Exploring the link between microbial community structure and flavour compounds of traditional fermented yak milk in Gannan region

Traditional fermented yak milk has immense cultural and nutritional significance for Tibetan herders. In this study, we investigated the microbial community structure and flavour compounds in traditional fermented yak milk from three distinct regions of Gannan to explore the relationship between microbial composition and flavour compounds. The findings revealed significant variations in flavour compounds and the bacterial microbiota among the samples from the three regions. The dominant species identified in fermented yak milk were Streptococcus salivarius subsp. Thermophilus, Lactobacillus helveticus, and Kluyveromyces marxianus. Bidirectional orthogonal partial least-squares (O2PLS) analysis highlighted five bacterial genera and three fungal genera as contributors to the production of flavour-related compounds. Furthermore, regression analysis revealed that the Lactobacillus and Streptococcus genera were associated with the production of 2,3-pentanedione as well as eight predicted KEGG pathways. These findings provide valuable insights into the intricate relationship between flavour compounds and microbiota in traditional fermented yak milk.

Proteomic Analysis Reveals the Effects of Different Dietary Protein Levels on Growth and Development of Jersey-Yak

Jersey-yak is a hybrid offspring of Jersey cattle and yak (Bos grunniens). Changing the feeding system of Jersey-yak can significantly improve its growth performance. In this study, tandem mass tag (TMT) proteomics technology was used to determine the differentially expressed proteins (DEPs) of the longissimus lumborum (LL) muscle of Jersey-yak fed different protein levels of diet. The results showed that compared with the traditional grazing feeding, the growth performance of Jersey-yaks was significantly improved by crude protein supplementation after grazing. A total of 3368 proteins were detected in these muscle samples, of which 3365 were quantified. A total of 434 DEPs were identified. Through analyses, it was found that some pathways related to muscle growth and development were significantly enriched, such as Rap1 signaling pathway, mTOR signaling pathway, and TGF-beta signaling pathway. A number of DEPs enriched in these pathways are related to muscle cell development, differentiation, and muscle development, including integrin subunit alpha 7 (ITGA7), myosin heavy chain 8 (MYH8), and collagen type XII alpha 1 chain (COL12A1). In conclusion, the results of this study provide insights into the proteomics of different feeding patterns of Jersey-yak, providing a stronger basis for further understanding the biological mechanism of hybrid varieties.

The potential mediation of hypoxia-inducible factor-1α in heat shock protein 27 translocations, caspase-3 and calpain activities and yak meat tenderness during postmortem aging

The present study aimed to characterize the influence of hypoxia-inducible factor-1α on heat shock protein 27 and cytochrome c translocation, yak meat microstructure destruction, and endogenous enzymes activities, refining the understanding of the tenderization process after slaughter. Postmortem yak longissimus thoracis et lumborum muscles were incubated with 0.9% saline or hypoxia-inducible factor-1α stabilizer dimethyloxaloylglycine at 4 °C for 6, 12, 24, 72, and 120 h. Results showed that hypoxia-inducible factor-1α activation promoted heat shock protein 27 migration and cytochrome c release, facilitating (P < 0.05) caspase-3 activity by mediating the heat shock protein 27/caspase-3 interaction but did not exert (P > 0.05) significant effects on the calpain-1 activity. Additionally, hypoxia-inducible factor-1α activation contributed to the mitochondrial apoptosis cascade, leading to a higher (P < 0.01) apoptosis rate. Therefore, these observations indicate that hypoxia-inducible factor-1α affects caspase-3 activity and tenderness of postmortem muscle through distinct regulatory mechanisms, possibly, in part, with heat shock protein 27 and cytochrome c mediation.

Effects of dietary crude protein levels in the concentrate supplement after grazing on rumen microbiota and metabolites by using metagenomics and metabolomics in Jersey-yak

Introduction

The crude protein level in the diet will affect the fermentation parameters, microflora, and metabolites in the rumen of ruminants. It is of great significance to study the effect of crude protein levels in supplementary diet on microbial community and metabolites for improving animal growth performance. At present, the effects of crude protein level in supplementary diet on rumen fermentation parameters, microbial community, and metabolites of Jersey-Yak (JY) are still unclear.

