Journal of Microbiology

Journal Articles

Gut Microbiota Dysbiosis Facilitates Susceptibility to Bloodstream Infection: Xiaomin Lin, Chun Lin, Xin Li, Fen Yao, Xiaoling Guo, Meimei Wang, Mi Zeng, Yumeng Yuan, Qingdong Xie, Xudong Huang, Xiaoyang Jiao; J. Microbiol. 2024;62(12):1113-1124. Published online December 2, 2024; DOI: https://doi.org/10.1007/s12275-024-00190-5

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Abstract: To study the role of intestinal flora in the development of bloodstream infections (BSIs). 42 patients and 19 healthy controls (HCs) were screened into the study and their intestinal flora was measured by 16S rRNA gene sequencing. The bacterial diversity was significantly lower in the BSI group compared with that in the HCs (P < 0.001), and beta diversity was significantly differentiated between the two groups (PERMANOVA, P = 0.001). The four keystone species [Roseburia, Faecalibacterium, Prevotella, and Enterococcus (LDA > 4)] differed significantly between the two groups. Dysbiosis of fecal microbial ecology is a common condition present in patients with BSI. The proliferation of certain pathogens or reduction of SCFA-producing bacteria would cause susceptibility to BSI.

The β‑Lactamase Activity at the Community Level Confers β‑Lactam Resistance to Bloom‑Forming Microcystis aeruginosa Ce: Yerim Park , Wonjae Kim , Minkyung Kim , Woojun Park; J. Microbiol. 2023;61(9):807-820. Published online October 18, 2023; DOI: https://doi.org/10.1007/s12275-023-00082-0

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Many freshwater cyanobacteria, including Microcystis aeruginosa, lack several known antibiotic resistance genes; however, both axenic and xenic M. aeruginosa strains exhibited high antibiotic resistance against many antibiotics under our tested concentrations, including colistin, trimethoprim, and kanamycin. Interestingly, axenic PCC7806, although not the xenic NIBR18 and NIBR452 strains, displayed susceptibility to ampicillin and amoxicillin, indicating that the associated bacteria in the phycosphere could confer such antibiotic resistance to xenic strains. Fluorescence and scanning electron microscopic observations revealed their tight association, leading to possible community-level β-lactamase activity. Combinatory treatment of ampicillin with a β-lactamase inhibitor, sulbactam, abolished the ampicillin resistance in the xenic stains. The nitrocefin-based assay confirmed the presence of significant community-level β-lactamase activity. Our tested low ampicillin concentration and high β-lactamase activity could potentially balance the competitive advantage of these dominant species and provide opportunities for the less competitive species, thereby resulting in higher bacterial diversity under ampicillin treatment conditions. Non-PCR-based metagenome data from xenic NIBR18 cultures revealed the dominance of blaOXArelated antibiotic resistance genes followed by other class A β-lactamase genes (AST-1 and FAR-1). Alleviation of ampicillin toxicity could be observed only in axenic PCC7806, which had been cocultured with β-lactamase from other freshwater bacteria. Our study suggested M. aeruginosa develops resistance to old-class β-lactam antibiotics through altruism, where associated bacteria protect axenic M. aeruginosa cells.

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Sustainable control of Microcystis aeruginosa, a harmful cyanobacterium, using Selaginella tamariscina extracts
Wonjae Kim, Yerim Park, Minkyung Kim, Yeji Cha, Jaejoon Jung, Che Ok Jeon, Woojun Park
Ecotoxicology and Environmental Safety.2024; 277: 116375. CrossRef
Microcystis abundance is predictable through ambient bacterial communities: A data-oriented approach
Mingyeong Kang, Dong-Kyun Kim, Ve Van Le, So-Ra Ko, Jay Jung Lee, In-Chan Choi, Yuna Shin, Kyunghyun Kim, Chi-Yong Ahn
Journal of Environmental Management.2024; 368: 122128. CrossRef
Enhanced mechanical properties of living and regenerative building materials by filamentous Leptolyngbya boryana
Yongjun Son, Jihyeon Min, Indong Jang, Jiyoon Park, Chongku Yi, Woojun Park
Cell Reports Physical Science.2024; 5(8): 102098. CrossRef
Food Webs and Feedbacks: The Untold Ecological Relevance of Antimicrobial Resistance as Seen in Harmful Algal Blooms
Aabir Banerji, Nichole E. Brinkman, Benjamin Davis, Alison Franklin, Michael Jahne, Scott P. Keely
Microorganisms.2024; 12(11): 2121. CrossRef
Extensive Genomic Rearrangement of Catalase-Less Cyanobloom-Forming Microcystis aeruginosa in Freshwater Ecosystems
Minkyung Kim, Jaejoon Jung, Wonjae Kim, Yerim Park, Che Ok Jeon, Woojun Park
Journal of Microbiology.2024; 62(11): 933. CrossRef
Biological and Chemical Approaches for Controlling Harmful Microcystis Blooms
Wonjae Kim, Yerim Park, Jaejoon Jung, Che Ok Jeon, Masanori Toyofuku, Jiyoung Lee, Woojun Park
Journal of Microbiology.2024; 62(3): 249. CrossRef
Alleviation of H2O2 toxicity by extracellular catalases in the phycosphere of Microcystis aeruginosa
Yerim Park, Wonjae Kim, Yeji Cha, Minkyung Kim, Woojun Park
Harmful Algae.2024; 137: 102680. CrossRef

