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Exploring the Molecular Diversity and Density of the Rumen Microbiome within the Impala (Aepyceros melampus melampus) from Pongola, South Africa
The rumen microbiome of domesticated ruminants has been studied extensively, but few studies have explored the microbiome of wild ruminants and no studies have used a metagenomic approach to examine the rumen microbiota within the impala (Aepyceros melampus melampus). Impala, like all domesticated ruminants, have a consortium of anaerobic microorganisms inhabiting their foregut (i.e. the rumen) that contribute to the feed efficiency of the animal, as well as greenhouse gas emissions. The present investigation seeks to expand our knowledge about the rumen microbial community of the impala while drawing comparisons to their domesticated relatives that could lead to advances in both feed efficiency and methane mitigation strategies.
The rumen contents from four male impala culled in the Kwazulu-Natal province of Pongola, South Africa were collected post-mortem. Once bacterial and archaeal amplicons were generated, next-generation sequencing techniques (i.e. Roche 454-pyrosequencing) were used to identify the diversity of bacterial and methanogenic archaeal (i.e. methanogens) 16S rRNA gene sequences. Real-time PCR amplification of the 16S rRNA gene was used to estimate the density of the bacterial population (R2 = 0.997), while the mcrA (methyl coenzyme-M reductase) gene was used to estimate the density of the methanogen population (R2= 0.997).
Using the bioinformatic platform, MOTHUR, a total of 20,124 methanogen sequence reads were assigned to 344 operational taxonomic units (OTUs) using a sequence identity cutoff of 3%. A high sampling efficiency was observed with OTU coverages greater than 99% for each individual impala, along with similar Shannon indices of 1.90 ± .003. The Ribosomal Database Project (RDP) Classifier classified 94.3% of the reads to the genus, Methanobrevibacter, 4.2% of the reads to the genus, Methanosphaera, with the remaining 1.5% of the reads being “unclassified.”
Most notably was the abundance of Methanobrevibacter thaueri-related methanogen sequence reads in all four impala samples, representing greater than 30% of each animal’s total sequences. This high abundance of Methanobrevibacter thaueri-related methanogen sequences has not been observed in previous studies of domesticated or wild ruminants, suggesting that either the diet and/or the rumen physiology of the impala may differ from previously studied ruminants. The diversity of the rumen bacteria will also be elucidated and discussed. Future studies to look at other factors that affect the rumen environment, like gender, should be performed to see if these findings are consistent.
Keywords: methanogens, bacteria, impala, rumen, Methanobrevibacter, operational taxonomic units