Pig gut metagenome isolate:Feces | breed:Duroc X Landrace X Yorkshire
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA595919 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10696800.fastq.gz | Fastqsanger.gz | |||
| SRR10696801_1.fastq.gz | Fastqsanger.gz | |||
| SRR10696801_2.fastq.gz | Fastqsanger.gz | |||
| SRR10696802.fastq.gz | Fastqsanger.gz | |||
| SRR10696803.fastq.gz | Fastqsanger.gz |
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Project description:Sperm contain microRNAs (miRNAs), which may have roles in epigenetic control. Regarding phylogenetic relationships among various swine breeds, Yorkshire and Landrace, are considered phenotypically and genetically very similar, but distinctly different from Duroc. The objective of the present study was to compare abundance of boar sperm miRNAs in these three breeds. Overall, 252 prioritized miRNAs were investigated using real-time PCR; relative expression of miRNAs in sperm was similar in Yorkshire and Landrace boars, but significantly different compared to Duroc. Seventeen miRNAs (hsa-miR-196a-5p, hsa-miR-514a-3p, hsa-miR-938, hsa-miR-372-3p, hsa-miR-558, hsa-miR-579-3p, hsa-miR-595, hsa-miR-648, hsa-miR-524-3p, hsa-miR-512-3p, hsa-miR-429, hsa-miR-639, hsa-miR-551a, hsa-miR-624-5p, hsa-miR-585-3p, hsa-miR-508-3p and hsa-miR-626) were down-regulated (P < 0.05; fold regulation ≤-2) in Yorkshire and Landrace sperm, compared to Duroc sperm. Furthermore, three miRNAs (hsa-miR-9-5p, hsa-miR-150-5p, and hsa-miR-99a-5p) were significantly up-regulated in Yorkshire and Landrace sperm compared to Duroc sperm, However, 240 miRNAs were not significantly different (within + 2 fold) between Yorkshire and Landrace sperm. We concluded that miRNAs in sperm were not significantly different between Yorkshire and Landrace boars, but there were significant differences between those two breeds and Duroc boars. Furthermore, integrated target genes for selected down-regulated miRNAs (identified via an in-silico method) appeared to participate in spermatogenesis and sperm functions.
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Project description:Sus scrofa strain:Duroc, Landrace, Yorkshire Metagenome
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Project description:ObjectiveTo investigate the effect of host genetics on gut microbial diversity, we performed a structural survey of the fecal microbiota of four purebred boar pig lines: Duroc, Landrace, Hampshire, and Yorkshire.MethodsThe V3-V4 regions of the 16S rRNA genes were amplified and sequenced.ResultsA total of 783 operational taxonomic units were shared by all breeds, whereas others were breed-specific. Firmicutes and Bacteroidetes dominated the majority of the fecal microbiota; Clostridia, Bacilli, and Bacteroidia were the major classes. Nine predominant genera were observed in all breeds and eight of them can produce short-chain fatty acids. Some bacteria can secrete cellulase to aid fiber digestion by the host. Butyric, isobutyric, valeric, and isovaleric acid levels were highest in Landrace pigs, whereas acetic and propionic acid were highest in the Hampshire breed. Heatmap was used to revealed breed-specific bacteria. Principal coordinate analysis of fecal bacteria revealed that the Landrace and Yorkshire breeds had high similarity and were clearly separated from the Duroc and Hampshire breeds.ConclusionOverall, this study is the first time to compare the fecal microbiomes of four breeds of boar pig by high-throughput sequencing and to use Spearman's rank correlation to analyze competition and cooperation among the core bacteria.
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Project description:The pig bone weight trait holds significant economic importance in southern China. To expedite the selection of the pig bone weight trait in pig breeding, we conducted molecular genetic research on these specific traits. These traits encompass the bone weight of the scapula (SW), front leg bone weight (including humerus and ulna) (FLBW), hind leg bone weight (including femur and tibia) (HLBW), and spine bone weight (SBW). Up until now, the genetic structure related to these traits has not been thoroughly explored, primarily due to challenges associated with obtaining the phenotype data. In this study, we utilized genome-wide association studies (GWAS) to discern single nucleotide polymorphisms (SNPs) and genes associated with four bone weight traits within a population comprising 571 Duroc × (Landrace × Yorkshire) hybrid pigs (DLY). In the analyses, we employed a mixed linear model, and for the correction of multiple tests, both the false discovery rate and Bonferroni methods were utilized. Following functional annotation, candidate genes were identified based on their proximity to the candidate sites and their association with the bone weight traits. This study represents the inaugural application of GWAS for the identification of SNPs associated with individual bone weight in DLY pigs. Our analysis unveiled 26 SNPs and identified 12 promising candidate genes (OPRM1, SLC44A5, WASHC4, NOPCHAP1, RHOT1, GLP1R, TGFB3, PLCB1, TLR4, KCNJ2, ABCA6, and ABCA9) associated with the four bone weight traits. Furthermore, our findings on the genetic mechanisms influencing pig bone weight offer valuable insights as a reference for the genetic enhancement of pig bone traits.