Diversity and Dynamics of Marine Arenicolous Fungi in Three Seasides of the Korean Peninsula: Jun Won Lee , Chang Wan Seo , Wonjun Lee , Ji Seon Kim , Ki Hyeong Park , Yoonhee Cho , Young Woon Lim; J. Microbiol. 2023;61(1):63-82. Published online January 30, 2023; DOI: https://doi.org/10.1007/s12275-023-00011-1

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Abstract

Various arenicolous fungal species have been detected from the beach sand in the coastal area. However, little has been revealed regarding their distribution and dynamics. To investigate the overall diversity of marine arenicolous fungi (MAFs) in Korea and whether the composition of MAFs is affected by ocean currents, we isolated and analyzed the fungal community from the western, southern, and eastern seasides of the Korean Peninsula. In total, 603 strains were isolated and identified as 259 species based on appropriate molecular markers for each genus (ITS, BenA, CaM, tef1, and act). The composition of MAFs showed differences among the seasides. Our results indicate that many MAFs inhabit the beach sand on the Korean Peninsula, and the composition of MAFs is also affected by ocean currents flowing along each coast.

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The genus Peniophora (Russulales, Basidiomycota) from Patagonia revisited
Mario Rajchenberg, Andrés de Errasti, Sergio Pérez Gorjón
Mycological Progress.2024;[Epub] CrossRef
Contributions to the Inocybe umbratica–paludinella (Agaricales) Group in China: Taxonomy, Species Diversity, and Molecular Phylogeny
Xin Chen, Wen-Jie Yu, Tolgor Bau, P. Brandon Matheny, Egon Horak, Yu Liu, Li-Wu Qin, Li-Ping Tang, Yu-Peng Ge, Tie-Zhi Liu, Yu-Guang Fan
Journal of Fungi.2024; 10(12): 893. CrossRef
Long-Term Investigation of Marine-Derived Aspergillus Diversity in the Republic of Korea
Jun Won Lee, Wonjun Lee, Rekhani Hansika Perera, Young Woon Lim
Mycobiology.2023; 51(6): 436. CrossRef

Flaviflexus equikiangi sp. nov. isolated from faeces of Equus kiang (Tibetan wild ass) and carrying a class 1 integron gene cassette in its genome: Caixin Yang , Xingxing Lian , Yanpeng Cheng , Yifan Jiao , Jing Yang , Kui Dong , Shan Lu , Xin-He Lai , Dong Jin , Han Zheng , Ji Pu , Suping Wang , Liyun Liu , Jianguo Xu; J. Microbiol. 2022;60(6):585-593. Published online April 18, 2022; DOI: https://doi.org/10.1007/s12275-022-1673-3

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Abstract: Two Gram-stain-positive, catalase-negative, non-spore-forming, cocci-shaped strains (dk850T and JY899) were isolated from the feces of Equus kiang in the Qinghai-Tibet Plateau of China. 16S rRNA gene sequence-based phylogenetic analyses showed that strains dk850T and JY899 belong to the genus Flaviflexus, closest to F. salsibiostraticola KCTC 33148T, F. ciconiae KCTC 49253T and F. huanghaiensis H5T. The DNA G + C content of strain dk850T was 62.9%. The digital DNADNA hybridization values of strain dk850T with the closely related species were below the 70% threshold for species demarcation. The two strains grew best at 28°C on brain heart infusion (BHI) agar with 5% sheep blood. All strains had C18:1ω9c and C16:0 as the major cellular fatty acids. MK-9(H4) was the major menaquinone in strain dk850T. The major polar lipids included diphosphatidylglycerol and an unidentified phospholipid. Strains dk850T and JY899 were identified as carrying a class 1 integron containing the aminoglycoside resistance gene aadA11, both strains were resistant to spectinomycin and streptomycin. Based on several lines of evidence from phenotypic and phylogenetic analyses, strains dk850T and JY899 represent a novel species of the genus Flaviflexus, for which the name Flaviflexus equikiangi sp. nov. is proposed. The type strain is dk850T (= CGMCC 1.16593T = JCM 33598T).

