- Sala cibi gen. nov., sp. nov., an extremely halophilic archaeon isolated from solar salt
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Hye Seon Song , Juseok Kim , Yeon Bee Kim , Se Hee Lee , Tae Woong Whon , Seong Woon Roh
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J. Microbiol. 2022;60(9):899-904. Published online July 14, 2022
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DOI: https://doi.org/10.1007/s12275-022-2137-5
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Two novel halophilic archaeal strains, CBA1133T and CBA-
1134, were isolated from solar salt in South Korea. The 16S
rRNA gene sequences of the isolates were identical to each
other and were closely related to the genera Natronomonas
(92.3–93.5%), Salinirubellus (92.2%), Halomarina (91.3–
92.0%), and Haloglomus (91.4%). The isolated strains were
coccoid, Gram-stain-negative, aerobic, oxidase-positive, and
catalase-negative. Growth occurred under temperatures of
25–50°C (optimum, 45°C), NaCl levels of 10–30% (optimum,
15%), pH levels of 6.0–8.5 (optimum, 7.0), and MgCl2 concentrations
of 0–500 mM (optimum, 100 mM). Digital DNADNA
hybridization values between the strains and related
genera ranged from 18.3% to 22.7%. The major polar lipids
of the strains were phosphatidyl glycerol, phosphatidyl glycerol
phosphate methyl ester, and phosphatidyl glycerol sulfate.
Genomic, phenotypic, physiological, and biochemical
analyses of the isolates revealed that they represent a novel
genus and species in the family Halobacteriaceae. The type
strain is CBA1133T (= KACC 22148T = JCM 34265T), for which
the name Sala cibi gen. nov., sp. nov. is proposed.
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Citations
Citations to this article as recorded by  - Phylogenomic and comparative analyses on protein sequences from Halobacteria to identify taxon-specific molecular markers which demarcate different Halobacteriaceae and Haloarculaceae genera
Radhey S. Gupta, Bashudev Rudra, Josh Tony, Sarah Bello
International Journal of Systematic and Evolutionary Microbiology
.2025;[Epub] CrossRef - Dominance and diversity of archaea in food-grade salts: insights for histamine degradation in salt-fermented foods
Jing Hou, Ya-Ling Mao, Na Li, Xiao-Yan Yang, Chidiebele Nwankwo, Heng-Lin Cui
International Journal of Food Science and Technology.2024; 59(12): 9490. CrossRef - Congregibacter variabilis sp. nov. and Congregibacter brevis sp. nov. Within the OM60/NOR5 Clade, Isolated from Seawater, and Emended Description of the Genus Congregibacter
Hyeonsu Tak, Miri S. Park, Hyerim Cho, Yeonjung Lim, Jang-Cheon Cho
Journal of Microbiology.2024; 62(9): 739. CrossRef - Genome-based classification of genera Halosegnis and Salella, and description of four novel halophilic archaea isolated from a tidal flat
Yao Hu, Xue Ma, Shun Tan, Xin-Xin Li, Mu Cheng, Jing Hou, Heng-Lin Cui
Antonie van Leeuwenhoek.2024;[Epub] CrossRef - Assessing the impact of heavy metals on bacterial diversity in coastal regions of Southeastern India
Chandra Veluchamy, Avinash Sharma, Kalaivani Thiagarajan
Environmental Monitoring and Assessment.2024;[Epub] CrossRef - Proposal of Eoetvoesiella gen. nov., Paludihabitans gen. nov., Rivihabitans gen. nov. and Salella gen. nov. as replacement names for the illegitimate prokaryotic generic names Eoetvoesia, Paludicola, Rivicola and Sala, respectively
Umakant Bhoopati Deshmukh, Aharon Oren
International Journal of Systematic and Evolutionary Microbiology
.2023;[Epub] CrossRef - Validation List no. 209. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology
.2023;[Epub] CrossRef - Halorarius litoreus gen. nov., sp. nov., Halorarius halobius sp. nov., Haloglomus halophilum sp. nov., Haloglomus salinum sp. nov., and Natronomonas marina sp. nov., extremely halophilic archaea isolated from tidal flat and marine solar salt
Ya-Ping Sun, Bei-Bei Wang, Zhang-Ping Wu, Xi-Wen Zheng, Jing Hou, Heng-Lin Cui
Frontiers in Marine Science.2023;[Epub] CrossRef - Naming new taxa of prokaryotes in the 21st century
Aharon Oren
Canadian Journal of Microbiology.2023; 69(4): 151. CrossRef
- Brachybacterium kimchii sp. nov. and Brachybacterium halotolerans subsp. kimchii subsp. nov., isolated from the Korean fermented vegetables, kimchi, and description of Brachybacterium halotolerans subsp. halotolerans subsp. nov.
