To explore the relationship among the level of fiber, gut microbiota, and nutritional substances, we applied the next generation sequencing technology for the identification of the composition and structure of microbiota in the gastrointestinal tract. In this study, a total of 25 phyla and 298 genera were identified from the gastrointestinal tract; Firmicutes, Bacteroidetes, and Proteobacteria were the predominant phyla. The ability of cecum in carbohydrate metabolism was significantly higher than that of the gizzard and ileum (P < 0.05). The bacterial community structure in various stages of the development of the cecum was different. In the different growth stages of cecum, the increase in the microbiota structure of the fiber level elevates the ability of carbon hydration. Second, the apparent metabolic rates of the other nutrients were affected by the fiber and period except for acid detergent fiber (P < 0.05); the apparent utilization rate of the nutrients increased with time. However, with the increase in the fiber level, the apparent utilization of nutrients was initially increased, followed by a decrease. Therefore, a correlation was established between the fiber level and gastrointestinal microbiota and apparent nutrient utilization rate of the 3 phyla. Our results suggest that the fiber level and growth stages could impact the composition of gut microbiota.

Subcutaneous adipose tissue is a loose connective tissue specializing in the regulation of energy storage and metabolization. In domesticated pigs (Sus scrofa), the temporal development of subcutaneous adipose tissue is critical for meat production. However, the regulation of adipose tissue development remains unclear. Here, the subcutaneous adipose tissue development was characterized and compared in lean (Danish-Landrace) and obese (Min) pigs at juvenile and the juvenile-to-adult growth stages. Using RNA sequencing, we profiled the transcriptome of subcutaneous adipose tissue isolated from 4- and 16-week-old pigs and identified 24,718 expressed transcription units. Of them, 6327 genes were differentially expressed between the breeds and/or developmental stages. Compared with obese pigs, upregulated genes in lean pigs showed significant function and pathway enrichment in fatty acid degradation and mitochondrial functions. Further analysis uncovered the distinct usage preferences of the three alternative peroxisome proliferator-activated receptor γ (PPARγ) promoters associated with the development of subcutaneous adipose tissue in both breeds. Transcriptome analysis of subcutaneous adipose tissue in lean and obese pigs suggested that marker-assisted selection of fatty acid degradation and PPARγ signaling pathways could be important directions for future pork quality improvement and modern breeding.

The intramuscular fat (IMF) content and fatty acid composition are important meat quality traits that are mostly affected by the cattle breed. Muscle, adipose tissue and liver are important organs involved in the development of intramuscular adipose tissue. Thus, we hypothesized that there were marked differences in the adipogenesis and lipid metabolism of these tissues between Wagyu-cross and Holstein steers during the finishing phases. To test this hypothesis, we analyzed the expression levels of adipogenesis- and lipid metabolism-related genes in longissimus muscle (LM), subcutaneous fat (SCF) and liver from Wagyu-cross and Holstein steers at 26 months of age. The IMF content and fatty acid profile of LM were determined. Wagyu-cross steers had a higher IMF content and MUFA percentages in the LM than Holstein steers (P<0.05). The relative expression of FGF2, COL1A1, SREBP1c, SCD1, GRP78 and LEP was greater in the LM of Wagyu-cross steers than in Holstein steers (P<0.05). In contrast, Holstein steer SCF had higher (P<0.05) mRNA expression levels of FABP4 and ADIPOQ than Wagyu-cross steers. In the liver, the expression of SREBP1c and GRP78 in Wagyu-cross steers was significantly higher than that in Holstein steers (P<0.05). The results demonstrate that both intramuscular adipogenesis and fibrogenesis are enhanced in Wagyu-cross steers compared with Holstein steers during the finishing phase and that IMF deposition is positively correlated with the maturity of SCF and hepatic lipid accumulation in Wagyu-cross steers.

