Pseudois nayaur szechuanensis
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA846117 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19570488_1.fastq.gz | Fastqsanger.gz | |||
| SRR19570488_2.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Pseudois_nayaur Genome sequencing and assembly
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Project description:BACKGROUND:Gastrointestinal microbiota play an important role in animal host immunity, nutrient metabolism, and energy acquisition, and have therefore drawn increasing attentions. This study compared the diversity of the gut microbiota of both wild and captive bharals, which is an ungulate herbivore of caprid from the Qinghai-Tibet plateau. RESULTS:The sequencing of the V4-V5 region of the 16S rRNA gene via high-throughput sequencing technology showed that the dominant bacterial phyla are Firmicutes and Bacteroides both in wild and captive bharals. However, their abundance differed significantly between groups. Firmicutes were significantly higher in wild bharals, while Bacteroides were significantly higher in captive bharals. Different diets are likely a key influencing factor in the diversity and abundance of gut microbiota in bharals. CONCLUSIONS:Changes in diets affect the diversity of gut microbiota and the relative abundance of pathogenic bacteria, increasing the risk of diseases outbreak in captive bharals. The results of this study suggest that the structure and function of the gut microbiota should be regulated via dietary intervention, accurate provision of an individualized diet, and optimization of the functional network of gut microbiota and its interaction with the host. This will improve the ex situ protection of wild animals.
| S-EPMC6626359 | biostudies-literature
Project description:Pseudois nayaur feces Raw sequence reads
| PRJNA660926 | ENA
Project description:Microbiota of the wild blue sheep (Pseudois nayaur) presents a seasonal variation due to different dietary selection and feeding strategies from different ecological niches chosen by different sex in summer. To address those issues, we analyzed the variation of gut microbiota based on the material from the feces, with 16S rRNA and meta-genome aimed to explore seasonal and gender differences. The results indicate that seasonal dietary changes and gender differentiation, as expected, cause the variation in sheep's gut microbiota structure. The variation of the former is more significant than the latter. Dominant Firmicutes exists a significantly higher abundance in summer than that in winter. Subordinate Bacteroides expresses no seasonal difference between the two seasons. Compared with the winter group, the summer group is featured by abundant enzymes digesting cellulose and generating short-chain fatty acids (SCFAs), such as beta-glucosidase (EC: 3.2.1.21) for cellulose digestion, and butyrate kinase (EC:2.7.2.7) in butyrate metabolism, implying that the changes of the composition in intestinal flora allow the sheep to adapt to the seasonalized dietary selection through alternated microbial functions to reach the goal of facilitating the efficiency of energy harvesting. The results also show that the blue sheep expresses a prominent sexual dimorphism in the components of gut microbiota, indicating that the two sexes have different adaptations to the dietary selection, and demands for physical and psychological purposes. Thus, this study provides an example of demonstrating the principles and regulations of natural selection and environmental adaptation.
| S-EPMC7332577 | biostudies-literature
Project description:BackgroundHaemonchus contortus is known among parasitic nematodes as one of the major veterinary pathogens of small ruminants and results in great economic losses worldwide. Human activities, such as the sympatric grazing of wild with domestic animals, may place susceptible wildlife hosts at risk of increased prevalence and infection intensity with this common small ruminant parasite. Studies on phylogenetic factors of H. contortus should assist in defining the amount of the impact of anthropogenic factors on the extent of sharing of agents such as this nematode between domestic animals and wildlife.MethodsH. contortus specimens (n = 57) were isolated from wild blue sheep (Pseudois nayaur) inhabiting Helan Mountains (HM), China and additional H. contortus specimens (n = 20) were isolated from domestic sheep that were grazed near the natural habitat of the blue sheep. Complete ITS2 (second internal transcribed spacer) sequences and partial sequences of the nad4 (nicotinamide dehydrogenase subunit 4 gene) gene were amplified to determine the sequence variations and population genetic diversities between these two populations. Also, 142 nad4 haplotype sequences of H. contortus from seven other geographical regions of China were retrieved from database to further examine the H. contortus population structure.ResultsSequence analysis revealed 10 genotypes (ITS2) and 73 haplotypes (nad4) among the 77 specimens, with nucleotide diversities of 0.007 and 0.021, respectively, similar to previous studies in other countries, such as Pakistan, Malaysia and Yemen. Phylogenetic analyses (BI, MP, NJ) of nad4 sequences showed that there were no noticeable boundaries among H. contortus populations from different geographical origin and population genetic analyses revealed that most of the variation (94.21%) occurred within H. contortus populations. All phylogenetic analyses indicated that there was little genetic differentiation but a high degree of gene flow among the H. contortus populations among wild blue sheep and domestic ruminants in China.ConclusionsThe current work is the first genetic characterization of H. contortus isolated from wild blue sheep in the Helan Mountains region. The results revealed a low genetic differentiation and high degree of gene flow between the H. contortus populations from sympatric wild blue sheep and domestic sheep, indicating regular cross-infection between the sympatrically reared ruminants.
