Integrated Analysis of Transcriptome and Metabolome Profiles in the Longissimus Dorsi Muscle of Buffalo and Cattle.

Buffalo meat is gaining popularity for its nutritional properties, such as its low fat and cholesterol content. However, it is often unsatisfactory to consumers due to its dark color and low tenderness. There is currently limited research on the regulatory mechanisms of buffalo meat quality. Xinglong buffalo are raised in the tropical Hainan region and are undergoing genetic improvement from draught to meat production. For the first time, we evaluated the meat quality traits of Xinglong buffalo using the longissimus dorsi muscle and compared them to Hainan cattle. Furthermore, we utilized a multi-omics approach combining transcriptomics and metabolomics to explore the underlying molecular mechanism regulating meat quality traits. We found that the Xinglong buffalo had significantly higher meat color redness but lower amino acid content and higher shear force compared to Hainan cattle. Differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) were identified, with them being significantly enriched in nicotinic acid and nicotinamide metabolic and glycine, serine, and threonine metabolic pathways. The correlation analysis revealed that those genes and metabolites (such as: GAMT, GCSH, PNP, L-aspartic acid, NADP+, and glutathione) are significantly associated with meat color, tenderness, and amino acid content, indicating their potential as candidate genes and biological indicators associated with meat quality. This study contributes to the breed genetic improvement and enhancement of buffalo meat quality.

Association between INHA gene polymorphisms and litter size in Hainan black goats.

Background: The inhibin alpha (INHA) gene is one of the important genes affecting the reproductive traits of animals. Hainan black goats are the main goat breed in Hainan Island (China), whose development is limited by low reproductive performance. However, the relationship between INHA gene and the reproductive performance of Hainan black goats is still unclear. Therefore, the purpose of this work was to explore the effect of INHA gene polymorphisms on the litter size of Hainan black goats. Methods: Single nucleotide polymorphisms (SNPs) of INHA were detected, and the genetic parameters and haplotype frequency of these SNPs were calculated and association analysis was performed for these SNPs with the litter size. Finally, the SNP with significant correlations to litter size was analyzed by Bioinformatics tools. Results: The results showed that the litter size of individuals with the AC genotype at loci g.28317663A>C of INHA gene was significantly higher than those with the AA genotype. This SNP changed the amino acid sequence, which may affect the function of INHA protein by affecting its structure. Our results suggest that g.28317663A>C loci may serve as a potential molecular marker for improving the reproductive traits in Hainan black goats.

A Novel System for the Detection of Spontaneous Abortion-Causing Aneuploidy and Its Erroneous Chromosome Origins through the Combination of Low-Pass Copy Number Variation Sequencing and NGS-Based STR Tests.

During the period of 2018-2020, we first combined reported low-pass whole genome sequencing and NGS-based STR tests for miscarriage samples analysis. Compared with G-banding karyotyping, the system increased the detection rate of chromosomal abnormalities in miscarriage samples to 56.4% in 500 unexplained recurrent spontaneous abortions. In this study, a total of 386 STR loci were developed on twenty-two autosomes and two sex chromosomes (X and Y chromosomes), which can help to distinguish triploidy, uniparental diploidy and maternal cell contamination and can trace the parental origin of erroneous chromosomes. It is not possible to accomplish this with existing methods of detection in miscarriage samples. Among the tested aneuploid errors, the most frequently detected error was trisomy (33.4% in total and 59.9% in the error chromosome group). In the trisomy samples, 94.7% extra chromosomes were of maternal origin and 5.31% were of paternal origin. This novel system improves the genetic analysis method of miscarriage samples and provides more reference information for clinical pregnancy guidance.

Association between body weight and distal gut microbes in Hainan black goats at weaning age.

