Browsing by Author "Cloete, Schalk"

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    Direct PCR offers a fast and reliable alternative to conventional DNA isolation methods for gut microbiomes
    (American Society for Microbiology, 2017) Videvall, Elin; Strandh, Maria; Engelbrecht, Anel; Cloete, Schalk; Cornwallis, Charlie K.
    The gut microbiome of animals is emerging as an important factor influencing ecological and evolutionary processes. A major bottleneck in obtaining microbiome data from large numbers of samples is the time-consuming laboratory procedures required, specifically the isolation of DNA and generation of amplicon libraries. Recently, direct PCR kits have been developed that circumvent conventional DNA extraction steps, thereby streamlining the laboratory process by reducing preparation time and costs. However, the reliability and efficacy of direct PCR for measuring host microbiomes have not yet been investigated other than in humans with 454 sequencing. Here, we conduct a comprehensive evaluation of the microbial communities obtained with direct PCR and the widely used Mo Bio PowerSoil DNA extraction kit in five distinct gut sample types (ileum, cecum, colon, feces, and cloaca) from 20 juvenile ostriches, using 16S rRNA Illumina MiSeq sequencing. We found that direct PCR was highly comparable over a range of measures to the DNA extraction method in cecal, colon, and fecal samples. However, the two methods significantly differed in samples with comparably low bacterial biomass: cloacal and especially ileal samples. We also sequenced 100 replicate sample pairs to evaluate repeatability during both extraction and PCR stages and found that both methods were highly consistent for cecal, colon, and fecal samples (rs > 0.7) but had low repeatability for cloacal (rs = 0.39) and ileal (rs = −0.24) samples. This study indicates that direct PCR provides a fast, cheap, and reliable alternative to conventional DNA extraction methods for retrieving 16S rRNA data, which can aid future gut microbiome studies.
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    Early-life gut dysbiosis linked to juvenile mortality in ostriches
    (BMC (part of Springer Nature), 2020-10-12) Videvall, Elin; Song, Se Jin; Bensch, Hanna M.; Strandh, Maria; Engelbrecht, Anel; Serfontein, Naomi; Hellgren, Olof; Olivier, Adriaan; Cloete, Schalk; Knight, Rob; Cornwallis, Charlie K.
    Background: Imbalances in the gut microbial community (dysbiosis) of vertebrates have been associated with several gastrointestinal and autoimmune diseases. However, it is unclear which taxa are associated with gut dysbiosis, and if particular gut regions or specific time periods during ontogeny are more susceptible. We also know very little of this process in non-model organisms, despite an increasing realization of the general importance of gut microbiota for health. Methods: Here, we examine the changes that occur in the microbiome during dysbiosis in different parts of the gastrointestinal tract in a long-lived bird with high juvenile mortality, the ostrich (Struthio camelus). We evaluated the 16S rRNA gene composition of the ileum, cecum, and colon of 68 individuals that died of suspected enterocolitis during the first 3 months of life (diseased individuals), and of 50 healthy individuals that were euthanized as age-matched controls. We combined these data with longitudinal environmental and fecal sampling to identify potential sources of pathogenic bacteria and to unravel at which stage of development dysbiosisassociated bacteria emerge. Results: Diseased individuals had drastically lower microbial alpha diversity and differed substantially in their microbial beta diversity from control individuals in all three regions of the gastrointestinal tract. The clear relationship between low diversity and disease was consistent across all ages in the ileum, but decreased with age in the cecum and colon. Several taxa were associated with mortality (Enterobacteriaceae, Peptostreptococcaceae, Porphyromonadaceae, Clostridium), while others were associated with health (Lachnospiraceae, Ruminococcaceae, Erysipelotrichaceae, Turicibacter, Roseburia). Environmental samples showed no evidence of dysbiosis-associated bacteria being present in either the food, water, or soil substrate. Instead, the repeated fecal sampling showed that pathobionts were already present shortly after hatching and proliferated in individuals with low microbial diversity, resulting in high mortality several weeks later. Conclusions: Identifying the origins of pathobionts in neonates and the factors that subsequently influence the establishment of diverse gut microbiota may be key to understanding dysbiosis and host development.
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    Exploration of the hypothalamic-pituitary-adrenal axis to improve animal welfare by mean of genetic selection : lessons from the South African merino
    (MDPI, 2013) Hough, Denise; Swart, Pieter; Cloete, Schalk
    It is a difficult task to improve animal production by means of genetic selection, if the environment does not allow full expression of the animal’s genetic potential. This concept may well be the future for animal welfare, because it highlights the need to incorporate traits related to production and robustness, simultaneously, to reach sustainable breeding goals. This review explores the identification of potential genetic markers for robustness within the hypothalamic-pituitary-adrenal axis (HPAA), since this axis plays a vital role in the stress response. If genetic selection for superior HPAA responses to stress is possible, then it ought to be possible to breed robust and easily managed genotypes that might be able to adapt to a wide range of environmental conditions whilst expressing a high production potential. This approach is explored in this review by means of lessons learnt from research on Merino sheep, which were divergently selected for their multiple rearing ability. These two selection lines have shown marked differences in reproduction, production and welfare, which makes this breeding programme ideal to investigate potential genetic markers of robustness. The HPAA function is explored in detail to elucidate where such genetic markers are likely to be found.
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    Genetic traits of relevance to sustainability of smallholder sheep farming systems in South Africa
    (MDPI, 2017) Molotsi, Annelin; Dube, Bekezela; Oosting, Simon; Marandure, Tawanda; Mapiye, Cletos; Cloete, Schalk; Dzama, Kennedy
    Sustainable livestock production is important to ensure continuous availability of resources for future generations. Most smallholder livestock farming systems in developing countries have been perceived to be environmentally, socially and economically unsustainable. Farming with livestock that is robust and adaptable to harsh environments is important in developing countries especially in semi-arid and arid environments. This review discusses the different sheep farming systems employed by smallholder farmers and associated sustainability problems facing them. The review also gives an overview of sustainability indicators and limitations to the sustainability for the different smallholder sheep production systems in South Africa. It is argued that genetic diversity is important for sustainability and needs to be maintained in sheep for sustainable production and reproduction performance. The application of traditional breeding and genomics to ensure sustainable production is explored. Animal breeding approaches, specifically genomics can be applied to improve areas of environmental sustainability of smallholder sheep farming systems but must be targeted to the specific production environments, challenges, and opportunities of smallholder production. The genetic traits important for sustainability, the role of genomics in improving these traits and linking these genetic traits to different farming systems in South Africa are discussed.