groups of genes (or genetic variants within) that are inherited together in organisms across entire populations (the haplome) [2] or in viruses, identifying strains related by mutations in a highly mutagenic environment (the quasispecies) [3].However many communities (and especially microbial communities) maintain a fine balance between stability and plasticity that is driven both by their genetic breadth and diversity [4,5,6,7]. This necessitates a more holistic approach to allow the simultaneous characterisation of all haplotypes of all organisms in a microbial community (the "metahaplome").…”