Gut microbiota plays a critical role in the healthy growth and development of young animals. However, there are few studies on the gut microbiota of young Hainan black goats. In this study, 12 three-month-old weaned lambs with the same birth date were selected and divided into the high body weight group (HW) and low body weight group (LW). The microbial diversity, composition, and predicted function in the feces of HW and LW groups were analyzed by collecting fecal samples and sequencing the 16S rRNA V3-V4 region. The results indicated that the HW group exhibited higher community diversity compared with the LW group, based on the Shannon index. The core phyla of the HW and LW groups were both Firmicutes and Bacteroidetes. Parabacteroides, UCG-005, and Bacteroides are the core genera of the HW group, and Bacteroides, Escherichia-Shigella, and Akkermansia are the core genera of the LW group. In addition, genera such as Ruminococcus and Anaerotruncus, which were positively correlated with body weight, were enriched in the HW group; those genera, such as Akkermansia and Christensenellaceae, which were negatively correlated with body weight, were enriched in the LW group. Differential analysis of the KEGG pathway showed that Amino Acid Metabolism, Energy Metabolism, Carbohydrate Metabolism, and Nucleotide Metabolism were enriched in the HW group, while Cellular Processes and Signaling, Lipid Metabolism, and Glycan Biosynthesis and Metabolism were enriched in the LW group. The results of this study revealed the gut microbial characteristics of Hainan black goats with different body weights at weaning age and identified the dominant flora that contributed to their growth.

The Association between Gut Microbiome Diversity and Composition and Heat Tolerance in Cattle.

Cattle are raised around the world and are frequently exposed to heat stress, whether in tropical countries or in regions with temperate climates. It is universally acknowledged that compared to those in temperate areas, the cattle breeds developed in tropical and subtropical areas have better heat tolerance. However, the underlying mechanism of heat tolerance has not been fully studied, especially from the perspective of intestinal microbiomics. The present study collected fecal samples of cattle from four representative climatic regions of China, namely, the mesotemperate (HLJ), warm temperate (SD), subtropical (HK), and tropical (SS) regions. Then, the feces were analyzed using high-throughput 16S rRNA sequencing. The results showed that with increasing climatic temperature from HLJ to SS, the abundance of Firmicutes increased, accompanied by an increasing Firmicutes to Bacteroidota ratio. Proteobacteria showed a trend of reduction from HLJ to SS. Patescibacteria, Chloroflexi, and Actinobacteriota were particularly highest in SS for adapting to the tropical environment. The microbial phenotype in the tropics was characterized by an increase in Gram-positive bacteria and a decrease in Gram-negative bacteria, aerobic bacteria, and the forming of_biofilms. Consistently, the functional abundances of organismal systems and metabolism were decreased to reduce the material and energy demands in a hot environment. Genetic information processing and information storage and processing may be how gut flora deals with hot conditions. The present study revealed the differences in the structure and function of gut microbes of cattle from mesotemperate to tropical climates and provided an important reference for future research on the mechanism of heat tolerance regulated by the gut microbiota and a potential microbiota-based target to alleviate heat stress.

First Report and Comparative Genomic Analysis of a Mycoplasma mycoides Subspecies capri HN-A in Hainan Island.

Mycoplasma mycoides subspecies capri (Mmc) is one of the six Mycoplasma mycoides cluster (Mm cluster) members, which can cause "MAKePS" (Mastitis, Arthritis, Keratoconjunctivitis, Pneumonia, Septicemia) syndrome in ruminants. These symptoms can occur alone or together in individuals or flocks of goats. However, little is known about the epidemic Mmc strains in Hainan Island, China. We aimed to isolate the endemic Mmc strains in Hainan Island and reveal their molecular characteristics by genomic sequencing and comparative genomics to mitigate the impact of Mmc on local ruminant farming. Here, the Mmc HN-A strain was isolated and identified for the first time in Hainan Island, China. The genome of Mmc HN-A was sequenced. It contains a 1,084,691 bp-long circular chromosome and 848 coding genes. The genomic analysis of Mmc HN-A revealed 16 virulence factors, 2 gene islands, and a bacterial type IV secretion system protein VirD4. Comparative genomics showed that the core genome of the five Mycoplasma mycoides contained 611 genes that could be exploited to develop drugs and endemic vaccines. Additionally, 36 specific genes were included in the Mmc HN-A genome, which could provide the possibility for the further control and prevention of the Mmc effects on local ruminants and enrich the information on Mmc strains.

The LiaFSR and BsrXRS Systems Contribute to Bile Salt Resistance in Enterococcus faecium Isolates.

