Distribution and associations for antimicrobial resistance and antibiotic resistance genes of Escherichia coli from musk deer (Moschus berezovskii) in Sichuan, China
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ABSTRACT:
SUBMITTER: Liu H
PROVIDER: S-EPMC10681177 | biostudies-literature | 2023 Jan
REPOSITORIES: biostudies-literature
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Project description:The forest musk deer, Moschus berezovskii, is one of seven musk deer (Moschus spp.) and is distributed in Southwest China. Akin to other musk deer, the forest musk deer has been traditionally and is currently hunted for its musk (i.e., global perfume industry). Considerable hunting pressure and habitat loss have caused significant population declines. Consequently, the Chinese government commenced captive breeding programs for musk harvesting in the 1950s. However, the prevalence of fatal diseases is considerably restricting population increases. Disease severity and extent are exacerbated by inbreeding and genetic diversity declines in captive musk deer populations. It is essential that knowledge of captive and wild forest musk deer populations' immune system and genome be gained in order to improve their physical and genetic health. We have thus sequenced the whole genome of the forest musk deer, completed the genomic assembly and annotation, and performed preliminary bioinformatic analyses. A total of 407 Gb raw reads from whole-genome sequencing were generated using the Illumina HiSeq 4000 platform. The final genome assembly is around 2.72 Gb, with a contig N50 length of 22.6 kb and a scaffold N50 length of 2.85 Mb. We identified 24,352 genes and found that 42.05% of the genome is composed of repetitive elements. We also detected 1,236 olfactory receptor genes. The genome-wide phylogenetic tree indicated that the forest musk deer was within the order Artiodactyla, and it appeared as the sister clade of four members of Bovidae. In total, 576 genes were under positive selection in the forest musk deer lineage. We provide the first genome sequence and gene annotation for the forest musk deer. The availability of these resources will be very useful for the conservation and captive breeding of this endangered and economically important species and for reconstructing the evolutionary history of the order Artiodactyla.
| S-EPMC5906906 | biostudies-literature
Project description:Myiasis is an infestation of maggots on living tissue in humans and animals all over the world. It is known to occur in wild animals, while no information is reported in forest musk deer (Moschus berezovskii). During our research on the conservation of forest musk deer, we found a new record of traumatic myiasis of an injured forest musk deer. The flies are likely Lucilia caesar (Linnaeus, 1758) according to the results of DNA barcoding technology. We report traumatic myiasis of forest musk deer for the first time, which expands the information on parasite and myiasis of forest musk deer and confirms the potential risk of traumatic myiasis of forest musk deer.
| S-EPMC8379354 | biostudies-literature
Project description:Shanxi Province is the northernmost distribution range of Chinese forest musk deer (Moschus berezovskii), with wild populations scattered across Zhongtiao (ZT), Lüliang (LL), and Taiyue (TY) mountain ranges. Using line transect surveys and local guide assistance, coupled with infrared camera data, this study systematically collected fecal samples from wild forest musk deer from five nature reserves across the three mountain ranges. Genetic diversity was analyzed using the mtDNA control region, which yielded 129 effective sequences of 656 bp and 20 distinct haplotypes. Haplotype and nucleotide diversities were 0.916 and 0.01505, respectively, indicating a relatively high overall genetic diversity in the studied populations. Significant genetic differentiation was observed between the Lüliang-Taiyue (LLTY) and ZT mountain range populations, with most of the genetic variation existing within the populations. No significant correlation was detected between the geographical and genetic distances of the samples, which may have resulted from historical agricultural activities in Shanxi impeding gene flow among populations. Therefore, genetic exchange programs are recommended to improve the genetic diversity and population fitness of forest musk deer in this region to facilitate their recovery and growth.
