Journal of Microbiology

Journal Articles

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; J. Microbiol. 2024;62(9):739-748. Published online July 18, 2024; DOI: https://doi.org/10.1007/s12275-024-00158-5

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Two Gram-stain-negative, aerobic, motile by means of flagella, short rod-shaped bacterial strains, designated IMCC43200(T) and IMCC45268(T), were isolated from coastal seawater samples collected from the South Sea of Korea. Strains IMCC43200(T) and IMCC45268(T) shared 98.6% 16S rRNA gene sequence similarity and were closely related to Congregibacter litoralis KT71(T) (98.8% and 98.7%, respectively). Complete whole-genome sequences of IMCC43200(T) and IMCC45268(T) were 3.93 and 3.86 Mb in size with DNA G + C contents of 54.8% and 54.2%, respectively. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the two strains were 74.5% and 23.4%, respectively, revealing that they are independent species. The two strains showed ANI values of ≤ 75.8% and dDDH values of ≤ 23.0% to the type and only species of the genus Congregibacter (C. litoralis), indicating that each strain represents a novel species. Both strains contained summed feature 3 (comprising C(16:1) ω6c and/or C(16:1) ω7c) and summed feature 8 (comprising C(18:1) ω6c and/or C(18:1) ω7c) as major fatty acid constituents. The predominant isoprenoid quinone detected in both strains was ubiquinone-8 (Q-8). The major polar lipids of the two strains were phosphatidylethanolamine, phosphatidylglycerol, phospholipids, and aminolipids. Based on the phylogenetic, genomic, and phenotypic characterization, strains IMCC43200(T) and IMCC45268(T) were considered to represent two novel species within the genus Congregibacter, for which the names Congregibacter variabilis sp. nov. and Congregibacter brevis sp. nov. are proposed with IMCC43200(T) (= KCTC 8133(T) = NBRC 116295(T) = CCTCC AB 2023139(T)) and IMCC45268(T) (= KCTC 92921(T) = NBRC 116135(T)) as the type strains, respectively.

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Leuconostoc aquikimchii sp. nov., a Lactic Acid Bacterium Isolated from Cabbage Watery Kimchi
Subin Kim, Se Hee Lee, Ki Hyun Kim, Misun Yun
Journal of Microbiology.2024; 62(12): 1089. CrossRef

Ship Hull‑Fouling Diatoms on Korean Research Vessels Revealed by Morphological and Molecular Methods, and Their Environmental Implications: Jaeyeong Park , Taehee Kim , Buhari Lawan Muhammad , Jang-Seu Ki; J. Microbiol. 2023;61(6):615-626. Published online May 25, 2023; DOI: https://doi.org/10.1007/s12275-023-00055-3

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Abstract

Ship biofouling is one of the main vectors for the introduction and global spread of non-indigenous organisms. Diatoms were the early colonizers of ship hulls; however, their community composition on ships is poorly understood. Herein, we investigated the diatom community on the hull samples collected from two Korean research vessels Isabu (IRV) and Onnuri (ORV) on September 2 and November 10, 2021, respectively. IRV showed low cell density (345 cells/cm2) compared to ORV (778 cells/cm2). We morphologically identified more than 15 species of diatoms from the two research vessels (RVs). The microalgae in both RVs were identified as Amphora, Cymbella, Caloneis, Halamphora, Navicula, Nitzschia, and Plagiogramma. Of them, the genus Halamphora was found to be predominant. However, both RVs had a varied dominant species with a significant difference in body size; Halamphora oceanica dominated at IRV, and Halamphora sp. at ORV, respectively. Molecular cloning showed similar results to morphological analysis, in which Halamphora species dominated in both RVs. The hull-attached species were distinct from species found in the water column. These results revealed diatoms communities that are associated with ship hull-fouling at an early stage of biofilm formation. Moreover, ships arriving from different regions could show some variation in species composition on their hull surfaces, with the potential for nonindigenous species introduction.

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Invasion and ecological impact of the biofouling tube worm Hydroides elegans (Polychaeta: Serpulidae) in Korean coastal waters
Sang Lyeol Kim, Ok Hwan Yu
Frontiers in Marine Science.2025;[Epub] CrossRef
High haplotype diversity and strong phylogeographic structure in the invasive jellyfish Blackfordia virginica population highlight its complex demographic history in Korea
Buhari Lawan Muhammad, Jinho Chae, Jang-Seu Ki
Marine Biodiversity.2024;[Epub] CrossRef

Comparison of Ganoderma boninense Isolate’s Aggressiveness Using Infected Oil Palm Seedlings: Mei Lieng Lo , Tu Anh Vu Thanh , Frazer Midot , Sharon Yu Ling Lau , Wei Chee Wong , Hun Jiat Tung , Mui Sie Jee , Mei-Yee Chin , Lulie Melling; J. Microbiol. 2023;61(4):449-459. Published online April 25, 2023; DOI: https://doi.org/10.1007/s12275-023-00040-w