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Project description:The study aimed to investigate the genetic parameters of the production and reproduction traits of Korean Duroc, Landrace, and Yorkshire pigs. Three production traits, namely average daily gain (ADG), age at 105 kg body weight (DAYS105) and backfat thickness (BFT), and three reproduction traits, namely age at first farrowing (AFF), total number of piglets born (TNB) and number of piglets born alive (NBA), were analyzed. The reproduction dataset was based on first-parity gilts only. However, the production dataset comprised pigs of both sexes. Genetic parameters were estimated from individual datasets using a multiple-trait animal model in AIREMLF90 software. The heritability values of ADG, DAYS105 and BFT were 0.34-0.36, 0.41-0.44 and 0.38-0.48, respectively, across breeds. Heritability values for AFF, TNB and NBA were 0.07-0.14, 0.09-0.11 and 0.09-0.10, respectively. Strong genetic correlations existed between ADG and DAYS105 (-0.97) and between TNB and NBA (0.90 to 0.96). In line with breeding goals, all productive traits in Duroc pigs, and all reproduction traits except AFF in Landrace and Yorkshire pigs, also showed noticeable improvements in recent years. In conclusion, we believe that our findings on economic traits would greatly assist future pig breeding decisions in Korea.
| S-EPMC8147943 | biostudies-literature
Project description:BackgroundThe health and welfare of pigs used in biomedical research is essential to research quality and compliance with the 3Rs (replacement, reduction, and refinement). Hematological variables are objective markers to quantitatively determine health issues and evaluate physiological differences before and after experimental procedures. There are no recent validated hematologic reference intervals (RIs) published for Danish crossbred Landrace Yorkshire Duroc (LYD) pigs to aid researchers and veterinarians in their decision-making. The objective of this study was to establish hematologic RIs for LYD pigs used for biomedical research. Blood samples were collected from healthy female LYD pigs (35-65 kg) and analyzed using the in-house ProCyte Dx Hematology Analyzer. Means with 90% confidence intervals for lower and upper limits were calculated according to guidelines by the American Society of Veterinary Clinical Pathology.ResultsInspection of 141 pigs led to 133 blood samples available for analyses after exclusions due to clinical signs of disease, inadequate tube filling or presence of macroscopic clots. Thirty-two samples reported platelet abnormalities and upon further investigation these samples were excluded when calculating RIs for platelets and platelet indices. Other measurements were not affected. The RI for red blood cells, hemoglobin, hematocrit and white blood cells were 5.10-7.00 × 106/µL, 9.36-12.29 g/dL, 30.46-40.47%, and 11.73-25.00 × 103/µL, respectively.ConclusionsOur study provides RIs for hematological variables in LYD pigs, revealing significant differences from published RIs of other breeds. These findings highlight the influence of factors like age, breed and health status on measurements, emphasizing the importance of using breed-specific RIs. This research supports the 3Rs, guiding better animal care and enhancing overall research quality.
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Project description:The gut microbiota plays an important role in pig health and performance, particularly in host growth and fecundity. In present study, the characteristics and diversity of gut microbiota in fine purebred boars from three-way crossbred "Duroc×Landrace×Yorkshire" pigs were investigated using 16 S rRNA gene sequencing. The results showed that the three breeds of boars shared similar gut microbiota, yet there remain slight differences at the family/genus level. At the family level, Ruminococcaceae, Streptococcaceae and Lactobacillaceae have the highest abundance in Landrace, while Rikenellaceae and f_p_251_o5 have the highest abundance in Duroc. The abundance of Prevotellaceae, Lachnospiraceae and Spirochaetaceae in intestinal of Yorkshire were higher than that of Landrace and Duroc. In addition, ten and six biomarkers were identified in the microbiota across breeds and months of age, respectively. Moreover, we evaluated the effect of gut microbiota on boar semen quality, revealing that Duroc had the strongest sperm vitality, significantly associated with the genus Rikenellaceae_PC9_gut_group. In addition, the spermatogenesis ability and sperm production improved gradually along with increase of age. In conclusion, this study provides a reference for understanding the gut microbiota composition of purebred boars used for three-way crosses and their impact on semen performance.
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Project description:Microbiome analysis has relied largely on metagenomics to characterize microbial populations and predict their functions. Here, we used a TMT LC-MSMS metaproteomic analysis of the fecal microbiome in piglets before and after weaning to compare protein abundances as they pertain to microbial populations specific to either a milk- or plant-based diet. Fecal samples were collected from six piglets on the day of weaning and four weeks after transitioning to a standard nursery diet. Using the 12,554 protein groups identified in samples, we confirmed the shift in protein composition that takes place in response to the microbial succession following weaning and demonstrated the redundancy in metabolic processes between taxa. We identified taxa with roles as primary degraders based on corresponding proteins synthesized, thereby providing evidence for cross-feeding. Proteins associated with the breakdown of milk-specific carbohydrates were common among pre-weaned pigs, whereas the proteome of post-weaned piglets contained a greater abundance of proteins involved in the breaking down plant-specific carbohydrates. Furthermore, output revealed that production of propionate takes place via the propionaldehyde pathway in pre-weaned piglets, but changes to production via the succinate pathway in post-weaned piglets. Finally, a disproportionate quantity of carbohydrate-active enzymes (CAZymes) (~8%) were produced by fungi, which typically only represent ~0.1% of the microbiome taxa. Information gathered through this characterization of the metaproteome before and after weaning revealed important differences regarding the role of members in the microbial community, thereby providing information for the optimization of diets and products for both piglet and microbiome health.
2025-05-26 | PXD063155 | Pride
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Project description:Hindgut microbiome of entire male pigs
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