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Yujin Kim , Yeon Bee Kim , Juseok Kim , Joon Yong Kim , Tae Woong Whon , Won-Hyong Chung , Eun-Ji Song , Young-Do Nam , Se Hee Lee , Seong Woon Roh
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J. Microbiol. 2022;60(7):678-688. Published online July 4, 2022
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DOI: https://doi.org/10.1007/s12275-022-1581-6
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Two Gram-stain-positive, oxidase-negative, catalase-positive,
and coccus-shaped bacterial strains, designated CBA3104T
and CBA3105T, were isolated from kimchi. Strain CBA3104T
and CBA3105T grew at 10–35°C (optimum, 25°C and 30°C,
respectively), at pH 6.0–8.5 (optimum, pH 6.5), and in the
presence of 0–15% (w/v) NaCl (optimum, 5%). A phylogenetic
analysis based on 16S rRNA gene sequences revealed
that strain CBA3104T formed a distinct phylogenetic lineage
within the genus Brachybacterium whereas strain CBA3105T
was closely positioned with Brachybacterium halotolerans
MASK1Z-5T. The 16S rRNA gene sequence similarity between
strains CBA3104T and CBA3105T was 99.9%, but ANI
and dDDH values between strains CBA3104T and CBA3105T
were 93.61% and 51.5%, respectively. Strain CBA3104T showed
lower ANI and dDDH values than species delineation against
three closely related strains and type species of the genus
Brachybacterium, however, strain CBA3105T showed 96.63%
ANI value and 69.6% dDDH value with Brachybacterium
halotolerans MASK1Z-5T. Among biochemical analysis results,
strain CBA3104T could uniquely utilize bromo-succinic
acid whereas only strain CBA3105T was positive for alkaline
phosphatase and α-fucosidase among two novel strains, closely
related strains, and type species of the genus Brachybacterium.
Compared with strain CBA3105T and Brachybacterium
halotolerans JCM 34339T, strain CBA3105T was differentially
positive for acid production of D-arabinose, D-adonitol, and
potassium 5-ketogluconate and enzyme activity of β-glucuronidase.
Both strains contained menaquinone-7 as the dominant
quinone. The cell-wall peptidoglycan of two novel
strains contained meso-diaminopimelic acid. The major fatty
acids of strains CBA3104T and CBA3105T were anteiso-C15:0,
anteiso-C17:0, and iso-C16:0. The major polar lipids of both
strains were phosphatidylglycerol and diphosphatidylglycerol.
Strain CBA3104T possessed a uniquely higher abundance of
tRNA (97 tRNAs) than four Brachybacterium strains used for
comparative taxonomic analysis (54–62 tRNAs). Both the
CBA3104T and CBA3105T strain harbored various oxidoreductase,
transferase, hydrolase, and lyase as strain-specific
functional genes compared to closely related strains and Brachybacterium
type species. The results of biochemical/physiological,
chemotaxonomic, and genomic analyses demonstrated
that strains CBA3104T and CBA3105T represent a novel species
of the genus Brachybacterium and a novel subspecies of
B. halotolerans, respectively, for which the names Brachybacterium
kimchii sp. nov. and B. halotolerans subsp. kimchii
subsp. nov. are proposed. The type strains of the novel
species and the novel subspecies are CBA3104T (= KCCM
43417T = JCM 34759T) and CBA3105T (= KCCM 43418T =
JCM 34760T), respectively.
-
Citations
Citations to this article as recorded by - Metagenomic Insights into the Taxonomic and Functional Features of Traditional Fermented Milk Products from Russia
Alexander G. Elcheninov, Kseniya S. Zayulina, Alexandra A. Klyukina, Mariia K. Kremneva, Ilya V. Kublanov, Tatiana V. Kochetkova
Microorganisms.2023; 12(1): 16. CrossRef - Validation List no. 208. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology
.2022;[Epub] CrossRef -
Complete Genome Sequence of
Brachybacterium
sp. Strain NBEC-018, Isolated from Nematode-Infected Potatoes
Ling Chen, Yueying Wang, Nanxi Liu, Lei Zhu, Yong Min, Yimin Qiu, Yuxi Tian, Xiaoyan Liu, David Rasko
Microbiology Resource Announcements.2022;[Epub] CrossRef
- Pathogenomics of Streptococcus ilei sp. nov., a newly identified pathogen ubiquitous in human microbiome
-
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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435
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10
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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.