Description of Microbacterium luteum sp. nov., Microbacterium cremeum sp. nov., and Microbacterium atlanticum sp. nov., three novel C50 carotenoid producing bacteria: Fuquan Xie , Siwen Niu , Xihuang Lin , Shengxiang Pei , Li Jiang , Yun Tian , Gaiyun Zhang; J. Microbiol. 2021;59(10):886-897. Published online September 7, 2021; DOI: https://doi.org/10.1007/s12275-021-1186-5

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Abstract

We have identified three Microbacterium strains, A18JL200T, NY27T, and WY121T, that produce C50 carotenoids. Taxonomy shows they represent three novel species. These strains shared < 98.5% 16S rRNA gene sequence identity with each other and were closely related to Microbacterium aquimaris JCM 15625T, Microbacterium yannicii JCM 18959T, Microbacterium ureisolvens CFH S00084T, and Microbacterium hibisci CCTCC AB 2016180T. Digital DNA-DNA hybridization (dDDH) values and average nucleotide identity (ANI) showed differences among the three strains and from their closest relatives, with values ranging from 20.4% to 34.6% and 75.5% to 87.6%, respectively. These values are below the threshold for species discrimination. Both morphology and physiology also differed from those of phylogenetically related Microbacterium species, supporting that they are indeed novel species. These strains produce C50 carotenoids (mainly decaprenoxanthin). Among the three novel species, A18JL200T had the highest total yield in carotenoids (6.1 mg/L or 1.2 mg/g dry cell weight). Unusual dual isoprenoid biosynthetic pathways (methylerythritol phosphate and mevalonate pathways) were annotated for strain A18JL200T. In summary, we found strains of the genus Microbacterium that are potential producers of C50 carotenoids, but their genome has to be investigated further.

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Identification, evaluation, control of yellow-causing bacteria and their influence on the quality of high moisture rice-based food
Sijie Zhang, Lin Ou, Cuiping Yi, Qiutao Xie, Yang Shan
Food Control.2025; 168: 110887. CrossRef
Chlamydomonas reinhardtii and Microbacterium forte sp. nov., a mutualistic association that favors sustainable hydrogen production
Neda Fakhimi, María Jesus Torres, Emilio Fernández, Aurora Galván, Alexandra Dubini, David González-Ballester
Science of The Total Environment.2024; 913: 169559. CrossRef
Discovery of a new bacterium, Microbacterium betulae sp. nov., in birch wood associated with hypersensitivity pneumonitis in woodworkers
Mariola Paściak, Krzysztof J. Pawlik, Dariusz Martynowski, Łukasz Łaczmański, Jarosław Ciekot, Bogumiła Szponar, Angelina Wójcik‐Fatla, Barbara Mackiewicz, Ewelina Farian, Grażyna Cholewa, Alicja Cholewa, Jacek Dutkiewicz
Environmental Microbiology Reports.2024;[Epub] CrossRef
Microbacterium aquilitoris sp. nov. and Microbacterium gwkjiense sp. nov., isolated from beach
Soon Dong Lee, Hong Lim Yang, Ji-Sun Kim, In Seop Kim
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Microbacterium algihabitans sp. nov., Microbacterium phycohabitans sp. nov., and Microbacterium galbum sp. nov., isolated from dried beach seaweeds
Soon Dong Lee, Hong Lim Yang, In Seop Kim
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Association between the gut microbiome and carotenoid plumage phenotype in an avian hybrid zone
Marcella D. Baiz, Andrew W. Wood, David P. L. Toews
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Description of Microbacterium dauci sp. nov., a plant growth hormone indoleacetic acid-producing and nitrogen-fixing bacterium isolated from carrot rhizosphere soil
Jiawen Zheng, Yunyu Liao, Yang Li, Dongsheng Li, Yaping Sun, Zijun Xiao
Archives of Microbiology.2024;[Epub] CrossRef
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Jian Xiao, Tian Liang, Shangdong Yang, Hongwei Tan
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Evaluation of Various Escherichia coli Strains for Enhanced Lycopene Production
Jun Ren, Junhao Shen, Thi Duc Thai, Min-gyun Kim, Seung Ho Lee, Wonseop Lim, Dokyun Na
Journal of Microbiology and Biotechnology.2023; 33(7): 973. CrossRef
Effects of flavonoids on membrane adaptation of food-associated bacteria
Maria Linden, Alexander Flegler, Michelle M. Feuereisen, Fabian Weber, André Lipski, Andreas Schieber
Biochimica et Biophysica Acta (BBA) - Biomembranes.2023; 1865(4): 184137. CrossRef
Four new Microbacterium species isolated from seaweeds and reclassification of five Microbacterium species with a proposal of Paramicrobacterium gen. nov. under a genome-based framework of the genus Microbacterium
Soon Dong Lee, Hong Lim Yang, In Seop Kim
Frontiers in Microbiology.2023;[Epub] CrossRef
Microbacterium Cluster EA Bacteriophages: Phylogenomic Relationships and Host Range Predictions
Mark Milhaven, Cyril J. Versoza, Aman Garg, Lindsey Cai, Sanjana Cherian, Kamalei Johnson, Kevin Salas Perez, Madison Blanco, Jackelyn Lobatos, Corinne Mitra, Maria Strasser, Susanne P. Pfeifer
Microorganisms.2023; 11(1): 170. 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

