- Pathogenomics of Streptococcus ilei sp. nov., a newly identified pathogen ubiquitous in human microbiome
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Dong-Wook Hyun , Jae-Yun Lee , Min-Soo Kim , Na-Ri Shin , Tae Woong Whon , Kyung Hyun Kim , Pil Soo Kim , Euon Jung Tak , Mi-Ja Jung , June Young Lee , Hyun Sik Kim , Woorim Kang , Hojun Sung , Che Ok Jeon , Jin-Woo Bae
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J. Microbiol. 2021;59(8):793-806.
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DOI: https://doi.org/10.1007/s12275-021-1165-x
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 Abstract
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Viridans group streptococci are a serious health concern because
most of these bacteria cause life-threatening infections,
especially in immunocompromised and hospitalized individuals.
We focused on two alpha-hemolytic Streptococcus
strains (I-G2 and I-P16) newly isolated from an ileostomy
effluent of a colorectal cancer patient. We examined their pathogenic
potential by investigating their prevalence in human
and assessing their pathogenicity in a mouse model. We also
predicted their virulence factors and pathogenic features by
using comparative genomic analysis and in vitro tests. Using
polyphasic and systematic approaches, we identified the isolates
as belonging to a novel Streptococcus species and designated
it as Streptococcus ilei. Metagenomic survey based on
taxonomic assignment of datasets from the Human Microbiome
Project revealed that S. ilei is present in most human
population and at various body sites but is especially abundant
in the oral cavity. Intraperitoneal injection of S. ilei was
lethal to otherwise healthy C57BL/6J mice. Pathogenomics
and in vitro assays revealed that S. ilei possesses a unique set
of virulence factors. In agreement with the in vivo and in vitro
data, which indicated that S. ilei strain I-G2 is more pathogenic
than strain I-P16, only the former displayed the streptococcal
group A antigen. We here newly identified S. ilei sp.
nov., and described its prevalence in human, virulence factors,
and pathogenicity. This will help to prevent S. ilei strain
misidentification in the future, and improve the understanding
and management of streptococcal infections.
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Citations
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Yingying Bi, Yuezhu Wang, Wu Li, Yuhang Chen, Jinlong Qin, Huajun Zheng
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Molecular characterization of a novel putative pathogen,
Streptococcus nakanoensis
sp. nov., isolated from sputum culture
Takeaki Wajima, Takashi Sugawara, Emi Tanaka, Kei-ichi Uchiya, Justin R. Kaspar
Microbiology Spectrum.2024;[Epub] CrossRef -
Streptococcus raffinosi sp. nov., isolated from human breast milk samples
Ha Viet Nguyen, Anh Thi Van Trinh, Linh Nguyen Hai Bui, Anh Thi Lan Hoang, Quyen Thi Le Tran, Trung Thanh Trinh
International Journal of Systematic and Evolutionary Microbiology
.2024;[Epub] CrossRef - Description of Streptococcus dentalis sp. nov., Streptococcus gingivalis sp. nov., and Streptococcus lingualis sp. nov., Isolated from Human Oral Cavities
Beom-Jin Goo, Young-Sik Choi, Do-Hun Gim, Su-Won Jeong, Jee-Won Choi, Hojun Sung, Jae-Yun Lee, Jin-Woo Bae
Journal of Microbiology.2024; 62(11): 973. CrossRef - Valid and accepted novel bacterial taxa derived from human clinical specimens and taxonomic revisions published in 2022
Erik Munson, Arianna Carella, Karen C. Carroll, Romney M. Humphries
Journal of Clinical Microbiology.2023;[Epub] CrossRef - Valid publication of new names and new combinations effectively published outside the IJSEM. Validation List no. 203
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology
.2022;[Epub] CrossRef - Modulation of gut microbiota and fecal metabolites by corn silk among high-fat diet-induced hypercholesterolemia mice
Lin Ding, Shan Ren, Yaoxin Song, Chuangang Zang, Yuchao Liu, Hao Guo, Wenqing Yang, Hong Guan, Jicheng Liu
Frontiers in Nutrition.2022;[Epub] CrossRef - Reclassification of Streptococcus ilei as a later heterotypic synonym of Streptococcus koreensis based on whole-genome sequence analysis
Sanjeet Kumar, Kanika Bansal, Santosh Kumar Sethi
Archives of Microbiology.2022;[Epub] CrossRef
- Omics in gut microbiome analysis
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Tae Woong Whon , Na-Ri Shin , Joon Yong Kim , Seong Woon Roh
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J. Microbiol. 2021;59(3):292-297. Published online February 23, 2021
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DOI: https://doi.org/10.1007/s12275-021-1004-0
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38
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Abstract
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Our understanding of the interactions between microbial communities
and their niche in the host gut has improved owing
to recent advances in environmental microbial genomics.
Integration of metagenomic and metataxonomic sequencing
data with other omics data to study the gut microbiome
has become increasingly common, but downstream analysis
after data integration and interpretation of complex omics
data remain challenging. Here, we review studies that have
explored the gut microbiome signature using omics approaches,
including metagenomics, metataxonomics, metatranscriptomics,
and metabolomics. We further discuss recent
analytics programs to analyze and integrate multi-omics datasets
and further utilization of omics data with other advanced
techniques, such as adaptive immune receptor repertoire sequencing,
microbial culturomics, and machine learning, to
evaluate important microbiome characteristics in the gut.
