Journal Article

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

St-Pierre, Benoit, van Hoven, Wouter, Wright, André-Denis G., Lachance, Hannah, Cersosimo, Laura M.

2015

Overview

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.

• Publisher: Springer-Verlag,Springer,Springer US,Springer Nature B.V
• Subject: adults / Aepyceros melampus / Aepyceros melampus melampus / Animals / Antelopes - microbiology / Archaea / Archaea - classification / Archaea - genetics / Archaea - isolation & purification / Bacteria / Bacteria - classification / Bacteria - genetics / Bacteria - isolation & purification / Biomedical and Life Sciences / Cupriavidus / data collection / DNA sequencing / Domestication / Dry season / Ecology / ENVIRONMENTAL MICROBIOLOGY / Firmicutes / Gastrointestinal Microbiome / Gene sequencing / Genera / Geoecology/Natural Processes / high-throughput nucleotide sequencing / Impalas / Life Sciences / Male / Melampus / Methanobrevibacter / Methanogenic archaea / Methanogenic bacteria / methanogens / Microbial Ecology / Microbiology / microbiome / Microbiomes / Molecular Sequence Data / Nature Conservation / Next-generation sequencing / Nucleotide sequence / nucleotide sequences / PCR / phylotype / Polymerase chain reaction / Prevotella / Proteobacteria / quantitative polymerase chain reaction / Real time / ribosomal RNA / RNA, Archaeal - genetics / RNA, Bacterial - genetics / RNA, Ribosomal, 16S - genetics / rRNA 16S / rumen / Rumen - microbiology / rumen bacteria / Rumen microorganisms / Ruminantia / ruminants / South Africa / Water Quality/Water Pollution