• Proceedings of the PSK Conference
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• 2002.04a
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• pp.94-95
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• 2002

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.245-250
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• 2003

There are currently about 6000 bacterial species with validly published names, but scientists assume that these may be less than 1% of bacterial species present on the earth. Microbial resource is one of the most important bioresources in bioinderstry and provides us with high economic values. To find missing ones, the studies of metagenome, metabolome, and proteome about microbes have started recently in developed countries. We construct the information system that integrates information on microbial genome resources and manages the information to support efficient research of microbial genome application, and name this system 'Bio-Meta Information System (Bio-MIS)'. Bio-MIS consists of integrated microbial genome resources database, microbial genome resources input system, integrated microbial genome resources search engine, microbial resources on-line distribution system, portal service and management via internet. In the future, we will include public database connection and implement useful bioinformatics software for analyzing microbial genome resources. The web-site is accessible at http://biomis.probionic.com

• Proceedings of the Microbiological Society of Korea Conference
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• 2000.05a
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• pp.52-57
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• 2000

• Journal of Microbiology and Biotechnology
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• v.31 no.7
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• pp.903-911
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• 2021

Previous studies have modified microbial genomes by introducing gene cassettes containing selectable markers and homologous DNA fragments. However, this requires several steps including homologous recombination and excision of unnecessary DNA regions, such as selectable markers from the modified genome. Further, genomic manipulation often leaves scars and traces that interfere with downstream iterative genome engineering. A decade ago, the CRISPR/Cas system (also known as the bacterial adaptive immune system) revolutionized genome editing technology. Among the various CRISPR nucleases of numerous bacteria and archaea, the Cas9 and Cas12a (Cpf1) systems have been largely adopted for genome editing in all living organisms due to their simplicity, as they consist of a single polypeptide nuclease with a target-recognizing RNA. However, accurate and fine-tuned genome editing remains challenging due to mismatch tolerance and protospacer adjacent motif (PAM)-dependent target recognition. Therefore, this review describes how to overcome the aforementioned hurdles, which especially affect genome editing in higher organisms. Additionally, the biological significance of CRISPR-mediated microbial genome editing is discussed, and future research and development directions are also proposed.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.83-85
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• 2000

A lot of microbial genome sequencing projects is being done in many genome centers around the world, since the first genome, Haemophilus influenzae, was sequenced in 1995. The deluge of microbial genome sequence data demands new and highly automatic data flow system in order for genome researchers to manage and analyze their own bulky sequence data from low-level to high-level. In such an aspect, we developed the automatic data management system for microbial genome projects, which consists mainly of local database, analysis programs, and user-friendly interface. We designed and implemented the local database for large-scale sequencing projects, which makes systematic and consistent data management and retrieval possible and is tightly coupled with analysis programs and web-based user interface, That is, parsing and storage of the results of analysis programs in local database is possible and user can retrieve the data in any level of data process by means of web-based graphical user interface. Contig assembly, homology search, and ORF prediction, which are essential in genome projects, make analysis programs in our system. All but Contig assembly program are open as public domain. These programs are connected with each other by means of a lot of utility programs. As a result, this system will maximize the efficiency in cost and time in genome research.

• The Korea Genome Conference
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• 2003.09a
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• pp.44.2-44.2
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• 2003

• Korean Journal of Microbiology
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• v.55 no.2
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• pp.167-170
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• 2019

Pantoea intestinalis SRCM103226, isolated from edible insect mealworm overproduces zeaxanthin as a main carotenoid. The complete genome of P. intestinalis SRCM103226 was sequenced using the Pacific Biosciences (PacBio) RS II platform. The genome of P. intestinalis SRCM103226 comprises a 4,784,919 bp circular chromosome (53.41% G+C content), and is devoid of any extrachromosomal plasmids. Annotation using the RAST server reveals 4,332 coding sequences and 107 RNAs (22 rRNA genes, 85 tRNA genes). Genome annotation analysis revealed that it has five genes involved in the carotenoid pathway. The genome information provides fundamental knowledge for comparative genomics studies of the zeaxanthin pathway.

• The Korea Genome Conference
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• 2003.09a
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• pp.44.1-44.1
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• 2003

• Microbiology and Biotechnology Letters
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• v.51 no.4
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• pp.559-561
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• 2023

Staphylococcus aureus is a ubiquitous pathogen associated with both human and animal diseases. In this study, we present the complete genome sequence of SA73-2, which was isolated from lettuce at an agricultural farm in South Korea. The assembled genome consists of a 2,750,304-bp circular chromosome and a 24,654-bp plasmid. This strain belongs to sequence type 188 (ST188), with spa type 189, and carries the β-lactamase gene (blaZ) on the plasmid.

• Journal of Microbiology and Biotechnology
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• v.16 no.10
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• pp.1650-1655
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• 2006

Bacteria belonging to the genus Paenibacillus are facultatively anaerobic endospore formers and are attracting growing ecological and agricultural interest, yet their genome information is very limited. The present study surveyed the genomic features of P. polymyxa ATCC $842^T$ using pulse-field gel electrophoresis of restriction fragments and sample genome sequencing of 1,747 reads (approximately 17.5% coverage of the genome). Putative functions were assigned to more than 60% of the sequences. Functional classification of the sequences showed a similar pattern to that of B. subtilis. Sequence analysis suggests nitrogen fixation and antibiotic production by P. polymyxa ATCC $842^T$, which may explain its plant growth-promoting effects.