Revealing the associated microflora hosted by the globally significant parasite Trichostrongylus colubriformis.

Trichostrongylus colubriformis is a parasitic helminth that primarily infects small ruminants, causing substantial economic losses in the livestock industry. Exploring the microbiome of this helminth might provide insights into the potential influence of its microbial community on the parasite's survival. We characterised the intestinal microbiome of T. colubriformis that had been collected from the duodenum of sheep, and compared the helminth microbiome with the duodenal microbiome of its host, aiming to identify contributions from the helminth's environment. At the same time, we explored the isolation of fastidious organisms from the harvested helminth. Primary alpha and beta diversity analyses of bacterial species revealed statistically significant differences between the parasite and the host, in terms of species richness and ecological composition. 16S rRNA differential abundance analysis showed that Mycoplasmoides and Stenotrophomonas were significantly present in T. colubriformis but not in the duodenal microbiome of the sheep. Furthermore, two bacteria, Aeromonas caviae and Aeromonas hydrophila, were isolated from T. colubriformis. Examinations of the genome highlight differences in genome size and profiles of antimicrobial resistance genes. Our results suggest that T. colubriformis carries a specific bacterial community that could be supporting the helminth's long-term survival in the host's digestive system.

Utilising male stimulus to improve the reproductive efficiency of 8-month-old nulliparous ewes and adult parous ewes.

We tested whether utilising the male effect to stimulate ewes before the mating period can reduce the time to conception following the introduction of entire rams, and increase fertility, prolificacy, and reproductive rate (number of fetuses per 100 ewes exposed to fertile rams). A retrospective analysis was used to analyse records from 59,716 ewes collected over 34 years (1986-2020) from seven genotypes: Border Leicester, Composite (crossbred), Dorset, Merino, Dorset x Polypay, Rambouillet, White Suffolk. The dataset also included nulliparous young ewes (mated at age 8 months) and adult parous ewes. Vasectomized rams were used to stimulate 20,632 ewes before a mating period that lasted 2 or 3 estrous cycles, and the outcomes were compared with those from 39,084 ewes that had not been stimulated. Independently of genotype, utilising the male stimulus advanced the average conception date by 8 days for young ewes (P < 0.0001) and by 1 day for adult ewes (P < 0.0001). The male stimulus also increased the proportion of ewes that conceived in their first cycle by 33 % for young ewes and by 6 % for adult ewes (P < 0.0001). For the cycle of conception, there were significant (P < 0.0001) effects of two interactions: male stimulus x age at mating and male stimulus x live weight at mating. The male stimulus improved fertility in both adult ewes (99.8 % vs 89 %; P < 0.001) and young ewes (77.7 % vs 81.3 %; P < 0.001). The male stimulus increased the number of young ewes (41.9 % vs 11.1 %; P < 0.001) and adult ewes (16.6 % vs 2.7 %; P < 0.001) that conceived multiple fetuses in the first 17 days of the mating period. The reproductive rate was improved by the male stimulus in young ewes (129 % vs 135 %; P < 0.001) but not in adult ewes (120 % vs 122 %; P = 0.12). When all animals for all breeds were included in the analyses, there were improvements in fertility, prolificacy, and reproductive rate as age and live weight increased at mating (P < 0.0001). We conclude that, independently of genotype, utilising the male stimulus before the mating period reduces the time to conception and improves reproductive performance in both young and adult ewes.

Chromosome-length genome assembly of Teladorsagia circumcincta - a globally important helminth parasite in livestock.

BACKGROUND: Gastrointestinal (GIT) helminthiasis is a global problem that affects livestock health, especially in small ruminants. One of the major helminth parasites of sheep and goats, Teladorsagia circumcincta, infects the abomasum and causes production losses, reductions in weight gain, diarrhoea and, in some cases, death in young animals. Control strategies have relied heavily on the use of anthelmintic medication but, unfortunately, T. circumcincta has developed resistance, as have many helminths. Vaccination offers a sustainable and practical solution, but there is no commercially available vaccine to prevent Teladorsagiosis. The discovery of new strategies for controlling T. circumcincta, such as novel vaccine targets and drug candidates, would be greatly accelerated by the availability of better quality, chromosome-length, genome assembly because it would allow the identification of key genetic determinants of the pathophysiology of infection and host-parasite interaction. The available draft genome assembly of T. circumcincta (GCA_002352805.1) is highly fragmented and thus impedes large-scale investigations of population and functional genomics. RESULTS: We have constructed a high-quality reference genome, with chromosome-length scaffolds, by purging alternative haplotypes from the existing draft genome assembly and scaffolding the result using chromosome conformation, capture-based, in situ Hi-C technique. The improved (Hi-C) assembly resulted in six chromosome-length scaffolds with length ranging from 66.6 Mbp to 49.6 Mbp, 35% fewer sequences and reduction in size. Substantial improvements were also achieved in both the values for N50 (57.1 Mbp) and L50 (5 Mbp). A higher and comparable level of genome and proteome completeness was achieved for Hi-C assembly on BUSCO parameters. The Hi-C assembly had a greater synteny and number of orthologs with a closely related nematode, Haemonchus contortus. CONCLUSION: This improved genomic resource is suitable as a foundation for the identification of potential targets for vaccine and drug development.