Hahyoungchilella caricis gen. nov., sp. nov., isolated from a rhizosphere mudflat of a halophyte (Carex scabrifolia), transfer of Thioclava arenosa Thongphrom et al. 2017 to Pseudothioclava as Pseudothioclava arenosa gen. nov., comb. nov. and proposal of Thioclava electrotropha Chang et al. 2018: Young-Ju Kim , Soon Dong Lee; J. Microbiol. 2019;57(12):1048-1055. Published online September 25, 2019; DOI: https://doi.org/10.1007/s12275-019-9260-y

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Abstract

A Gram-stain-negative, strictly aerobic, marine bacterium, designated GH2-2T, was isolated from a rhizosphere mudflat of a halophyte (Carex scabrifolia) in Gangwha Island, the Republic of Korea. The cells of the organism were oxidase- positive, catalase-positive, flagellated, short rods that grew at 10–40°C, pH 4–10, and 0–13% (w/v) NaCl. The predominant ubiquinone was Q-10. The major polar lipids were phosphatidylcholine, phosphatidylethanolamine, and phosphatidylglycerol. The major fatty acid is C18:1. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the novel isolate formed an independent lineage at the base of the radiation encompassing members of the genus Thioclava, except for Thioclava arenosa. The closest relatives were T. nitratireducens (96.03% sequence similarity) and T. dalianensis (95.97%). The genome size and DNA G+C content were 3.77 Mbp and 59.6 mol%, respectively. Phylogenomic analysis supported phylogenetic distinctness based on 16S rRNA gene sequences. Average nucleotide identity values were 73.6–74.0% between the novel strain and members of the genus Thioclava. On the basis of data obtained from a polyphasic approach, the strain GH2-2T (= KCTC 62124T = DSM 105743T) represents a novel species of a new genus for which the name Hahyoungchilella caricis gen. nov., sp. nov. is proposed. Moreover, the transfer of Thioclava arenosa Thongphrom et al. 2017 to Pseudothioclava gen. nov. as Pseudothioclava arenosa comb. nov. is also proposed. Finally, Thioclava electrotropha Chang et al. 2018 is proposed to be a later heterosynonym of Thioclava sediminum Liu et al. 2017.

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Genome-based analysis of the family Paracoccaceae and description of Ostreiculturibacter nitratireducens gen. nov., sp. nov., isolated from an oyster farm on a tidal flat
Zhaobin Huang, Meiqin Li, Aharon Oren, Qiliang Lai
Frontiers in Microbiology.2024;[Epub] CrossRef
Sustainable agricultural management of saline soils in arid and semi-arid Mediterranean regions through halophytes, microbial and soil-based technologies
Salvadora Navarro-Torre, Pedro Garcia-Caparrós, Amaia Nogales, Maria Manuela Abreu, Erika Santos, Ana Lúcia Cortinhas, Ana Delaunay Caperta
Environmental and Experimental Botany.2023; 212: 105397. CrossRef
Notification of changes in taxonomic opinion previously published outside the IJSEM
Aharon Oren, George Garrity
International Journal of Systematic and Evolutionary Microbiology .2020; 70(7): 4061. CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George Garrity
International Journal of Systematic and Evolutionary Microbiology .2020; 70(7): 4043. CrossRef

Martelella lutilitoris sp. nov., isolated from a tidal mudflat: Young-Ju Kim , Soon Dong Lee; J. Microbiol. 2019;57(11):976-981. Published online September 25, 2019; DOI: https://doi.org/10.1007/s12275-019-9259-4

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Abstract

A novel, Gram-stain-negative, marine bacterium, designated GH2-6T, was isolated from a rhizosphere mudflat of a halophyte (Carex scabrifolia) collected in Gangwha Island, the Republic of Korea. The cells of the organism were strictly aerobic, oxidase- and catalase-positive, non-flagellated rods. Growth occurred at 20–45°C, pH 5–10, and 0.5–9 (w/v) NaCl. The requirement of Na+ for growth (0.5–3%) was observed. The major respiratory quinone was Q-10. The major polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an aminolipid and a glycolipid. The predominant fatty acids were C18:1 ω7c, C18:0, C16:0, C19:0 cyclo ω8c, C18:1 ω7c 11-methyl and summed feature 2 (C14:0 3-OH and/or C16:1 iso I). The genome size was 4.45 Mb and the G+C content of the genomic DNA was 61.9 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain GH2-6T belonged to genus Martelella and formed a tight cluster with M. radicis BM5-7T and M. endophytica YC6887T. Levels of 16S rRNA gene sequence similarity between the novel isolate and members of the genus were 99.3–95.5%, but strain GH2-6T possessed an extended loop (49 nucleotides in length) between positions 187 and 213 of the 16S rRNA gene sequence (E. coli numbering). DDH values in vitro between the novel isolate and the closest relatives were 23.2±12.8 – 46.3±5.2%. On the basis of polyphasic data presented in this study, the type strain GH2-6T (= KACC 19403T = KCTC 62125T = NBRC 113212T) represents a novel species of the genus Martelella for which the name Martelella lutilitoris sp. nov. is proposed.

