Journal of Microbiology

Volume 53(11); November 2015

Review

MINIREVIEW] Stress responses in Streptococcus species and their effects on the host: Cuong Thach Nguyen , Sang-Sang Park , Dong-Kwon Rhee; J. Microbiol. 2015;53(11):741-749. Published online October 28, 2015; DOI: https://doi.org/10.1007/s12275-015-5432-6

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Streptococci cause a variety of diseases, such as dental caries, pharyngitis, meningitis, pneumonia, bacteremia, endocarditis, erysipelas, and necrotizing fasciitis. The natural niche of this genus of bacteria ranges from the mouth and nasopharynx to the skin, indicating that the bacteria will inevitably be subjected to environmental changes during invasion into the host, where it is exposed to the host immune system. Thus, the Streptococcus-host interaction determines whether bacteria are cleared by the host’s defenses or whether they survive after invasion to cause serious diseases. If this interaction was to be deciphered, it could aid in the development of novel preventive and therapeutic agents. Streptococcus species possess many virulent factors, such as peroxidases and heat-shock proteins (HSPs), which play key roles in protecting the bacteria from hostile host environments. This review will discuss insights into the mechanism(s) by which streptococci adapt to host environments. Additionally, we will address how streptococcal infections trigger host stress responses; however, the mechanism by which bacterial components modulate host stress responses remains largely unknown.

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Research Support, Non-U.S. Gov'ts

Spirosoma pulveris sp. nov., a bacterium isolated from a dust sample collected at Chungnam province, South Korea: Eun Sun Joo , Jae-Jin Lee , Seho Cha , Weonhwa Jheong , Taegun Seo , Sangyong Lim , Sun-wook Jeong , Sathiyaraj Srinivasan; J. Microbiol. 2015;53(11):750-755. Published online October 28, 2015; DOI: https://doi.org/10.1007/s12275-015-5263-5

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Abstract

Strain JSH 5-14T, a Gram-negative, non-motile, and curved rod-shaped bacterium, was isolated from a dust sample collected at Nonsan, Chungnam province, South Korea, and was characterized to determine its taxonomic position. Phylogenetic analysis based on the 16S rRNA gene sequence of strain JSH 5-14T revealed that it belongs to the genus Spirosoma, family Cytophagaceae, class Cytophagia. The highest degree of sequence similarities of strain JSH 5-14T were found with Spirosoma liguale DSM 74T (97.8%) and Spirosoma endophyticum EX 36T (96.2%). The predominant fatty acids were summed feature 3 (composed of C16:1 ω7c/C16:1 ω6c) and C16:1ω5c. The major polar lipid was phosphatidylethanolamine, and the predominant respiratory quinone was MK-7. Based on the phylogenetic, chemotaxonomic, and phenotypic data, we propose the strain JSH 5-14T (=KCTC 42550T =JCM 30688T =KEMB 9004-165T) should be classified as a type strain of a novel species, for which the name Spirosoma pulveris sp. nov., is proposed.

