Depicting Fecal Microbiota Characteristic in Yak, Cattle, Yak-Cattle Hybrid and Tibetan Sheep in Different Eco-Regions of Qinghai-Tibetan Plateau

Comparative Analysis of Gut Bacterial Diversity in Wild and Domestic Yaks on the Qinghai-Tibetan Plateau

The gut microbiota is a diverse and complex population, and it has a key role in the host's health and adaptability to the environment. The present study investigated the fecal bacterial community of wild grazing (WG) and domestic grazing (DG) yaks on natural grazing pastures, analyzing the gut microbiota using 16S rRNA sequencing to assess bacterial diversity. A total of 48 yak fecal samples were selected from two different grazing habitats. The DG group had more crude proteins and non-fiber carbohydrates. The WG group had more OM, insoluble dietary fiber such as NDF, ADF, ether extract, and TC. There were 165 and 142 unique operational taxonomic units (OTUs) in the WG and DG groups, respectively. Shannon index analysis revealed a higher bacterial diversity in the WG group than in the DG group. At the phylum level, Firmicutes were the dominant bacterial taxa in both groups. The relative abundance of Firmicutes in the WG group was higher than in the DG group. At the family level, the WG group had a significantly higher abundance of Ruminococcaceae (p < 0.001) and Rikenellaceae (p < 0.001) than the DG group. The abundances of Alloprevotella and Succinivibrio were more pronounced in the DG group than in the WG group at the genus level. This study presents a novel understanding of the bacterial communities of ruminants and their potential applications for livestock production.

Survey of the fecal microbiota of indigenous small ruminants living in different areas of Guizhou

Introduction

Gut microbiota are associated with the health and performance of ruminant species, and they are affected by altitude, host genetics, and sex. However, there has been little research on comparing the fecal microbiota of indigenous small ruminants such as sheep and goats in Guizhou province, China. In the present study, we revealed the effect of altitude, genetics, and sex on fecal microbiota profiles and enterotypes in indigenous small ruminants of Guizhou province, China.

Methods

Fecal samples were collected from Hei and Qianbei Ma goats and Weining sheep in the Chinese province of Guizhou. 16S rRNA gene sequencing targeting the V3-V4 region was performed using the Illumina MiSeq platform. Sequences were processed using QIIME2, and the qualified sequences were processed using the plugin DADA2 to generate amplicon sequence variants (ASVs). The statistical analysis was performed using R studio.

Results

The fecal microbial profile was found to vary by herd (influenced by genetics/altitude) and sex. All samples were categorized into two enterotypes. The first enterotype is dominated by UCG-005, and the second enterotype is dominated by the Christensenellaceae_R-7_group, which may be highly driven by the host's genetics (breed). The predicted functional profiles of the fecal microbiota were also assigned to two clusters that corresponded exactly to the enterotypes. Cluster 1 of the functional profiling was characterized by biosynthesis pathways, and cluster 2 was characterized by energy metabolism pathways.

Discussion

Our findings may provide new insights into the fecal microbial community and enterotypes in small ruminants by herds, offering clues for understanding the mechanisms by which the fecal microbiota contribute to divergent host phenotypes in indigenous small ruminants in Guizhou.

Faecal microbial diversity in a cattle herd infected by Mycobacterium avium subsp. paratuberculosis: a possible effect of production status