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Abstract

Basal stem rot incidence caused by a white-rot fungus, Ganoderma boninense, is the major disease of oil palm in Southeast Asia. The rate of disease transmission and host damage are affected by variations in pathogen aggressiveness. Several other studies have used the disease severity index (DSI) to determine G. boninense aggressiveness levels while verifying disease using a culture-based method, which might not provide accurate results or be feasible in all cases. To differentiate G. boninense aggressiveness, we employed the DSI and vegetative growth measurement of infected oil palm seedlings. Disease confirmation was performed through scanning electron microscopy and molecular identification of fungal DNA from both infected tissue and fungi isolated from Ganoderma selective medium. Two-month-old oil palm seedlings were artificially inoculated with G. boninense isolates (2, 4A, 5A, 5B, and 7A) sampled from Miri (Lambir) and Mukah (Sungai Meris and Sungai Liuk), Sarawak. The isolates were categorized into three groups: highly aggressive (4A and 5B), moderately aggressive (5A and 7A), and less aggressive (2). Isolate 5B was identified as the most aggressive, and it was the only one to result in seedling mortality. Out of the five vegetative growth parameters measured, only the bole size between treatments was not affected. The integration of both conventional and molecular approaches in disease confirmation allows for precise detection.

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An In-Depth Study of Phytopathogenic Ganoderma: Pathogenicity, Advanced Detection Techniques, Control Strategies, and Sustainable Management
Samantha C. Karunarathna, Nimesha M. Patabendige, Wenhua Lu, Suhail Asad, Kalani K. Hapuarachchi
Journal of Fungi.2024; 10(6): 414. CrossRef
Advancements in the nanodelivery of azole-based fungicides to control oil palm pathogenic fungi
Azren Aida Asmawi, Fatmawati Adam, Nurul Aini Mohd Azman, Mohd Basyaruddin Abdul Rahman
Heliyon.2024; 10(18): e37132. CrossRef
Characterizations of Ganoderma species causing basal stem rot disease in coconut tree
Umesh Sajjan, Manjunath Hubballi, Abhay K. Pandey, V. Devappa, H. P. Maheswarappa
3 Biotech.2024;[Epub] CrossRef

Structural and biochemical analysis of the PTPN4 PDZ domain bound to the C-terminal tail of the human papillomavirus E6 oncoprotein: Hye Seon Lee , Hye-Yeoung Yun , Eun-Woo Lee , Ho-Chul Shin , Seung Jun Kim , Bonsu Ku; J. Microbiol. 2022;60(4):395-401. Published online January 28, 2022; DOI: https://doi.org/10.1007/s12275-022-1606-1

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Abstract

High-risk genotypes of human papillomaviruses (HPVs) are directly implicated in various abnormalities associated with cellular hyperproliferation, including cervical cancer. E6 is one of two oncoproteins encoded in the HPV genome, which recruits diverse PSD-95/Dlg/ZO-1 (PDZ) domain-containing human proteins through its C-terminal PDZ-binding motif (PBM) to be degraded by means of the proteasome pathway. Among the three PDZ domain-containing protein tyrosine phosphatases, protein tyrosine phosphatase non-receptor type 3 (PTPN3) and PTPN13 were identified to be recognized by HPV E6 in a PBM-dependent manner. However, whether HPV E6 associates with PTPN4, which also has a PDZ domain and functions as an apoptosis regulator, remains undetermined. Herein, we present structural and biochemical evidence demonstrating the direct interaction between the PBM of HPV16 E6 and the PDZ domain of human PTPN4 for the first time. X-ray crystallographic structure determination and binding measurements using isothermal titration calorimetry demonstrated that hydrophobic interactions in which Leu158 of HPV16 E6 plays a key role and a network of intermolecular hydrogen bonds sustain the complex formation between PTPN4 PDZ and the PBM of HPV16 E6. In addition, it was verified that the corresponding motifs from several other highrisk HPV genotypes, including HPV18, HPV31, HPV33, and HPV45, bind to PTPN4 PDZ with comparable affinities, suggesting that PTPN4 is a common target of various pathogenic HPV genotypes.

