Ontology highlight
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PROVIDER: PRJNA672957 | ENA |
REPOSITORIES: ENA
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Project description:Antimicrobial resistance E_coli in a high artic reindeer subspecies
| PRJEB40996 | ENA
Project description:Svalbard reindeer (Rangifer tarandus platyrhynchus) is a non-migratory subspecies of reindeer inhabiting the high-arctic archipelago of Svalbard. In contrast to other Rangifer tarandus subspecies, Svalbard reindeer graze exclusively on natural sources of food and have no chance of ingestion of any crops. We report the use of a non-invasive method for analysis of fecal microbiome by means of sequencing the 16S rDNA extracted from the fecal microbiota of R. tarandus platyrhynchus from a small, isolated population in Hornsund, South Spitsbergen National Park. Analyses of all samples showed that 99% of the total reads were represented by Bacteria. Taxonomy-based analysis showed that fecal bacterial communities consisted of 14 phyla. The most abundant phyla across the population were Firmicutes and Bacteroidetes, and those phyla jointly accounted for more than 95% of total bacterial sequences (ranging between 90.14 and 98.19%). Specifically, Firmicutes comprised 56.53% (42.98-63.64%) and Bacteroidetes comprised 39.17% (34.56-47.16%) of the total reads. The remaining 5% of the population reads comprised of Tenericutes, Cyanobacteria, TM7, Actinobacteria, Proteobacteria, Verrucomicrobia, Elusimicrobia, Planctomycetes, Fibrobacteres, Spirochaetes, Chloroflexi, and Deferribacteres. Differences in the fecal bacteria composition between particular reindeer were not statistically significant which may reflect the restricted location and similar diet of all members of the local population.
2016-01-01 | S-EPMC4763015 | BioStudies
Project description:Reindeer species (Rangifer tarandus, Linnaeus, 1758) includes wild and semi-domesticated ruminants belonging to Capreaolinae subfamily of Cervidae family reared in Eurasia (reindeer subspecies) and North America (caribou subspecies). Herding of reindeer has a great historical, socio-economic and ecological importance, especially to indigenous ethnic minorities. Infectious disease threats may therefore impact not solely the animal population driving it to further extinction and irreversible alterations to the wild environments of northern hemisphere, but also add to cultural changes observed as negative impact of globalization. Introduction of new technologies to control of reindeer migration between dwindling pasture areas and intensification of reindeer husbandry may facilitate the intra- and interspecies transmission of pathogens. The role of the reindeer as a potential BVDV reservoir has been studied, however, the number of publications is rather limited. The observed seroprevalences of the virus varied significantly between different geographical regions with different epidemiological situation. Most frequently limited number of animals studied and the differences in the sensitivities and specificities of the diagnostic test used could have also influenced on the differences between the studies. No pestivirus has been ever detected in free-ranging reindeer, however, a putative pestivirus strain named V60-Krefeld has been isolated from reindeer kept at a German Zoo in the 1990's. The virus was characterized as border disease virus type 2 (BDV-2) closely related to German ovine strains. The cross-neutralization studies of the semi-domesticated reindeer sera from Sweden suggested infection with a strain related to BDV-1 or BDV-2. The available data indicates that reindeer might be infected by a endemic species-specific BDV-like strain. However, the interspecies transmission of BVDV from domestic animals should not be excluded, since the susceptibility of reindeer to BVDV-1 has been confirmed under experimental conditions.