-
Citations
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Yingying Bi, Yuezhu Wang, Wu Li, Yuhang Chen, Jinlong Qin, Huajun Zheng
BMC Microbiology.2025;[Epub] CrossRef - Characterization of blood microbial population in beef calves with clinical signs of sepsis using 16S rRNA gene sequencing
Giuliano Borriello, Flaminia Valentini, Sara Ferrini, Giorgia Di Muro, Giulia Cagnotti, Elena Grego, Angela Maria Catania, Maria Cristina Stella, Ugo Ala, Patrizia Nebbia, Antonio D’Angelo, Claudio Bellino, Ulrike Gertrud Munderloh
PLOS One.2025; 20(5): e0324469. CrossRef - Alterations of Gut Microbiome and Serum Short‐Chain Fatty Acids in Children With Enthesitis‐Related Arthritis
Qi Zheng, Yiping Xu, Xubo Qian, Bin Hu, Qian Ma, Li Guo, Robert M. Dorazio, Meiping Lu
International Journal of Rheumatic Diseases.2025;[Epub] CrossRef -
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
-
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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383
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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.
-
Citations
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Myungji Kang, Jihye Jo, Hwarang Shin, Hyun Wook Kang
Journal of Photochemistry and Photobiology B: Biology.2025; 269: 113201. CrossRef - Bee gut microbiota as an emerging endpoint for the environmental risk assessment of pesticides
Annelise Rosa-Fontana, Daniel Aguado-López, Clara Jabal Uriel, María Buendía Abad, Mariano Higes, M. Alice Pinto, Dora Henriques, Simone Tosi, Juan Miguel Rodríguez, Claudio Alba, Raquel Martín-Hernández
Science of The Total Environment.2025; 993: 179977. CrossRef - Multi-omics reveals effects of diet FNDF/starch level on growth performance and rumen development of Hu sheep
Haibi Zhao, Jiqing Wang, Zhiyun Hao, Pengfei Yin, Shanglong Wang, Yanli Guo, Chunyan Ren
Frontiers in Microbiology.2025;[Epub] CrossRef - The Microbiome as a Protagonist of Xylophagous Insects in Adaptation to Environmental Conditions and Climate Change
Alexander Kuprin, Vladislava Baklanova
International Journal of Molecular Sciences.2025; 26(20): 10143. CrossRef -
Effect of alfalfa supplementary change dietary non-fibrous carbohydrate (NFC) to neutral detergent fiber (NDF) ratio on rumen fermentation and microbial function in Gansu alpine fine wool sheep (
Ovis aries
)
Qian Chen, Yun-feng Cui, Zhao-xi Zhang, Fu-cheng Jiang, Xiang-yu Meng, Jin-jin Li, Da-yong Cui, Jian-lei Jia
Animal Biotechnology.2024;[Epub] CrossRef - Effect of Pharmaceutically Active Antibiotics on Gut Metagenome of Mother and Infant
Ruchi Yadav
Journal of Preventive, Diagnostic and Treatment Strategies in Medicine.2024; 3(4): 284. CrossRef - Effects of gnotobiotic fermentation on global gene expression of germ‐free vegetables
Yujin Kim, Hojun Sung, Yeon Bee Kim, Hye Seon Song, Mi‐Ja Jung, Jisu Lee, Min Ji Lee, Se Hee Lee, Seong Woon Roh, Jin‐Woo Bae, Tae Woong Whon
Physiologia Plantarum.2024;[Epub] CrossRef - Intestinal biofilms: pathophysiological relevance, host defense, and therapeutic opportunities
Bernhard Jandl, Satish Dighe, Christoph Gasche, Athanasios Makristathis, Markus Muttenthaler, Christopher Staley, Giovanni Di Bonaventura
Clinical Microbiology Reviews.2024;[Epub] CrossRef - The role of insect gut microbiota in host fitness, detoxification and nutrient supplementation
U. Shamjana, Deepa Azhchath Vasu, Preety Sweta Hembrom, Karunakar Nayak, Tony Grace
Antonie van Leeuwenhoek.2024;[Epub] CrossRef - Effect of florfenicol administered through feed on Atlantic salmon (Salmo salar) gut and its microbiome
Giovanna Monticelli, Joseph H. Bisesi, Jason T. Magnuson, Daniel Schlenk, Carlos Zarza, David Peggs, Daniela M. Pampanin
Aquaculture.2024; 580: 740310. CrossRef - Advances in Culturomics Research on the Human Gut Microbiome: Optimizing Medium Composition and Culture Techniques for Enhanced Microbial Discovery
Hye Seon Song, Yeon Bee Kim, Joon Yong Kim, Seong Woon Roh, Tae Woong Whon
