- Intestinibaculum porci gen. nov., sp. nov., a new member of the family Erysipelotrichaceae isolated from the small intestine of a swine
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Ji-Sun Kim , Hanna Choe , Yu-Ri Lee , Kyung Mo Kim , Doo-Sang Park
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J. Microbiol. 2019;57(5):381-387. Published online February 22, 2019
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DOI: https://doi.org/10.1007/s12275-019-8631-8
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A strictly anaerobic, Gram-stain-positive, catalase-negative,
non-motile, rod-shaped bacterium, designated SG0102T, was
isolated from the small intestine of a swine. Optimal growth
occurred at 37°C and pH 7.0. Furthermore, growth was observed
in the presence of up to 3% (w/v) NaCl but not at
salinity levels higher than 4%. The comparative analysis of
16S rRNA gene sequences showed that strain SG0102T was
most closely related to Kandleria vitulina DSM 20405T (93.3%),
followed by Catenibacterium mitsuokai KCTC 5053T (91.1%),
Sharpea azabuensis KCTC 15217T (91.0%), and Eggerthia catenaformis
DSM 5348T (89.6%). The average nucleotide identity
values between strain SG0102T and related species, K. vitulina
DSM 20405T, C. mitsuokai KCTC 5053T, S. azabuensis
KCTC 15217T, and E. catenaformis DSM 5348T, were 71.0,
69.3, 70.0, and 69.2%, respectively. The phylogenetic analysis
based on 16S rRNA gene sequence revealed that strain
SG0102T belonged to the family Erysipelotrichaceae in the
class Erysipelotrichia. The DNA G+C content of the strain
SG0102T was 39.5 mol%. The major cellular fatty acids (> 10%)
of strain SG0102T were C16:0, C16:0 dimethyl acetal, and C18:2
ω9/12c. The cell wall peptidoglycan of strain SG0102T contained
the meso-diaminopimelic acid. The strain SG0102T
produced lactic acid as a major end product of fermentation.
These distinct phenotypic and phylogenetic properties suggest
that strain SG0102T represents a novel species in a novel
genus of the family Erysipelotrichaceae, for which the name
Intestinibaculum porci gen. nov. sp. nov. is proposed. The
type strain is SG0102T (= KCTC 15725T = NBRC 113396T).
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Citations
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- PyroTrimmer: a Software with GUI for Pre-Processing 454 Amplicon Sequences
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Jeongsu Oh , Byung Kwon Kim , Wan-Sup Cho , Soon Gyu Hong , Kyung Mo Kim
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J. Microbiol. 2012;50(5):766-769. Published online November 4, 2012
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DOI: https://doi.org/10.1007/s12275-012-2494-6
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802
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The ultimate goal of metagenome research projects is to understand the ecological roles and physiological functions of the microbial communities in a given natural environment. The 454 pyrosequencing platform produces the longest reads among the most widely used next generation sequencing platforms. Since the relatively longer reads of the 454 platform provide more information for identification of microbial sequences, this platform is dedicated to microbial community and population studies. In order to accurately perform the downstream analysis of the 454 multiplex datasets, it is necessary to remove artificially designed sequences located at either ends of individual reads and to correct lowquality sequences. We have developed a program called Pyro-Trimmer that removes the barcodes, linkers, and primers, trims sequence regions with low quality scores, and filters out low-quality sequence reads. Although these functions have previously been implemented in other programs as well, PyroTrimmer has novelty in terms of the following features: i) more sensitive primer detection using Levenstein distance and global pairwise alignment, ii) the first stand-alone software with a graphic user interface, and iii) various options for trimming and filtering out the low-quality sequence reads. PyroTrimmer, written in JAVA, is compatible with multiple operating systems and can be downloaded free at http://pyrotrimmer.kobic.re.kr.
