Browsing by Author "Wells, Felicia"

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    Investigating the developmental changes in the gut microbiome of naturally reared ostrich chicks.
    (Stellenbosch : Stellenbosch University, 2021-03) Wells, Felicia; Botes, Annelise; Bellstedt, D. U.; Stellenbosch University. Faculty of Science. Dept. of Biochemistry.
    ENGLISH ABSTRACT: The South African ostrich industry has suffered losses due to premature losses of intensively reared ostrich chicks because of gastrointestinal tract (GIT) infections. It is known that survival increases with less GIT infections observed if a production system is used where chicks are raised naturally with the hen. The purpose of this study was therefore to evaluate the change in gut bacteria of naturally reared ostrich chicks during the first three months post hatch. To this end, Ion Torrent 16S-fragment metagenomic sequencing was used in combination with the Ion Reporter pipeline for analysis of sequence data. Different genomic (gDNA) isolation protocols were evaluated as well as the use of a stabilising solution to allow for sampling in remote areas. Overall, the protocol using the PSP® Spin Stool DNA Plus Kit, outperformed the rest of the protocols regarding time, efficiency and extracting the most and most highly diverse bacteria. Although the stabilising solution improved the ease of sampling, repeated freezing and thawing reduced gDNA yield. Results also indicated that the targeting of multiple 16S V-regions with Ion Torrent improved the identification of microbial taxa. Analysis of samples at weeks 0, 2, 4, 6 and 12 after hatch from different sections of the ostrich chick GIT indicated that the chicks already have a bacterial microbiome present within their GIT at hatch. A substantial bacterial shift was observed between week 0 and week 2, and another from week 6-12. The changes from weeks 0-2 can be attributed to the change from yolk as main nutrient to feed whilst the gradual stabilization in bacterial population from week 6-12 is the result of the chick developing an adult-like hindgut fermenter. A comparison of microbiome of the different GIT sections with each other, showed that the stool sample, colon and caecum had the same dominant phyla (Figure 4.16: B), classes and families (Figure 4.19), however, at the genus level the differentiation between the stool sample, colon and caecum became more distinct (Figure 4.20: A). These changes between the different GIT sections are attributed to the unique physiological environments within each GIT section. Thus, the extrapolation of the ostrich chick GIT microbiome from a stool sample only must be done with caution. The microbiome data obtained in this study could in future studies be compared to that obtained for intensively reared ostrich chicks to shed some light on the impact of production systems on the intestinal health of ostrich chicks.