Journal of Microbiology and Biotechnology.2024; 34(4): 757. CrossRef - Deciphering the microbial map and its implications in the therapeutics of neurodegenerative disorder
Shrutikirti Vashishth, Rashmi K. Ambasta, Pravir Kumar
Ageing Research Reviews.2024; 100: 102466. CrossRef - Emerging importance of stool preservation methods in OMICS studies with special focus on cancer biology
Parul Mehra, Anil Kumar
Cell Biochemistry and Function.2024;[Epub] CrossRef - Gut microbiota and metabolic modulation by supplementation of polysaccharide-producing Bacillus licheniformis from Tibetan Yaks: A comprehensive multi-omics analysis
Zhibo Zeng, Chuxian Quan, Shimeng Zhou, Saisai Gong, Mudassar Iqbal, Muhammad Fakhar-e-Alam Kulyar, Shah Nawaz, Kewei Li, Jiakui Li
International Journal of Biological Macromolecules.2024; 254: 127808. CrossRef - The Microbiome Matters: Its Impact on Cancer Development and Therapeutic Responses
In-Young Chung, Jihyun Kim, Ara Koh
Journal of Microbiology.2024; 62(3): 137. CrossRef - Deciphering the gut microbiome: The revolution of artificial intelligence in microbiota analysis and intervention
Mohammad Abavisani, Alireza Khoshrou, Sobhan Karbas Foroushan, Negar Ebadpour, Amirhossein Sahebkar
Current Research in Biotechnology.2024; 7: 100211. CrossRef - Should Routine Diagnostics Implement Gut Microbiota Analysis?
Giuseppe Guido Maria Scarlata, Ludovico Abenavoli
The International Journal of Gastroenterology and Hepatology Diseases.2024;[Epub] CrossRef - Microbiome and pancreatic cancer: time to think about chemotherapy
Juliana de Castilhos, Katharina Tillmanns, Jana Blessing, Arnelyn Laraño, Vadim Borisov, Christoph K. Stein-Thoeringer
Gut Microbes.2024;[Epub] CrossRef - Microbiota in Irritable Bowel Syndrome and Endometriosis: Birds of a Feather Flock Together—A Review
Noemi Salmeri, Emanuele Sinagra, Carolina Dolci, Giovanni Buzzaccarini, Giulio Sozzi, Miriam Sutera, Massimo Candiani, Federica Ungaro, Luca Massimino, Silvio Danese, Francesco Vito Mandarino
Microorganisms.2023; 11(8): 2089. CrossRef - Revelation of the sciences of traditional foods
Zhen Jia, Boce Zhang, Arnav Sharma, Nathalie S. Kim, Sonia M. Purohit, Madison M. Green, Michelle R. Roche, Emma Holliday, Hongda Chen
Food Control.2023; 145: 109392. CrossRef - The gut microbiota: A new perspective for tertiary prevention of hepatobiliary and gallbladder diseases
Xiaoyu Huang, Yi Yang, Xueli Li, Xiaoya Zhu, Dan Lin, Yueran Ma, Min Zhou, Xiangyi Cui, Bingyu Zhang, Dongmei Dang, Yuhong Lü, Changwu Yue
Frontiers in Nutrition.2023;[Epub] CrossRef - Environmental factors and gut microbiota: Toward better conservation of deer species
Yu Wang, Bo Xu, Huan Chen, Fang Yang, Jinlin Huang, Xin’an Jiao, Yunzeng Zhang
Frontiers in Microbiology.2023;[Epub] CrossRef - Potential role of gut microbes in the efficacy and toxicity of immune checkpoints inhibitors
Jingxin Ma, Qi Wei, Xin Cheng, Jie Zhang, Zhongtao Zhang, Jianrong Su
Frontiers in Pharmacology.2023;[Epub] CrossRef - Microbiota-Gut-Brain Axis in Neurological Disorders: From Leaky Barriers
Microanatomical Changes to Biochemical Processes
Irene Neri, Elisa Boschetti, Matilde Yung Follo, Roberto De Giorgio, Lucio Ildebrando Cocco, Lucia Manzoli, Stefano Ratti
Mini-Reviews in Medicinal Chemistry.2023; 23(3): 307. CrossRef - Effects of microbial-derived biotics (meta/pharma/post-biotics) on the modulation of gut microbiome and metabolome; general aspects and emerging trends
Alireza Sadeghi, Maryam Ebrahimi, Mohammad Saeed Kharazmi, Seid Mahdi Jafari
Food Chemistry.2023; 411: 135478. CrossRef - Interkingdom interactions between Pseudomonas aeruginosa and Candida albicans affect clinical outcomes and antimicrobial responses
Lisa J Kahl, Nina Stremmel, M Alejandra Esparza-Mora, Rachel M Wheatley, R Craig MacLean, Markus Ralser
Current Opinion in Microbiology.2023; 75: 102368. CrossRef - Molecular Insights Into the Role of Gut Microbiota in Antibiotic Therapy Selection and Resistance Mitigation
Mihaela Andreescu
Cureus.2023;[Epub] CrossRef - Gut Microbiota Composition and Cardiovascular Disease: A Potential New Therapeutic Target?