Methods

The purpose of this experiment was to study the appropriate crude protein level in the diet of JY. The rumen fermentation indexes (volatile fatty acids and pH) were determined by supplementary diets with crude protein levels of 15.16 and 17.90%, respectively, and the microbial community and metabolites of JYs were analyzed by non-target metabonomics and metagenome sequencing technology, and the changes of rumen fermentation parameters, microbial flora, and metabolites in the three groups and their interactions were studied.

Results and Discussion

The crude protein level in the supplementary diet had significant effects on pH, valeric acid, and the ratio of acetic acid to propionic acid (p < 0.05). The protein level had no significant effect on the dominant microflora at the phylum level (p > 0.05), and all three groups were Bacteroides and Firmicutes. The results of metabolite analysis showed that the crude protein level of supplementary diet significantly affected the metabolic pathways such as Bile secretion and styrene degradation (p < 0.05), and there were different metabolites between the LP group and HP group, and these different metabolites were related to the dominant microbial to some extent. To sum up, in this experiment, the effects of crude protein level in supplementary diet on rumen microorganisms and metabolites of JY and their relationship were studied, which provided the theoretical basis for formulating a more scientific and reasonable supplementary diet in the future.

Transcriptome-Wide Study of mRNAs and lncRNAs Modified by m6A RNA Methylation in the Longissimus Dorsi Muscle Development of Cattle-Yak

Cattle-yak is a hybrid F₁ generation of cattle and yak, which has a history of more than 3000 years and has shown better production performance and higher economic benefits than those of yaks. However, up to now, there has been no study on the transcriptome-wide m⁶A methylation profile of bovine skeletal muscle and its potential biological function during muscle development. Here, we observed significant changes in the expression levels of muscle-related marker genes and methylation-related enzymes during the development of cattle-yak, and the overall m⁶A content in the Longissimus dorsi muscle of 18-month-old cattle-yak decreased significantly. A total of 36,602 peaks, 11,223 genes and 8388 lncRNAs were identified in the two groups, including 2989 differential peaks (427 up-regulated peaks and 2562 down-regulated peaks), 1457 differentially expressed genes (833 up-regulated genes and 624 down-regulated genes) and 857 differentially expressed lncRNAs (293 up-regulated lncRNAs and 564 down-regulated lncRNAs). GO and KEGG analysis revealed that they were significantly enriched in some muscle-related pathways (Wnt signaling pathway and MAPK signaling pathway) and high-altitude adaptation-related pathway (HIF-1 signaling pathway). Moreover, m⁶A abundance was positively correlated with gene expression levels, while it was negatively correlated with lncRNA expression levels. This indicates that m⁶A modification played an important role in the Longissimus dorsi muscle development of cattle-yak; however, the regulation mechanism of m⁶A-modified mRNA and lncRNA may be different. This study was the first report of transcriptome-wide m⁶A-modified mRNAs and lncRNAs atlas in the Longissimus dorsi muscle development of cattle-yak, one which will provide new perspectives for genetic improvement in bovines.

Genomic analyses of wild argali, domestic sheep, and their hybrids provide insights into chromosome evolution, phenotypic variation, and germplasm innovation