Mycobacterium avium subsp. paratuberculosis (MAP) causes Johne's disease, or paratuberculosis (PTB) in ruminants, besides having zoonotic potential. It possibly changes the gut microbiome, but no conclusive data are available yet. This study aimed at investigating the influence of MAP on the faecal microbiome of cattle naturally infected with PTB. In a follow up period of 10 months, PTB status was investigated in a herd of dairy cattle with history of clinical cases. Each animal was tested for MAP infection using serum and milk ELISA for MAP anti-bodies and IS900 real-time PCR and recombinase polymerase amplification assays for MAP DNA in the faeces and milk monthly for 4 successive months, then a last one after 6 months. The faecal samples were subjected to 16S rDNA metagenomic analysis using Oxford Nanopore Sequencing Technology. The microbial content was compared between animal groups based on MAP positivity rate and production status. All animals were MAP positive by one or more tests, but two animals were consistently negative for MAP DNA in the faeces. In all animals, the phyla firmicutes and bacteroidetes were highly enriched with a small contribution of proteobacteria, and increased abundance of the families Oscillospiraceae, Planococcaceae, and Streptococcacaceae was noted. Animals with high MAP positivity rate showed comparable faecal microbial content, although MAP faecal positivity had no significant effect (p > 0.05) on the microbiome. Generally, richness and evenness indices decreased with increasing positivity rate. A significantly different microbial content was found between dry cows and heifers (p < 0.05). Particularly, Oscillospiraceae and Rikenellaceae were enriched in heifers, while Planococcaceae and Streptococcaceae were overrepresented in dry cows. Furthermore, abundance of 72 genera was significantly different between these two groups (p < 0.05). Changes in faecal microbiome composition were notably associated with increasing MAP shedding in the faeces. The present findings suggest a combined influence of the production status and MAP on the cattle faecal microbiome. This possibly correlates with the fate of the infection, the concern in disease control, again remains for further investigations.

Yaks Are Dependent on Gut Microbiota for Survival in the Environment of the Qinghai Tibet Plateau

The yak (Poephagus grunniens) has evolved unique adaptations to survive the harsh environment of the Qinghai-Tibetan Plateau, while their gut microorganisms play a crucial role in maintaining the health of the animal. Gut microbes spread through the animal population not only by horizontal transmission but also vertically, which enhances microbial stability and inheritance between generations of the population. Homogenization of gut microbes in different animal species occurs in the same habitat, promoting interspecies coexistence. Using the yak as a model animal, this paper discusses the adaptive strategies under extreme environments, and how the gut microbes of the yak circulate throughout the Tibetan Plateau system, which not only affects other plateau animals such as plateau pikas, but can also have a profound impact on the health of people. By examining the relationships between yaks and their gut microbiota, this review offers new insights into the adaptation of yaks and their ecological niche on the Qinghai-Tibetan plateau.

Characterization of lipid composition and nutritional quality of yak ghee at different altitudes: A quantitative lipidomic analysis

Efficient and comprehensive analysis of lipid profiles in yak ghee samples collected from different elevations is crucial for optimal utilization of these resources. Unfortunately, such research is relatively rare. Yak ghee collected from three locations at different altitudes (S2: 2986 m; S5: 3671 m; S6: 4508 m) were analyzed by quantitative lipidomic. Our analysis identified a total of 176 lipids, and 147 s lipid of them were upregulated and 29 lipids were downregulated. These lipids have the potential to serve as biomarkers for distinguishing yak ghee from different altitudes. Notably, S2 exhibited higher levels of fatty acids (21:1) and branched fatty acid esters of hydroxy fatty acids (14:0/18:0), while S5 showed increased levels of phosphatidylserine (O-20:0/19:1) and glycerophosphoric acid (19:0/22:1). S6 displayed higher levels of triacylglycerol (17:0/20:5/22:3), ceramide alpha-hydroxy fatty acid-sphingosine (d17:3/34:2), and acyl glucosylceramides (16:0-18:0-18:1). Yak ghee exhibited a high content of neutralizing glycerophospholipids and various functional lipids, including sphingolipids and 21 newly discovered functional lipids. Our findings provide insights into quantitative changes in yak ghee lipids during different altitudes, development of yak ghee products, and screening of potential biomarkers.

Multi-omics data elucidate parasite-host-microbiota interactions and resistance to Haemonchus contortus in sheep

BACKGROUND

The integration of molecular data from hosts, parasites, and microbiota can enhance our understanding of the complex biological interactions underlying the resistance of hosts to parasites. Haemonchus contortus, the predominant sheep gastrointestinal parasite species in the tropics, causes significant production and economic losses, which are further compounded by the diminishing efficiency of chemical control owing to anthelmintic resistance. Knowledge of how the host responds to infection and how the parasite, in combination with microbiota, modulates host immunity can guide selection decisions to breed animals with improved parasite resistance. This understanding will help refine management practices and advance the development of new therapeutics for long-term helminth control.