Martina Belli, Lucy Barone, Susanna Longo, Francesca Romana Prandi, Dalgisio Lecis, Rocco Mollace, Davide Margonato, Saverio Muscoli, Domenico Sergi, Massimo Federici, Francesco Barillà
International Journal of Molecular Sciences.2023; 24(15): 11971. CrossRef - Old Folks, Bad Boon: Antimicrobial Resistance in the Infant Gut Microbiome
Silvia Saturio, Alejandra Rey, Anna Samarra, Maria Carmen Collado, Marta Suárez, Laura Mantecón, Gonzalo Solís, Miguel Gueimonde, Silvia Arboleya
Microorganisms.2023; 11(8): 1907. CrossRef - A New Biomarker Profiling Strategy for Gut Microbiome Research: Valid Association of Metabolites to Metabolism of Microbiota Detected by Non-Targeted Metabolomics in Human Urine
Sijia Zheng, Lina Zhou, Miriam Hoene, Andreas Peter, Andreas L. Birkenfeld, Cora Weigert, Xinyu Liu, Xinjie Zhao, Guowang Xu, Rainer Lehmann
Metabolites.2023; 13(10): 1061. CrossRef - Causal discovery for the microbiome
Jukka Corander, William P Hanage, Johan Pensar
The Lancet Microbe.2022; 3(11): e881. CrossRef - Play the plug: How bacteria modify recognition by host receptors?
Suma Tiruvayipati, Dharjath S. Hameed, Niyaz Ahmed
Frontiers in Microbiology.2022;[Epub] CrossRef - Intestinal virome: An important research direction for alcoholic and nonalcoholic liver diseases
Yan Li, Wen-Cheng Liu, Bing Chang
World Journal of Gastroenterology.2022; 28(26): 3279. CrossRef - Regulator of RNase E activity modulates the pathogenicity of Salmonella Typhimurium
Jaejin Lee, Eunkyoung Shin, Ji-Hyun Yeom, Jaeyoung Park, Sunwoo Kim, Minho Lee, Kangseok Lee
Microbial Pathogenesis.2022; 165: 105460. CrossRef - Long-term high loading intensity of aerobic exercise improves skeletal muscle performance via the gut microbiota-testosterone axis
Lidong Zhang, Hedong Lang, Li Ran, Guoliang Tian, Hui Shen, Jundong Zhu, Qianyong Zhang, Long Yi, Mantian Mi
Frontiers in Microbiology.2022;[Epub] CrossRef - In sickness and in health: Insights into the application of omics in aquaculture settings under a microbiological perspective
Anna Luiza Bauer Canellas, Wellington Felipe Costa, Jéssyca Freitas-Silva, Isabelle Rodrigues Lopes, Bruno Francesco Rodrigues de Oliveira, Marinella Silva Laport
Aquaculture.2022; 554: 738132. CrossRef - The gut microbiome in human health and disease—Where are we and where are we going? A bibliometric analysis
Zhiqiang Huang, Kun Liu, Wenwen Ma, Dezhi Li, Tianlu Mo, Qing Liu
Frontiers in Microbiology.2022;[Epub] CrossRef - Standards for Collection, Preservation, and Transportation of Fecal Samples in TCM Clinical Trials
Wenquan Su, Yawei Du, Fengmei Lian, Hui Wu, Xinrong Zhang, Wenli Yang, Yunfeng Duan, Yuanming Pan, Weijng Liu, Aiming Wu, Bowen Zhao, Chongming Wu, Shengxian Wu
Frontiers in Cellular and Infection Microbiology.2022;[Epub] CrossRef - Global research trends on the links between the gut microbiota and diabetes between 2001 and 2021: A bibliometrics and visualized study
Boxun Zhang, Zishan Jin, Tiangang Zhai, Qiyou Ding, Haoyu Yang, Jia Wang, Lili Zhang, Linhua Zhao
Frontiers in Microbiology.2022;[Epub] CrossRef - Regulator of ribonuclease activity modulates the pathogenicity of Vibrio vulnificus
Jaejin Lee, Eunkyoung Shin, Jaeyeong Park, Minho Lee, Kangseok Lee
Journal of Microbiology.2021; 59(12): 1133. CrossRef - Omics-based microbiome analysis in microbial ecology: from sequences to information
Jang-Cheon Cho
Journal of Microbiology.2021; 59(3): 229. CrossRef - Genome-Scale Metabolic Modeling Enables In-Depth Understanding of Big Data
Anurag Passi, Juan D. Tibocha-Bonilla, Manish Kumar, Diego Tec-Campos, Karsten Zengler, Cristal Zuniga
Metabolites.2021; 12(1): 14. CrossRef
- Paenibacillus marinisediminis sp. nov., a Bacterium Isolated from Marine Sediment
-
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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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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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).
