Faecal microbiota of Svalbard reindeer Rangifer tarandus platyrhynchus from Hornsund, southwest Spitsbergen
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REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR768125_1.fastq.gz | Fastqsanger.gz | |||
| ERR768125_2.fastq.gz | Fastqsanger.gz | |||
| ERR768126_1.fastq.gz | Fastqsanger.gz | |||
| ERR768126_2.fastq.gz | Fastqsanger.gz | |||
| ERR768127_1.fastq.gz | Fastqsanger.gz |
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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.
| S-EPMC4763015 | biostudies-literature
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.
| S-EPMC4620691 | biostudies-literature
Project description:BackgroundThe reindeer (Rangifer tarandus) is the only fully domesticated species in the Cervidae family, and it is the only cervid with a circumpolar distribution. Unlike all other cervids, female reindeer, as well as males, regularly grow cranial appendages (antlers, the defining characteristics of cervids). Moreover, reindeer milk contains more protein and less lactose than bovids' milk. A high-quality reference genome of this species will assist efforts to elucidate these and other important features in the reindeer.FindingsWe obtained 615 Gb (Gigabase) of usable sequences by filtering the low-quality reads of the raw data generated from the Illumina Hiseq 4000 platform, and a 2.64-Gb final assembly, representing 95.7% of the estimated genome (2.76 Gb according to k-mer analysis), including 92.6% of expected genes according to BUSCO analysis. The contig N50 and scaffold N50 sizes were 89.7 kilo base (kb) and 0.94 mega base (Mb), respectively. We annotated 21 555 protein-coding genes and 1.07 Gb of repetitive sequences by de novo and homology-based prediction. Homology-based searches detected 159 rRNA, 547 miRNA, 1339 snRNA, and 863 tRNA sequences in the genome of R. tarandus. The divergence time between R. tarandus and ancestors of Bos taurus and Capra hircus is estimated to be about 29.5 million years ago.ConclusionsOur results provide the first high-quality reference genome for the reindeer and a valuable resource for studying the evolution, domestication, and other unusual characteristics of the reindeer.
| S-EPMC5726476 | biostudies-literature
Project description:BackgroundSemi-domesticated reindeer represent an important livestock industry and livelihood for a proportion of the human population in northern Fennoscandia. Reindeer husbandry is considered an extensive animal husbandry, where the animals are kept mostly on natural pastures, although sometimes kept in fenced areas for shorter periods. These reindeer may harbour a variety of parasites that may affect animal health and production. The relatively limited close contact between herds and owners gives limited opportunities for diagnosis and treatment of diseases in general. Furthermore, the effects of subclinical parasitism in livestock are commonly expressed as a reduction in productivity rather than clinical disease and mortality. Thus, specific knowledge of endoparasites and parasitic infections in these herds is scarce. This study investigated the occurrence of various endoparasites in reindeer by analysis of a total of 114 faecal samples from winter-slaughtered reindeer from two different grazing areas in Troms and Finnmark, Norway.ResultsUsing a McMaster method, a Baermann technique, and a direct immunofluorescent antibody test, the following parasites were identified in the faecal samples with the occurrence data given as percentages: Strongylid eggs (62%), Nematodirinae spp. eggs (24%), Capillaria sp. eggs (42%) and Moniezia spp. eggs (17%), Dictyocaulus spp. larvae (14%) protostrongylid larvae (40%), Eimera spp. oocysts (23%), and Giardia duodenalis cysts (5%). Cryptosporidium oocysts were not detected. Parasite eggs, oocysts, and cysts were quantified. Molecular analysis revealed G. duodenalis sub-assemblage AI, a potentially zoonotic genotype not previously reported in reindeer from this region. Morphological analyses of Eimeria oocysts identified two species, Eimeria mayeri and Eimeria rangiferis, and molecular analyses of the cytochrome C oxidase I (coi) gene and 18 s rRNA (18SSU) gene of Eimeria confirmed the presence of Eimeria species that are specific to reindeer.ConclusionsA high prevalence, but low burden, of endoparasites was detected in samples from these semi-domesticated reindeer. The samples were collected during winter, when adult gastrointestinal parasites usually produce only low numbers of transmission stages. Therefore, together with the low number of samples, detailed and definitive conclusions regarding parasite status of semi-domesticated reindeer are avoided. Nevertheless, these data provide a snapshot overview of parasite occurrence in a semi-domesticated animal group vulnerable to the various environmental changes to which they are exposed.
| S-EPMC7985575 | biostudies-literature
Project description:Svalbard reindeer adaptation genomics
| PRJEB80888 | ENA
Project description:Chronic wasting disease (CWD), a transmissible spongiform encephalopathy of cervids, remains prevalent in North American elk, white-tailed deer and mule deer. A natural case of CWD in reindeer (Rangifer tarandus tarandus) has not been reported despite potential habitat overlap with CWD-infected deer or elk herds. This study investigates the experimental transmission of CWD from elk or white-tailed deer to reindeer by the oral route of inoculation. Ante-mortem testing of the three reindeer exposed to CWD from white-tailed deer identified the accumulation of pathological PrP (PrP(CWD)) in the recto-anal mucosa associated lymphoid tissue (RAMALT) of two reindeer at 13.4 months post-inoculation. Terminal CWD occurred in the two RAMALT-positive reindeer at 18.5 and 20 months post-inoculation while one other reindeer in the white-tailed deer CWD inoculum group and none of the 3 reindeer exposed to elk CWD developed disease. Tissue distribution analysis of PrP(CWD) in CWD-affected reindeer revealed widespread deposition in central and peripheral nervous systems, lymphoreticular tissues, the gastrointestinal tract, neuroendocrine tissues and cardiac muscle. Analysis of prion protein gene (PRNP) sequences in the 6 reindeer identified polymorphisms at residues 2 (V/M), 129 (G/S), 138 (S/N) and 169 (V/M). These findings demonstrate that (i) a sub-population of reindeer are susceptible to CWD by oral inoculation implicating the potential for transmission to other Rangifer species, and (ii) certain reindeer PRNP polymorphisms may be protective against CWD infection.