Backgrounds As osteoarthritis (OA) disease-modifying therapies are not available, novel therapeutic targets need to be discovered and prioritized. Here, we aim to identify miRNA signatures in patients to fully elucidate regulatory mechanism of OA pathogenesis and advance in basic understanding of the genetic etiology of OA. Methods Six participants (3 OA and 3 controls) were recruited and serum samples were assayed through RNA sequencing (RNA-seq). And, RNA-seq dataset was analysed to identify genes, pathways and regulatory networks dysregulated in OA. The overlapped differentially expressed microRNAs (DEMs) were further screened in combination with the microarray dataset GSE143514. The expression levels of candidate miRNAs were further validated by quantitative real-time PCR (qRT-PCR) based on the GEO dataset (GSE114007). Results Serum samples were sequenced interrogating 382 miRNAs. After screening of independent samples and GEO database, the two comparison datasets shared 19 overlapped candidate micRNAs. Of these, 9 up-regulated DEMs and 10 down-regulated DEMs were detected, respectively. There were 236 target genes for up-regulated DEMs and 400 target genes for those down-regulated DEMs. For up-regulated DEMs, the top 10 hub genes were KRAS, NRAS, CDC42, GDNF, SOS1, PIK3R3, GSK3B, IRS2, GNG12, and PRKCA; for down-regulated DEMs, the top 10 hub genes were NR3C1, PPARGC1A, SUMO1, MEF2C, FOXO3, PPP1CB, MAP2K1, RARA, RHOC, CDC23, and CREB3L2. Mir-584-5p-KRAS, mir-183-5p-NRAS, mir-4435-PIK3R3, and mir-4435-SOS1 were identified as four potential regulatory pathways by integrated analysis. Conclusions We have integrated differential expression data to reveal putative genes and detected four potential miRNA-target gene pathways through bioinformatics analysis that represent new mediators of abnormal gene expression and promising therapeutic targets in OA.

Backgrounds: Given the roles of microRNA (miRNA) in human diseases and the high incidence of gestational diabetes mellitus (GDM), the aim of the study was to examine miRNA signatures and crucial pathways, as well as possible biomarkers for GDM diagnosis.Methods: We conducted a two-stage study to explore functional miRNA and those target genes. Twelve participants (6 GDM and 6 non-GDM) were first enrolled and performed RNA sequencing analysis. The overlapped candidate genes were further screened in combination with differentially expressed genes (DEGs) of GEO datasets (GSE87295, GSE49524 and GSE19649) and potential target genes of DEMs. Candidate genes, critical pathways, small molecular compounds and regulatory networks were identified using bioinformatic analysis. The potential candidate genes were then investigated using the GEO dataset (GSE103552) of 19 participants in the validation stage (11 GDM and 8 non-GDM women).Results: Briefly, blood samples were sequenced interrogating 50 miRNAs, including 20 upregulated and 30 downregulated differentially expressed microRNAs(DEMs) in our internal screening dataset. After screening GEO databases, 123 upregulated and 70 downregulated genes were overlapped through DEGs of GEO datasets and miRNA-target genes. MiR-29b-1-5p-TGFB2, miR-142-3p-TGFB2, miR-9-5p-FBN2, miR-212-5p-FBN2, miR-542-3p-FBN1, miR-9-5p-FBN1, miR-508-3p-FBN1, miR-493-5p-THBS1, miR-29b-3p-COL4A1, miR-432-5p-COL5A2, miR-9-5p-TGFBI, miR-486-3p-SLC7A5 and miR-6515-5p-SLC1A5 were revealed as thirteen possible regulating pathways by integrative analysis.Conclusion: Overall, thirteen candidate miRNA-target gene regulatory pathways representing potentially novel biomarkers of GDM diseases were revealed. Ten chemicals were identified as putative therapeutic agents for GDM. This study examined a series of DEGs that are associated with epigenetic alternations of miRNA through an integrated approach and gained insight into biological pathways in GDM. Precise diagnosis and therapeutic targets of GDM would be further explored through putative genes in the future.