| S-EPMC11829026 | biostudies-literature
Project description:Musk is a secretion of the forest musk deer (Moschus berezovskii). Normal musk is a brown solid secretion with a light fragrance. In this study, abnormal types of musk, namely, white and black musks, were discovered during the musk collection process. Researchers have long been concerned with the components of musk. Herein, GC-MS, headspace solid-phase microextraction (HS-SPME), and nonmetric multidimensional scaling (NMDS) were used to analyze the nonpolar organic components, volatile organic components, and sample similarities among different musks, respectively. Abundant steroid hormones and proteins were also found in the musk. The steroid hormone concentrations were detected using a radioimmunoassay (RIA). Proteins in the samples were hydrolyzed and the amino acids concentrations were detected. The steroid hormone and amino acid concentrations in white musk were significantly lower than in normal and black musks (p<0.05). The components were subjected to NMDS analysis to understand the differences in components among different types of musk, with the results suggesting that white musk was different from normal and black musks.
| S-EPMC7963063 | biostudies-literature
Project description:BackgroundThe formation of musk is a complex biophysical and biochemical process that change with the rut of male forest musk deer. We have reported that the mating status of male forest musk deer might result to the variations of chemical composition and microbiota of musk and its yields. Critical roles for microRNAs (miRNAs) of multi-tissues were profiled in our previous study; however, the role for miRNAs of the musk gland remains unclear in this species.MethodsIn this study, we used Illumina deep sequencing technology to sequence the small RNA transcriptome of unmated male (UM) and mated male (UM) of Chinese forest musk deer.ResultsWe identified 1,652 known miRNAs and 45 novel miRNAs, of which there were 174 differentially expressed miRNAs between UM and MM. chi-miR-21-5p, ipu-miR-99b and bta-miR-26a were up-regulated in UM among the 10 most differentially expressed miRNAs. Functional enrichment of the target genes showed that monosaccharide biosynthetic process, protein targeting, cellular protein catabolic process enriched higher in MM. Meanwhile, structural molecule activity, secretion by cell, regulated exocytosis and circulatory system process enriched more in UM, hinting that the formation of musk in UM was mediated by target genes related to exocytosis. The miRNA-mRNA pairs such as miR-21: CHD7, miR143: HSD17B7, miR-141/200a: Noc2 might involve in musk gland development and musk secretion, which need to be verified in future study.
| S-EPMC8710055 | biostudies-literature
Project description:The forest musk deer (Moschus berezovskii) is a high elevation species distributed across western China and northern Vietnam. Once abundant, habitat loss and poaching has led to a dramatic decrease in population numbers prompting the IUCN to list the species as endangered. Here, we characterized the genetic diversity of a Major Histocompatibility Complex (MHC) locus and teased apart driving factors shaping its variation. Seven DRB exon 2 alleles were identified among a group of randomly sampled forest musk deer from a captive population in the Sichuan province of China. Compared to other endangered or captive ungulates, forest musk deer have relatively low levels of MHC genetic diversity. Non-synonymous substitutions primarily occurred in the putative peptide-binding region (PBR), with analyses suggesting that recombination and selection has shaped the genetic diversity across the locus. Specifically, inter-allelic recombination generated novel allelic combinations, with evidence for both positive selection acting on the PBR and negative selection on the non-PBR. An improved understanding of functional genetic variability of the MHC will facilitate better design and management of captive breeding programs for this endangered species.
