Characterising the gut microbiome of ostrich chicks reared under intensive conditions

Heitmann, Sinjon (2020-12)

Thesis (MSc)--Stellenbosch University, 2020.

Thesis

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.

AFRIKAANSE OPSOMMING: Elke jaar ly die volstruisbedryf aan ernstige verliese as gevolg van die hoë vrektesyfer van intensief geproduseerde volstruiskuikens tydens vroeë na-uitbroei ontwikkeling. Een van die hoof bydraers tot die hoë mortaliteit is enteritis, 'n enteriese siekte wat grootliks uit ‘n mikrobiese wanbalans spruit. Pogings om enteriese siektes in volstruiskuikens te verminder en te voorkom vereis deels 'n uitgebreide begrip van die veranderinge in mikrobiese samestelling binne die spysverteringskanaal. Hierdie studie kenmerk die opeenvolgende ontwikkeling van die mikrobiota wat teenwoordig is in die spysverteringskanaal van volstruiskuikens, geproduseer onder intensiewe toestande, binne die eerste drie maande na uitbroei. Deur die mikrobiota in die dunderm, sekum, kolon en feses te teiken, bied die veranderinge in bakteriële samestelling en voorkoms insigte wat uniek is tot die ontwikkeling daarvan in die spesifieke dermdele en die ontwikkeling van die spysverteringskanaal self. Om dit te bereik, is monsters vanaf drie volstruiskuikens, by vyf tydspunte (15 kuikens) geneem. Op elke tydspunt is die monsters per dermdeel saamgevoeg, die mikrobiese genomiese DNS geïsoleer en vir 16S metagenomiese-opeenvolging op die Ion Torrent-platvorm gebruik. Om definisie by laer taksonomiese vlakke te verbeter, was die geenvolgorde van sewe van die nege hiperveranderlike areas in die 16S rRNA-geen bepaal. Die rou volgordedata is verwerk, en die bioinformatiese ontledings uitgevoer met behulp van die Ion Reporter sagteware. Ontledings van die dermdele het oor tyd 'n progressiewe toename in bakteriële diversiteit en stabiliteit getoon ten spyte van die teenwoordigheid van beide kolonisasie- en uitwissingsgebeurtenisse. Die aanvanklike kolonisasie van die spysverteringskanaal teen week 2 het saamgeval met die verandering in voedingsbron van dooier na voer, en tesame daarmee die bekendstelling van 'n wye verskeidenheid van taksa insluitend lede van die Firmicutes, Bacteroidetes, Proteobakterie en Tenericutes fila. Tog was die veranderinge in bakteriële samestelling en voorkoms met verloop van tyd nie eenvormig tussen dermdele nie. Daar is gevind dat die dunderm en kolondele aansienlike verskille gehad het in vergelyking met die oorblywende dermdele van week 0 - 4 en week 6 - 12 onderskeidelik. Die oorgang van die dunderm na die kolon is gekenmerk deur die chronologiese verskuiwing van sommige spesies soos C. butyricum, C. disporicum en T. sanguinis, en saam met hulle, die lokale vermeerdering van potensieel patogeniese spesies. Die beweging van C. butyricum weg van die dunderm af mag dus sy beskermende invloed verwyder en die opportunistiese vermeerdering van patogeniese spesies toelaat. Die oorgang tussen die dunderm en die kolon korreleer beide met die verandering in dieet, as 'n deel van die intensiewe produksiestelsel, en die ontwikkeling van die kolon in 'n meer doeltreffende fermentasie kamer. Verder het die ontwikkelde kolon nie die groter voorkoms van fibrolitiese spesies uit die Ruminococcaceae of Bacteroidaceae families getoon soos verwag nie. Daar was eerder 'n groter voorkoms van fibrolitiese spesies vanuit die Clostridiaceae familie soos C. butyricum, C. chartatabidum, C. disporicum en C. Paraputrificum teenwoordig, wat dui op 'n versameling van weerstandige stysel en styselkomponente in die kolon. Verdermeer was verskille in bakteriese samestelling in die kern mikrobiota van die verskillende dermdele daargestel wat toon dat feses monsters nie 'n volledige voorstelling van die spysverteringskanaal mikrobiota bied nie. Ideaal behoort die dermdele individueel en saam ondersoek te word om die volle impak, wat ‘n veranderinge in dieet op die spysverteringskanaal het, te verstaan. 'n Ondersoek van die verspreidingsdata van relatiewe voorkoms kan dien as n verwysing in die aanpassing van voedingsstrategieë en strategieë om dermkanaalinfeksies in intensief grootgemaakte volstruiskuikens te bestuur.

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