2015-01-01 | S-EPMC4620691 | BioStudies
Project description:The faecal microbiota of muskoxen (n=3) pasturing on Ryøya (69° 33' N 18° 43' E), Norway, in late September was characterized using high-throughput sequencing of partial 16S rRNA gene regions. A total of 16 209 high-quality sequence reads from bacterial domains and 19 462 from archaea were generated. Preliminary taxonomic classifications of 806 bacterial operational taxonomic units (OTUs) resulted in 53.7-59.3 % of the total sequences being without designations beyond the family level. Firmicutes (70.7-81.1 % of the total sequences) and Bacteroidetes (16.8-25.3 %) constituted the two major bacterial phyla, with uncharacterized members within the family Ruminococcaceae (28.9-40.9 %) as the major phylotype. Multiple-library comparisons between muskoxen and other ruminants indicated a higher similarity for muskoxen faeces and reindeer caecum (P>0.05) and some samples from cattle faeces. The archaeal sequences clustered into 37 OTUs, with dominating phylotypes affiliated to the methane-producing genus Methanobrevibacter (80-92 % of the total sequences). UniFrac analysis demonstrated heterogeneity between muskoxen archaeal libraries and those from reindeer and roe deer (P=1.0e-02, Bonferroni corrected), but not with foregut fermenters. The high proportion of cellulose-degrading Ruminococcus-affiliated bacteria agrees with the ingestion of a highly fibrous diet. Further experiments are required to elucidate the role played by these novel bacteria in the digestion of this fibrous Artic diet eaten by muskoxen.
2016-01-01 | S-EPMC5343138 | BioStudies
Project description:Reindeer herding probably developed during the Late Iron Age onwards and is still an important part of the subsistence and culture of many peoples in northern Eurasia. However, despite the importance of this husbandry in the history of these Arctic people, the period and place of the origin as well as the spread of domestic reindeer is still highly debated. Besides the existence of different breeding methods in these territories, identifying domesticated individuals in the archaeological record is complicated because reindeers are considered to still be in the early phases of the domestication process. Indeed, the traditional morphological markers used in zooarchaeology to decipher the domestication syndrome are hardly perceptible in these early stages. In this work, we propose solutions for identifying domestic reindeer bones using 3D geometric morphometrics on isolated elements from the long bones of the forelimb (i.e. humerus, radio-ulna and metacarpal). These bones are important to understand both the feeding behaviour and the mobility of reindeer, and the potential effect of load-carrying or draught in the case of domestic reindeer. We analysed 123 modern specimens from Fennoscandia, including the two interbreeding subspecies currently present in these territories: mountain reindeer (Rangifer tarandus tarandus) and forest reindeer (R.t. fennicus); and where the sex and the lifestyle were known (i.e. free-ranging, racing or draught and captive individuals). A good level of discrimination between the size and shape variables of the bones of the forelimb was found among both subspecies and sexes. Moreover, individuals bred in captivity had smaller bone elements and a thinner and more slender morphology than free-ranging individuals. This demonstrates that the long bones of the forelimb can provide information on changes in feeding and locomotor behaviour prompted by the domestication process, like control and/or reduction of mobility and food of individual reindeer by humans. This also demonstrates that analysis in 3D geometric morphometrics is useful in detecting reindeer incipient domestication markers. Our results can be used by archaeologists to trace the early stages of domestication from fossil reindeer remains, and aid in reconstructing the socio-economic changes of past Arctic populations over time.
2020-01-01 | S-EPMC7366605 | BioStudies
Project description:The ecology of the uncultured, but large and morphologically conspicuous, rumen bacterium Oscillospira spp. was studied. Oscillospira-specific 16S rRNA gene sequences were detected in North American domestic cattle, sheep from Australia and Japan, and Norwegian reindeer. Phylogenetic analysis of the sequences obtained allowed definition of three operational taxonomic units within the Oscillospira clade. Consistent with this genetic diversity, we observed atypical smaller morphotypes by using an Oscillospira-specific fluorescence in situ hybridization probe. Despite the visual disappearance of typical large Oscillospira morphotypes, the presence of Oscillospira spp. was still detected by Oscillospira-specific PCR in the rumen of cattle and sheep. These observations suggest the broad presence of Oscillospira species in various rumen ecosystems with the level, and most likely the morphological form, dependent on diet. An ecological analysis based on enumeration of the morphologically conspicuous, large-septate form confirms that the highest counts are associated with the feeding of fresh forage diets to cattle and sheep and in two different subspecies of reindeer investigated.