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Bioinformatics Analysis of Human Papillomavirus 16 Integration in Cervical Cancer: Changes in MAGI-1 Expression in Premalignant Lesions and Invasive Carcinoma
Oscar Catalán-Castorena, Olga Lilia Garibay-Cerdenares, Berenice Illades-Aguiar, Rocio Castillo-Sánchez, Ma. Isabel Zubillaga-Guerrero, Marco Antonio Leyva-Vazquez, Sergio Encarnacion-Guevara, Eugenia Flores-Alfaro, Mónica Ramirez-Ruano, Luz del Carmen Al
Cancers.2024; 16(12): 2225. CrossRef
Comparative structural studies on Bovine papillomavirus E6 oncoproteins: Novel insights into viral infection and cell transformation from homology modeling and molecular dynamics simulations
Lucas Alexandre Barbosa de Oliveira Santos, Tales de Albuquerque Leite Feitosa, Marcus Vinicius de Aragão Batista
Genetics and Molecular Biology.2024;[Epub] CrossRef
Crystal Structures of Plk1 Polo-Box Domain Bound to the Human Papillomavirus Minor Capsid Protein L2-Derived Peptide
Sujin Jung, Hye Seon Lee, Ho-Chul Shin, Joon Sig Choi, Seung Jun Kim, Bonsu Ku
Journal of Microbiology.2023; 61(8): 755. CrossRef
The effects of HPV oncoproteins on host communication networks: Therapeutic connotations
Josipa Skelin, Ho Yin Luk, Dražan Butorac, Siaw Shi Boon, Vjekoslav Tomaić
Journal of Medical Virology.2023;[Epub] CrossRef
Structural analysis of human papillomavirus E6 interactions with Scribble PDZ domains
Bryce Z. Stewart, Sofia Caria, Patrick O. Humbert, Marc Kvansakul
The FEBS Journal.2023; 290(11): 2868. CrossRef
Viral manipulation of cell polarity signalling
Airah Javorsky, Patrick O. Humbert, Marc Kvansakul
Biochimica et Biophysica Acta (BBA) - Molecular Cell Research.2023; 1870(7): 119536. CrossRef
Mechanistic role of HPV-associated early proteins in cervical cancer: Molecular pathways and targeted therapeutic strategies
Rahul Bhattacharjee, Sabya Sachi Das, Smruti Sudha Biswal, Arijit Nath, Debangshi Das, Asmita Basu, Sumira Malik, Lamha Kumar, Sulagna Kar, Sandeep Kumar Singh, Vijay Jagdish Upadhye, Danish Iqbal, Suliman Almojam, Shubhadeep Roychoudhury, Shreesh Ojha, J
Critical Reviews in Oncology/Hematology.2022; 174: 103675. CrossRef

Diluted conventional media improve the microbial cultivability from aquarium seawater: Jing Sun , Jiazhen Guo , Qian Yang , Jie Huang; J. Microbiol. 2019;57(9):759-768. Published online August 3, 2019; DOI: https://doi.org/10.1007/s12275-019-9175-7

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Abstract

The cultivation of microbial species remains a primary challenge in microbiology and obtaining pure cultures is essential for the study of microbial physiology and function. When isolating microorganisms from aquaculture environments, Vibrio are the most dominate isolates on the media that are commonly used. In order to expand our ability to study microbial species, an easy-operation and low-cost medium that can reduce the interference of Vibrio strains and increase the cultivability of other bacteria is urgently needed. We compared viable cell counts on conventional media (CM; including Marine Agar 2216 and LB media) and diluted media (DM; including 1/10-Marine Agar 2216, 1/10-LB). We also assessed the diversity of cultivable microorganisms under high and low nutrient conditions by a plate-wash strategy coupled with high-throughput sequencing of the V4 hypervariable region of the 16S rRNA gene. The results show that microbial communities from DM, especially 1/10-Marine Agar 2216, are more diverse than those obtained from CM. Vibrio isolates were reduced on DM. PICRUSt analysis revealed that nutrient composition is a significant contributor to the diversity and function of the cultivable microbial communities. Bacteria grown on CM possess more pathogenic characteristics, whereas DM favors the growth of bacteria that have multiple metabolic functions. Collectively, our data provide strong evidence that dilution of CM influences the cultivability of bacteria from aquaculture seawater. It also supports that DM can expand the range of microbial species that can be cultivated. This study also provides insights for media design in microbial cultivation from aquaculture systems.

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Unexpected methane oxidation acceleration by two species of bacteria from the rainwater promoting Methylomonas sp. in the soil
Yuxuan Sang, Jia Tang, Oumei Wang, Qinqin Hao, Shiling Zheng, Fanghua Liu
Journal of Environmental Chemical Engineering.2024; 12(5): 113895. CrossRef
Glucose addition improves the culture performance of Pacific white shrimp by regulating the assembly of Rhodobacteraceae taxa in gut bacterial community
Pengsheng Dong, Haipeng Guo, Lei Huang, Demin Zhang, Kai Wang
Aquaculture.2023; 567: 739254. CrossRef
Reaching unreachables: Obstacles and successes of microbial cultivation and their reasons
Gabriela Kapinusova, Marco A. Lopez Marin, Ondrej Uhlik
Frontiers in Microbiology.2023;[Epub] CrossRef
The Metabolomics Changes in Luria–Bertani Broth Medium under Different Sterilization Methods and Their Effects on Bacillus Growth
Haifeng Wang, Juan Guo, Xing Chen, Hongxuan He
Metabolites.2023; 13(8): 958. CrossRef
Conjugative Transfer of Acute Hepatopancreatic Necrosis Disease-Causing pVA1-Type Plasmid Is Mediated by a Novel Self-Encoded Type IV Secretion System
Dehao Wang, Liying Wang, Dexi Bi, Jipeng Song, Guohao Wang, Ye Gao, Kathy F. J. Tang, Fanzeng Meng, Jingmei Xie, Fan Zhang, Jie Huang, Jianliang Li, Xuan Dong, Jennifer M. Auchtung, Songzhe Fu
Microbiology Spectrum.2022;[Epub] CrossRef
Culturomics of Bacteria from Radon-Saturated Water of the World’s Oldest Radium Mine
Gabriela Kapinusova, Kunal Jani, Tereza Smrhova, Petr Pajer, Irena Jarosova, Jachym Suman, Michal Strejcek, Ondrej Uhlik, Jing Han
Microbiology Spectrum.2022;[Epub] CrossRef
Diluted Luria-Bertani medium vs. sewage sludge as growth media: comparison of community structure and diversity in the culturable bacteria
Kazuo Yamamoto, Shotaro Toya, Sarah Sabidi, Yuki Hoshiko, Toshinari Maeda
Applied Microbiology and Biotechnology.2021; 105(9): 3787. CrossRef
Plant Broth- (Not Bovine-) Based Culture Media Provide the Most Compatible Vegan Nutrition for In Vitro Culturing and In Situ Probing of Plant Microbiota
Hend Elsawey, Sascha Patz, Rahma A. Nemr, Mohamed S. Sarhan, Mervat A. Hamza, Hanan H. Youssef, Mohamed R. Abdelfadeel, Hassan-Sibroe A. Daanaa, Mahmoud El-Tahan, Mohamed Abbas, Mohamed Fayez, Katja Witzel, Silke Ruppel, Nabil A. Hegazi
Diversity.2020; 12(11): 418. CrossRef

