Effects of oat (Avena sativa L.) hay diet supplementation on the intestinal microbiome and metabolome of Small-tail Han sheep

Supplementation of the sheep diet with oats (Avena sativa L.) improves animal growth and meat quality, however effects on intestinal microbes and their metabolites was not clear. This study aimed to establish the effect of dietary oat supplementation on rumen and colonic microbial abundance and explore the relationship with subsequent changes in digesta metabolites. Twenty Small-tail Han sheep were randomly assigned to a diet containing 30 g/100 g of maize straw (Control) or oat hay (Oat). After 90-days on experimental diets, rumen and colon digesta were collected and microbial diversity was determined by 16S rRNA gene Illumina NovaSeq sequencing and metabolomics was conducted using Ultra-high performance liquid chromatography Q-Exactive mass spectrometry (UHPLC-QE-MS). Compared to Control group, oat hay increased the abundance of Bacteroidetes and Fibrobacteres as well as known short-chain fatty acid (SCFA) producers Prevotellaceae, Ruminococcaceae and Fibrobacteraceae in rumen (p < 0.05). In rumen digesta, the Oat group showed had higher levels of (3Z,6Z)-3,6-nonadienal, Limonene-1,2-epoxide, P-tolualdehyde, and Salicylaldehyde compared to Control (p < 0.05) and these metabolites were positively correlated with the abundance of cecal Prevotellaceae NK3B31. In conclusion, supplementation of the sheep diet with oat hay improved desirable microbes and metabolites in the rumen, providing insight into mechanisms whereby meat quality can be improved by oat hay supplementation

Transcriptome Dynamics Reveal Stage-Specific and Melatonin-Triggered Gene Expression Patterns During The Cashmere Growth Cycle in Capra Hircus

Abstract Background Cashmere goat is famous for its high-quality fibers. The growth of cashmere in secondary hair follicles exhibits a seasonal pattern arising from circannual changes in the natural photoperiod. Although several studies have compared and analyzed the differences in gene expression between different cashmere growth stages, the selection of samples in these studies relies on research experience or morphological evidence. Distinguishing cashmere growth cycle according to gene expression patterns may help to explore the regulation mechanisms related to cashmere growth and the effect of melatonin from a molecular level more accurately. Results In this study, we applied RNA-sequencing to the hair follicles of three normal and three melatonin-treated Inner Mongolian cashmere goats sampled every month during a whole cashmere growth cycle. A total of 3559 and 988 genes were subjected as seasonal changing genes (SCGs) in the control and treated groups, respectively. The SCGs in the normal group are divided into three clusters, and their specific expression patterns help to group the cashmere growth cycle into anagen, catagen and telogen stages. Some canonical pathways such as Wnt, TGF-beta and Hippo signaling pathways are detected as promoting the cashmere growth, while Cell adhesion molecules (CAMs), Cytokine-cytokine receptor interaction, Jak-STAT, Fc epsilon RI, NOD-like receptor, Rap1, PI3K-Akt, cAMP, NF-kappa B and many immune-related pathways are detected in the catagen and telogen stages. The PI3K-Akt signaling, ECM-receptor interaction and Focal adhesion are found in the transition stage between telogen to anagen, which may serve as candidate biomarkers for telogen-anagen regeneration. Pairwise comparisons between the control and melatonin-treated groups also indicate 941 monthly differentially expressed genes (monthly DEGs). These monthly DEGs are mainly distributed from April and September, which reveal a potential signal pathway map regulating the anagen stage triggered by melatonin. Enrichment analysis shows that Wnt, Hedgehog, ECM, Chemokines and NF-kappa B signaling pathways may be involved in the regulation of non-quiescence and secondary shedding under the influence of melatonin. Conclusions Our study decodes the key regulators of the whole cashmere growth cycle, laying the foundation for the control of cashmere growth and improvement of cashmere yield.</jats:p

Transcriptome Dynamics Reveal Stage-specific and Melatonin-triggered Gene Expression Patterns During the Cashmere Growth Cycle in Capra Hircus

Abstract Background: Cashmere goat is famous for its high-quality fibers. The growth of cashmere in secondary hair follicles exhibits a seasonal pattern arising from circannual changes in the natural photoperiod. Although several studies have compared and analyzed the differences in gene expression between different cashmere growth stages, the selection of samples in these studies relies on research experience or morphological evidence. Distinguishing cashmere growth cycles according to gene expression patterns may help to explore the regulation mechanisms related to cashmere growth and the effect of melatonin from a molecular level more accurately. Results: In this study, we applied RNA-sequencing to the hair follicles of three normal and three melatonin-treated Inner Mongolian cashmere goats sampled every month during a whole cashmere growth cycle. A total of 3559 and 988 genes were subjected as seasonal changing genes (SCGs) in the control and treated groups, respectively. The SCGs in the normal group are divided into three clusters, and their specific expression patterns help to group the cashmere growth cycle into anagen, catagen and telogen stages. Some canonical pathways such as Wnt, TGF-beta and Hippo signaling pathways are detected as promoting the cashmere growth, while Cell adhesion molecules (CAMs), Cytokine-cytokine receptor interaction, Jak-STAT, Fc epsilon RI, NOD-like receptor, Rap1, PI3K-Akt, cAMP, NF-kappa B and many immune-related pathways are detected in the catagen and telogen stages. The PI3K-Akt signaling, ECM-receptor interaction and Focal adhesion are found in the transition stage between telogen to anagen, which may serve as candidate biomarkers for telogen-anagen regeneration. Pairwise comparisons between the control and melatonin-treated groups also indicate 941 monthly differentially expressed genes (monthly DEGs). These monthly DEGs are mainly distributed from April and September, which reveal a potential signal pathway map regulating the anagen stage triggered by melatonin. Enrichment analysis shows that Wnt, Hedgehog, ECM, Chemokines and NF-kappa B signaling pathways may be involved in the regulation of non-quiescence and secondary shedding under the influence of melatonin. Conclusions: Our study decodes the key regulators of the whole cashmere growth cycle, laying the foundation for the control of cashmere growth and improvement of cashmere yield.</jats:p