2003-01-01 | S-EPMC262257 | BioStudies
Project description:Polymorphisms within the prion protein gene (Prnp) are an intrinsic factor that can modulate chronic wasting disease (CWD) pathogenesis in cervids. Although wild European reindeer (Rangifer tarandus tarandus) were infected with CWD, as yet there have been no reports of the disease in North American caribou (R. tarandus spp.). Previous Prnp genotyping studies on approximately 200 caribou revealed single nucleotide polymorphisms (SNPs) at codons 2 (V/M), 129 (G/S), 138 (S/N), 146 (N/n) and 169 (V/M). The impact of these polymorphisms on CWD transmission is mostly unknown, except for codon 138. Reindeer carrying at least one allele encoding for asparagine (138NN or 138SN) are less susceptible to clinical CWD upon infection by natural routes, with the majority of prions limited to extraneural tissues. We sequenced the Prnp coding region of two caribou subspecies (n = 986) from British Columbia, Saskatchewan, Yukon, Nunavut and the Northwest Territories, to identify SNPs and their frequencies. Genotype frequencies at codon 138 differed significantly between barren-ground (R. t. groenlandicus) and woodland (R. t. caribou) caribou when we excluded the Chinchaga herd (p < .05). We also found new variants at codons 153 (Y/F) and 242 (P/L). Our findings show that the 138N allele is rare among caribou in areas with higher risk of contact with CWD-infected species. As both subspecies are classified as Threatened and play significant roles in North American Indigenous culture, history, food security and the economy, determining frequencies of Prnp genotypes associated with susceptibility to CWD is important for future wildlife management measures.
2020-01-01 | S-EPMC7590118 | BioStudies
Project description:<b>Purpose: </b>Most patients with early-stage breast cancer are treated with adjuvant radiotherapy (RT) after breast-conserving surgery (BCS) to prevent locoregional recurrence (LRR). However, no genomic tools are used currently to select the optimal RT strategy.<br><br><b>Methods: </b>We profiled the transcriptome of primary tumors on a clinical grade assay from the SweBCG91-RT trial, in which patients with node-negative breast cancer were randomly assigned to either whole-breast RT after BCS or no RT. We derived a new classifier, Adjuvant Radiotherapy Intensification Classifier (ARTIC), comprising 27 genes and patient age, in three publicly available cohorts, then independently validated ARTIC for LRR in 748 patients in SweBCG91-RT. We also compared previously published genomic signatures for ability to predict benefit from RT in SweBCG91-RT.<br><br><b>Results: </b>ARTIC was highly prognostic for LRR in patients treated with RT (hazard ratio [HR], 3.4; 95% CI, 2.0 to 5.9; <i>P</i> < .001) and predictive of RT benefit (<i>P</i><sub>interaction</sub> = .005). Patients with low ARTIC scores had a large benefit from RT (HR, 0.33 [95% CI, 0.21 to 0.52], <i>P</i> < .001; 10-year cumulative incidence of LRR, 6% <i>v</i> 21%), whereas those with high ARTIC scores benefited less from RT (HR, 0.73 [95% CI, 0.44 to 1.2], <i>P</i> = .23; 10-year cumulative incidence of LRR, 25% <i>v</i> 32%). In contrast, none of the eight previously published signatures were predictive of benefit from RT in SweBCG91-RT.<br><br><b>Conclusion: </b>ARTIC identified women with a substantial benefit from RT as well as women with a particularly elevated LRR risk in whom whole-breast RT was not sufficiently effective and, thus, in whom intensified treatment strategies such as tumor-bed boost, and possibly regional nodal RT, should be considered. To our knowledge, ARTIC is the first classifier validated as predictive of benefit from RT in a phase III clinical trial with patients randomly assigned to receive or not receive RT.
2019-01-01 | S-EPMC6901281 | BioStudies