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Genomic Analysis of Halotolerant Bacterial Strains Martelella soudanensis NC18T and NC20
Jung-Yun Lee, Dong-Hun Kim
Journal of Microbiology and Biotechnology.2022; 32(11): 1427. CrossRef
Description of Polaribacter batillariae sp. nov., Polaribacter cellanae sp. nov., and Polaribacter pectinis sp. nov., novel bacteria isolated from the gut of three types of South Korean shellfish
Su-Won Jeong, Jeong Eun Han, June-Young Lee, Ji-Ho Yoo, Do-Yeon Kim, In Chul Jeong, Jee-Won Choi, Yun-Seok Jeong, Jae-Yun Lee, So-Yeon Lee, Euon Jung Tak, Hojun Sung, Hyun Sik Kim, Pil Soo Kim, Dong-Wook Hyun, Jin-Woo Bae
Journal of Microbiology.2022; 60(6): 576. CrossRef
Martelella alba sp. nov., isolated from mangrove rhizosphere soil within the Beibu Gulf
Mi Li, Chenghai Gao, Yuyao Feng, Kai Liu, Pei Cao, Yonghong Liu, Xiangxi Yi
Archives of Microbiology.2021; 203(4): 1779. CrossRef
Insights from comparative proteomic analysis into degradation of phenanthrene and salt tolerance by the halophilic Martelella strain AD-3
Xin Chen, Weiwei Wang, Haiyang Hu, Hongzhi Tang, Yongdi Liu, Ping Xu, Kuangfei Lin, Changzheng Cui
Ecotoxicology.2021; 30(7): 1499. CrossRef
Duganella aceris sp. nov., isolated from tree sap and proposal to transfer of Rugamonas aquatica and Rugamonas rivuli to the genus Duganella as Duganella aquatica comb. nov., with the emended description of the genus Rugamonas
Dabin Jeon, In Seop Kim, Hanna Choe, Ji-Sun Kim, Soon Dong Lee
Archives of Microbiology.2021; 203(6): 2843. CrossRef
Characterization of Martelella soudanensis sp. nov., Isolated from a Mine Sediment
Jung-Yun Lee, Dong-Hun Lee, Dong-Hun Kim
Microorganisms.2021; 9(8): 1736. CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George Garrity
International Journal of Systematic and Evolutionary Microbiology .2020; 70(7): 4043. CrossRef
Hahyoungchilella caricis gen. nov., sp. nov., isolated from a rhizosphere mudflat of a halophyte (Carex scabrifolia), transfer of Thioclava arenosa Thongphrom et al. 2017 to Pseudothioclava as Pseudothioclava arenosa gen. nov., comb. nov. and proposal of
Young-Ju Kim, Soon Dong Lee
Journal of Microbiology.2019; 57(12): 1048. CrossRef

Comparative portrayal of ocular surface microbe with and without dry eye: ZhenHao Li , Yufang Gong , ShuZe Chen , SiQi Li , Yu Zhang , HuiMin Zhong , ZhouCheng Wang , YiFan Chen , QiXin Deng , YuTing Jiang , LiYing Li , Min Fu , GuoGuo Yi; J. Microbiol. 2019;57(11):1025-1032. Published online August 28, 2019; DOI: https://doi.org/10.1007/s12275-019-9127-2

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Abstract

To compare the ocular surface (OS) microbial communities and diversity between dry eye (DE) and non-DE (NDE). Furthermore, we compared meibomian gland dysfunction (MGD) and non-MGD (NMGD) among DE subjects. The V3-V4 region of 16S rRNA gene high-throughput sequencing was performed in the conjunctival swab samples to investigate the composition of the OS bacterial community in DE (n=35) and NDE (n=54) and compared the composition of MGD (n=25) and NMGD (n=10) among DE subjects. Deep sequencing of OS 16S rDNA from DE (n=35) and NDE (n=54) demonstrated great a difference in alpha and beta diversity between the OS bacterial flora (P < 0.05). The similar OS microbial structures were shown at the phylum and genus levels by bioinformatics analysis between them, and in LEfSe (linear discriminant analysis effect size) analysis, Bacteroidia and Bacteroidetes were enriched in DE, while Pseudomonas was plentiful in NDE (linear discriminant analysis [LDA] > 4.0). Among the DE group, there was no significant difference in α and β diversity between MGD and NMGD (P > 0.05). Surprisingly, Bacilli was the dominant microbe in MGD, and Bacteroidetes was the superior bacteria in NMGD among DE subjects (LDA > 4.0). Different diversity of OS bacteria composition between DE and NDE and the altered diversity of OS bacteria may play an important role in DE. Moreover, the lower dominance of OS bacteria in DE may be associated with the occurrence and development of DE. Although there was no significant difference in alpha and beta analysis, the OS dominant microbe between MGD and NMGD among DE was different.

