Developmental Dynamics of the Gut Virome in Tibetan Pigs at High Altitude: A Metagenomic Perspective across Age Groups.

Tibetan pig is a geographically isolated pig breed that inhabits high-altitude areas of the Qinghai-Tibetan plateau. At present, there is limited research on viral diseases in Tibetan pigs. This study provides a novel metagenomic exploration of the gut virome in Tibetan pigs (altitude ≈ 3000 m) across three critical developmental stages, including lactation, nursery, and fattening. The composition of viral communities in the Tibetan pig intestine, with a dominant presence of Microviridae phages observed across all stages of development, in combination with the previous literature, suggest that it may be associated with geographical locations with high altitude. Functional annotation of viral operational taxonomic units (vOTUs) highlights that, among the constantly increasing vOTUs groups, the adaptability of viruses to environmental stressors such as salt and heat indicates an evolutionary response to high-altitude conditions. It shows that the lactation group has more abundant viral auxiliary metabolic genes (vAMGs) than the nursery and fattening groups. During the nursery and fattening stages, this leaves only DNMT1 at a high level. which may be a contributing factor in promoting gut health. The study found that viruses preferentially adopt lytic lifestyles at all three developmental stages. These findings not only elucidate the dynamic interplay between the gut virome and host development, offering novel insights into the virome ecology of Tibetan pigs and their adaptation to high-altitude environments, but also provide a theoretical basis for further studies on pig production and epidemic prevention under extreme environmental conditions.

Study on the genotypes of Echinococcus granulosus in yaks and sheep from Langkazi County in Tibet Autonomous Region of China based on mitochondrial cox1 and nad1.

To determine the genotypes of the epidemic strains of Echinococcus granulosus in livestock in Tibet, samples of E. granulosus cysts were collected from 11 yaks and 62 sheep. Genomic DNA was extracted from these samples, and gene fragments of mitochondrial cytochrome c oxidase subunit I (cox1) and NADH dehydrogenase subunit I (nad1) were amplified by PCR and sequenced. DNASTAR and MAGA7.0 were employed for homology analysis and phylogenetic tree construction. Echinococcus granulosus cysts were detected in 56.2% (41/73) of the samples screened. Of these, 63.4% (26/41) were identified as E. granulosus G1 genotype (common sheep strain), 24.4% (10 /41) as G3 genotype (buffalo strain), and 12.2% (5/41) were G6 genotype (camel strain). The study concludes that yaks and sheep in Langkazi county, Tibet, carry three E. granulosus genotypes (G1, G3, and G6), with the G1 genotype the predominant genotype in the region. This study clarifies the distribution of E. granulosus genotypes, providing genetic data and insight for the surveillance and prevention of echinococcosis.

Antimicrobial susceptibility and multilocus sequence typing of Clostridium perfringens isolated from yaks in Qinghai-Tibet plateau, China.

Clostridium perfringens (C. perfringens) is an opportunistic pathogen that cause necrotic enteritis, food poisoning and even death in animals. In this study, we explored the prevalence, antibiotic resistance and genetic diversity of Clostridium perfringens isolated from yak in the Qinghai-Tibet plateau, China. A total of 744 yak fecal samples were collected and assessed for toxin genes, antimicrobial susceptibility and multilocus sequence typing (MLST). Results indicated that 144 out of 744 (19.35%) yak fecal samples were tested to be positive for C. perfringens, 75% (n = 108, 108/144) were C. perfringens type A, 17.36% (n = 25, 25/144) were C. perfringens type C, 2.78% (n = 4, 4/144) were C. perfringens type D, and 4.86% (n = 7, 7/144) were C. perfringens type F. In addition, 2.78% (n = 4, 4/144) of the isolates were positive for cpb2 toxin gene. Antimicrobial susceptibility testing revealed that 98.61% (142/144) of the isolates showed multiple-antibiotic resistance. According to MLST and phylogenetic tree, 144 yak-derived C. perfringens isolates had an average of 12.95 alleles and could be divided into 89 sequence types (STs) and clustered in 11 clonal complexes (CCs). The most of isolates belong to type A with a considerable genetic diversity, having Simpson index up to 0.9754. MLST and phylogenetic analysis showed that the isolates under the same clade came from multiple regions. Cross-transmission among isolates and interconnectedness were observed in the genetic evolution. According to the study, the most of the isolates exhibited broad-spectrum antibacterial resistance, diverse alleles, and multiple lethal toxin genes of C. perfringens.