Understanding the genetic mechanisms of phenotypic variation in hybrids between domestic animals and their wild relatives may aid germplasm innovation. Here, we report the high-quality genome assemblies of a male Pamir argali (O ammon polii, 2n = 56), a female Tibetan sheep (O aries, 2n = 54), and a male hybrid of Pamir argali and domestic sheep, and the high-throughput sequencing of 425 ovine animals, including the hybrids of argali and domestic sheep. We detected genomic synteny between Chromosome 2 of sheep and two acrocentric chromosomes of argali. We revealed consistent satellite repeats around the chromosome breakpoints, which could have resulted in chromosome fusion. We observed many more hybrids with karyotype 2n = 54 than with 2n = 55, which could be explained by the selfish centromeres, the possible decreased rate of normal/balanced sperm, and the increased incidence of early pregnancy loss in the aneuploid ewes or rams. We identified genes and variants associated with important morphological and production traits (e.g., body weight, cannon circumference, hip height, and tail length) that show significant variations. We revealed a strong selective signature at the mutation (c.334C > A, p.G112W) in TBXT and confirmed its association with tail length among sheep populations of wide geographic and genetic origins. We produced an intercross population of 110 F2 offspring with varied number of vertebrae and validated the causal mutation by whole-genome association analysis. We verified its function using CRISPR-Cas9 genome editing. Our results provide insights into chromosomal speciation and phenotypic evolution and a foundation of genetic variants for the breeding of sheep and other animals.

Comparison of Dynamics of Udder Skin Microbiota From Grazing Yak and Cattle During the Perinatal Period on the Qinghai–Tibetan Plateau

The perinatal period has an important impact on the health of ruminants, and the imbalance of udder skin microbiota might be an important inducement of bovine mastitis. However, it is not clear how the perinatal period affects the microbial structure and stability of the udder skin of yak and cattle. Here, we used 16S rRNA gene high-throughput sequencing to analyze the udder skin microbiota of yak and cattle during the perinatal period. We found that the diversity and richness of microbiota of bovine udder skin during 1–2 weeks postpartum were significantly lower than those in the 1–2 weeks prenatal and 1-month postpartum period (Wilcoxon, p < 0.05). Besides, we found sharing of 2,533 OTUs in the udder skin microbiota of yak and cattle during the perinatal period, among which the core microbiota at the genera level was mainly composed of Staphylococcus, Moraxella, and Acinetobacter. However, the genus Acinetobacter was significantly abundant in the udder skin of cattle during 1–2 weeks postpartum. The NMDS and LEfSe results showed that the perinatal period had more effects on the composition and stability of microbial community in the udder skin of cattle compared to yak, particularly during 1–2 weeks postpartum. In addition, the average content of total whey proteins and immunoglobulin G of whey protein were significantly higher in the yak colostrum when compared to those found in the cattle (p < 0.05). In conclusion, the structure of udder skin microbiota of yak during the perinatal period is more stable than that of cattle in the same habitat, and 1–2 weeks postpartum may be a potential window period to prevent cattle mastitis.

Comprehensive Analysis of mRNA, lncRNA, circRNA, and miRNA Expression Profiles and Their ceRNA Networks in the Longissimus Dorsi Muscle of Cattle-Yak and Yak

Cattle-yak, as the hybrid offspring of cattle (Bos taurus) and yak (Bos grunniens), demonstrates obvious heterosis in production performance. Male hybrid sterility has been focused on for a long time; however, the mRNAs and non-coding RNAs related to muscle development as well as their regulatory networks remain unclear. The phenotypic data showed that the production performance (i.e., body weight, withers height, body length, and chest girth) of cattle-yak was significantly better than that of the yak, and the economic benefits of the cattle-yak were higher under the same feeding conditions. Then, we detected the expression profiles of the longissimus dorsi muscle of cattle-yak and yak to systematically reveal the molecular basis using the high-throughput sequencing technology. Here, 7,126 mRNAs, 791 lncRNAs, and 1,057 circRNAs were identified to be differentially expressed between cattle-yaks and yaks in the longissimus dorsi muscle. These mRNAs, lncRNA targeted genes, and circRNA host genes were significantly enriched in myoblast differentiation and some signaling pathways related to muscle development (such as HIF-1 signaling pathway and PI3K-Akt signaling pathway). We constructed a competing endogenous RNA (ceRNA) network and found that some non-coding RNAs differentially expressed may be involved in the regulation of muscle traits. Taken together, this study may be used as a reference tool to provide the molecular basis for studying muscle development.