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B. Barrera, A. Bustamante, M. Marín-Cornuy, P. Aguila-Torres
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Virginie G Peter, Sophia C Morandi, Elio L Herzog, Martin S Zinkernagel, Denise C Zysset-Burri
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Mesorhizobium denitrificans sp. nov., a novel denitrifying bacterium isolated from sludge: Muhammad Zubair Siddiqi , Ngo Thi Phuong Thao , Gyumin Choi , Dae-Cheol Kim , Young-Woo Lee , Sang Young Kim , Ji-Hyang Wee , Wan-Taek Im; J. Microbiol. 2019;57(4):238-242. Published online March 30, 2019; DOI: https://doi.org/10.1007/s12275-019-8590-0

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Abstract

A Gram-stain-negative, non-spore-forming, facultative, rodshaped bacterium (designated LA-28T) was isolated from a sludge sample from a wastewater treatment plant in Hanam city, Republic of Korea. On the basis of 16S rRNA gene sequencing, strain LA-28T clustered with species of the genus Mesorhizobium and appeared closely related to M. jarvisii LMG 28313T (96.8%), M. waimense ICMP 19557T (96.7%), and M. huakuii LMG 14107T (96.7%). Growth occurs at 18– 40°C on R2A medium in the presence of 1–4% NaCl (w/v) and at pH 6–8. The DNA G+C content was 61.2 mol%, and the predominant quinone was ubiquinone-10 (Q-10). The major cellular fatty acids (> 5%) were C16:0, C19:0 ω8c cyclo, C18:1 ω7c 11-methyl, and C18:1 ω7c and/or C18:1 ω6c (summed feature 8). Major polar lipids were phosphatidylglycerol (PG), phosphatidylethanolamine (PE), phosphatidyl-N-methylethanolamine (PME), and phosphatidylcholine (PC). Physiological and biochemical characteristics indicated that strain LA-28T represents a novel species of the genus Mesorhizobium, for which the name Mesorhizobium denitrificans sp. nov. is proposed. The type strain is LA-28T (= KACC 19675T = LMG 30806T).

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Lysobacter panacihumi sp. nov., isolated from ginseng cultivated soil: Yue Huo , Jong-Pyo Kang , Joon Hurh , Yaxi Han , Jong-Chan Ahn , Ramya Mathiyalagan , Chunhong Piao , Deok-Chun Yang; J. Microbiol. 2018;56(10):748-752. Published online September 28, 2018; DOI: https://doi.org/10.1007/s12275-018-8202-4

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Abstract

A Gram-negative, non-motile, aerobic, catalase-, and oxidasepositive bacterial strain, designated DCY117T, was isolated from ginseng cultivated soil in Gochang-gun, Republic of Korea, and was characterized taxonomically using a multifaceted approach. 16S rRNA gene sequence analysis revealed that strain DCY117T showed highest similarity to Lysobacter ruishenii CTN-1T (95.3%). Phylogenetic analysis revealed that closely related relatives of strain DCY117T were L. aestuarii S2-CT (95.1%), L. daejeonensis GH1-9T (95.0%), and L. caeni BUT-8T (94.9%). Diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), and phosphatidylethanolamine (PE) were the major polar lipids of strain DCY117T. The major isoprenoid quinone was Q-8. The major cellular fatty acids of strain DCY117T were iso-C15:0, iso-C16:0, and summed feature 9 (comprising iso-C17:1 ω9c and/or 10-methyl-C16:0). Genomic DNA G + C content was 61.8 mol%. On the basis of our findings, strain DCY117T is a novel species in the genus Lysobacter. We propose the name Lysobacter panacihumi sp. nov., and the type strain is DCY117T (= KCTC 62019T = JCM 32168T).