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Jihye Jung, Dawon Jo, Myoungjoo Riu, Seongho Ahn, Do-Hyun Kim
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Spirosoma oryzicola sp. nov., isolated from dried rice husk
Miyoung Won, Jun Heo, Hang-Yeon Weon, Daseul Lee, Byeong-Hak Han, Seung-Beom Hong, Soon-Wo Kwon
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Spirosoma rhododendri sp. nov., isolated from a flower of royal azalea (Rhododendron schlippenbachii)
Miyoung Won, Seung-Beom Hong, Byeong-Hak Han, Soon-Wo Kwon
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
Spirosoma taeanense sp. nov., a radiation resistant bacterium isolated from a coastal sand dune
Ji Hee Lee, Jong-Hyun Jung, Min-Kyu Kim, Han Na Choe, Chi Nam Seong, Sangyong Lim
Antonie van Leeuwenhoek.2021; 114(2): 151. CrossRef
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Heeyoung Kang, Inseong Cha, Haneul Kim, Kiseong Joh
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Complete Genome Sequence of Spirosoma sp. Strain KCTC 42546, Isolated from a Reservoir in South Korea
Pokchut Kusolkumbot, Song-Gun Kim, Chatrudee Suwannachart, Kenneth M. Stedman
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Guillaume Tahon, Liesbeth Lebbe, Anne Willems
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Li Weilan, Jae-Jin Lee, Seung-Yeol Lee, Sangkyu Park, Leonid N. Ten, Hee-Young Jung
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Leonid N. Ten, Nabil Elderiny, Jae-Jin Lee, Seung-Yeol Lee, Sangkyu Park, Dae Sung Lee, Myung Kyum Kim, Hee-Young Jung
Current Microbiology.2018; 75(2): 179. CrossRef
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Weilan Li, Seung-Yeol Lee, In-Kyu Kang, Leonid N. Ten, Hee-Young Jung
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Weilan Li, Leonid N. Ten, Seung-Yeol Lee, In-Kyu Kang, Hee-Young Jung
International Journal of Systematic and Evolutionary Microbiology.2018; 68(3): 930. CrossRef
Spirosoma daeguensis sp. nov., isolated from beach soil
Nabil Elderiny, Leonid N. Ten, Jae-Jin Lee, Seung-Yeol Lee, Sangkyu Park, Young-Je Cho, Myung Kyum Kim, Hee-Young Jung
Journal of Microbiology.2017; 55(9): 678. CrossRef
Spirosoma migulaei sp. nov., isolated from soil
Joseph Okiria, Leonid N. Ten, Su-Jin Park, Seung-Yeol Lee, Dong Hoon Lee, In-Kyu Kang, Dae Sung Lee, Hee-Young Jung
Journal of Microbiology.2017; 55(12): 927. CrossRef
Spirosoma litoris sp. nov., a bacterium isolated from beach soil
Joseph Okiria, Leonid N. Ten, Jae-Jin Lee, Seung-Yeol Lee, Young-Je Cho, Myung Kyum Kim, Hee-Young Jung
International Journal of Systematic and Evolutionary Microbiology.2017; 67(12): 4986. CrossRef
Spirosoma flavus sp. nov., a novel bacterium from soil of Jeju Island
Nabil Elderiny, Seung-Yeol Lee, Sangkyu Park, In-Kyu Kang, Myung Kyum Kim, Dae Sung Lee, Leonid N. Ten, Hee-Young Jung
Journal of Microbiology.2017; 55(11): 850. CrossRef
Complete genome sequence of Spirosoma pulveris JSH 5-14T, a bacterium isolated from a dust sample
Myung Kyum Kim, Ju-Young Kim, Su Jeong Kim, Min Ji Kim, Ju Yeon Lee, Chang-Gyeom Kim, Sathiyaraj Srinivasan
Molecular & Cellular Toxicology.2017; 13(4): 373. CrossRef
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Seon Hwa Jeon, Myung-Suk Kang, Eun Sun Joo, Eun Bit Kim, Sangyong Lim, Sun-wook Jeong, Hee-Young Jung, Sathiyaraj Srinivasan, Myung Kyum Kim
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List of new names and new combinations previously effectively, but not validly, published
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Flavobacterium jejuensis sp. nov., isolated from marine brown alga Ecklonia cava: So-Hyun Park , Ji-Young Kim , Young-Ju Kim , Moon-Soo Heo; J. Microbiol. 2015;53(11):756-761. Published online October 28, 2015; DOI: https://doi.org/10.1007/s12275-015-5280-4