Characterization of Flavobacterium aquimarinum sp. nov., a halotolerant bacterium isolated from seawater: Sylvia Kristyanto , Tuan Manh Nguyen , Dhiraj Kumar Chaudhary , Sang-Seob Lee , Jaisoo Kim; J. Microbiol. 2018;56(5):317-323. Published online May 2, 2018; DOI: https://doi.org/10.1007/s12275-018-7454-3

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Abstract

A novel, aerobic, Gram-stain-negative, non-motile, non-spore forming, rod-shaped bacterium, designated strain Dol 15-39T, was isolated from a seawater sample near Geoje Island in the South Sea, Republic of Korea. The strain was found to be oxidase-negative and catalase-positive. The isolate was observed to grow at temperatures from 4 to 37°C, at salinities of up to 7%, and at pH levels from 6 to 9; moreover, it was not able to degrade starch, DNA, esculin, or tyrosine. Phylogenetic analysis based on 16S rRNA gene sequences showed that Dol 15-39T was most closely related to Flavobacterium jumunjinense HME7102T with a sequence similarity of 97.3%. However, the levels of DNA-DNA relatedness between Dol 15-39T and the most closely related species were much lower than 70%, confirming that they represented distinct genomic species. The genomic DNA G + C content of Dol 15-39T was calculated to be 32.6 mol%. MK-6 was the predominant respiratory quinine, while iso-C15:0 (25.0%), iso- C15:1 G (17.0%), and iso-C17:0 3-OH (10.4%) were the major cellular fatty acids. Phosphatidylethanolamine was identified as a major polar lipid, while various unidentified aminolipids and polar lipids were also detected. Based on polyphasic taxonomic data, Dol 15-39T represents a novel species of the genus Flavobacterium, for which the name F. aquimarinum sp. nov. is proposed. The type strain is accessible under the culture collection numbers (KEMB 9005-617T = JCM 31930T).

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Flavobacterium adhaerens sp. nov. and Flavobacterium maritimum sp. nov., two novel flavobacteria isolated from the Pearl River Estuary
Zi-Qi Peng, Jia-Ling Li, Zi-Wen Yang, Pan-Deng Wang, Dan-Yuan Guo, Xiao-Qing Luo, Qi-Qi Deng, Qi Li, Ting-Ting She, Wen-Jun Li
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Flavobacterium frigoritolerans sp. nov. and Flavobacterium shii sp. nov., isolated from glaciers on the Tibetan Plateau
Lei-Lei Yang, Hong-Can Liu, Yu-Hua Xin, Qing Liu
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Identification of Flavobacterium algoritolerans sp. nov. and Flavobacterium yafengii sp. nov., two novel members of the genus Flavobacterium
Ce-Ce Yin, Lei-Lei Yang, Yu-Hua Xin, Jian Ye, Qing Liu
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Ten Novel Species Belonging to the Genus Flavobacterium, Isolated from Freshwater Environments: F. praedii sp. nov., F. marginilacus sp. nov., F. aestivum sp. nov., F. flavigenum sp. nov., F. luteolum sp. nov., F. gelatinilyticum sp. nov., F. aquiphilum s
Hyunyoung Jo, Miri S. Park, Yeonjung Lim, Ilnam Kang, Jang-Cheon Cho
Journal of Microbiology.2023; 61(5): 495. CrossRef
Description of Flavobacterium cyclinae sp. nov. and Flavobacterium channae sp. nov., isolated from the intestines of Cyclina sinensis (Corb shell) and Channa argus (Northern snakehead)
Seomin Kang, Jae-Yun Lee, Jeong Eun Han, Yun-Seok Jeong, Do-Hun Gim, Jin-Woo Bae
Journal of Microbiology.2022; 60(9): 890. CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology.2018; 68(9): 2707. CrossRef

