Abstract:
Although the rumen microbiome of domesticated
ruminants has been evaluated, few studies have explored the
rumen microbiome of wild ruminants, and no studies have
identified the rumen microbiome in the impala (Aepyceros
melampus melampus). In the present study, next-generation
sequencing and real-time polymerase chain reaction were
used to investigate the diversity and density of the bacteria
and methanogenic archaea residing in the rumen of five adult
male impalas, culled during the winter dry season in Pongola,
South Africa. A total of 15,323 bacterial 16S rRNA gene
sequences (from five impala), representing 3,892 different
phylotypes, were assigned to 1,902 operational taxonomic
units (OTUs). A total of 20,124 methanogen 16S rRNA gene
sequence reads (from four impala), of which 5,028 were
unique, were assigned to 344 OTUs. From the total sequence
reads, Bacteroidetes, Proteobacteria, and Firmicutes were the
most abundant bacterial phyla. While the majority of the
bacterial genera found were unclassified, Prevotella and
Cupriavidus were the most abundant classified genera. For
methanogens, the genera Methanobrevibacter and
Methanosphaera represented 94.3 % and 4.0 % of the classified
sequences, respectively. Most notable was the identification
of Methanobrevibacter thaueri-like 16S rRNA gene sequence
reads in all four impala samples, representing greater than 30 % of each individual’s total sequences. Both data sets
are accessible through NCBI’s Sequence Read Archive (SRA),
under study accession number SRP [048619]. The densities of
bacteria (1.26×1010–3.82×1010 cells/ml whole rumen contents)
and methanogens (4.48×108–7.2×109 cells/ml of whole
rumen contents) from five individual impala were similar to
those typically observed in domesticated ruminants.