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Abstract

A bacterial strain, designated EC11T was isolated from brown alga Ecklonia cava collected from Jeju Island, Korea. EC11T was identified as a Gram-negative, rod-shaped and yellowpigmented bacterial strain. The strain EC11T grew over a temperature range of 10°C to 30°C (optimally at 25°C), and a pH range of 6.0–10.5 (optimally at pH 7.5). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain EC11T belongs to the genus Flavobacterium. Strain EC11T shared close similarity with Flavobacterium jumunjinense HME7102T (96.4%), Flavobacterium dongtanense LW30T (95.8%), Flavobacterium haoranii LQY-7T (95.3%), and Flavobacterium urocaniciphilum (95.1%). The major fatty acids (> 5%) were iso-C17:0 3-OH (22.4%), iso-C15:0 3-OH (19.0%), C15:0 (12.4%), summed feature 3 (comprising C16:1 ω7c/ C16:1 ω6c; 9.78%), iso-C15:1 G (9.6%), and iso-C16:0 3-OH (9.0%). The DNA G+C content was 28.1 mol% and the strain contained MK-6 as the predominant menaquinone. The major polar lipids were phosphatidylethanolamine, two unknown aminolipids and three unknown polar lipids. Based on phenotypic, chemotaxonomic and phylogenetic analysis, strain EC11T represents a novel species of the Flavobacterium genus, for which the name Flavobacterium jejuensis sp. nov. is proposed. The type strain of F. jejuensis is EC11T (=KCTC 42149T = JCM 30735T).

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Winogradskyella vincentii sp. nov. and Winogradskyella alexanderae sp. nov., two novel bacteria isolated from intertidal sediment
Yu-Yan Yue, Yu-Qi Ye, Zi-Yang Zhou, Meng-Di Zhang, Ya-Wei Jia, Zong-Jun Du
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
Microbiome structure in biofilms from a volcanic island in Maritime Antarctica investigated by genome-centric metagenomics and metatranscriptomics
V.B. Centurion, S. Campanaro, A. Basile, L. Treu, V.M. Oliveira
Microbiological Research.2022; 265: 127197. CrossRef
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Xiaogang Chen, Qi Ye, Christian J. Sanders, Jinzhou Du, Jing Zhang
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Qian Wang, Sheng-Dong Cai, Jie Liu, De-Chao Zhang
International Journal of Systematic and Evolutionary Microbiology .2020; 70(6): 3633. CrossRef
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Xiangyuan Mei, Chunhui Wu, Jin Zhao, Tian Yan, Peng Jiang
Frontiers in Microbiology.2019;[Epub] CrossRef
Isolation and genome analysis of Winogradskyella algicola sp. nov., the dominant bacterial species associated with the green alga Dunaliella tertiolecta
Jaeho Song, Yeonjung Lim, Hye-Jin Jang, Yochan Joung, Ilnam Kang, Seong-Joo Hong, Choul-Gyun Lee, Jang-Cheon Cho
Journal of Microbiology.2019; 57(11): 982. CrossRef
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Inhyup Kim, Jiyoun Kim, Geeta Chhetri, Taegun Seo
Journal of Microbiology.2019; 57(12): 1079. CrossRef
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Dorji Phurbu, Hubin Lu, Xiaofeng Xue, Yanling Tian, Yangzom Pema, Chao Ma, Peng Xing
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Sooyeon Park, Jeehyun Choi, Su Jung Choi, Jung-Hoon Yoon
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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
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List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George M. Garrity
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Niabella ginsenosidivorans sp. nov., isolated from compost: Kwon-Jung Yi , Wan-Taek Im , Dong-Woon Kim , Qing Mei Liu , Soo-Ki Kim; J. Microbiol. 2015;53(11):762-766. Published online October 28, 2015; DOI: https://doi.org/10.1007/s12275-015-5463-z

