• Food Science of Animal Resources
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• v.41 no.4
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• pp.701-714
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• 2021

In this study, the microbial community succession and the protein hydrolysis of donkey meat during refrigerated (4℃) storage were investigated. 16S rDNA sequencing method was used to analyze the bacteria community structure and succession in the level of genome. Meanwhile, the volatile base nitrogen (TVB-N) was measured to evaluate the degradation level of protein. After sorting out the sequencing results, 1,274,604 clean data were obtained, which were clustered into 2,064 into operational taxonomic units (OTUs), annotated to 32 phyla and 527 genus. With the prolonging of storage time, the composition of microorganism changed greatly. At the same time, the diversity and richness of microorganism decreased and then increased. During the whole storage period, Proteobacteria was the dominant phyla, and the Photobacterium, Pseudompnas, and Acinetobacter were the dominant genus. According to correlation analysis, it was found that the abundance of these dominant bacteria was significantly positively correlated with the variation of TVB-N. And Pseudomonas might play an important role in the production of TVB-N during refrigerated storage of donkey meat. The predicted metabolic pathways, based on PICRUSt analysis, indicated that amino metabolism in refrigerated donkey meat was the main metabolic pathways. This study provides insight into the process involved in refrigerated donkey meat spoilage, which provides a foundation for the development of antibacterial preservative for donkey meat.

• Animal Bioscience
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• v.34 no.9
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• pp.1559-1568
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• 2021

Objective: Bedding materials directly contact hooves of dairy cows and they may serve as environmental sources of lameness-associated pathogen. However, the specific composition of bacteria hidden in bedding materials is still not clear. The aim of this study was to determine the effect bedding material and its bacterial composition has on lameness of Holstein heifers. Methods: Forty-eight Holstein heifers with similar body weights were randomly assigned into three groups including sand bedding (SB), concrete floor (CF), and compost bedding (CB). Hock injuries severity and gait performance of dairy cows were scored individually once a week. Blood samples were collected at the end of the experiment and bedding material samples were collected once a week for Illumina sequencing. Results: The CF increased visible hock injuries severity and serum biomarkers of joint damage in comparison to SB and CB groups. Besides, Illumina sequencing and analysis showed that the bacterial community of CB samples had higher similarity to that of SB samples than CF samples. Bacteria in three bedding materials were dominated by gastrointestinal bacteria and organic matter-degrading bacteria, such as Actinobacteria, Firmicutes, and norank JG30-KF-cM45. Lameness-associated Spirochaetaceae and Treponeme were only detected in SB and CB samples with a very low relative abundance (0% to 0.08%). Conclusion: The bacterial communities differed among bedding materials. However, the treponemes pathogens involved in the pathogenesis of lameness may not be a part of microbiota in bedding materials of dairy cows.

• Journal of Microbiology and Biotechnology
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• v.33 no.8
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• pp.1013-1022
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• 2023

Arbuscular mycorrhizal fungi (AMF) are widespread soil endophytic fungi, forming mutualistic relationships with the vast majority of land plants. Biochar (BC) has been reported to improve soil fertility and promote plant growth. However, limited studies are available concerning the combined effects of AMF and BC on soil community structure and plant growth. In this work, a pot experiment was designed to investigate the effects of AMF and BC on the rhizosphere microbial community of Allium fistulosum L. Using Illumina high-throughput sequencing, we showed that inoculation of AMF and BC had a significant impact on soil microbial community composition, diversity, and versatility. Increases were observed in both plant growth (the plant height by 8.6%, shoot fresh weight by 12.1%) and root morphological traits (average diameter by 20.5%). The phylogenetic tree also showed differences in the fungal community composition in A. fistulosum. In addition, Linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed that 16 biomarkers were detected in the control (CK) and AMF treatment, while only 3 were detected in the AMF + BC treatment. Molecular ecological network analysis showed that the AMF + BC treatment group had a more complex network of fungal communities, as evidenced by higher average connectivity. The functional composition spectrum showed significant differences in the functional distribution of soil microbial communities among different fungal genera. The structural equation model (SEM) confirmed that AMF could improve the microbial multifunctionality by regulating the rhizosphere fungal diversity and soil properties. Our findings provide new information on the effects of AMF and biochar on plants and soil microbial communities.

• Asian-Australasian Journal of Animal Sciences
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• v.27 no.11
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• pp.1521-1525
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• 2014

This study investigated heritability for bovine growth estimated with genomewide single nucleotide polymorphism (SNP) information obtained from a DNA microarray chip. Three hundred sixty seven Korean cattle were genotyped with the Illumina BovineSNP50 BeadChip, and 39,112 SNPs of 364 animals filtered by quality assurance were analyzed to estimate heritability of body weights at 6, 9, 12, 15, 18, 21, and 24 months of age. Restricted maximum likelihood estimate of heritability was obtained using covariance structure of genomic relationships among animals in a mixed model framework. Heritability estimates ranged from 0.58 to 0.76 for body weights at different ages. The heritability estimates using genomic information in this study were larger than those which had been estimated previously using pedigree information. The results revealed a trend that the heritability for body weight increased at a younger age (6 months). This suggests an early genetic evaluation for bovine growth using genomic information to increase genetic merits of animals.