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Citations
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Marine Chemistry.2026; : 104677. CrossRef - Music of metagenomics—a review of its applications, analysis pipeline, and associated tools
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Functional & Integrative Genomics.2022; 22(1): 3. CrossRef - Microbiome in Cladonia squamosa Is Vertically Stratified According to Microclimatic Conditions
Hyun-Ju Noh, Yung Mi Lee, Chae Haeng Park, Hong Kum Lee, Jang-Cheon Cho, Soon Gyu Hong
Frontiers in Microbiology.2020;[Epub] CrossRef - DNA Sequencing Technologies
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Frontiers in Microbiology.2018;[Epub] CrossRef - Biogeochemical evidence of anaerobic methane oxidation on active submarine mud volcanoes on the continental slope of the Canadian Beaufort Sea
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Biogeosciences.2018; 15(24): 7419. CrossRef - Niche specialization of bacteria in permanently ice‐covered lakes of the McMurdo Dry Valleys, Antarctica
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Environmental Microbiology.2017; 19(6): 2258. CrossRef - Geographical structure of endosymbiotic bacteria hosted by Bathymodiolus mussels at eastern Pacific hydrothermal vents
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The Korean Journal of Microbiology.2016; 52(1): 49. CrossRef - Aboveground Whitefly Infestation-Mediated Reshaping of the Root Microbiota
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PLOS ONE.2016; 11(3): e0151064. CrossRef - Bacterial communities in Antarctic lichens
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Antarctic Science.2016; 28(6): 455. CrossRef - Soil development and bacterial community shifts along the chronosequence of the Midtre Lovénbreen glacier foreland in Svalbard
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Journal of Ecology and Environment.2015; 38(4): 461. CrossRef - Improved pipeline for reducing erroneous identification by 16S rRNA sequences using the Illumina MiSeq platform
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PLOS ONE.2015; 10(3): e0119966. CrossRef - Algal and Fungal Diversity in Antarctic Lichens
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- A Genome-Wide Identification of Genes Potentially Associated with Host Specificity of Brucella Species
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Kyung Mo Kim , Kyu-Won Kim , Samsun Sung , Heebal Kim
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J. Microbiol. 2011;49(5):768-775. Published online November 9, 2011
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DOI: https://doi.org/10.1007/s12275-011-1084-3
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Brucella species are facultative intracellular pathogenic α-Proteobacteria that can cause brucellosis in humans and domestic animals. The clinical and veterinary importance of the bacteria has led to well established studies on the molecular mechanisms of Brucella infection of host organisms. However, to date, no genome-wide study has scanned for genes related to the host specificity of Brucella spp. The majority of bacterial genes related to specific environmental adaptations such as host specificity are well-known to have evolved under positive selection pressure. We thus detected signals of positive selection for individual orthologous genes among Brucella genomes and identified genes related to host specificity. We first determined orthologous sets from seven completely sequenced Brucella genomes using the Reciprocal Best Hits (RBH). A maximum likelihood analysis based on the branch-site test was accomplished to examine the presence of positive selection signals, which was subsequently confirmed by phylogenetic analysis. Consequently, 12 out of 2,033 orthologous genes were positively selected by specific Brucella lineages, each of which belongs to a particular animal host. Extensive literature reviews revealed that half of these computationally identified genes are indeed involved in Brucella host specificity. We expect that this genome-wide approach based on positive selection may be reliably used to screen for genes related to environmental adaptation of a particular species and that it will provide a set of appropriate candidate genes.
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Citations
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Molecular Phylogenetics and Evolution.2016; 100: 31. CrossRef - Identification of Recombination and Positively Selected Genes in Brucella
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Genomics.2015; 106(1): 43. CrossRef - Complete Genome Sequence of Brucella canis Strain 118, a Strain Isolated from Canine
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Journal of Bacteriology.2012; 194(23): 6680. CrossRef - Complete Genome Sequence of Brucella canis BCB018, a Strain Isolated from a Human Patient
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Journal of Bacteriology.2012; 194(23): 6697. CrossRef
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