Arcobacter acticola sp. nov., isolated from seawater on the East Sea in South Korea: Sooyeon Park , Yong-Taek Jung , Sona Kim , Jung-Hoon Yoon; J. Microbiol. 2016;54(10):655-659. Published online September 30, 2016; DOI: https://doi.org/10.1007/s12275-016-6268-4

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Abstract

A Gram-stain-negative, facultative aerobic, non-flagellated, and rod-shaped bacterium, designated AR-13T, was isolated from a seawater on the East Sea in South Korea, and subjected to a polyphasic taxonomic study. Strain AR-13T grew optimally at 30°C, at pH 7.0–8.0 and in the presence of 0–0.5% (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences showed that strain AR-13T fell within the clade comprising the type strains of Arcobacter species, clustering coherently with the type strain of Arcobacter venerupis. Strain AR-13T exhibited 16S rRNA gene sequence similarity values of 98.1% to the type strain of A. venerupis and of 93.2–96.9% to the type strains of the other Arcobacter species. Strain AR-13T contained MK-6 as the only menaquinone and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), C16:0, C18:1 ω7c, and summed feature 2 (iso-C16:1 I and/or C14:0 3-OH) as the major fatty acids. The major polar lipids detected in strain AR-13T were phosphatidylethanolamine, phosphatidylglycerol, and one unidentified aminophospholipid. The DNA G+C content was 28.3 mol% and its mean DNA-DNA relatedness value with the type strain of A. venerupis was 21%. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain AR-13T is separated from recognized Arcobacter species. On the basis of the data presented, strain AR-13T is considered to represent a novel species of the genus Arcobacter, for which the name Arcobacter acticola sp. nov. is proposed. The type strain is AR-13T (=KCTC 52212T =NBRC 112272T).