- NOTE] Oceanobacillus kimchii sp. nov. Isolated from a Traditional Korean Fermented Food
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Tae Woong Whon , Mi-Ja Jung , Seong Woon Roh , Young-Do Nam , Eun-Jin Park , Kee-Sun Shin , Jin-Woo Bae
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J. Microbiol. 2010;48(6):862-866. Published online January 9, 2011
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DOI: https://doi.org/10.1007/s12275-010-0214-7
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A moderate halophile, strain X50T, was isolated from mustard kimchi, a traditional Korean fermented food. The organism grew under conditions ranging from 0-15.0% (w/v) NaCl (optimum: 3.0%), pH 7.0-10.0 (optimum: pH 9.0) and 15-45°C (optimum: 37°C). The morphological, physiological, and biochemical features and the 16S rRNA gene sequences of strain X50T were characterized. Colonies of the isolate were creamcolored and the cells were rod-shaped. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain X50T belongs to the genus Oceanobacillus and is closely related phylogenetically to the type strain O. iheyensis HTE831T (98.9%) and O. oncorhynchi subsp. oncorhynchi R-2T (97.0%). The cellular fatty acid profiles predominately included anteiso-C15:0 and iso-C15:0. The G+C content of the genomic DNA of the isolate was 37.9 mol% and the major isoprenoid quinone was MK-7. Analysis of the 16S rRNA gene sequences, DNA-DNA relatedness and physiological and biochemical tests indicated genotypic and
phenotypic differences among strain X50T and reference species in the genus Oceanobacillus. Therefore, strain X50T was proposed as a novel species and named Oceanobacillus kimchii. The type strain of the new species is X50T (=JCM 16803T =KACC 14914T =DSM 23341T).
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Citations
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Xu Liu, Jun-Jie Fu, Han-Jun Shen, Li-Juan Chai, Xiao-Juan Zhang, Hong-Yu Xu, Song-Tao Wang, Su-Yi Zhang, Cai-Hong Shen, Jin-Song Shi, Zhen-Ming Lu, Zheng-Hong Xu
Process Biochemistry.2025; 150: 68. CrossRef - Unveiling the microbiome during post-partum uterine infection: a deep shotgun sequencing approach to characterize the dairy cow uterine microbiome
Carl Basbas, Adriana Garzon, Cory Schlesener, Machteld van Heule, Rodrigo Profeta, Bart C. Weimer, Noelia Silva-del-Rio, Barbara A. Byrne, Betsy Karle, Sharif S. Aly, Fabio S. Lima, Richard V. Pereira
Animal Microbiome.2023;[Epub] CrossRef - Phenotypic characteristics, phylogenetic analysis and characterization of alkaline proteases of marine bacteria Geomicrobium halophilum, Oceanobacillus oncorhynchi, and Oceanobacillus khimchii
Vikram H. Raval, Rupal H. Joshi, Hitarth B. Bhatt, Satya P. Singh
Biologia.2022; 77(8): 2405. CrossRef - Draft Genome Sequence of Oceanobacillus jordanicus Strain GSFE11, a Halotolerant Plant Growth-Promoting Bacterial Endophyte Isolated From the Jordan Valley
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Annals of Laboratory Medicine.2022; 42(2): 290. CrossRef - Oceanobacillus alkalisoli sp. nov., an alkaliphilic bacterium isolated from saline-alkaline soil
Pin-Jiao Jin, Lei Sun, Manik Prabhu Narsing Rao, Jian-Yu Jiao, Xiu-Jun Sun, Wen-Jun Li, Shuang Wang
International Journal of Systematic and Evolutionary Microbiology