| S-EPMC3377593 | biostudies-literature
Project description:BackgroundTwo outbreaks of the disease contagious ecthyma were reported in 1999 and 2000 in Norwegian semi-domesticated reindeer (Rangifer tarandus tarandus). Contagious ecthyma is an epidermal disease of sheep and goats worldwide, which is caused by the zoonotic parapoxvirus orf virus. Characterisation of clinical samples from the two outbreaks in semi-domesticated reindeer in Norway by electron microscopy and PCR (B2L) revealed typical parapoxvirus particles and partial gene sequences corresponding to parapoxvirus, respectively. If contagious ecthyma in reindeer is caused by orf virus, the virus may be transferred from sheep and goats, via people, equipment and common use of pastures and corrals, to reindeer. Another possibility is that contagious ecthyma in reindeer is caused by a hitherto unclassified member of the parapoxvirus genus that circulates among reindeer herds and remains endemic in Norway.ResultsGenomic comparisons of one standard orf strain (orf NZ2) and the reindeer isolates, employing restriction fragment length polymorphism (RFLP) and random amplified polymorphic DNA (RAPD) analysis, demonstrated high similarity between the reindeer viruses and known orf virus strains. Partial DNA sequences of two different viral genes were determined for the different isolates and compared with corresponding parapoxvirus genebank sequences. The comparison/alignment and construction of phylogenetic trees also point to an affiliation of the reindeer viruses to the species orf virus.ConclusionThe results of this work imply that the parapoxvirus causing contagious ecthyma in Norwegian semi-domesticated reindeer belongs to the species orf virus and that the orf virus crosses the host species barrier from sheep and goat to semi-domesticated reindeer.
| S-EPMC1242257 | biostudies-literature
Project description:The most southern population of reindeer (Rangifer tarandus) inhabits northeastern China, but the migration route and origin of this population have not been confirmed. The sequences of mitochondrial DNA control regions from domestic and wild herds from Eurasia and China were analysed. The results showed that the Chinese reindeer population originated independently from north-central Russian domestic herds, belonging to a large reindeer population that was present across Beringia during the last glacial period. Some studies have reported that the Chinese reindeer population is closely related to wild forest reindeer herds in Russia. Our results, however, indicate that wild forest reindeer herds of southeastern Russia contributed little or nothing to the Chinese reindeer herd gene pool. Chinese reindeer herds have a much greater genetic similarity to more northerly distributed tundra-type herds that inhabit open areas. The present findings will be essential for future conservation planning for Chinese reindeer.
| S-EPMC6853604 | biostudies-literature
Project description:To efficiently investigate the forage preference of Svalbard reindeer (Rangifer tarandus platyrhynchus), we applied length-heterogeneity polymerase chain reaction (LH-PCR) based on length differences of internal transcribed spacer (ITS) regions of ribosomal RNA (rRNA) to fecal samples from R. tarandus platyrhynchus. A length-heterogeneity (LH) database was constructed using both collected potential food sources of Svalbard reindeer and fecal samples, followed by PCR, cloning and sequencing. In total, eighteen fecal samples were collected between 2011 and 2012 from 2 geographic regions and 15 samples were successfully amplified by PCR. The LH-PCR analysis detected abundant peaks, 18.6 peaks on an average per sample, ranging from 100 to 500 bp in size and showing distinct patterns associated with both regions and years of sample collection. Principal component analysis (PCA) resulted in clustering of 15 fecal samples into 3 groups by the year of collection and region with a statistically significant difference at 99.9% level. The first 2 principal components (PCs) explained 71.1% of the total variation among the samples. Through comparison with LH database and identification by cloning and sequencing, lichens (Stereocaulon sp. and Ochrolechia sp.) and plant species (Salix polaris and Saxifraga oppositifolia) were detected as the food sources that contributed most to the Svalbard reindeer diet. Our results suggest that the use of LH-PCR analysis would be a non-invasive and efficient monitoring tool for characterizing the foraging strategy of Svalbard reindeer. Additionally, combining sequence information would increase its resolving power in identification of foraged diet components.
| S-EPMC3950246 | biostudies-literature
Project description:We report here Taenia lynciscapreoli metacestode from the lung lobe of a semi-domesticated reindeer (Rangifer tarandus tarandus). The specimen was detected within a development project concerning remote post mortem inspection at a reindeer abattoir in Sweden. Post mortem inspection was performed according to a routine on-site official meat inspection protocol. The species identification to T. lynciscapreoli was confirmed based on the DNA extracted from the metacestode, which was analysed by sequencing of the cytochrome c oxidase subunit 1. Firstly, our finding shows that semi-domesticated reindeer in addition to several other cervids can act as an additional intermediate host for T. lynciscapreoli. Secondly, it further confirms that this parasite is more widely distributed on the Scandinavian peninsula than what has previously been shown. This is in line with a previous molecular finding of adult T. lynciscapreoli from the Eurasian lynx (Lynx lynx) in Sweden and demonstrates that new intermediate host can be detected. Whether the present finding can be regarded as accidental or have created opportunities for an expansion throughout the northernmost Scandinavian Peninsula remains to be seen.
| S-EPMC9108717 | biostudies-literature