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Cultivable butyrate-producing bacteria of elderly Japanese diagnosed with Alzheimer’s disease: Thi Thuy Tien Nguyen , Yuta Fujimura , Iyo Mimura , Yusuke Fujii , Ngoc Luong Nguyen , Kensuke Arakawa , Hidetoshi Morita; J. Microbiol. 2018;56(10):760-771. Published online August 22, 2018; DOI: https://doi.org/10.1007/s12275-018-8297-7

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Abstract

The group of butyrate-producing bacteria within the human gut microbiome may be associated with positive effects on memory improvement, according to previous studies on dementia- associated diseases. Here, fecal samples of four elderly Japanese diagnosed with Alzheimer’s disease (AD) were used to isolate butyrate-producing bacteria. 226 isolates were randomly picked, their 16S rRNA genes were sequenced, and assigned into sixty OTUs (operational taxonomic units) based on BLASTn results. Four isolates with less than 97% homology to known sequences were considered as unique OTUs of potentially butyrate-producing bacteria. In addition, 12 potential butyrate-producing isolates were selected from the remaining 56 OTUs based on scan-searching against the PubMed and the ScienceDirect databases. Those belonged to the phylum Bacteroidetes and to the clostridial clusters I, IV, XI, XV, XIVa within the phylum Firmicutes. 15 out of the 16 isolates were indeed able to produce butyrate in culture as determined by high-performance liquid chromatography with UV detection. Furthermore, encoding genes for butyrate formation in these bacteria were identified by sequencing of degenerately primed PCR products and included the genes for butyrate kinase (buk), butyryl-CoA: acetate CoAtransferase (but), CoA-transferase-related, and propionate CoA-transferase. The results showed that eight isolates possessed buk, while five isolates possessed but. The CoA-transfer- related gene was identified as butyryl-CoA:4-hydroxybutyrate CoA transferase (4-hbt) in four strains. No strains contained the propionate CoA-transferase gene. The biochemical and butyrate-producing pathways analyses of butyrate producers presented in this study may help to characterize the butyrate-producing bacterial community in the gut of AD patients.

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Brevibacterium anseongense sp. nov., isolated from soil of ginseng field: Mi-Seon Jung , Xiao-Tian Quan , Muhammad Zubair Siddiqi , Qingzhen Liu , Sang Yong Kim , Ji-Hyang Wee , Wan Taek Im; J. Microbiol. 2018;56(10):706-712. Published online August 22, 2018; DOI: https://doi.org/10.1007/s12275-018-8181-5

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Abstract

A Gram-positive, aerobic, non-motile, pale-yellow, and rodshaped bacterium, designated as Gsoil 188T, was isolated from the soil of a ginseng field in Pocheon, South Korea. A phylogenetic analysis based on 16S rRNA gene sequence comparison revealed that the strain formed a distinct lineage within the genus Brevibacterium and was most closely related to B. epidermidis NBRC 14811T (98.4%), B. sediminis FXJ8.269T (98.2%), B. avium NCFB 3055T (98.1%), and B. oceani BBH7T (98.1%), while it shared less than 98.1% identity with the other species of this genus. The DNA G + C content was 68.1 mol%. The predominant quinone was MK-8(H2). The major fatty acids were anteiso-C15:0 and anteiso-C17:0. The cell wall peptidoglycan of strain Gsoil 188T contained meso-diaminopimelic acid. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, and an unidentified aminolipid. The physiological and biochemical characteristics, low DNA-DNA relatedness values, and taxonomic analysis allowed the differentiation of strain Gsoil 188T from the other recognized species of the genus Brevibacterium. Therefore, strain Gsoil 188T represents a novel species of the genus Brevibacterium, for which the name Brevibacterium anseongense sp. nov. is proposed, with the type strain Gsoil 188T (= KACC 19439T = LMG 30331T).

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Su-Won Jeong, Jeong Eun Han, June-Young Lee, Ji-Ho Yoo, Do-Yeon Kim, In Chul Jeong, Jee-Won Choi, Yun-Seok Jeong, Jae-Yun Lee, So-Yeon Lee, Euon Jung Tak, Hojun Sung, Hyun Sik Kim, Pil Soo Kim, Dong-Wook Hyun, Jin-Woo Bae
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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(5): 1247. CrossRef

Terrabacter ginsengisoli sp. nov., isolated from ginseng cultivating soil: Mei-Fang Jin , Xiao-Tian Quan , Muhammad Zubair Siddiqi , Qing-Zhen Liu , Hong-Shan Yu , Wan-Taek Im; J. Microbiol. 2018;56(5):331-336. Published online May 2, 2018; DOI: https://doi.org/10.1007/s12275-018-8098-z