Two-component systems (TCSs) are dominant regulating components in bacteria for responding to environmental stimuli. However, little information is available on how TCSs in Enterococcus faecium respond to bile salts - an important environmental stimulus for intestinal bacteria. In this study, the gene expression of 2 TCSs, BsrXRS and LiaFSR, was positively correlated with survival rates of different E. faecium isolates during exposure to ox gall. Moreover, gene disruptions of bsrR, bsrS, liaS, and liaR significantly reduced the survival rates of E. faecium in the presence of ox gall. Finally, EMSA results indicated that BsrR functioned as a transcription regulator for expression of its own gene as well as lipoate-protein ligase A (lplA). Additional 27 potential target genes by BsrR were revealed through in silico analyses. These findings suggest that BsrXRS and LiaFSR systems play important roles in bile salt resistance in E. faecium.

Preliminary evaluation of the potential role of ß-elemene in reversing erlotinib-resistant human NSCLC A549/ER cells.

ß-elemene (ß-ELE) is a natural compound extracted from Curcuma zedoaria Roscoe that has shown promise as a novel anticancer drug to treat malignant tumors. Recent studies have demonstrated that ß-ELE can reverse the drug resistance of tumor cells. To the best of our knowledge, there are no reports concerning the reversal of erlotinib resistance by ß-ELE in human non-small cell lung cancer (NSCLC) cells. Therefore, the present study investigated the effects of ß-ELE on erlotinib-resistant human NSCLC A549/ER cells in vitro and its possible mechanism of action. The sensitivity of A549/ER cells to erlotinib, the cytotoxicity of ß-ELE on the growth of A549/ER cells and the effects of ß-ELE on the reversal of drug resistance in A549/ER cells were determined by MTT assay. The cell apoptosis rate, cell cycle phase distribution and intracellular rhodamine 123 (Rh123) fluorescence intensity were detected by flow cytometry. The expression level of P-glycoprotein (P-gp) was detected by western blotting. A549/ER cells had a stable drug-resistance to erlotinib. ß-ELE inhibited the proliferation of A549/ER cells in a time- and dose-dependent manner, enhanced the sensitivity of A549/ER cells to erlotinib and reversed the drug resistance in A549/ER cells. Treatment with 15 µg/ml ß-ELE combined with 10 µmol/l erlotinib caused an increased rate of cell apoptosis and G0/G1 phase arrest. Furthermore, ß-ELE reduced the efflux of Rh123 from A549/ER cells, increased the intracellular accumulation of Rh123 and decreased the expression of P-gp. The results of the present study indicated that ß-ELE could reverse drug resistance in erlotinib-resistant human NSCLC A549/ER cells in vitro through a mechanism that may involve the decreased expression of P-gp, inhibition of P-gp dependent drug efflux and the increased intracellular concentration of anticancer drugs.

Effective Antimicrobial Activity of Plectasin-Derived Antimicrobial Peptides against Staphylococcus aureus Infection in Mammary Glands.

Staphylococcus aureus (S. aureus) is the causative agent for a wide variety of illnesses ranging from minor skin infections to life-threatening diseases. Development of antibiotic resistance by the bacteria has rendered many antibiotics ineffective. It has been known that plectasin-derived antimicrobial peptides (AMPs; NZ2114 and MP1102) are promising alternatives to antibiotics. However, their activities against S. aureus in mammary glands were unknown. Our objective was to assess the antimicrobial activities of NZ2114 and MP1102 against S. aureus in milk, in cultured mammary epithelial cells, and in a mouse model in order to evaluate their potentials as anti-mastitis agents. NZ2114 and MP1102 showed in vitro bactericidal effects against S. aureus in both the culture medium and the milk. NZ2114 and MP1102 at the concentration of 100 µg/mL reduced the number of S. aureus by almost 100% within 4 h in processed bovine milk. Similarly, both NZ2114 and MP1102 were efficient to reduce the number of internalized S. aureus in cultured mammary epithelial cells. Finally, both AMPs significantly reduced the S. aureus load and concentrations of TNF-α and IL-6 in mammary glands, compared to a buffer control in the mouse model. Our results suggest that NZ2114 and MP1102 may be used to treat S. aureus-induced mastitis.