• Journal of Forest and Environmental Science
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• v.34 no.3
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• pp.258-261
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• 2018

Drought alters soil microorganisms; however, it is still not clear how soil microbes respond to severe drought conditions. In this study, the responses of soil bacterial community to experimental drought in a coniferous stand were examined. Six $6m{\times}6m$ plots with three replicates of control and drought treatments were delimited. PCR amplification and Illumina sequencing were conducted for cluster analysis of soil bacterial community and species richness and species diversity was analyzed. Along the 393 days of simulated drought from July 2016 to October 2017, soil bacterial species diversity slightly increased whereas species richness decreased in both control and roof plots. Moreover, soil bacterial species richness more decreased in roof plots than in controls. Combining these results, soil bacterial activity might have been altered by simulated drought.

• International Journal of Industrial Entomology and Biomaterials
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• v.35 no.2
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• pp.97-99
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• 2017

Eleven polymorphic microsatellite loci were developed and characterized for Dorcus hopei in this study. The number of alleles varied from 2 to 21. The observed heterozygosity and expected heterozygosity ranged from 0.1058 to 0.9744 and 0.0997 to 0.8941, respectively. Two loci showed low polymorphism, while the rest were highly polymorphic. Six loci deviated from Hardy-Weinberg Equilibrium. The set of markers will provide effective tools for examining the population genetic structures and be helpful for managing wild population in D. hopei.

• Korean Journal of Plant Taxonomy
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• v.51 no.3
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• pp.332-336
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• 2021

The complete chloroplast (cp) genome sequence of Neolitsea sericea was determined by Illumina sequencing. The complete cp genome was 152,446bp in length, containing a large single-copy region of 93,796 bp and a small single-copy region of 18,506bp, which were separated by a pair of 20,072bp inverted repeats. A total of 112 unique genes were annotated, including 78 protein-coding genes (PCGs), 30 transfer RNAs, and four ribosomal RNAs. Among the PCGs, 18 genes contained one or two introns. A very low level of sequence variation between two cp genomes of N. sericea was found with seven insertions or deletions and only one single nucleotide polymorphism. An analysis using the maximum likelihood method showed that N. sericea was closely related to Actinodaphne trichocarpa.

• Journal of Animal Science and Technology
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• v.62 no.6
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• pp.952-955
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• 2020

Bacteroides sp. CACC 737 was isolated from a feline, and its potential probiotic properties were characterized using functional genome analysis. Whole-genome sequencing was performed using the PacBio RSII and Illumina HiSeq platforms. The complete genome of strain CACC 737 contained 4.6 Mb, with a guanine (G) + cytosine (C) content of 45.8%, six cryptic plasmids, and extracellular polysaccharide gene as unique features. The strain was beneficial to animal health when consumed as feed, for example, for ameliorating immunological dysfunctions and metabolic disorders. The genome information adds to the comprehensive understanding of Bacteroides sp. and suggests potential animal-related industrial applications for this strain.

• Genomics & Informatics
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• v.19 no.3
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• pp.32.1-32.10
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• 2021

Semisulcospira libertina, a species of freshwater snail, is widespread in East Asia. It is important as a food source. Additionally, it is a vector of clonorchiasis, paragonimiasis, metagonimiasis, and other parasites. Although S. libertina has ecological, commercial, and clinical importance, its whole-genome has not been reported yet. Here, we revealed the genome of S. libertina through de novo assembly. We assembled the whole-genome of S. libertina and determined its transcriptome for the first time using Illumina NovaSeq 6000 platform. According to the k-mer analysis, the genome size of S. libertina was estimated to be 3.04 Gb. Using RepeatMasker, a total of 53.68% of repeats were identified in the genome assembly. Genome data of S. libertina reported in this study will be useful for identification and conservation of S. libertina in East Asia.

• Genomics & Informatics
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• v.18 no.3
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• pp.32.1-32.7
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• 2020

The mitochondrial genome of a species is an essential resource for its effective conservation and phylogenetic studies. In this article, we present sequencing and characterization of the complete mitochondrial genome of a threatened labeonine fish, Cirrhinus reba collected from Khulna region of Bangladesh. The complete mitochondrial genome was 16,597 bp in size, which formed a circular double-stranded DNA molecule containing a total of 37 mitochondrial genes (13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes) with two non-coding regions, an origin of light strand replication (OL) and a displacement loop (D-loop), similar structure with other fishes of Teleostei. The phylogenetic tree demonstrated its close relationship with labeonine fishes. The complete mitogenome of Cirrhinus reba (GenBank no. MN862482) showed 99.96% identity to another haplotype of Cirrhinus reba (AP013325), followed by 90.18% identity with Labeo bata (AP011198).