Characterization of cecal microbiome of the emu (Dromaius novaehollandiae)

Abstract

Emus (Dromaius novaehollandiae), large flightless ratites native to Australia, are farmed for their fat and meat. They are omnivorous, feeding on a wide variety of plants and insects, preferring high quality items in which nutrients are concentrated. They have a relatively simple gastrointestinal tract, with a relatively short mean digesta retention time. However, despite these limitations, emus are able to digest 35 to 45% of the ingested dietary neutral detergent fiber, which may contribute up to 50% of their maintenance energy requirement. Vertebrates lack endogenous enzymes that are capable of digesting complex carbohydrates and therefore rely on microbial organisms in their gastrointestinal tract to accomplish this. However, nothing is known about the microbial diversity in the emu hindgut. In this study, we evaluated the phylogenetic diversity of the cecal microbiome of 4 emus fed a barley-alfalfa-canola based diet, using 454 pyrotag sequencing after amplification for v3–v5 region of bacterial 16s rRNA gene. After very stringent quality trimming on raw data, 96,118 16S rDNA sequence reads (24,030 ± 2495 reads/sample) with an average read length of 508 bp were generated. A mean 727 (418- 1108) operational taxonomic units (OTUs) belonging to 9 bacterial phyla were identified. The most predominant bacterial phyla were Bacteroidetes (44% of total classified diversity), Proteobacteria (39%), Fusobacteria (9%), and Firmicutes (6%). Microbes from the remaining phyla together accounted for less than 1% of the total classified diversity. The estimated microbial richness (Chao1) was 1481 ± 331 OTUs, whereas the Shannon diversity index was 4.5 ± 0.3. These results indicated emus’ ceca may have higher bacterial diversity than that of chickens. This is the first study to characterize the microbial community of the gastrointestinal tract of a ratite using pyrosequencing, providing a baseline for further study.