Contribution of the Immune Response in the Ileum to the Development of Diarrhoea caused by Helminth Infection: Studies with the Sheep Model.

Gastrointestinal helminths are a global health issue, for humans as well as domestic animals. Most studies focus on the tissues that are infected with the parasite, but here we studied the ileum, a tissue that is rarely infected by helminths. We tested whether inflammation in the ileum contributes to the development and severity of diarrhoea, by comparing sheep that are susceptible (n = 4) or resistant (n = 4) to the disease. We analyzed the ileum transcriptome using RNASeq sequencing approach and various bioinformatics tools including FastQC, STAR, featureCounts, DESeq2, DAVID, clusterProfiler, Cytoscape (ClusterONE) and EnrichR. We identified 243 differentially expressed genes (DEGs), of which 118 were up-regulated and 125 were down-regulated DEGs in the diarrhoea-susceptible animals compared to the diarrhoea-resistant animals. The resulting DEGs were functionally enriched for biological processes, pathways and gene set enrichment analysis. The up-regulated DEGs suggested that an inflammatory immune response was coupled with genes involved in 'Th2 immune response' and 'anti-inflammatory response'. The down-regulated DEGs were related to ion transport, muscle contraction and pathways preventing inflammation. We conclude that i) susceptibility to helminth-induced diarrhoea involves an inflammatory response at a non-infectious site; ii) down-regulation of pathways preventing inflammation can contribute to the severity of diarrhoea; and iii) genes involved in anti-inflammatory responses can reduce the inflammation and diarrhoea.

Bacterial communities in the gastrointestinal tract segments of helminth-resistant and helminth-susceptible sheep.

BACKGROUND: Helminth parasitism is a world-wide problem in livestock industries, with major impacts on health, welfare and productivity. The role of the gut microbiota in host-helminth interactions in ruminants has been extensively examined and the present study added to this body of knowledge by assessing the effects of resistance and susceptibility to helminth infection in the gastro-intestinal tract (GIT). Australian Sheep Breeding Values (ASBVs) for faecal egg count (FEC) were used to select the 10 highly helminth-susceptible (High-FEC) and 10 highly helminth-resistant (Low-FEC) sheep. FEC status was confirmed during the experiment. Using samples from the faeces and the lumen of the rumen, abomasum, duodenum, jejunum, ileum, caecum, and colon, DNA was extracted and used for 16 rRNA gene amplicon sequencing. RESULTS: The most frequent genera identified along the GIT were Eubacterium, Oscillibacter, and Ruminococcus. Intersectoral-specialization zones were identified along the GIT, with the duodenum displaying major differences between the High-FEC and Low-FEC animals in values for alpha and beta diversity. After taking all samples into account and adjusting for GIT segment, the High-FEC and Low-FEC sheep differed significantly for four genera Butyrivibrio, Mycoplasma, Lachnoclostridium and Succiniclasticum. In the duodenum, the abundances of Aminipila, Lachnoclostridium and Mogibacterium differed significantly between the High-FEC and Low-FEC sheep. In the ileum, on the other hand, the genus Mycoplasma was significantly depleted in the Low-FEC group. CONCLUSIONS: The gastro-intestinal microbial profile varies widely between helminth-resistant and helminth-susceptible sheep. Each GIT section appears to support a particular bacterial composition leading to inter-sectoral differences among the various microbial communities. The microbial populations were most rich and diverse in the duodenum of helminth-resistant sheep, comprising bacterial genera that generally ferment carbohydrates. This observation suggests that helminth-resistant sheep can reorganize the duodenal microbiome taxa which may restrict the development of parasites.

Investigating the development of diarrhoea through gene expression analysis in sheep genetically resistant to gastrointestinal helminth infection.

Gastrointestinal helminths infect livestock causing health problems including severe diarrhoea. To explore the underlying biological mechanisms relating to development and control of diarrhoea, we compared 4 sheep that were susceptible to development of diarrhoea with 4 sheep that were diarrhoea-resistant. Transcriptomes in the tissues where the parasites were located were analyzed using RNASeq. By considering low-diarrhoea sheep as control, we identified 114 genes that were down-regulated and 552 genes that were up-regulated genes in the high-diarrhoea phenotype. Functional analysis of DEGs and PPI sub-network analysis showed that down-regulated genes in the high-diarrhoea phenotype were linked to biological processes and pathways that include suppression of 'antigen processing and presentation', 'immune response', and a list of biological functional terms related to 'suppression in immune tolerance'. On the other hand, up-regulated genes in the high-diarrhoea phenotype probably contribute to repair processes associated with tissue damage, including 'extracellular matrix organization', 'collagen fibril organization', 'tissue morphogenesis', 'circulatory system development', 'morphogenesis of an epithelium', and 'focal adhesion'. The genes with important roles in the responses to helminth infection could be targeted in breeding programs to prevent diarrhoea.

