Determining the culturability of the rumen bacterial microbiome

Abstract

The goal of the Hungate1000 project is to generate a reference set of rumen microbial genome sequences. Toward this goal we have carried out a meta-analysis using information from culture collections, scientific literature, and the NCBI and RDP databases and linked this with a comparative study of several rumen 16S rRNA gene-based surveys. In this way we have attempted to capture a snapshot of rumen bacterial diversity to examine the culturable fraction of the rumen bacterial microbiome. Our analyses have revealed that for cultured rumen bacteria, there are many genera without a reference genome sequence. Our examination of culture-independent studies highlights that there are few novel but many uncultured taxa within the rumen bacterial microbiome. Taken together these results have allowed us to compile a list of cultured rumen isolates that are representative of abundant, novel and core bacterial species in the rumen. In addition, we have identified taxa, particularly within the phylum Bacteroidetes, where further cultivation efforts are clearly required. This information is being used to guide the isolation efforts and selection of bacteria from the rumen microbiota for sequencing through the Hungate1000.

Figure 1

Inverted circular phylogenetic tree of the 2405 rumen bacterial OTUs identified as part of this analysis. The blue graph in the middle represents the average scaled proportion of each OTU from across the seven datasets analysed. The colour gradient surrounding that represents the prevalence of each OTU across all seven datasets analysed (dark = most prevalent, light = least prevalent). The major groups of bacteria that are represented in the tree are indicated. The clades that are most abundant in the rumen are indicated in red and numbered I to VIII in order of abundance. The statistics associated with clades numbered I to VIII are detailed in Supporting Information Table S4.

Figure 2

On both plots, the x-axis shows the scaled phylogenetic distance from the nearest cultured isolate and the y-axis the average scaled abundance for each OTU. A. The circles are coloured according to their prevalence across the seven datasets as indicated by the colour gradient. The black dotted line illustrates the 0.25 cut-off discussed in the text. B. The subplot of only those 98 core OTUs colour-coded according to taxonomy.

Figure 3

Bacteriodetes-specific tree of OTUs, including those from the RDP database. OTUs which contain sequences from the RDP database are marked with a red dot. The green dots highlight OTUs, which contain RDP isolates that have been annotated as of rumen origin. The statistics associated with clades numbered 1 to 10 are detailed in Supporting Information Table S4.