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Abstract

A Gram-positive, strictly aerobic, nonmotile, yellowish, coccus- rod-shaped bacterium (designated Gsoil 653T) isolated from ginseng cultivating soil was characterized using a polyphasic approach to clarify its taxonomic position. The strain Gsoil 653T exhibited optimal growth at pH 7.0 on R2A agar medium at 30°C. Phylogenetic analysis based on 16S rRNA gene sequence similarities, indicated that Gsoil 653T belongs to the genus Terrabacter of the family Humibacillus, and was closely related to Terrabacter tumescens DSM 20308T (98.9%), Terrabacter carboxydivorans PY2T (98.9%), Terrabacter terrigena ON10T (98.8%), Terrabacter terrae PPLBT (98.6%), and Terrabacter lapilli LR-26T (98.6%). The DNA G + C content was 70.5 mol%. The major quinone was MK-8(H4). The primary polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidyl-ethanolamine. The predominant fatty acids were iso-C15:0, iso-C16:0, iso-C14:0, and anteiso-C15:0, as in the case of genus Terrabacter, thereby supporting the categorization of strain Gsoil 653T. However, the DNA-DNA relatedness between Gsoil 653T and closely related strains of Terrabacter species was low at less than 31%. Moreover, strain Gsoil 653T could be both genotypically and phenotypically distinguished from the recognized species of the genus Terrabacter. This isolate, therefore, represents a novel species, for which the name Terrabacter ginsengisoli sp. nov. is proposed with the type strain Gsoil 653T (= KACC 19444T = LMG 30325T).

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Phosphorus fertilizer application and tillage practices influence bacterial community composition: implication for soil health
R.A. Adeleke, C. C. Obieze, C. Mukoro, C. B. Chikere, S. Tsipinana, A. Nciizah
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International Journal of Molecular Sciences.2020; 21(24): 9746. 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(5): 1247. CrossRef

Bacillus spongiae sp. nov., isolated from sponge of Jeju Island: Ga-Eun Lee , Wan-Taek Im , Jin-Sook Park; J. Microbiol. 2018;56(4):217-222. Published online February 28, 2018; DOI: https://doi.org/10.1007/s12275-018-7511-y

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Abstract

A Gram-reaction-positive, strictly aerobic, motile, endospore- forming, and rod-shaped bacterial strain designated 135PIL107-10T was isolated from a sponge on Jeju Island, and its taxonomic position was investigated using a polyphasic approach. Strain 135PIL107-10T grew at 20–37°C (optimum temperature, 25°C) and pH 6.0–10.0 (optimum pH, 6.0) on marine and R2A agars. Based on 16S rRNA gene phylogeny analysis, the novel strain formed a new branch within the genus Bacillus of the family Bacillaceae, and formed clusters with Bacillus thaohiensis NHI-38T (96.8%), Bacillus fengqiuensis NPK15T (96.7%), and Bacillus songklensis CAU 1033T (96.7%). Lower sequence similarities (97.0%) were found with the type strains of all other recognized members of the genus Bacillus (95.6–96.8% similarity). The G + C content of the genomic DNA was 43.6 mol%. The predominant respiratory quinone was menaquinone-7 and the major fatty acids were iso-C15:0 and iso-C17:1ω10c. The overall polar lipid patterns were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The isolate therefore represents a novel species, for which the name Bacillus spongiae sp. nov. is proposed, with the type strain 135PIL107-10T (= KACC 19275T = LMG 30080T).

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Antimicrobial Biosynthetic Potential and Phylogenetic Analysis of Culturable Bacteria Associated with the Sponge Ophlitaspongia sp. from the Yellow Sea, China
Lei Chen, Xue-Ning Wang, Hong-Yu Bi, Guang-Yu Wang
Marine Drugs.2022; 20(10): 588. 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(5): 1247. CrossRef

Lysobacter spongiae sp. nov., isolated from spongin: Heejae Choi , Wan-Taek Im , Jin-Sook Park; J. Microbiol. 2018;56(2):97-103. Published online February 2, 2018; DOI: https://doi.org/10.1007/s12275-018-7462-3

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Abstract

A Gram-negative, motile, aerobic and rod-shaped bacterial strain designated 119BY6-57T was isolated from spongin. The taxonomic position of the novel isolate was confirmed using the polyphasic approach. Strain 119BY6-57T grew well at 25– 30°C on marine agar. On the basis of 16S rRNA gene sequence similarity, strain 119BY6-57T belongs to the family Xanthomonadaceae and is related to Lysobacter aestuarii S2-CT (99.8% sequence similarity), L. maris KMU-14T (97.5%), and L. daejeonensis GH1-9T (97.3%). Lower sequence similarities (97.0%) were found with all of the other recognized members of the genus Lysobacter. The G + C content of the genomic DNA was 69.9 mol%. The major respiratory quinone was Q-8 and the major fatty acids were C16:0 iso, C15:0 iso, summed feature 9 (comprising C17􍾙:1 iso ω9c and/or C16:0 10-methyl), summed feature 3 (comprising C16􍾙:1 ω7c and/or C16:1 ω6c), and C11:0 iso 3-OH. The polar lipids were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, three unidentified phospholipids, and an unidentified polar lipid. DNADNA relatedness values between strain 119BY6-57T and its closest phylogenetically neighbors were below 48.0 ± 2.1%. Based on genotypic and phenotypic characteristics, it is concluded that strain 119BY6-57T is a new member within the genus Lysobacter, for which the name Lysobacter spongiae sp. nov. is proposed. The type strain is 119BY6-57T (= KACC 19276T = LMG 30077T).

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