Microbiome community of farmed Common eland (Taurotragus oryx) under varied forage quality regimes

Bc. Lucie Benešová

Master's thesis

Abstract:

Ruminants are one of the most successful groups of herbivorous mammals. Their evolutionary success is greatly influenced by the microbiome, which is helping them to degrade cellulose, as well as it serves as a direct source of microbial protein. The majority of research of ruminant gastrointestinal tract (GIT) microbiome is focused on the rumen microbes of cattle. But there is not so much known about the faecal microbiome, even if the collection of faecal samples is not invasive and could be used also for wild species of ruminants. The aim of this research was to identify faecal and rumen microbiome of farmed Common Eland (Taurotragus oryx), to detect whether the faecal and rumen microbiome varies between each other and to determine if there are differences in microbiome due to changing diets. The research was done on the University Farm Estate Lány in the Czech Republic. Six adult eland males were involved in 3 treatments. The first treatment was grass hay only diet, the second treatment was alfalfa silage diet and the third treatment (control) was a common daily diet composed by a mixture of corn silage, alfalfa hay, meadow grass hay and barley straw. There were collected fresh faecal samples, post-mortem rectum and rumen samples. The samples were analyzed by molecular methods. Changes of faecal microbiome due to different diets were analyzed using PCR-amplified 16S rRNA, primarily by DGGE (degradation gradient gel electrophoresis) with following sequencing of important bands. There were also done Next Generation Sequencing (NGS). There were major changes of microbiome due to varied diets as well as significant difference between rumen and faecal samples. In all faecal samples, the most abundant phyla were Firmicutes (58-70%), on the other hand, the dominant phylum in rumen samples was Bacteroidetes (60.22%). The interesting difference between grass hay diet and alfalfa silage was in the phylum Proteobacteria, which were in the alfalfa diet represented only by 0.65%, but in the grass hay diet, their abundance was 17.62%.

Keywords

microbiome, antelope, large animal husbandry, ruminant physiology, nutrition, diet quality

Jazyk práce: English

Datum vytvoření / odevzdání či podání práce: 27. 4. 2018

Obhajoba závěrečné práce

• Vedúci: prof. RNDr. Pavla Hejcmanová, Ph.D.

Czech University of Life Sciences Prague

Faculty of Tropical AgriSciences

Master programme / odbor:
Tropical Agriculture / Wildlife Management in the Tropics and Subtropics