| S-EPMC5606089 | biostudies-literature
Project description:The gut microbiota is a complex and essential system organ that plays an integrative role in balancing key vital functions in the host. Knowledge of the impact of altitude on the gut microbiota of European mouflon (Ovis orientalis musimon) and blue sheep (Pseudois nayaur) is currently limited. In this study, we compared the characteristics of gut microbiota in 5 mouflon at low altitude (K group), 4 mouflon at high altitude (L group), 4 blue sheep at low altitude (M group), and 4 blue sheep at high altitude (N group). The V3-V4 region of the 16S rRNA gene was analyzed using high-throughput sequencing. Analyses based on the operational taxonomic units showed significant changes in the gut microbial communities between groups at different altitudes. At the phylum level, groups at the high altitudes had a higher relative abundance of Firmicutes and a lower relative abundance of Bacteroidetes than those at the low altitudes. A higher Firmicutes:Bacteroidetes ratio is beneficial to animals in terms of the gut microbiota-mediated energy harvest. The relative abundance of Proteobacteria was significantly higher in the gut microbiota of mouflon sheep at high altitudes. At the genus level, the Bacteroides:Prevotella ratio was significantly higher in the low-altitude group (than the high-altitude group) of mouflon sheep and the ratio was significantly higher in the high-altitude group (than the low-altitude group) in blue sheep. In addition, the Ruminococcaceae_UCG-005 related to cellulose and starch digestion was the predominant genus in blue sheep and the relative abundance of the genus was significant higher in the high-altitude group than the low-altitude group of blue sheep (P < 0.01). In conclusion, our results suggested that the gut microbiota of high-altitude groups of sheep had stronger abilities related to energy metabolism and the decomposition of substances, e.g., fiber and cellulose, and that such abilities are associated with high-altitude adaptation.
| S-EPMC6682669 | biostudies-literature
Project description:gut metagenome
| PRJNA837737 | ENA
Project description:BackgroundBenzimidazole (BZ) resistance is an increasingly serious problem due to the excessive use of this anthelmintic for controlling Haemonchus contortus, which is one of the major gastrointestinal nematodes infecting small ruminants worldwide. Three known single nucleotide polymorphisms (SNPs), F167Y (TAC), E198A (GCA) and F200Y (TAC), in the isotype-1 β-tubulin gene of H. contortus are associated with BZ resistance. Comprehending the spread and origins of BZ resistance-associated SNPs has important implications for the control of this nematode.ResultsTwenty-seven adult H. contortus were harvested from wild blue sheep (Pseudois nayaur), small wild ruminants sympatric with domestic ruminants, inhabiting the Helan Mountains, China, to monitor the status of BZ resistance. In addition, 20 adult H. contortus from domestic sheep sympatric with this wild ruminant and 36 isotype-1 β-tubulin haplotype sequences of H. contortus (two of these haplotypes, E198A3 and E198A4, possessed resistance-associated SNP E198A (GCA) from domestic ruminants in eight other geographical regions of China were used to further define the origins of BZ resistance-associated SNPs within the worms collected from blue sheep. The BZ resistance-associated SNP E198A was detected, whereas SNPs F167Y (TAC) and F200Y (TAC) were not found within the worms collected from blue sheep, and the frequency of homozygous resistant E198A (GCA) was 7.40%. The evolutionary tree and network showed consistent topologies for which there was no obvious boundary among the worms from the wild and domestic hosts, and two haplotypes (E198A1 and E198A2) possessing E198A from the wild blue sheep had two different independent origins. E198A1 had the same origin with E198A3 but E198A2 had a different origin with them. Population genetic analyses revealed a low level of Fst values (ranging from 0 to 0.19749) between all H. contortus worm groups in China.ConclusionsResults of the current study of the three BZ resistance-associated SNPs of H. contortus from wild blue sheep suggested that only E198A (GCA) was present within the worms collected from the wild ruminants and had multiple independent origins.
| S-EPMC6416841 | biostudies-literature
Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
| 2533916 | ecrin-mdr-crc