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Authigenic carbonate and native sulfur formation in Messinian (upper Miocene) marine sediments: Sedimentological, petrographical and geochemical constraints
M. Natalicchio, D. Birgel, S. Giunti, L. Guibourdenche, L. Pellegrino, G. Aloisi, J. Peckmann, F. Dela Pierre
Marine and Petroleum Geology.2024; 165: 106889. CrossRef
Arcobacter roscoffensis sp. nov., a marine bacterium isolated from coastal seawater
Javier Pascual, Cendrella Lepleux, Anika Methner, Cathrin Spröer, Boyke Bunk, Jörg Overmann
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Widespread Multidrug Resistance of Arcobacter butzleri Isolated from Clinical and Food Sources in Central Italy
Claudia Gabucci, Giulia Baldelli, Giulia Amagliani, Giuditta Fiorella Schiavano, David Savelli, Ilaria Russo, Stefania Di Lullo, Giuliana Blasi, Maira Napoleoni, Francesca Leoni, Sara Primavilla, Francesca Romana Massacci, Giuliano Garofolo, Annalisa Petr
Antibiotics.2023; 12(8): 1292. CrossRef
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Rajani Ghaju Shrestha, Yasuhiro Tanaka, Eiji Haramoto
Water.2022; 14(8): 1266. CrossRef
RETRACTED: Improving tilapia (Oreochromis mossambicus) resistance to streptococcal disease by improving the gut biome through administration of the microorganisms Bacillus subtilis and Enterococcus faecalis
Xianhui Pan, Qian Liu, Luting Wen, Yin Huang, Huawei Ma, Yong Lin, Zhong Chen, Junqi Qin, Xuesong Du
Aquaculture Reports.2021; 20: 100636. CrossRef
A Systematic Analysis of Research on Arcobacter: Public Health Implications from a Food–Environment Interphase Perspective
Chidozie Declan Iwu, Temitope Cyrus Ekundayo, Anthony Ifeanyin Okoh
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Corey C Holt, Mark van der Giezen, Carly L Daniels, Grant D Stentiford, David Bass
The ISME Journal.2020; 14(2): 531. CrossRef
Aliarcobacter vitoriensis sp. nov., isolated from carrot and urban wastewater
Rodrigo Alonso, Cecilia Girbau, Irati Martinez-Malaxetxebarria, Alba Pérez-Cataluña, Nuria Salas-Massó, Jesús L. Romalde, María José Figueras, Aurora Fernandez-Astorga
Systematic and Applied Microbiology.2020; 43(4): 126091. CrossRef
Complete Genome Sequencing of FourArcobacterSpecies Reveals a Diverse Suite of Mobile Elements
William G Miller, Emma Yee, James L Bono, Howard Ochman
Genome Biology and Evolution.2020; 12(2): 3850. CrossRef
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Yukino Mizutani, Shunpei Iehata, Tetsushi Mori, Ryota Oh, Satoshi Fukuzaki, Reiji Tanaka
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Susana Ferreira, Ângelo Luís, Mónica Oleastro, Luísa Pereira, Fernanda C. Domingues
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Francesca Fanelli, Angela Di Pinto, Anna Mottola, Giuseppina Mule, Daniele Chieffi, Federico Baruzzi, Giuseppina Tantillo, Vincenzina Fusco
Frontiers in Microbiology.2019;[Epub] CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology.2019; 69(1): 5. CrossRef
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Alba Pérez-Cataluña, Nuria Salas-Massó, María José Figueras
International Journal of Systematic and Evolutionary Microbiology.2019; 69(11): 3326. CrossRef
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Alba Pérez-Cataluña, Luis Collado, Oscar Salgado, Violeta Lefiñanco, María J. Figueras
Frontiers in Microbiology.2018;[Epub] CrossRef
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William G. Miller, Emma Yee, James L. Bono, Jason Stajich
Microbiology Resource Announcements.2018;[Epub] CrossRef
Revisiting the Taxonomy of the Genus Arcobacter: Getting Order From the Chaos
Alba Pérez-Cataluña, Nuria Salas-Massó, Ana L. Diéguez, Sabela Balboa, Alberto Lema, Jesús L. Romalde, Maria J. Figueras
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Sofia Vicente-Martins, Mónica Oleastro, Fernanda C. Domingues, Susana Ferreira
Food Control.2018; 85: 107. CrossRef
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William G. Miller, Emma Yee, Steven Huynh, Craig T. Parker, David A. Baltrus
Microbiology Resource Announcements.2018;[Epub] CrossRef
Arcobacter canalis sp. nov., isolated from a water canal contaminated with urban sewage
Alba Pérez-Cataluña, Nuria Salas-Massó, María José Figueras
International Journal of Systematic and Evolutionary Microbiology.2018; 68(4): 1258. CrossRef
Comparative isolation and genetic diversity ofArcobactersp. from fish and the coastal environment
S. Rathlavath, S. Kumar, B.B. Nayak
Letters in Applied Microbiology.2017; 65(1): 42. CrossRef
Arcobacter: an emerging food-borne zoonotic pathogen, its public health concerns and advances in diagnosis and control – a comprehensive review
Thadiyam Puram Ramees, Kuldeep Dhama, Kumaragurubaran Karthik, Ramswaroop Singh Rathore, Ashok Kumar, Mani Saminathan, Ruchi Tiwari, Yashpal Singh Malik, Raj Kumar Singh
Veterinary Quarterly.2017; 37(1): 136. CrossRef
Occurrence, genetic diversity and antibiotic resistance of Arcobacter sp. in a dairy plant
S. Ferreira, M. Oleastro, F.C. Domingues
Journal of Applied Microbiology.2017; 123(4): 1019. CrossRef
Arcobacter haliotis sp. nov., isolated from abalone species Haliotis gigantea
Reiji Tanaka, Ilse Cleenwerck, Yukino Mizutani, Shunpei Iehata, Peter Bossier, Peter Vandamme
International Journal of Systematic and Evolutionary Microbiology.2017; 67(8): 3050. CrossRef
Occurrence of putative virulence genes onArcobacter butzleriisolated from three different environmental sites throughout the dairy chain
S. Piva, G.R. Gariano, P. Bonilauri, F. Giacometti, L. Decastelli, D. Florio, E. Massella, A. Serraino
Journal of Applied Microbiology.2017; 122(4): 1071. CrossRef
Antimicrobial susceptibility, virulence potential and sequence types associated with Arcobacter strains recovered from human faeces
Alba Pérez-Cataluña, Josepa Tapiol, Clara Benavent, Carolina Sarvisé, Frederic Gómez, Bruno Martínez, Margarida Terron-Puig, Gemma Recio, Angels Vilanova, Isabel Pujol, Frederic Ballester, Antonio Rezusta, María Jose Figueras
Journal of Medical Microbiology .2017; 66(12): 1736. CrossRef

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Aquimarina litoralis sp. nov., Isolated from a Coastal Seawater: You-Sung Oh , Hyung-Yeel Kahng , Young Sun Lee , Byoung-Jun Yoon , Sang-Bin Lim , Jae Sung Jung , Duck-Chul Oh , Dong-Heon Lee; J. Microbiol. 2010;48(4):433-437. Published online August 20, 2010; DOI: https://doi.org/10.1007/s12275-010-0088-8

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Abstract: A strictly aerobic, red-pigmented, non-motile, catalase- and oxidase-positive, Gram-staining-negative bacterium, designated strain CNURIC011T, was isolated from seawater off the coast of Jeju Island in Korea. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain CNURIC011T belongs to the genus Aquimarina in the family Flavobacteriaceae. 16S rRNA gene sequence analysis revealed that the close relatives of the novel strain are Aquimarina latercula ATCC 23177T, Aquimarina marcrocephali JAMB N27T, Aquimarina intermedia KMM 6258T, Aquimarina muelleri KMM 6020T, and Aquimarina brevivitae SMK-19T, with sequence similarities of 97.6, 96.6, 96.0, 95.6, and 94.2%, respectively. DNA-DNA hybridization revealed that the level of relatedness between strain CNURIC011T and Aquimarina latercula ATCC 23177T (=KCTC 2912T) was 4.9%. The DNA G+C content was 35.8 mol% and the major respiratory quinone was MK-6. The major fatty acids were iso-C15:0 (14.9%), C15:0 (13.9%), iso-C17:0 3-OH (12.6%), iso-C15:1 G (7.3%), and iso-C17:1 ω9c (7.2%). On the basis of phenotypic, phylogenetic, and genotypic data, strain CNURIC011T represents a novel species within the genus Aquimarina, for which the name Aquimarina litoralis sp. nov. is proposed. The type strain is CNURIC011T (=KCTC 22614T =JCM 15974T).

