Examination of the rumen bacteria and methanogenic archaea of wild impalas (Aepyceros melampus melampus) from Pongola, South Africa

摘要

Although the rumen microbiome of domesticatedruminants has been evaluated, few studies have explored therumen microbiome of wild ruminants, and no studies haveidentified the rumen microbiome in the impala (Aepycerosmelampus melampus). In the present study, next-generationsequencing and real-time polymerase chain reaction wereused to investigate the diversity and density of the bacteriaand methanogenic archaea residing in the rumen of five adultmale impalas, culled during the winter dry season in Pongola,South Africa. A total of 15,323 bacterial 16S rRNA genesequences (from five impala), representing 3,892 differentphylotypes, were assigned to 1,902 operational taxonomicunits (OTUs). A total of 20,124 methanogen 16S rRNA genesequence reads (from four impala), of which 5,028 wereunique, were assigned to 344 OTUs. From the total sequencereads, Bacteroidetes, Proteobacteria, and Firmicutes were themost abundant bacterial phyla. While the majority of thebacterial genera found were unclassified, Prevotella andCupriavidus were the most abundant classified genera. Formethanogens, the genera Methanobrevibacter andMethanosphaera represented 94.3 % and 4.0 % of the classifiedsequences, respectively. Most notable was the identificationof Methanobrevibacter thaueri-like 16S rRNA gene sequencereads in all four impala samples, representing greater than 30 % of each individual’s total sequences. Both data setsare accessible through NCBI’s Sequence Read Archive (SRA),under study accession number SRP [048619]. The densities ofbacteria (1.26×1010–3.82×1010 cells/ml whole rumen contents)and methanogens (4.48×108–7.2×109 cells/ml of wholerumen contents) from five individual impala were similar tothose typically observed in domesticated ruminants.