.2022;[Epub] CrossRef - ODFM, an omics data resource from microorganisms associated with fermented foods
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Scientific Data.2021;[Epub] CrossRef -
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Wentao Zhu, Junqin Li, Xiaoxia Wang, Jing Yang, Shan Lu, Xin-He Lai, Dong Jin, Yuyuan Huang, Sihui Zhang, Ji Pu, Juan Zhou, Zhihong Ren, Ying Huang, Xiaomin Wu, Jianguo Xu
International Journal of Systematic and Evolutionary Microbiology
.2020; 70(6): 3763. CrossRef - Two novel species of the family Bacillaceae: Oceanobacillus piezotolerans sp. nov. and Bacillus piezotolerans sp. nov., from deep-sea sediment samples of Yap Trench
Libo Yu, Xixiang Tang, Shiping Wei, Yinkun Qiu, Xiashutong Xu, Guangxin Xu, Qilin Wang, Qian Yang
International Journal of Systematic and Evolutionary Microbiology.2019; 69(10): 3022. CrossRef - Oceanobacillus timonensis sp. nov. and Oceanobacillus senegalensis sp. nov., two new moderately halophilic, Gram-stain positive bacteria isolated from stools sample of healthy young Senegalese
Bruno Senghor, Hubert Bassène, Saber Khelaifia, Catherine Robert, Pierre-Edouard Fournier, Raymond Ruimy, Cheikh Sokhna, Didier Raoult, Jean-Christophe Lagier
Antonie van Leeuwenhoek.2019; 112(5): 785. CrossRef - Characterizing the metabolites and the microbial communities of the soy sauce mash affected by temperature and hydrostatic pressure
Ru Liang, Jun Huang, Xueming Wu, Yi Xu, Jun Fan, Chongde Wu, Yao Jin, Rongqing Zhou
Food Research International.2019; 123: 801. CrossRef - Microbial communities and their predicted metabolic functions in a desiccating acid salt lake
Elena Zaikova, Kathleen C. Benison, Melanie R. Mormile, Sarah Stewart Johnson
Extremophiles.2018; 22(3): 367. CrossRef - Microbial Culturomics to Map Halophilic Bacterium in Human Gut: Genome Sequence and Description of Oceanobacillus jeddahense sp. nov.
Saber Khelaifia, Jean-Christophe Lagier, Fehmida Bibi, Esam Ibraheem Azhar, Olivier Croce, Roshan Padmanabhan, Asif Ahmad Jiman-Fatani, Muhammad Yasir, Catherine Robert, Claudia Andrieu, Pierre-Edouard Fournier, Didier Raoult
OMICS: A Journal of Integrative Biology.2016; 20(4): 248. CrossRef -
Draft Genome Sequence of an
Oceanobacillus
sp. Strain Isolated from Soil in a Burial Crypt
Ilargi Martínez-Ballesteros, Ylenia Arizaga, Joseba Bikandi, Javier Garaizar, Giulia Ganau, Bianca Paglietti, Manuela Murgia, Massimo Deligios, Salvatore Rubino
Genome Announcements.2016;[Epub] CrossRef -
Oceanobacillus halophilus sp. nov., a novel moderately halophilic bacterium from a hypersaline lake
Mohammad Ali Amoozegar, Maryam Bagheri, Ali Makhdoumi, Mahdi Moshtaghi Nikou, Seyed Abolhassan Shahzadeh Fazeli, Peter Schumann, Cathrin Spröer, Cristina Sánchez-Porro, Antonio Ventosa
International Journal of Systematic and Evolutionary Microbiology
.2016; 66(3): 1317. CrossRef - Genome sequence of Oceanobacillus picturae strain S1, an halophilic bacterium first isolated in human gut
Jean-Christophe Lagier, Saber Khelaifia, Esam Ibraheem Azhar, Olivier Croce, Fehmida Bibi, Asif Ahmad Jiman-Fatani, Muhammad Yasir, Huda Ben Helaby, Catherine Robert, Pierre-Edouard Fournier, Didier Raoult
Standards in Genomic Sciences.2015;[Epub] CrossRef -
Oceanobacillus arenosus sp. nov., a moderately halophilic bacterium isolated from marine sand
Wonyong Kim, Chatuphon Siamphan, Jong-Hwa Kim, Ampaitip Sukhoom