Gaetbulibacter jejuensis sp. nov., Isolated from Seawater: You-Sung Oh , Sang-Bin Lim , Hyung-Yeel Kahng , Byoung-Jun Yoon , Duck-Chul Oh , Jae-Ho Joa , Dong-Heon Lee; J. Microbiol. 2010;48(3):307-311. Published online June 23, 2010; DOI: https://doi.org/10.1007/s12275-010-9232-8

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Abstract: A novel marine bacterium, designated strain CNURIC014T was isolated from coastal seawater of Jeju Island in Korea. Strain CNURIC014T formed yellow colonies on marine agar 2216 and the cells were Gram-negative, non-motile, strictly aerobic, rod-shaped. The temperature, pH and NaCl ranges for growth were 15-37°C, pH 6.0-9.0 and 1.0-7.0% NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CNURIC014T was most closely related to Gaetbulibacter marinus and Gaetbulibacter saemankumensis, with a sequence similarity of 95.1% and 94.6%, respectively. The DNA G+C content of the strain was 33.1 mol% and the major respiratory quinone was menaquinone-6. The major cellular fatty acids were iso-C15:1 (22.8%), iso-C15:0 (18.8%), summed feature 3 (iso-C15:0 2-OH/C16:1 ω7c, 12.9%) and iso-C17:0 3-OH (11.5%). On the basis of phenotypic, phylogenetic, and genotypic data, strain CNURIC014T represents a novel species within the genus Geatbulibacter, for which the name Gaetbulibacter jejuensis sp. nov. is proposed. The type strain is CNURIC014T (=KCTC 22615T =JCM 15976T).

Antarcticimonas flava gen. nov., sp. nov., Isolated from Antarctic Coastal Seawater: Seung-Jo Yang , Hyun-Myung Oh , Sangyun Chung , Jang-Cheon Cho; J. Microbiol. 2009;47(5):517-523. Published online October 24, 2009; DOI: https://doi.org/10.1007/s12275-009-0225-4

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Abstract: A marine bacterium, designated IMCC3175T, was isolated from a seawater sample collected off the Antarctic coast. The strain was Gram-negative, obligately aerobic, carotenoid pigment-containing, and rod-shaped bacterium that divided by binary fission. As determined by 16S rRNA gene sequence comparisons, the most closely related genera were Formosa (92.9~93.3%), Bizionia (91.6~93.2%), Gaetbulibacter (91.5~92.8%), Sediminibacter (92.7%), Yeosuana (92.6%), Subsaximicrobium (92.1~92.2%), and Gillisia (89.5~92.2%). Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain formed a monophyletic clade together with the genera Sediminibacter and Subsaximicrobium but represented an independent phyletic line in this clade of the family Flavobacteriaceae. The DNA G+C content of the strain was 37.3 mol%. The major respiratory quinone was MK-6 and the predominant cellular fatty acids were C16:1 ω7c and/or iso-C15:0 2-OH (12.8%), anteiso-C15:0 (9.4%), and iso-C16:1 (9.4%). Low 16S rRNA gene sequence similarity, formation of a distinct phylogenetic branch, and several phenotypic characteristics, including a narrow range of temperature and salinity for growth, differentiated strain IMCC3175T from other related genera in the family Flavobacteriaceae. Therefore the name Antarcticimonas flava gen. nov., sp. nov. is proposed, with strain IMCC3175T (=KCCM 42713T =NBRC 103398T) as the type strain.

Prevalence of Tetracycline Resistance Genes in Greek Seawater Habitats: Theodora L. Nikolakopoulou , Eleni P. Giannoutsou , Adamandia A. Karabatsou , Amalia D. Karagouni; J. Microbiol. 2008;46(6):633-640. Published online December 24, 2008; DOI: https://doi.org/10.1007/s12275-008-0080-8

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Abstract: The presence of selected tetracycline resistance (TcR) genes was studied in different Greek seawater habitats, originated from wastewater treatment facilities, fishfarm, and coastal environments. The methods employed included assessment of the presence of twelve gene clusters by PCR, followed by hybridization with specific probes, in habitat extracted DNA, TcR bacteria, and exogenous isolated plasmids conferring TcR. The direct DNA-based analysis showed that tet(Α) and tet(K) genes were detected in all habitats, whilst tet(C) and tet(E) were present in fishfarm and wastewater effluent samples and tet(M) was detected in fishfarm and coastal samples. Resistance genes tet(A), tet(C), tet(K), and tet(M) were detected in 60 of the 89 isolates screened. These isolates were identified by fatty acid methyl ester analysis (FAME) as Stenotrophomonas, Acinetobacter, Pseudomonas, Bacillus, and Staphylococcus strains. The presence of the TcR genes in 15% of the bacterial isolates coincided with the presence of IncP plasmids. A habitat-specific dissemination of IncP alpha plasmids in wastewater effluent isolates and of IncP beta plasmids in fishfarm isolates was observed. Exogenous isolation demonstrated the presence of plasmids harbouring TcR genes in all the habitats tested. Plasmids were shown to carry tet(A), tet(C), tet(E), and tet(K) genes. It is concluded that TcR genes are widespread in the seawater habitats studied and often occur on broad host range plasmids that seem to be well disseminated in the bacterial communities.

