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Papers by Adriaan Olivier

Additional file 1. Supplementary figures.

Additional file 2. Supplementary Table S1. Significant differentially abundant OTUs in the ileum.

Additional file 7. Supplementary Table S6. Fecal samples metadata.

Additional file 4. Supplementary Table S3. Significant differentially abundant OTUs in the cecum.

Additional file 5. Supplementary Table S4. Predicting patterns of mortality from fecal microbiota... more Additional file 5. Supplementary Table S4. Predicting patterns of mortality from fecal microbiota during preceding ages using Cox proportional hazard models.

Additional file 3. Supplementary Table S2. Significant differentially abundant OTUs in the caecum.

Additional file 6. Supplementary Table S5. Intestinal and environmental samples metadata.

Microbiome

Background Imbalances in the gut microbial community (dysbiosis) of vertebrates have been associa... more 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 envir...

Preventive Veterinary Medicine

Dysbiosis in the vertebrate gut microbiome has been associated with several diseases. However, it... more 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 la...

The development of gut microbiota during ontogeny in vertebrates is emerging as an important proc... more 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 diversit...

Frontiers in Immunology

In ostriches, the population densities resulting from intensive rearing increases susceptibility ... more In ostriches, the population densities resulting from intensive rearing increases susceptibility to pathogens such as mycoplasmas. In addition to good management practices, vaccination offers an attractive alternative for controlling mycoplasma infections in food animals, instead of using antibiotics, which often leave unacceptable residues. The use of live attenuated vaccines, however, carry the concern of reversion to virulence or genetic recombination with field strains. Currently there are no commercially available vaccines against ostrich-infecting mycoplasmas and this study therefore set out to develop and evaluate the use of a DNA vaccine against mycoplasma infections in ostriches using an OppA protein as antigen. To this end, the oppA gene of "Mycoplasma nasistruthionis sp. nov." str. Ms03 was cloned into two DNA vaccine expression vectors after codon correction by site-directed mutagenesis. Three-months-old ostriches were then vaccinated intramuscularly at different doses followed by a booster vaccination after 6 weeks. The ability of the DNA vaccines to elicit an anti-OppA antibody response was evaluated by ELISA using the recombinant OppA protein of Ms03 as coating antigen. A statistically significant anti-OppA antibody response could be detected after administration of a booster vaccination indicating that the OppA protein was successfully immunogenic. The responses were also both dose and vector dependent. In conclusion, the DNA vaccines were able to elicit an immune response in ostriches and can therefore be viewed as an option for the development of vaccines against mycoplasma infections.

Anatomical record (Hoboken, N.J. : 2007), Aug 21, 2016

In ostrich husbandry, economic losses have mainly been attributed to low hatchability of eggs, wh... more In ostrich husbandry, economic losses have mainly been attributed to low hatchability of eggs, which has mostly been attributed to the structure of the eggshell. The main aim of this study was to investigate the morphology and the morphometry of the ostrich eggshell using micro-focus X-ray computer tomography and scanning electron microscopy. The mean weight and volume of the eggs were 1,312±56SE g and 1,333±44SE cm(3) , respectively. The mean thickness and the mean surface area of the eggshell was 1.83±0.10SE mm and 619±15SE cm(2) respectively and the mean total number of pores in the shell was 40,596±1832SE. No significant correlations were found between the thickness of the shell and the weight of the eggs, the volume of the egg and the thickness of the shell, the diameter of the pores and the number of pores, the volume of the pores and the number of pores or the surface area of the pores and the number of pores. The mean diameters of the pores on the blunt (air cell)- (0.02±0.0...

Virus Genes, 2007

The first recorded outbreak of avian influenza (AI) in South African chickens (low pathogenicity ... more The first recorded outbreak of avian influenza (AI) in South African chickens (low pathogenicity H6N2) occurred at Camperdown, KwaZulu/Natal Province (KZN) in June 2002. To determine the source of the outbreak, we defined the phylogenetic relationships between various H6N2 isolates, and the previously unpublished gene sequences of an H6N8 virus isolated in 1998 from ostriches in the Leeu Gamka region (A/Ostrich/South Africa/KK98/98). We demonstrated that two distinct genetic H6N2 lineages (sub-lineages I and II) circulated in the Camperdown area, which later spread to other regions. Sub-lineages I and II shared a recent common H6N2 ancestor, which arose from a reassortment event between two South African ostrich isolates A/Ostrich/South Africa/9508103/95 and (H9N2) /Ostrich/South Africa/KK98/98 (H6N8). Furthermore, the H6N2 sub-lineage I viruses had several molecular genetic markers including a 22-amino acid stalk deletion in the neuraminidase (NA) protein gene, a predicted increased Nglycosylation, and a D144 mutation of the HA protein gene, all of which are associated with the adaptation of AI viruses to chickens. The H6N2 NS1 and PB1 genes shared recent common ancestors with those of contemporary Asian HPAI H5N1 viruses. Our results suggest that ostriches are potential mixing vessels for avian influenza viruses (AIV) outbreak strains and support other reports that H6 viruses are capable of forming stable lineages in chickens.

Avian Pathology, 2010

In the present study we collected 177 serum samples from ostriches (Struthio camelus) infected ex... more In the present study we collected 177 serum samples from ostriches (Struthio camelus) infected experimentally with A/ostrich/South Africa/Middleton/2004 (H5N2) highly pathogenic avian influenza virus. We tested these samples using the haemagglutination inhibition (HI) test, the agar gel immunodiffusion test and three enzyme-linked immunosorbent assay kits. We considered the HI test, with homologous antigen and including pre-treatment of sera with 10% chicken red blood cells, as the gold standard. Detectable specific antibodies appeared on day 7 post-infection and persisted until the termination of the experiment. The relative sensitivity and specificity of the tests under evaluation and Cohen's K value were calculated. The results reported herein could be of assistance to decision-makers in drafting guidelines for the definition of the health status of ostriches and for trade purposes.

Avian Pathology, 2013

An ostrich farm of 929 birds that tested polymerase chain reaction-positive for highly pathogenic... more An ostrich farm of 929 birds that tested polymerase chain reaction-positive for highly pathogenic avian influenza H5N2 in a single sample was designated for culling, despite no evidence of sero-conversion as assessed by haemagglutination inhibition (HI) tests. A month later and immediately prior to culling, all birds were bled and tested with an IDEXX avian influenza virus (AIV) nucleoprotein (NP)-specific enzyme-linked immunosorbent assay (ELISA) and a high sero-prevalence was detected. To address the question of whether the NP-specific antibodies detected indicated exposure to H5 or non-H5 subtypes (H6N2 and H1N2 strains were also circulating regionally at the time), we developed two H5-specific ELISAs, both based on a recombinant H5 HA1 antigen. The H5 indirect ELISA used a horseradish peroxidase ostrich IgY conjugate that we produced in chicken eggs. The single-chain variable fragment (scFv) competitive ELISA (H5 scFv cELISA) used a scFv derived from an H5-immune chicken scFv library. By comparing IDEXX AIV ELISA results with those of the two H5-specific ELISAs and HI tests, we determined that up to 89% of the flock had been exposed to H5N2 AIV. We also detected evidence of suspected vaccination, since 17% of sera contained antibodies against the H5 glycoprotein but not the NP protein. Comparative analytical sensitivity indicated that HI tests are likely to miss up to 35% of H5-positive samples, and thus we consider that H5/H7-specific ELISAs should replace HI tests for ostrich testing in future.