Masters Degrees (Animal Sciences)

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Browsing Masters Degrees (Animal Sciences) by browse.metadata.advisor "Burger, Johan T."

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    Molecular characterization of the penile microbiome of Dorper rams (Ovis aries)
    (Stellenbosch : Stellenbosch University, 2017-03) Courchay, Auberi Marie Madeleine; Lambrechts, Helet; Burger, Johan T.; Stellenbosch University. Faculty of AgriSciences. Dept. of Animal Sciences.
    ENGLISH ABSTRACT: Characterizing the bacterial community inhabiting the penile environment of Dorper rams may provide insight into the aetiology of ulcerative balanoposthitis (UB), a venereal disease of unknown aetiology, which occurs predominantly in this breed, and that is of great economic importance to the mutton industry in South Africa. Profiling of the bacteria present in the penile environment of healthy and diseased rams was carried out previously using culture-based methods. These culture-based studies identified Mycoplasma mycoides mycoides large colony (MMMLC) and Trueperella pyogenes as potentially contributing to the incidence of UB. Although cultured-based methods have been described as the gold standard for identification of bacteria, many bacteria are uncultivable or grow slowly and poorly in-vitro. The advent of high throughput next generation sequencing (HT-NGS), a culture-independent bacterial identification approach, has offered high coverage and depths in determining the bacterial penile community. Thus, this study aimed to characterize and compare the penile bacterial microbiome of Dorper rams that were healthy and diseased by means of 16S amplicon sequencing, a method of HT-NGS. Swab samples of the preputial and penile mucosa were collected from 113 rams, of which 40 Dorper ram samples (20 infected, 20 healthy) were chosen for further analysis in this study. Genomic DNA was extracted and amplified based on the V3V4 hypervariable region of the 16S rRNA bacterial gene. Bioinformatics analysis was performed using UPARSE and the ecological and statistical analyses such as Principal Coordinate Analysis (PCoA) was performed in QIIME and XLSTAT. Additional analyses comparing the predicted bacterial microbiota in healthy and diseased populations was carried out using LEfSe. A total of 789 OTUs from 9 964 842 sequences of high quality were obtained from the healthy and diseased communities indicating a high bacterial diversity in the penile environment, higher than previously reported and isolated using culture-based bacterial identification methods. The genus Corynebacterium was the most dominant genus identified (20.9%), irrespective of health status. A high inter-sample variation in microbiota was revealed. There were no significant differences in bacterial diversity or community composition between the healthy and diseased ram groups. The microbiota population was thus similar, with a few OTUs of high biological relevance belonging to genera Fusobacterium and Porphyromonas, as well as uncharacterized genera within Aerococaceae and Bacteroidales that were enriched in the diseased community. MMMLC and Trueperella pyogenes were not associated with UB in this study, which is contradictory to previous reports. However, a new Mycoplasma species, Mycoplasma hyopharyngis, not previously isolated in sheep and in cases of UB in Dorper rams, was identified and although not significantly different, had a higher abundance in the diseased population. The prevalence and predominance of Corynebacterium across all samples suggests this genus forms part of the core microbiome of the penile environment. High inter-sample variation in microbiota may depict true biological representation, however, future studies using homogenous ram populations (i.e. same type, same age) under the same environmental factors (i.e. management, feeding regime, etc.) should be conducted to validate these findings. Ulcerative balanoposthitis is not caused as a result of a change in bacterial diversity or community composition but OTUs enriched in the diseased ram population may be disease-specific/disease-associated and their role in UB warrants further investigation. No definitive aetiological agent was thus identified but the OTUs enriched in diseased rams can help direct future studies towards the identification of an aetiological agent of UB.