Fecal Microbiota Dynamics Reveal the Feasibility of Early Weaning of Yak Calves under Conventional Grazing System

Simple Summary

Yak (Bos grunniens) is the most economically and culturally important domestic bovine species adapted to the extreme ecological environment of the Qinghai–Tibetan Plateau (QTP), which provides milk, meat, transportation, fuel (yak dung), and wool for local nomads as well as major sources of income. Calves are an important part of the sustainable development of the yak industry on the QTP, and the quality of calf rearing directly determines the production performance of adult animals. Under the traditional grazing management, late weaning (>180 days) of yak calves seriously affects the improvement of their production performance. A comparative study of fecal microbiota dynamics of yak and cattle (Bos taurus) calves in different months after weaning will help to understand the changes in intestinal microbiota structure, and will aid in in improving growth rate and survivability of early weaned calves. Our research will contribute to the development of appropriate strategies to regulate the gut microbiome and thus improve the growth and health of the grazing ruminants on the QTP.

Abstract

Background: The gut microbiota plays an important role in the health and production of animals. However, little information is available on the dynamic variations and comparison of intestinal microbiota in post-weaning yak calves living on the QTP. Methods: We explored the fecal bacterial microbiota succession of yak calves at different months after early weaning (60 d) compared with cattle calves by 16S rRNA gene amplicon sequencing and functional composition prediction. Results: We found no significant difference in blood biochemical parameters related to glucose and lipid metabolism between yaks and calves in different months after weaning. The core fecal bacterial microbiota from both species of calves was dominated by Ruminococcaceae, Rikenellaceae, and Bacteroidaceae. The fecal microbial community has a great alteration within the time after weaning in both cattle and yak calves, but cattle showed a larger change. After five months, the microbiota achieves a stable and concentrated state. This is also similar to the functional profile. Conclusions: Based on the exploration of dynamic changes in the fecal microbiota at an early stage of life, our results illustrated that there were no negative effects of intestinal microbiota succession on yak calves when early weaning was employed.

Characterization of the complete mitochondrial genome of Tibet Gaoshan Yak (Bos grunniens)

Tibet Gaoshan Yak (Bos grunniens) is a local Yak breed that mainly produces meat in Tibet Autonomous Region, China. In this study, the complete mitochondrial genome of Tibet Gaoshan Yak was sequenced. The total length of the mitochondrial genome is 16,323 bp, and the base composition is 33.71% for A, 13.21% for G, 27.27% for T, and 25.81% for C. The genome includes 13 protein-coding genes (ND1-ND6, ND4L, COX1-COX3, ATP6, ATP8, and CYTB), two rRNA genes (12S rRNA and 16SrRNA), 22 tRNA genes, and a noncoding control region (D-loop). Phylogenetic analysis showed that Tibet Gaoshan Yak has the closest relationship with Polled Yak. The sequence analysis provided in this study will be helpful to the management of Yak breeds, the origin, and evolution of Yak, and the protection and utilization of genetic resources.

Characterization of the complete mitochondrial genome of the Qiaoke sheep (Ovis aries)

Qiaoke sheep (Ovis aries) is a local sheep breed in Gansu province, China. It is a kind of Tibetan sheep that used for both meat and wool after long-term breeding. In this paper, the complete mitochondrial genome of Qiaoke sheep was sequenced. The total length of the mitochondrial genome is 16616 bp, and the base composition is 33.65% A, 13.14% G, 25.88% C and 27.33% T. The genome has a total of 37 genes, including 13 protein-coding genes, 22 tRNA genes, two ribosomal RNA genes and a control region (D-loop region). This complete sequence would enlarge useful genomic information for further studies.