International Journal of Systematic and Evolutionary Microbiology
.2015; 65(Pt_9): 2943. CrossRef - Oceanobacillus bengalensis sp. nov., a bacterium isolated from seawater of the Bay of Bengal
Ouyang Yongchang, Wenzhou Xiang, Guanghua Wang
Antonie van Leeuwenhoek.2015; 108(5): 1189. CrossRef - Oceanobacillus damuensis sp. nov. and Oceanobacillus rekensis sp. nov., isolated from saline alkali soil samples
Xiufeng Long, Renyuan Ye, Shuai Zhang, Bo Liu, Yuqin Zhang, Zhigang Zeng, Yongqiang Tian
Antonie van Leeuwenhoek.2015; 108(3): 731. CrossRef -
Oceanobacillus limi sp. nov., a moderately halophilic bacterium from a salt lake
Mohammad Ali Amoozegar, Maryam Bagheri, Ali Makhdoumi-Kakhki, Maryam Didari, Peter Schumann, Cathrin Spröer, Cristina Sánchez-Porro, Antonio Ventosa
International Journal of Systematic and Evolutionary Microbiology
.2014; 64(Pt_4): 1284. CrossRef - Oceanobacillus-like bacterium isolated from Vyhna travertine spring
P. Pristas, M. Cunderlikova, J. Judova
Folia Microbiologica.2014; 59(2): 141. CrossRef - Oceanobacillus gochujangensis sp. nov., isolated from gochujang a traditional Korean fermented food
Seo-Jung Jang, Yu-Jin Kim, Sul-Hee Lee, Young-Seo Park, Jung-Min Park, Dong-Hoon Bai
Journal of Microbiology.2014; 52(12): 1050. CrossRef -
Oceanobacillus pacificus sp. nov., isolated from a deep-sea sediment
Cong Yu, Shaolan Yu, Zenghu Zhang, Zhao Li, Xiao-Hua Zhang
International Journal of Systematic and Evolutionary Microbiology
.2014; 64(Pt_4): 1278. CrossRef -
Oceanobacillus
luteolus sp. nov., isolated from soil
Min Wu, Guiqin Yang, Zhen Yu, Li Zhuang, Yingqiang Jin, Shungui Zhou
International Journal of Systematic and Evolutionary Microbiology
.2014; 64(Pt_5): 1495. CrossRef -
Evolution in the
Bacillaceae
Patricia Fajardo-Cavazos, Heather Maughan, Wayne L. Nicholson, Patrick Eichenberger, Adam Driks
Microbiology Spectrum.2014;[Epub] CrossRef -
Oceanobacillus
polygoni sp. nov., a facultatively alkaliphile isolated from indigo fermentation fluid
Kikue Hirota, Yoshiko Hanaoka, Yoshinobu Nodasaka, Isao Yumoto
International Journal of Systematic and Evolutionary Microbiology
.2013; 63(Pt_9): 3307. CrossRef -
Oceanobacillus indicireducens sp. nov., a facultative alkaliphile that reduces an indigo dye
Kikue Hirota, Kenichi Aino, Yoshinobu Nodasaka, Isao Yumoto
International Journal of Systematic and Evolutionary Microbiology
.2013; 63(Pt_4): 1437. CrossRef - Non-contiguous finished genome sequence and description of Oceanobacillus massiliensis sp. nov.
Véronique Roux, Matthieu Million, Catherine Robert, Alix Magne, Didier Raoult
Standards in Genomic Sciences.2013; 9(2): 370. CrossRef -
Oceanobacillus
chungangensis sp. nov., isolated from a sand dune
Dong Chae Lee, Hyeonji Kang, Veeraya Weerawongwiwat, Beomjoon Kim, Young-Wan Choi, Wonyong Kim
International Journal of Systematic and Evolutionary Microbiology
.2013; 63(Pt_10): 3666. CrossRef - Naturally Occurring Culturable Aerobic Gut Flora of Adult Phlebotomus papatasi, Vector of Leishmania major in the Old World
Jaba Mukhopadhyay, Henk R. Braig, Edgar D. Rowton, Kashinath Ghosh, Markus M. Heimesaat
PLoS ONE.2012; 7(5): e35748. CrossRef - List of new names and new combinations previously effectively, but not validly, published
International Journal of Systematic and Evolutionary Microbiology
.2011; 61(5): 1011. CrossRef
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