Behavior and Electrophysiological Response of Gravid and Non-Gravid Lucilia cuprina (Diptera: Calliphoridae) to Carrion-Associated Compounds.

The Australian blow fly, Lucilia cuprina Wiedmann (Diptera: Calliphoridae), is a major cause of myiasis (flystrike) in Merino sheep in Australia and New Zealand and, as a primary colonizer of fresh carrion, also an important species in forensic investigations. Olfaction is considered the most important cue for insects to rapidly locate carrion over long distances, so the first carrion visitors are predicted to be very sensitive to carrion-related volatile compounds. We studied the responses of the Australian blow fly, Lucilia cuprina, to the carrion-associated compounds dimethyl trisulfide (DMTS), butyric acid, 1-octen-3-ol and indole. We also tested 2-mercaptoethanol, a compound commonly used in fly traps in Australia. We investigated whether responses of the flies are affected by their ovarian status by comparing responses of gravid and non-gravid L. cuprina in electroantennography (EAG) and two-choice laboratory bioassays. All four compounds evoked an EAG response, while only DMTS evoked responses in gas chromatography-mass spectrometry electroantennographic detection (GCMS-EAD) analyses and two-choice bioassays. Gravid flies detected lower doses of the test compounds than non-gravid flies. Our results indicate that DMTS is an important semiochemical for L. cuprina to locate carrion resources, and has potential for use in fly traps for flystrike control. Our observations also suggest that the greater sensitivity of gravid L. cuprina allows them to find fresh carrion quickly to maximize reproductive success by avoiding unsuitable degraded carrion.

Assessing carcass and meat characteristics of Damara, Dorper and Australian Merino lambs under restricted feeding.

Seasonal weight loss (SWL) is the most pressing constraint in ruminant production systems in tropical climates. SWL is controlled using supplementation, which is costly and difficult to implement in extensive systems, or using breeds adapted to tropical hot dry climates, like the Damara and Dorper. Albeit 15 years in Australia, little is known on how these sheep compare to Australian Merino. Here, the responses of the Damara, Dorper and Merino breeds to nutritional stress were compared. Seventy-two 6-month-old ram lambs, 24 from each breed, were allocated to growth (gaining 100 g/day) or restricted diets (losing 100 g/day, 85% of maintenance needs). Animals were weighed and carcass and meat characteristics determined. Results point out to the existence of important differences between the three genotypes, in particular between the Merino and the Southern African breeds. Additionally, Merino ram lambs seem to have been more influenced by SWL than the other two, with consequences on meat characteristics.

A note on the reproductive performance of Damara, Dorper and Merino sheep under optimum management and nutrition for Merino ewes in the eastern wheatbelt of Western Australia.

The reproductive performance of 48 Damara, 42 Dorper and 46 Merino ewes was evaluated under an optimum nutritional regime for Merino ewes that included one annual joining in a mixed (cropping and sheep) farming system in the eastern wheatbelt of Western Australia (W.A.) over a 3-year period. In 2005, when the Damara, Dorper and Merino ewes were aged between 8 and 9 months at joining and weighed 41.2, 42.4 and 33.3 kg with average body condition scores of 2.3, 2.4 and 1.8, respectively, their weaning rates were 71% (Damara), 81% (Dorper) and 13% (Merino). The Merino ewes had significantly lighter body weights and were lower conditioned (p < 0.001) resulting in significantly lower weaning rates (p < 0.001). In 2006, the Damara, Dorper and Merino ewes weighed 61.9, 69.5 and 61.6 kg at joining, with body condition scores of 2.8, 3.3 and 2.8, respectively, resulting in weaning rates of 52% (Damara), 122% (Dorper) and 117% (Merino). While the Damara and Merino weights and body condition scores were not different (p > 0.05), the Damara weaning rates were significantly lower compared with the Dorper and Merino groups (p < 0.001). The Dorpers were heavier and greater conditioned (p < 0.001); however, the weaning rates between the Dorper and Merino were not different (p > 0.05). In 2007, the Damara, Dorper and Merino ewes weighed 71.6, 77.1 and 70.2 kg at joining with body condition scores of 2.8, 2.8 and 2.5, respectively. Again, the Dorper ewes were heavier (p < 0.001) than the Damaras and Merinos, which were not different (p > 0.05). The Damara and Dorper had the same body condition while the Merino ewes were less and different (p < 0.05). However, there were differences in weaning rates between the three breeds (p < 0.001), of 64% (Damara), 105% (Dorper) and 134% (Merino). Over the 3-year period, under a nutritional management system optimal for Merino sheep and with one annual joining, with increasing age the Merino ewes weaned more lambs. However, while the Damara and Dorper ewes conceived and weaned relatively high lamb numbers when they were joined as lambs, their reproductive performance decreased over time. This nutritional regime resulted in increased levels of fatness of the Damara and Dorper ewes with no increase in reproduction rates under an annual joining system. A significant factor for the lower conception and weaning rates in the Damara ewes was the enlarged fat tail due to the increased fat levels, which made it difficult for the rams to impregnate the ewes.