METHODS

Eggs per gram (EPG) of feces were obtained from Morada Nova sheep subjected to two artificial infections with H. contortus and used as a proxy to select animals with high resistance or susceptibility for transcriptome sequencing (RNA-seq) of the abomasum and 50 K single-nucleotide genotyping. Additionally, RNA-seq data for H. contortus were generated, and amplicon sequence variants (ASV) were obtained using polymerase chain reaction amplification and sequencing of bacterial and archaeal 16S ribosomal RNA genes from sheep feces and rumen content.

RESULTS

The heritability estimate for EPG was 0.12. GAST, GNLY, IL13, MGRN1, FGF14, and RORC genes and transcripts were differentially expressed between resistant and susceptible animals. A genome-wide association study identified regions on chromosomes 2 and 11 that harbor candidate genes for resistance, immune response, body weight, and adaptation. Trans-expression quantitative trait loci were found between significant variants and differentially expressed transcripts. Functional co-expression modules based on sheep genes and ASVs correlated with resistance to H. contortus, showing enrichment in pathways of response to bacteria, immune and inflammatory responses, and hub features of the Christensenellaceae, Bacteroides, and Methanobrevibacter genera; Prevotellaceae family; and Verrucomicrobiota phylum. In H. contortus, some mitochondrial, collagen-, and cuticle-related genes were expressed only in parasites isolated from susceptible sheep.

CONCLUSIONS

The present study identified chromosome regions, genes, transcripts, and pathways involved in the elaborate interactions between the sheep host, its gastrointestinal microbiota, and the H. contortus parasite. These findings will assist in the development of animal selection strategies for parasite resistance and interdisciplinary approaches to control H. contortus infection in sheep.

Rumen microbiota of indigenous and introduced ruminants and their adaptation to the Qinghai-Tibetan plateau

The grassland in the Qinghai-Tibetan plateau provide habitat for many indigenous and introduced ruminants which perform important ecological functions that impact the whole Qinghai-Tibetan plateau ecosystem. These indigenous Tibetan ruminants have evolved several adaptive traits to withstand the severe environmental conditions, especially cold, low oxygen partial pressure, high altitude, strong UV radiation, and poor forage availability on the alpine rangelands. Despite the challenges to husbandry associated with the need for enhanced adaptation, several domesticated ruminants have also been successfully introduced to the alpine pasture regions to survive in the harsh environment. For ruminants, these challenging conditions affect not only the host, but also their commensal microbiota, especially the diversity and composition of the rumen microbiota; multiple studies have described tripartite interactions among host-environment-rumen microbiota. Thus, there are significant benefits to understanding the role of rumen microbiota in the indigenous and introduced ruminants of the Qinghai-Tibetan plateau, which has co-evolved with the host to ensure the availability of specific metabolic functions required for host survival, health, growth, and development. In this report, we systemically reviewed the dynamics of rumen microbiota in both indigenous and introduced ruminants (including gut microbiota of wild ruminants) as well as their structure, functions, and interactions with changing environmental conditions, especially low food availability, that enable survival at high altitudes. We summarized that three predominant driving factors including increased VFA production, enhanced fiber degradation, and lower methane production as indicators of higher efficiency energy harvest and nutrient utilization by microbiota that can sustain the host during nutrient deficit. These cumulative studies suggested alteration of rumen microbiota structure and functional taxa with genes that encode cellulolytic enzymes to potentially enhance nutrient and energy harvesting in response to low quality and quantity forage and cold environment. Future progress toward understanding ruminant adaptation to high altitudes will require the integration of phenotypic data with multi-omics analyses to identify host-microbiota co-evolutionary adaptations enabling survival on the Qinghai-Tibetan plateau.