Fatty acid profiles of milk from Holstein cows, Jersey cows, buffalos, yaks, humans, goats, camels, and donkeys based on gas chromatography-mass spectrometry.

Due to the diversity and limitation of determination methods, published data on the fatty acid (FA) compositions of different milk samples have contributed to inaccurate comparisons. In this study, we developed a high-throughput gas chromatography-mass spectrometry method to determinate milk FA, and the proposed method had satisfactory linearity, sensitivity, accuracy, and precision. We also analyzed the FA compositions of 237 milk samples from Holstein cows, Jersey cows, buffalos, yaks, humans, goats, donkeys, and camels. Holstein, Jersey, goat, and buffalo milks contained high content of even-chain saturated FA, whereas goat milk had higher content of medium- and short-chain FA (MSCFA). Yak and camel milk are potential functional foods due to their high levels of odd- and branched-chain FA and low ratios of n-6 to n-3 polyunsaturated FA (PUFA). Human milk contained lower levels of saturated FA, MSCFA, and conjugated linoleic acid, and higher levels of monounsaturated FA and PUFA. As a special nonruminant milk, donkey milk contained low levels of monounsaturated FA and high levels of PUFA and MSCFA. Based on the FA profiles of 8 types of milk, nonruminant milk was distinct from ruminant milk, whereas camel and yak milk were different from other ruminant milks and considered as potential functional foods for balanced human diet.

Effects of Sugar Cane Molasses Addition on the Fermentation Quality, Microbial Community, and Tastes of Alfalfa Silage.

The objective was to study the effects of sugar cane molasses addition on the fermentation quality and tastes of alfalfa silage. Fresh alfalfa was ensiled with no additive (Control), 1% molasses (M1), 2% molasses (M2), and 3% molasses (M3) for 206 days. The chemical composition and fermentation characteristics of the alfalfa silages were determined, the microbial communities were described by 16S rRNA sequencing, and the tastes were evaluated using an electronic tongue sensing system. With the amount of added molasses (M), most nutrition (dry matter and crude protein) was preserved and water-soluble carbohydrates (WSC) were sufficiently used to promote the fermentation, resulting in a pH reduction from 5.16 to 4.48. The lactic acid (LA) content and LA/acetic acid (AA) significantly increased, indicating that the fermentation had turned to homofermentation. After ensiling, Enterococcus and Lactobacillus were the dominant genus in all treatments and the undesirable microbes were inhibited, resulting in lower propionic acid (PA), butyric acid (BA), and NH3-N production. In addition, bitterness, astringency, and sourness reflected tastes of alfalfa silage, while umami and sourness changed with the amount of added molasses. Therefore, molasses additive had improved the fermentation quality and tastes of alfalfa silage, and the M3 group obtained the ideal pH value (below 4.5) and the best condition for long-term preservation.

Metagenomic insights into the diversity of carbohydrate-degrading enzymes in the yak fecal microbial community.

