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.

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

“…Scaling these numbers according to average genome sizes using sequenced organisms from these groups actually increases this trend (Supplementary Table S3; Figure 5). However our estimates of the proportion of archaeal genes in the rumen metagenome from Methanobrevibacter (76.47%) and the relative proportions of genes from the major groups of bacteria are similar to those that were previously reported (Janssen and Kirs, 2008;Creevey et al, 2014), suggesting no sampling bias.…”

“…In contrast, microbial community profiling using 16S ribosomal RNA has revealed core communities can be defined for many environments (Turnbaugh et al, 2009;Lundberg et al, 2012;Creevey et al, 2014;Otani et al, 2014), indicating that niche specialisation of specific groups of organisms is somehow maintained even under the continued influence of horizontal gene transfer. One explanation may be that the horizontal acquisition of a single isoform of a novel gene is not enough to maintain a competitive advantage in fluctuating environmental conditions where a range of isoforms may be required to, for instance, maintain enzymatic activity (Stewart, 1976;Nevo, 2001).…”

Aspects of rumen adaptation in dairy cattle : morphological, functional, and gene expression changes of the rumen papillae and changes of the rumen microbiota during the transition period

“…These rumen specific bacteria, archaea, protozoa, yeasts and fungi are likely transferred to the calf via direct or indirect contact with saliva from ruminants with established rumen fermentation (Mizrahi, 2013). The fully developed rumen contains approximately 10 6 protozoa and 10 10 bacteria per ml of rumen contents, with both protozoa and bacteria each accounting for 45% of the total microbial mass (Creevey et al, 2014;. Genomic studies have shown that the rumen bacteria taxa are most numerous with 100s to 1000s possible species identified (McCann et al, 2014;Creevey et al, 2014;, depending on technique and sequencing depth used (Henderson et al, 2013).…”

“…The fully developed rumen contains approximately 10 6 protozoa and 10 10 bacteria per ml of rumen contents, with both protozoa and bacteria each accounting for 45% of the total microbial mass (Creevey et al, 2014;. Genomic studies have shown that the rumen bacteria taxa are most numerous with 100s to 1000s possible species identified (McCann et al, 2014;Creevey et al, 2014;, depending on technique and sequencing depth used (Henderson et al, 2013). However, only a small fraction of these bacterial species are represented by a cultured isolate (~150 different cultures known; Creevey et al, 2014), thus the vast majority are essentially unknown except for their genetic fingerprint.…”

“…Genomic studies have shown that the rumen bacteria taxa are most numerous with 100s to 1000s possible species identified (McCann et al, 2014;Creevey et al, 2014;, depending on technique and sequencing depth used (Henderson et al, 2013). However, only a small fraction of these bacterial species are represented by a cultured isolate (~150 different cultures known; Creevey et al, 2014), thus the vast majority are essentially unknown except for their genetic fingerprint. Compared with the bacteria, the number of taxa of protozoa and archaea is far smaller, with 12 genera of protozoa and 34 species-level groups of archaea covering > 99% of their respective communities .…”