Different Planctomycetes Diversity Patterns in Latitudinal Surface Seawater of the Open Sea and in Sediment: Qinglong Shu , Nianzhi Jiao; J. Microbiol. 2008;46(2):154-159. Published online June 11, 2008; DOI: https://doi.org/10.1007/s12275-008-0002-9

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Abstract: The 16S rRNA gene approach was applied to investigate the diversity of Planctomycetes in latitudinal surface seawater of the Western Pacific Ocean. The results revealed that the Pirellula-Rhodopirellula-Blastopirellula clade dominated the Planctomycetes community at all surface seawater sites while the minority genera Gemmata and Planctomyces were only found at sites H5 and H2 respectively. Although the clone frequency of the PRB clade seemed stable (between 83.3% and 94.1%) for all surface seawater sites, the retrieved Pirellula-Rhodopirellula-Blastopirellula clade presented unexpected diversity. Interestingly, low latitude seawater appeared to have higher diversity than mid-latitudes. ∫-LIBSHUFF software analysis revealed significantly different diversity patterns between in latitudinal surface seawater and in the sediment of South China Sea station M2896. Our data suggested that different hydrological and geographic features contributed to the shift of Planctomycetes diversity in marine environments. This is, to our knowledge, the first systematic assessment of Planctomycetes in latitudinal surface seawater of the open sea and the first comparison of diversity pattern between surface seawater and sediments and has broadened our understanding of Planctomycetes diversity in marine environments.

The Diversity of Multi-drug Resistance Profiles in Tetracycline-Resistant Vibrio Species Isolated from Coastal Sediments and Seawater: Farzana Ashrafi Neela , Lisa Nonaka , Satoru Suzuki; J. Microbiol. 2007;45(1):64-68.; DOI: https://doi.org/2489 [pii]

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Abstract: In this study we examined the multi-drug resistance profiles of the tetracycline (TC) resistant genus Vibrio to determine its susceptibility to two β-lactams, ampicillin (ABPC), and mecillinam (MPC), as well as to macrolide, erythromycin (EM). The results showed various patterns of resistance among strains that were isolated from very close geographical areas during the same year, suggesting diverse patterns of drug resistance in environmental bacteria from this area. In addition, the cross-resistance patterns suggested that the resistance determinants among Vibrio spp. are acquired differently within the sediment and seawater environments.

Bacterial Diversity of Culturable Isolates from Seawater and a Marine Coral, Plexauridae sp., near Mun-Sum, Cheju-Island: Jung-Hyun Lee , Hyun-Hee Shin , Deuk-Soo Lee , Kae Kyung Kwon , Sang-Jin Kim , Hong Kum Lee; J. Microbiol. 1999;37(4):193-199.

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Abstract: Fifty-eight strains showing different colony morphological characteristics on various media were isolated from marine coral (Plexauridae sp.) and ambient seawater near Mun-Sum, Cheju-Island in 1998. Bacterial diversity was studies by phylogenetic analysis of the partial 16S rRNA gene sequences. All isolates representing the bacterial domain included affiliates of the high G+C (59%) and los G+C (3%) subdivision of Gram positive bacteria, and the alpha (33%) and gamma (5%) subdivision of the Proteobacteria. The 16S rDNA sequence similarity of the isolates was in the 88.3 to 100% range (average, 95.6%) to reported sequence data. In the comparison of the isolates from marine coarl and ambient seawater, more diverse groups belonging to alpha-proteobacteria were preferentially obtained from seawater.

Freezing Seawater for the Long-term Storage of Bacterial Cells for Microscopic Enumeration: Jung-Ho Hyun , Eun-Jin Yang; J. Microbiol. 2003;41(3):262-265.

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Abstract: Although enumerating bacterial cells is a fundamental step in understanding microbial ecosystems in marine environments, substantial decrease in bacterial counts with increasing sample storage time hampers the accurate estimation of bacterial biomass. We compared the variations in bacterial cell numbers caused by freezing and thawing of sample bottles or slides. Bacterial counts of seawater samples frozen only once in a sampling bottle yielded approximately 95% of the original numbers after 90 days, whereas 80% of the original count was obtained for samples prepared on slides. Only 67% and 58% of the original counts were recovered in samples repeatedly frozen and thawed in bottles or on slides, respectively. The results indicated that freezing a seawater sample in a bottle increased the consistency of the epifluorescence microscopic enumeration of bacterial cells.

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