Investigating the developmental changes in the gut microbiome of naturally reared ostrich chicks.

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dc.contributor.advisorBotes, Anneliseen_ZA
dc.contributor.advisorBellstedt, D. U.en_ZA
dc.contributor.authorWells, Feliciaen_ZA
dc.contributor.otherStellenbosch University. Faculty of Science. Dept. of Biochemistry.en_ZA
dc.date.accessioned2021-03-03T08:44:55Z
dc.date.accessioned2021-04-22T10:13:22Z
dc.date.available2021-03-03T08:44:55Z
dc.date.issued2021-03
dc.descriptionThesis (MSc)--Stellenbosch University, 2021. en_ZA
dc.description.abstractENGLISH 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 PSPĀ® 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.en_ZA
dc.description.abstractAFRIKAANSE OPSOMMING: Die Suid-Afrikaanse volstruis bedryf het hewige verlies deur gemaak as gevolg van voortydige verliese van intensief grootgemaakte volstruiskuikens as gevolg van dermkanaal infeksies. Dit is bekend dat oorlewing verhoog, met minder dermkanaal infeksies waarneembaar, wanneer die kuikens natuurlik grootgemaak word saam met die hen. Die doel van hierdie studie was dus om die veranderinge in dermkanaal bakterieĆ« te evalueer van natuurlik grootgemaakte volstruiskuikens, gedurende die eerste drie maande na uitbroei. Sodoende was Ion Torrent 16S-fragment metagenomiese volgordebepaling gebruik in kombinasie met die Ion Reporter pyplyn vir data analise van die volgorde data. Verskillende genomiese DNA (gDNA) isolasie protokolle was geĆ«valueer asook die gebruik van ā€˜n stabilisering oplossing om in afgeleĆ« plekke bemonstering te kan doen. Oorhoofs, het die protokol van die ā€œPSPĀ® Spin Stool DNA Plus Kitā€ die beste presteer relatief tot die res van die protokolle met betrekking tot tyd, effektiwiteit en isolasie van die meeste en hoogs diverse bakterieĆ«. Alhoewel die stabilisering oplossing die bemonstering proses vergemaklik het, het die gDNA opbrengs afgeneem wanneer dit herhaaldelik gevries en ontdooi was. Die resultate het ook aangetoon dat as veelvuldige 16S V-areas geteiken word met Ion Torrent verbeter die mikrobiese taksa identifikasie. Analise van monsters by week 0, 2, 4, 6 en 12 vanaf die verskillende dele van die volstruiskuiken se dermkanaal het aangedui dat die kuikens reeds met uitbroei ā€˜n bakteriese mikrobioom teenwoordig het in hulle dermkanaal. ā€˜n Groot verskuiwing van die bakterieĆ« was opgelet tussen week 0 en week 2, en dan weer vanaf week 6-12. Die verandering vanaf week 0-2 kan toegeskryf word aan die verandering vanaf eiergeel as hoof voedingstof na voer, terwyl die bakteriese populasie geleidelik stabiliseer vanaf week 6-12. Hierdie geleidelike stabilisering is as gevolg van die kuiken se dermkanaal wat ontwikkel in ā€˜n meer volwasse agterderm verteerder. Deur die verskillende dermdele met mekaar te vergelyk, het die mismonster, kolon en sekum dieselfde dominante fila (Figuur 4.16: B), klasse en familie (Figuur 4.19) gehad, maar op genus vlak kon die mismonster, kolon en sekum duidelik van mekaar onderskei word (Figuur 4.20: A). Hierdie veranderinge tussen die verskillende dermdele kan toegeskryf word aan die unieke fisiologiese omgewings in elk van die dermdele. Afleidings oor die volstruiskuiken se dermkanaal mikrobioom vanaf ā€˜n mismonster moet dus met omsigtigheid gedoen word. Die mikrobioom data verkry uit hierdie studie kan in die toekoms vergelyk word met dit verkry vanaf intensief grootgemaakte volstruiskuikens, om sodoende insig te kry oor die impak van produksie sisteme op die gesondheid van die volstruiskuikens se dermkanaal.af_ZA
dc.description.versionMastersen_ZA
dc.embargo.lift2023-12-31
dc.embargo.terms2023-12-31
dc.format.extentviii, 343 pages : illustrationsen_ZA
dc.identifier.urihttp://hdl.handle.net/10019.1/110308
dc.language.isoen_ZAen_ZA
dc.publisherStellenbosch : Stellenbosch Universityen_ZA
dc.rights.holderStellenbosch Universityen_ZA
dc.subject.lcshOstriches -- Breeding -- South Africaen_ZA
dc.subject.lcshChicks -- Developmenten_ZA
dc.subject.lcshOstrich chicks -- Growthen_ZA
dc.subject.lcshOstrich chicks -- Diseases -- South Africaen_ZA
dc.subject.lcshGastrointestinal system -- Infectionsen_ZA
dc.subject.lcshGut microbiome -- Infections -- Pathogenesisen_ZA
dc.subject.lcshMicrobiomes -- Data processingen_ZA
dc.subject.lcshGenomics -- Evaluationen_ZA
dc.subject.nameUCTDen_ZA
dc.titleInvestigating the developmental changes in the gut microbiome of naturally reared ostrich chicks.en_ZA
dc.typeThesisen_ZA
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