| S-EPMC4658564 | biostudies-literature
Project description:BackgroundGiardia duodenalis and Enterocytozoon bieneusi are widespread pathogens that can infect humans and various animal species. Thus far, there are only a few reports of G. duodenalis and E. bieneusi infections in ruminant wildlife. Thus, the objective of this study was to examine the prevalence of G. duodenalis and E. bieneusi in forest musk deer in Sichuan, China, as well as identifying their genotypes.ResultsIn total, we collected 223 faecal samples from musk deer at the Sichuan Institute of Musk Deer Breeding in Dujiangyan (n = 80) and the Maerkang Breeding Institute (n = 143). Five (2.24%) faecal samples were positive for G. duodenalis; three belonged to assemblage E, and two belonged to assemblage A based on the sequence analysis of the β-giardin (bg) gene. One sample each was found to be positive based on the glutamate dehydrogenase (gdh) and triosephosphate isomerase (tpi) gene, respectively. Thirty-eight (17.04%) faecal samples were found to be E. bieneusi-positive based on the internal transcribed spacer (ITS) sequence, and only SC03 genotype was identified, which belonged to the zoonotic group 1 according to the phylogenic analysis. The infection rates were significantly different among the different geographical areas and age groups but had no apparent association with gender or clinical symptoms.ConclusionsTo our knowledge, this was the first molecular characterisation of G. duodenalis and E. bieneusi in musk deer. Identification of the zoonotic genotypes indicated a potential public health threat, and our study suggested that the forest musk deer is an important carrier of these parasites.
| S-EPMC5870929 | biostudies-literature
Project description:Among the artiodactyls, male animals belonging to the Family Moschidae have a unique tissue, the musk gland, with the capability of musk synthesis. However, the genetic basis of musk gland formation and musk production are still poorly understood. Here, musk gland tissues from two juvenile and three adult Chinese forest musk deer (Moschus berezovskii) were utilized to analyze genomic evolution events, evaluate mRNA profiles and investigate cell compositions. By performing genome reannotation and comparison with 11 ruminant genomes, three expanded gene families were identified in the Moschus berezovskii genome. Transcriptional analysis further indicated that the musk gland displayed a prostate-like mRNA expression pattern. Single-cell sequencing revealed that the musk gland is composed of seven distinguishable cell types. Among them, sebaceous gland cells and luminal epithelial cells play important roles in musk synthesis, while endothelial cells master the regulation of cell-to-cell communication. In conclusion, our study provides insights into musk gland formation and the musk-synthesizing process.
| S-EPMC10203155 | biostudies-literature
Project description:Musk is a precious raw material and ingredient in Chinese traditional medicine. The production of unqualified musk has become a puzzling problem in forest musk deer (FMD) breeding. However, what the essential differences between so-called unqualified musk and mature qualified musk have not yet been elucidated. In this study, 12 musk samples were collected and separated into two groups according to their external properties. One group is white or black cream-like secretion with sour or unpleasant odour (MM); the other group is brown or blackish brown solid secretion with pleasant fragrance (DM). Next-generation sequencing and gas chromatography-mass spectrometry were used to explore the essential differences between the DM and MM groups in microbial and chemical compositions. The results indicate that the DM group has more heterogenous microbial structure but simpler relationships among microbial communities. LEfSe analysis showed that 14 taxa at the genus level could be used to distinguish the DM and MM groups and Bacillus, Paracoccus, tenoteophomonas, Mycobacterium and Leuconostoc were more abundant in the DM group (P < 0.05). In addition, six compounds were identified to specifically distinguish the DM and MM groups under the OPLS-DA model. PICRUSt analysis revealed that metabolic pathways such as carbohydrate metabolism, nucleotide metabolism, energy metabolism, transport and catabolism were enriched in the DM group. All these findings of differences in microbiota and chemical compositions would provide potential clues for MM quality improvement and new evidence for the scientific establishment of a quality evaluation standard for musk.
| S-EPMC9151339 | biostudies-literature
Project description:Moschus berezovskii is an endangered species, but its captive populations are valuable on musk secretions in traditional Chinese medicine and perfume manufacture. The mitogenome of M. berezovskii was 16,353 bp in size. Stop codons in 13 PCGs were all typical types except incomplete stop codon T for COX3, ND2 and ND4, and TA for ND3. No tandem repeat was found in control region. Phylogenetic analysis indicated that Moschidae has the closest relationship with Bovidae. We supported that M. berezovskii should be categorized into two subspecies, and suggested that the status of M. chrysogaster JQ608470 should be further investigated.
| S-EPMC7800556 | biostudies-literature