• Journal of Animal Science and Technology
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• v.65 no.5
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• pp.1105-1109
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• 2023

Pedi coccus acidilactici CACC 537 was isolated from canine feces and reported to have probiotic properties. We aimed to characterize the potential probiotic properties of this strain by functional genomic analysis. Complete genome sequencing of P. acidilactici CACC 537 was performed using a PacBio RSII and Illumina platform, and contained one circular chromosome (2.0 Mb) with a 42% G + C content. The sequences were annotation revealed 1,897 protein-coding sequences, 15 rRNAs, and 56 tRNAs. It was determined that P. acidilactici CACC 537 genome carries genes known to be involved in the immune system, defense mechanisms, restriction-modification (R-M), and the CRISPR system. CACC 537 was shown to be beneficial in preventing pathogen infection during the fermentation process, help host immunity, and maintain intestinal health. These results provide for a comprehensive understanding of P. acidilactici and the development of industrial probiotic feed additives that can help improve host immunity and intestinal health.

• Journal of Animal Science and Technology
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• v.66 no.1
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• pp.232-236
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• 2024

Ligilactobacillus is a genus of Gram-positive lactobacilli commonly found in the intestinal tracts of vertebrates. It has been granted a Qualified Presumption of Safety (QPS) status from the European Food Safety Authority (EFSA). One specific strain, Ligilactobacillus salivarius B4311, was isolated from fecal samples of broiler chickens from a farm associated with Chung-Ang University (Anseong, Korea). This strain was observed to have inhibitory effects against Listeria monocytogenes. In this paper, we present the complete genome sequence of Lig. salivarius B4311. The whole genome of strain B4311 comprises 2,071,255 bp assembled into 3 contigs representing a chromosome, repA-type megaplasmid, and small plasmid. The genome contains 1,963 protein-coding sequences, 22 rRNA genes, and 78 tRNA genes, with a guanine + cytosine (GC) content of 33.1%. The megaplasmid of strain B4311 was found to contain the bacteriocin gene cluster for salivaricin P, a two-peptide bacteriocin belonging to class IIb.

• Food Science of Animal Resources
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• v.35 no.1
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• pp.86-90
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• 2015

In this study, we reported the morphogenetic analysis and genome sequence by genomic analysis of the newly isolated staphylococcal phage SMSAP5 from soil of slaughterhouses for cattle. Based on transmission electron microscopy evident morphology, phage SMSAP5 belonged to the Siphoviridae family. Phage SMSAP5 had a double-stranded DNA genome with a length of 45,552 bp and 33 % G+C content. Bioinformatics analysis of the phage genome revealed 43 open reading frames. A blastn search revealed that its nucleotide sequence shared a high degree of similarity with that of the Staphylococcus phage tp310-2. In conclusion, this study is the first report to show the morphological features and the complete genome sequence of the phage SMSAP5 from soil of slaughterhouses for cattle.

• Genomics & Informatics
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• v.4 no.4
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• pp.182-187
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• 2006

6-Phosphogluconolactonase (6PGL) is one of the key enzymes in the ubiquitous pathways of central carbon metabolism, but bacterial 6PGL had been long known as a missing enzyme even after complete bacterial genome sequence information became available. Although recent experimental characterization suggests that there are two types of 6PGLs (DevB and YbhE), their phylogenetic distribution is severely biased. Here we present that proteins in COG group previously described as 3-oarboxymuconate cyclase (COG2706) are actually the YbhE-type 6PGLs, which are widely distributed in Proteobacteria and Fimicutes. This case exemplifies how erroneous functional description of a member in the reference database commonly used in transitive genome annotation cause systematic problem in the prediction of genes even with universal cellular functions.

