Biology subjects

Cloete, S.

Publications and source records attributed to Cloete, S..

6 recordsLinked to original sources

bioRxiv2026

Development shapes molecular responses to thermal extremes in a desert bird

Thermal extremes are among the most immediate environmental challenges faced by animals. Coping with these conditions across life is complex because growth changes body size, heat exchange and thermoregulatory demands. Consequently, adaptive responses in young, small individuals may be maladaptive, or require adjustment, later in life. However, in endotherms we know very little about how thermoregulatory responses to hot and cold temperatures change during development, or about the molecular mechanisms regulating responses. We examined the molecular responses to acute heat (40{degrees}C), cold (12{degrees}C) and benign (23{degrees}C) conditions in 1- and 8-week-old ostrich chicks (Struthio camelus), a rapidly growing species exposed to strong daily and seasonal temperature variation. We found that in 1-week-old chicks, 44% of temperature-related genes were involved in both heat and cold responses, indicating that responses to opposing temperatures involve overlapping molecular pathways. However, the response of 76% of these genes changed during development. For example, some genes that increased with heat exposure when young decreased with heat exposure later in development, and vice versa. Such opposing selection pressures may maintain genetic variation in thermoregulatory pathways. Consistent with this prediction, comparisons between ostrich subspecies adapted to different thermal environments revealed patterns of genomic variation compatible with balancing selection in differentially expressed genes. Our results show that hot and cold temperatures trigger overlapping molecular responses that change during development, which shape genetic variation in the thermoregulatory system.

evolutionary biology↗

bioRxiv2021

Evolutionary trade-offs between heat and cold tolerance limit responses to fluctuating climates

The evolutionary potential of species to cope with short-term temperature fluctuations during reproduction is critical to predicting responses to future climate change. Despite this, vertebrate research has focused on reproduction under high or low temperatures in relatively stable temperate climates. Here, we characterize the genetic basis of reproductive thermal tolerance to temperature fluctuations in the ostrich that lives in tropical and sub-tropical Africa. Both heat and cold tolerance are under selection and heritable, indicating that evolutionary responses to mean temperature change are possible. However, a negative, genetic correlation between heat and cold tolerance limits the potential for adaptation to fluctuating temperatures. Genetic constraints between heat and cold tolerance appears a crucial, yet underappreciated, factor influencing responses to climate change. One-sentence summaryReproductive success in fluctuating climates is constrained by a negative genetic correlation between heat and cold tolerance

evolutionary biology↗

bioRxiv2019

Early-life gut dysbiosis linked to mass mortality in ostriches

Dysbiosis in the vertebrate gut microbiome has been associated with several diseases. However, it is unclear whether particular gut regions or specific time periods during ontogeny are responsible for the development of dysbiosis, especially in non-model organisms. Here we examine the microbiome associated with dysbiosis in different parts of the gastrointestinal tract (ileum, caecum, colon) in a long-lived bird with high juvenile mortality, the ostrich. Individuals that died of gut disease (n=68) had substantially different microbial composition from age-matched controls (n=50) throughout the gut. Several taxa were associated with mortality (Enterobacteriaceae, Peptostreptococcaceae, Porphyromonadaceae, Clostridium) and some with survival (Lachnospiraceae, Ruminococcaceae, Erysipelotrichaceae, Turicibacter). Repeated faecal sampling showed that pathobionts were already present shortly after hatching and proliferated in individuals with low diversity, resulting in mortality weeks later. The factors influencing seeding of the gut microbiota may therefore be key to understanding dysbiosis and host development.

microbiology↗

bioRxiv2018

The development of gut microbiota in ostriches and its association with growth

The development of gut microbiota during ontogeny in vertebrates is emerging as an important process influencing physiology, immune system, health, and adult fitness. However, we have little knowledge of how the gut microbiome is colonised and develops in non-model organisms, and to what extent microbial diversity and specific taxa influence changes in fitness-related traits. Here, we used 16S rRNA gene sequencing to describe the successional development of the faecal microbiota in juvenile ostriches (Struthio camelus; n = 71) over their first three months of life, during which time a five-fold difference in weight was observed. We found a gradual increase in microbial diversity with age, an overall convergence in community composition among individuals, multiple colonisation and extinction events, and major taxonomic shifts coinciding with the cessation of yolk absorption. In addition, we discovered significant but complex associations between juvenile growth and microbial diversity, and identified distinct bacterial groups that had positive (Bacteroidaceae) and negative (Enterobacteriaceae, Enterococcaceae, Lactobacillaceae) correlations with the growth of individuals at specific ages. These results have broad implications for our understanding of the development of gut microbiota and its association with juvenile growth.

microbiology↗

bioRxiv2017

Direct PCR offers a fast and reliable alternative to conventional DNA isolation methods for animal gut microbiomes

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, 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 the direct PCR method for measuring host microbiomes has 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 MoBio PowerSoil DNA extraction kit in five distinct gut sample types (ileum - caecum - colon - faeces - 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 caecal, colon, and faecal samples. However, the two methods recovered significantly different microbiomes in 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 caecal, colon, and faecal 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 data, which will aid future gut microbiome studies of animals.

microbiology↗

bioRxiv2017

Measuring the gut microbiome in birds: comparison of faecal and cloacal sampling

The gut microbiomes of birds and other animals are increasingly being studied in ecological and evolutionary contexts. While methods for preserving samples and processing high-throughput sequence data to characterise bacterial communities have received considerable attention, there has been little evaluation of non-invasive sampling methods. Numerous studies on birds and reptiles have made inferences about gut microbiota using cloacal sampling, however, it is not known whether the bacterial community of the cloaca provides an accurate representation of the avian gut microbiome. We examined the accuracy with which cloacal swabs and faecal samples measure the microbiota in three different parts of the gastrointestinal tract (ileum, caecum, and colon) using a case study on juvenile ostriches, Struthio camelus, and high-throughput 16S rRNA sequencing. We found that faeces were significantly better than cloacal swabs in representing the bacterial community of the colon. Cloacal samples had a higher abundance of Gammaproteobacteria and fewer Clostridia relative to the gut and faecal samples. However, both faecal and cloacal samples were poor representatives of the microbial communities in the caecum and ileum. Furthermore, the accuracy of the sampling methods in measuring the abundance of different bacterial taxa was highly variable: Bacteroidetes was the most highly correlated phylum between all three gut sections and both methods, whereas colonic Actinobacteria correlated strongly only with faecal samples. This study demonstrates that sampling methods can have significant effects on the inferred gut microbiome in studies of birds. Based on our results, we recommend sampling faeces, whenever possible, as this provides the most accurate assessment of the colon microbiome. The fact that neither sampling technique portrayed the bacterial community of the ileum or the caecum illustrates the difficulty in non-invasively monitoring gut bacteria located further up in the gastrointestinal tract. These results have important implications for the interpretation of avian gut microbiome studies.

ecology↗