Browsing by Author "Heitmann, Sinjon"
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- ItemCharacterising the gut microbiome of ostrich chicks reared under intensive conditions(Stellenbosch : Stellenbosch University, 2020-12) Heitmann, Sinjon; Botes, Annelise; Stellenbosch University. Faculty of Science. Dept. of Biochemistry.ENGLISH ABSTRACT: Every year the ostrich industry suffers severe losses from the high mortality rate of intensively farmed ostrich chicks during early post-hatch development. One of the major contributors to the high mortality is enteritis, an enteric disease that stems largely from microbial imbalance. Efforts to reduce and prevent enteric diseases in ostrich chicks requires in part an extensive understanding of the changes in microbial composition within gastrointestinal tract (GIT). This study characterises the successional development of the microbiota present in the GIT of ostrich chicks reared under intensive conditions within the first three months post-hatch. In targeting the microbiota present in the small intestine, caeca, colon and faeces, the changes in bacterial composition and abundance provide insights unique to its development in the gut region and the development of the GIT. To achieve this, samples were taken from three ostrich chicks at five time points (15 chicks). For each time point the samples per gut region were pooled, microbial genomic DNA extracted and used for 16S metagenomic sequencing on the Ion Torrent platform. To improve definition at lower taxonomic levels, seven of the nine hypervariable regions in the 16S rRNA gene were sequenced. The raw sequence data was processed, and the bioinformatic analyses performed using the Ion Reporter software. Analyses of the gut regions over time found a progressive increase in bacterial diversity and stability despite the presence of both colonisation and extinctions events. Initial colonization of the GIT by week 2 coincided with the change in nutritive source from yolk to feed, and with it the introduction of a wide range of taxa including members from the Firmicutes, Bacteroidetes, Proteobacteria and Tenericutes phyla. Yet the changes in bacterial composition and abundance over time were not uniform between gut regions. The small intestine and colon regions were found to have substantial dissimilarities to remaining gut regions from week 0 - 4 and week 6 - 12, respectively. The changeover from small intestine to the colon was marked by the chronological shift of some species such as C. butyricum, C. disporicum and T. sanguinis, and with them the localised proliferation of potentially pathogenic species. The movement of C. butyricum away from the small intestine may remove its protective influence and allow the opportunistic proliferation of pathogenic species. The changeover between the small intestine and colon correlated both with the change in diet, as a part of the intensive rearing system, and the development of the colon into a more efficient fermentation chamber. Furthermore, the developed colon did not present the greater abundance of fibrolytic species from the Ruminococcaceae or Bacteroidaceae families as anticipated. Rather, a greater abundance of fibrolytic species from the Clostridiaceae family were present such as C. butyricum, C. chartatabidum, C. disporicum and C. paraputrificum, which suggest an accumulation of resistant starches and starch components in the colon. Furthermore, differences in bacterial composition were established in the core microbiota of the different gut regions, which shows that faecal samples do not provide a complete representation of GIT microbiota. Ideally the gut regions should be examined individually and together to understand the full impact that changes in diet have on the GIT. An examination of the distribution of relative abundance data may serve as a reference in adapting feeding strategies and strategies to manage GIT infections in intensively reared ostrich chicks.