BACKGROUND: Yaks are able to utilize the gastrointestinal microbiota to digest plant materials. Although the cellulolytic bacteria in the yak rumen have been reported, there is still limited information on the diversity of the major microorganisms and putative carbohydrate-metabolizing enzymes for the degradation of complex lignocellulosic biomass in its gut ecosystem. RESULTS: Here, this study aimed to decode biomass-degrading genes and genomes in the yak fecal microbiota using deep metagenome sequencing. A comprehensive catalog comprising 4.5 million microbial genes from the yak feces were established based on metagenomic assemblies from 92 Gb sequencing data. We identified a full spectrum of genes encoding carbohydrate-active enzymes, three-quarters of which were assigned to highly diversified enzyme families involved in the breakdown of complex dietary carbohydrates, including 120 families of glycoside hydrolases, 25 families of polysaccharide lyases, and 15 families of carbohydrate esterases. Inference of taxonomic assignments to the carbohydrate-degrading genes revealed the major microbial contributors were Bacteroidaceae, Ruminococcaceae, Rikenellaceae, Clostridiaceae, and Prevotellaceae. Furthermore, 68 prokaryotic genomes were reconstructed and the genes encoding glycoside hydrolases involved in plant-derived polysaccharide degradation were identified in these uncultured genomes, many of which were novel species with lignocellulolytic capability. CONCLUSIONS: Our findings shed light on a great diversity of carbohydrate-degrading enzymes in the yak gut microbial community and uncultured species, which provides a useful genetic resource for future studies on the discovery of novel enzymes for industrial applications.

Characterization of Metagenome-Assembled Genomes and Carbohydrate-Degrading Genes in the Gut Microbiota of Tibetan Pig.

Tibetan pig is an important domestic mammal, providing products of high nutritional value for millions of people living in the Qinghai-Tibet Plateau. The genomes of mammalian gut microbiota encode a large number of carbohydrate-active enzymes, which are essential for the digestion of complex polysaccharides through fermentation. However, the current understanding of microbial degradation of dietary carbohydrates in the Tibetan pig gut is limited. In this study, we produced approximately 145 gigabases of metagenomic sequence data for the fecal samples from 11 Tibetan pigs. De novo assembly and binning recovered 322 metagenome-assembled genomes taxonomically assigned to 11 bacterial phyla and two archaeal phyla. Of these genomes, 191 represented the uncultivated microbes derived from novel prokaryotic taxa. Twenty-three genomes were identified as metagenomic biomarkers that were significantly abundant in the gut ecosystem of Tibetan pigs compared to the other low-altitude relatives. Further, over 13,000 carbohydrate-degrading genes were identified, and these genes were more abundant in some of the genomes within the five principal phyla: Firmicutes, Bacteroidetes, Spirochaetota, Verrucomicrobiota, and Fibrobacterota. Particularly, three genomes representing the uncultivated Verrucomicrobiota encode the most abundant degradative enzymes in the fecal microbiota of Tibetan pigs. These findings should substantially increase the phylogenetic diversity of specific taxonomic clades in the microbial tree of life and provide an expanded repertoire of biomass-degrading genes for future application to microbial production of industrial enzymes.

Characterization of Two Bovine viral diarrhea virus Strains Originating from Cattle in Tibet, China.

Here, we report two strains of Bovine viral diarrhea virus (BVDV), named XZ01 and XZ02, that were isolated from cattle in Tibet, China. They belong to subgenotype 1b. This report will help in understanding the molecular characteristics of BVDV in Tibetan cattle.

Identification and characterization of a protective antigen, PlpB of bovine Pasteurella multocida strain LZ-PM.

The Pasteurella multocida lipoprotein B (PlpB) was cloned from Pasteurella multocida (P. multocida) strain LZ-PM (serotype A) and expressed in Escherichia coli (E. coli). Sequence analysis showed that PlpB from different strains of P. multocida exhibited 80.8-99.4% sequence identity to each other, suggesting that PlpB might serve as a cross-protective antigen. The purified PCR product of PlpB gene consisting of 831 base pairs was inserted into the pET-32a (+) plasmid, and then transferred into E. coli. The protective immunity conferred by recombinant PlpB (rPlpB) on mice was evaluated. The results showed that mice immunized with 200 µg of purified rPlpB were protected (60% survival rate) against challenge infection with 1 MLD of P. multocida strain LZ-PM. In conclusion, our data indicated that the PlpB protein may be a potential target as a candidate subunit vaccine for P. multocida infection.