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- Acinetobacter apis sp. nov., Isolated from the Intestinal Tract of a Honey Bee, Apis mellifera
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Pil Soo Kim , Na-Ri Shin , Joon Yong Kim , Ji-Hyun Yun , Dong-Wook Hyun , Jin-Woo Bae
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J. Microbiol. 2014;52(8):639-645. Published online August 1, 2014
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DOI: https://doi.org/10.1007/s12275-014-4078-0
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Abstract
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A novel Gram-negative, obligate aerobic, non-motile, and both coccobacillus- and bacillus-shaped bacterium, designated strain HYN18T, was isolated from the intestinal tract of a honey bee (Apis mellifera). The isolate was oxidasenegative
and catalase-positive. Strain HYN18T showed optimum growth at 25°C, pH 6–7, and in the presence of 1% (w/v) NaCl in trypticase soy broth medium. The isolate was
negative for hydrolyses of starch, casein, gelatin and urea, indole production from tryptone and hemolysis on sheep blood agar. A phylogenetic analysis based on the 16S rRNA gene and rpoB gene sequence showed that strain HYN18T was most closely related to Acinetobacter nectaris SAP 763.2T and A. boissieri SAP 284.1T with 98.3% and 98.1% similarity (16S rRNA gene), respectively, and 84.4% similarity with Acinetobacter nectaris SAP 763.2T (rpoB gene). The major cellular fatty acids were summed features 3 (comprising C16:1ω7c/C16:1ω6c), C12:0 and C16:0. The main isoprenoid quinone was ubiquinone-9 (Q-9). The polar lipids of strain
HYN18T were phosphatidylethanolamine, three unidentified lipids, an unidentified phospholipid and an unidentified glycolipid. The DNA G+C content was 40.6 mol%. DNADNA hybridization experiments indicated less than 33 ± 10% relatedness to the closest phylogenetic species, Acinetobacter nectaris SAP 763.2T. Thus, the phenotypic, phylogenetic and genotypic analyses indicate that strain HYN18T is a novel species within the genus Acinetobacter, for which the name Acinetobacter apis is proposed. The type strain is HYN18T (=KACC 16906T =JCM 18575T).
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- Paenibacillus marinisediminis sp. nov., a Bacterium Isolated from Marine Sediment
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Hae-Won Lee , Seong Woon Roh , Kyung June Yim , Na-Ri Shin , Jina Lee , Tae Woong Whon , Joon Yong Kim , Dong-Wook Hyun , Daekyung Kim , Jin-Woo Bae
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J. Microbiol. 2013;51(3):312-317. Published online June 28, 2013
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DOI: https://doi.org/10.1007/s12275-013-3198-2
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Abstract
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A Gram-negative, nonmotile, endospore-forming, rod-shaped bacterial strain LHW35T, which belonged to the genus Paenibacillus, was isolated from marine sediment collected from the south coast of the Republic of Korea. A phylogenetic analysis of 16S rRNA gene sequences indicated that strain LHW35T was most closely related to Paenibacillus taiwanensis G-soil-2-3T (97.2% similarity). The optimal growth conditions for strain LHW35T were 37°C, pH 6.0, and 0% (w/v) NaCl. The main isoprenoid quinone was menaquinone-7 (MK-7) and the major polyamine was spermidine. The diamino acid present in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major fatty acids were anteiso-C15:0 and C16:0. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, unidentified aminohospholipids, unidentified phospholipids, and unidentified polar lipids. A DNA-DNA hybridization experiment using the type strain of P. taiwanensis indicated <40% relatedness. The DNA G+C content was 45.0 mol%. Based on these phylogenetic, genomic, and phenotypic analyses, strain LHW35T should be classified as a novel species within the genus Paenibacillus, for which the name Paenibacillus marinisediminis sp. nov. is proposed. The type strain is LHW35T (=KACC 16317T =JCM 17886T).
- Rhodopirellula rosea sp. nov., a Novel Bacterium Isolated from an Ark Clam Scapharca broughtonii
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Seong Woon Roh , Hae-Won Lee , Kyung June Yim , Na-Ri Shin , Jina Lee , Tae Woong Whon , Na-Lae Lim , Daekyung Kim , Jin-Woo Bae
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J. Microbiol. 2013;51(3):301-304. Published online June 28, 2013
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DOI: https://doi.org/10.1007/s12275-013-3210-x
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Abstract
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A novel Gram-negative, motile, and ovoid-shaped strain, LHWP3T, which belonged to the family Planctomycetaceae in the phylum Planctomycetes, was isolated from a dead ark clam Scapharca broughtonii collected during a mass mortality event on the south coast of Korea. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that the isolate was most closely related to the type strain of Rhodopirellula baltica, with a shared 16S rRNA gene sequence similarity of 94.8%. The isolate grew optimally at 30°C in 4–6% (w/v) NaCl, and at pH 7. The major isoprenoid quinone was menaquinone-6 (MK-6). The dominant polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, and unidentified polar lipids. The predominant cellular fatty acids were C16:0, C18:1 ω9c, and C18:0. The genomic DNA G+C content of strain LHWP3T was 53.0 mol%. Based on polyphasic taxonomic analyses, strain LHWP3T should be classified as a novel species in the genus Rhodopirellula in the family Planctomycetaceae, for which the name Rhodopirellula rosea sp. nov. is proposed. The type strain is LHWP3T (=KACC 15560T =JCM 17759T).
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