Time-course RNA-seq analysis reveals stage-specific and melatonin-triggered gene expression patterns during the hair follicle growth cycle in Capra hircus

Abstract Background Cashmere goat is famous for its high-quality fibers. The growth of cashmere in secondary hair follicles exhibits a seasonal pattern arising from circannual changes in the natural photoperiod. Although several studies have compared and analyzed the differences in gene expression between different hair follicle growth stages, the selection of samples in these studies relies on research experience or morphological evidence. Distinguishing hair follicle growth cycle according to gene expression patterns may help to explore the regulation mechanisms related to cashmere growth and the effect of melatonin from a molecular level more accurately. Results In this study, we applied RNA-sequencing to the hair follicles of three normal and three melatonin-treated Inner Mongolian cashmere goats sampled every month during a whole hair follicle growth cycle. A total of 3559 and 988 genes were subjected as seasonal changing genes (SCGs) in the control and treated groups, respectively. The SCGs in the normal group were divided into three clusters, and their specific expression patterns help to group the hair follicle growth cycle into anagen, catagen and telogen stages. Some canonical pathways such as Wnt, TGF-beta and Hippo signaling pathways were detected as promoting the hair follicle growth, while Cell adhesion molecules (CAMs), Cytokine-cytokine receptor interaction, Jak-STAT, Fc epsilon RI, NOD-like receptor, Rap1, PI3K-Akt, cAMP, NF-kappa B and many immune-related pathways were detected in the catagen and telogen stages. The PI3K-Akt signaling, ECM-receptor interaction and Focal adhesion were found in the transition stage between telogen to anagen, which may serve as candidate biomarkers for telogen-anagen regeneration. A total of 16 signaling pathways, 145 pathway mRNAs, and 93 lncRNAs were enrolled to construct the pathway-mRNA-lncRNA network, which indicated the function of lncRNAs through interacting with their co-expressed mRNAs. Pairwise comparisons between the control and melatonin-treated groups also indicated 941 monthly differentially expressed genes (monthly DEGs). These monthly DEGs were mainly distributed from April and September, which revealed a potential signal pathway map regulating the anagen stage triggered by melatonin. Enrichment analysis showed that Wnt, Hedgehog, ECM, Chemokines and NF-kappa B signaling pathways may be involved in the regulation of non-quiescence and secondary shedding under the influence of melatonin. Conclusions Our study decoded the key regulators of the whole hair follicle growth cycle, laying the foundation for the control of hair follicle growth and improvement of cashmere yield. </jats:sec

Genetic Diversity Analysis of Dermacentor Nuttalli within Inner Mongolia, China

Abstract BackgroundTicks (Arthropoda, Ixodida), after mosquitoes, are the next most prevalent vector of infectious diseases; and are responsible for spreading a multitude of pathogens and threatening the health and welfare of animals and human beings. Yet, given the history of tick-borne pathogen infections in the Inner Mongolia Autonomous region of China, neither the genetic diversity nor the spatial distribution of haplotypes within ticks has been studied. MethodsWe characterized the haplotype distribution of Dermacentor nuttalli in four main pastoral areas of the Inner Mongolia Autonomous region, by sampling 109 individuals (recovered from sheep) in April-August 2019. The 16S rRNA gene, Cytochrome c Oxidase Subunit Ⅰ, and the Internal Transcribed Spacer 2 region were amplified and sequenced from extracted DNA.Results 82 haplotypes were identified, the most prevalent of which was H32. 12 sequences (11 of all sequences) represented the most abundant haplotypes, with a highly scattered distribution. Total haplotype diversity was 0.98318, while total nucleotide diversity was 0.11369. Neutrality tests revealed negative results in the four locations analyzed, which is indicative of an excess of recently derived haplotypes. Fixation index values (FST) indicate that the degree of genetic differentiation amongst some sampled populations were small, while others were moderate. Conclusion The genetic diversity of D.nuttalli populations in our region can likely adapt to different geographical environments, thereby leading to genetic diversity, and creating genetic differentiation amongst different populations. However, genetic differentiation is cryptic and does not form the pedigree geographical structure.</jats:p

Additional file 9 of Time-course RNA-seq analysis reveals stage-specific and melatonin-triggered gene expression patterns during the hair follicle growth cycle in Capra hircus

Additional file 9. Detailed genes of 3 clusters in the melatonin-treated group (MC1, MC2 and MC3)

Additional file 11 of Time-course RNA-seq analysis reveals stage-specific and melatonin-triggered gene expression patterns during the hair follicle growth cycle in Capra hircus

Additional file 11. The KEGG analysis results of monthly DEGs