• Korean Journal of Plant Taxonomy
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• v.46 no.1
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• pp.60-64
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• 2016

Scopolia parviflora of the family Solanaceae is an endemic species of Korea and a traditional Korean medicinal plant. The plastid genome was sequenced by next-generation sequencing (NGS) method. The characterized cp genome is 156,193 bp in size; the large single-copy (LSC) region is 86,364 bp, the inverted repeat (IR) is 25,905 bp, and the small single copy (SSC) region is 18,019 bp. The overall GC content of the plastid genome amounts to 37.61%. The cp genome contains 113 genes and 21 introns, including 80 proteincoding genes, four RNA genes, 30 tRNA genes, 20 group II introns, and one group I intron. A phylogenetic analysis showed that Scopolia parviflora was closely related to Hyoscyamus niger.

• 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.

• Microbiology and Biotechnology Letters
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• v.51 no.3
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• pp.325-327
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• 2023

This paper presents the complete genome sequence of a novel marine actinomycete, Streptomyces sp. MMBL 11-1. The genome of Streptomyces sp. MMBL 11-1 was obtained through next-generation sequencing using the PacBio Sequel system and Illumina platform provided by Macrogen, Korea. The assembled genome consists of five contigs, with a total length of 8,496,900 bp and a G+C content of 71.6%. The genome harbors multiple biosynthetic gene clusters (BGCs) associated with producing microbial natural products (MNPs). The comprehensive genomic information of this type of strain will serve as a valuable resource for identifying other marine actinomycetes strains.

• BMB Reports
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• v.49 no.12
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• pp.653-654
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• 2016

The human reference genome, maintained by the Genome Reference Consortium, is conceivably the most complete genome assembly ever, since its first construction. It has continually been improved by incorporating corrections made to the previous assemblies, thanks to various technological advances. Many currently-ongoing population sequencing projects have been based on this reference genome, heightening hopes of the development of useful medical applications of genomic information, thanks to the recent maturation of high-throughput sequencing technologies. However, just one reference genome does not fit all the populations across the globe, because of the large diversity in genomic structures and technical limitations inherent to short read sequencing methods. The recent success in de novo construction of the highly contiguous Asian diploid genome AK1, by combining single molecule technologies with routine sequencing data without resorting to traditional clone-by-clone sequencing and physical mapping, reveals the nature of genomic structure variation by detecting thousands of novel structural variations and by finally filling in some of the prior gaps which had persistently remained in the current human reference genome. Now it is expected that the AK1 genome, soon to be paired with more upcoming de novo assembled genomes, will provide a chance to explore what it is really like to use ancestry-specific reference genomes instead of hg19/hg38 for population genomics. This is a major step towards the furthering of genetically-based precision medicine.

• Korean Journal of Microbiology
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• v.55 no.2
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• pp.171-173
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• 2019

The genus Cohnella, which belongs to the family Paenibacillaceae, inhabits a wide range of environmental niches. Here, we report the complete genome sequence of Cohnella sp. HS21, which was isolated from the rhizospheric soil of Korean fir (Abies koreana) on the top of Halla Mountain in the Republic of Korea. Strain HS21 features a 7,059,027 bp circular chromosome with 44.8% GC-content. Its genome contains 5,939 protein-coding genes, 78 transfer RNA (tRNA) genes, 27 ribosomal RNA (rRNA) genes, 4 noncoding RNA genes (ncRNA), and 90 pseudogenes. The bacterium contains antibiotic-related gene clusters and genes encoding plant cell wall-degrading enzymes.

• Korean Journal of Microbiology
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• v.55 no.3
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• pp.303-305
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• 2019

An actinobacterial strain designated Gordonia sp. MMS17-SY073 (=KCTC 49257) was isolated from a coastal soil of an island, and its complete genome was analyzed. A single contig consisting of 5,962,176 bp with the G + C content of 67.4% was obtained, and the annotation resulted in 5,201 protein-coding genes, 6 rRNA genes and 45 tRNA genes. Strain MMS17-SY073 was closest to the type strain of Gordonia soli based on the 16S rRNA gene sequence comparison, sharing 98.5% sequence similarity. A number of biosynthetic gene clusters for secondary metabolites, non-ribosomal peptide synthetase types in particular, could be identified from the genome.