Supplementary feeding of cattle-yak in the cold season alters rumen microbes, volatile fatty acids, and expression of SGLT1 in the rumen epithelium

Cattle-yak, a hybrid offspring of yak (Bos grunniens) and cattle (Bos taurus), inhabit the Qinghai-Tibet Plateau at an altitude of more than 3,000 m and obtain nutrients predominantly through grazing on natural pastures. Severe shortages of pasture in the cold season leads to reductions in the weight and disease resistance of grazing cattle-yak, which then affects their production performance. This study aimed to investigate the effect of supplementary feeding during the cold season on the rumen microbial community of cattle-yak. Six cattle-yak (bulls) were randomly divided into two groups-"grazing + supplementary feeding" (G+S) (n = 3) and grazing (G) (n = 3)-and rumen microbial community structure (based on 16S rRNA sequencing), volatile fatty acids (VFAs), and ruminal epithelial sodium ion-dependent glucose transporter 1 (SGLT1) expression were assessed. There were significant differences in the flora of the two groups at various taxonomic classification levels. For example, Bacteroidetes, Rikenellaceae, and Rikenellaceae_RC9_gut_group were significantly higher in the G+S group than in the G group (P < 0.05), while Firmicutes and Christensenellaceae_R-7_group were significantly lower in the G+S group than in the G group (P < 0.05). Kyoto Encyclopedia of Genes and Genomes (KEGG) and Clusters of Orthologous Groups (COG) analyses revealed that functions related to carbohydrate metabolism and energy production were significantly enriched in the G+S group (P < 0.05). In addition, the concentration of total VFAs, along with concentrations of acetate, propionate, and butyrate, were significantly higher in the G+S group than in the G group (P < 0.05). Furthermore, SGLT1 expression in ruminal epithelial tissue was significantly lower in the G+S group (P < 0.01). Supplementary feeding of cattle-yak after grazing in the cold season altered the microbial community structure and VFA contents in the rumen of the animals, and decreased ruminal epithelial SGLT1 expression. This indicated that supplementary feeding after grazing aids rumen function, improves adaptability of cattle-yak to the harsh environment of the Qinghai-Tibet Plateau, and enhances ability of the animals to overwinter.

Interactions Between Rumen Microbes, VFAs, and Host Genes Regulate Nutrient Absorption and Epithelial Barrier Function During Cold Season Nutritional Stress in Tibetan Sheep

As one of the important ruminants of the Qinghai-Tibet Plateau, Tibetan sheep are able to reproduce and maintain their population in this harsh environment of extreme cold and low oxygen. However, the adaptive mechanism of Tibetan sheep when nutrients are scarce in the cold season of the Plateau environment is unclear. We conducted comparative analysis rumen fermentation parameters, rumen microbes, and expression of host genes related to nutrient absorption and rumen epithelial barrier function in cold and warm season Tibetan sheep. We found that concentrations of the volatile fatty acids (VFAs) acetate, propionate and butyrate of Tibetan sheep in the cold season were significantly higher than in the warm season (P < 0.05). Microbial 16S rRNA gene analysis revealed significant differences in rumen microbiota between the cold and warm seasons, and the abundance of microbial in the cold season was significantly higher than that in the warm season (P < 0.05), and the lack of nutrients in the cold season led to a significant reduction in the expression of SGLT1, Claudin-4, and ZO-1 genes in the rumen epithelium. Correlation analysis revealed significant associations of some rumen microorganisms with the fermentation product acetate and the rumen epithelial genes SGLT1, Claudin-4, and ZO-1.

The complete mitochondrial genome sequence and phylogenetic analysis of Niangya yak (Bos grunniens)

In the present study, we report the complete mitochondrial genome of Niangya yak (Bos grunniens) and its phylogenetic inferences. The complete mitochondrial DNA is a circular molecule with 16,322 bp length consisting of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a non-coding control region(D-loop). Both ND6 and 7 tRNAs (tRNA-Pro, tRNA-Glu, tRNA-Tyr, tRNA-Cys, tRNA-Asn, tRNA-Ala and tRNA-Gln) are encoded on the light strand, and the remaining genes are encoded on the heavy strand. The overall nucleotide composition is A(33.73%), T(27.28%), C(25.80%), G(13.19%) respectively. The content of C + G is 38.99%. Given that yak is indispensable for the Tibetan people, it is important to understand the genetic status of the population for further systematic genetics, evolutionary significance and protection of genetic resources. Therefore, to understand the evolutionary history of Niangya yak, the complete mitochondrial genome of Niangya yak was sequenced and compared with the mitochondrial genome of closely related Bos species.