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Abstract

A Gram-reaction negative, strictly aerobic, non-motile, orange colored, and rod-shaped bacterium (designated BS26T) isolated from compost, was characterized by a polyphasic approach to clarify its taxonomic position. Strain BS26T was observed to grow optimally at 25–30°C and at pH 7.0 on R2A and nutrient media. Strain BS26T showed β-glucosidase activity that was responsible for its ability to transform ginsenoside Rb1 (one of the active components of ginseng) to ginsenoside compound-K (C-K). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain BS26T belongs to the genus Niabella of family Chitinophagaceae and was most closely related to Niabella soli DSM 19437T (94.5% similarity), N. yanshanensis CCBAU 05354T (94.3%), and N. aurantiaca DSM 17617T (93.8%). The G+C content of genomic DNA was 47.3 mol%. Chemotaxonomic data [predominant isoprenoid quinone-MK-7, major fatty acids–iso-C15:0, iso-C15:1 G, iso-C17:0 3-OH, and summed feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c)] supported the affiliation of strain BS26T to the genus Niabella. However, strain BS26T could be differentiated genotypically and phenotypically from the recognized species of the genus Niabella. The novel isolate therefore represents a novel species, for which the name Niabella ginsenosidivorans sp. nov. is proposed, with the type strain BS26T (=KACC 16620T =JCM 18199T).

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Niabella digestorum sp. nov., a High Cell-Surface Hydrophobic Bacterium Isolated from Waste Digestion System
Ling Zhang, Chuansheng Geng, Xingjuan Chen, Letian Chen, Tongchu Deng, Meiying Xu
Current Microbiology.2024;[Epub] CrossRef
Niabella beijingensis sp. nov. and Thermomonas beijingensis sp. nov., two bacteria from constructed wetland
Sheng-Zhi Guo, Tong Wu, Hai-Zhen Zhu, Lei Yan, Zhi-Pei Liu, De-Feng Li, Cheng-Ying Jiang, Shuang-Jiang Liu, Xi-Hui Shen
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
List of new names and new combinations previously effectively, but not validly, published
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International Journal of Systematic and Evolutionary Microbiology .2019; 69(5): 1247. CrossRef
Niabella hibiscisoli sp. nov., isolated from soil of a Rose of Sharon garden
Hien T. T. Ngo, Huan Trinh, Zheng-Fei Yan, Gabriela Moya, MooChang Kook, Tae-Hoo Yi
International Journal of Systematic and Evolutionary Microbiology.2017; 67(4): 784. CrossRef
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International Journal of Systematic and Evolutionary Microbiology.2016; 66(8): 2774. CrossRef

Enhanced method for microbial community DNA extraction and purification from agricultural yellow loess soil: Mathur Nadarajan Kathiravan , Geun Ho Gim , Jaewon Ryu , Pyung Il Kim , Chul Won Lee , Si Wouk Kim; J. Microbiol. 2015;53(11):767-775. Published online October 28, 2015; DOI: https://doi.org/10.1007/s12275-015-5454-0

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Abstract

In this study, novel DNA extraction and purification methods were developed to obtain high-quantity and reliable quality DNA from the microbial community of agricultural yellow loess soil samples. The efficiencies of five different soil DNAextraction protocols were evaluated on the basis of DNA yield, quality and DNA shearing. Our suggested extraction
method
, which used CTAB, EDTA and cell membrane lytic enzymes in the extraction followed by DNA precipitation using isopropanol, yielded a maximum DNA content of 42.28 ± 5.59 μg/g soil. In addition, among the five different purification protocols, the acid-treated polyvinyl polypyrrolidone (PVPP) spin column purification method yielded high-quality DNA and recovered 91% of DNA from the crude DNA. Spectrophotometry revealed that the ultraviolet A260/A230 and A260/A280 absorbance ratios of the purified DNA were 1.82 ± 0.03 and 1.94 ± 0.05, respectively. PCR-based 16S rRNA amplification showed clear bands at ~1.5 kb with acid-treated PVPP–purified DNA templates. In conclusion, our suggested extraction and purification protocols can be used to recover high concentration, high purity, and high-molecular-weight DNA from clay and silica-rich agricultural soil samples.

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The crystal structure of the D-alanine-D-alanine ligase from Acinetobacter baumannii suggests a flexible conformational change in the central domain before nucleotide binding: Kim-Hung Huynh , Myoung-ki Hong , Clarice Lee , Huyen-Thi Tran , Sang Hee Lee , Yeh-Jin Ahn , Sun-Shin Cha , Lin-Woo Kang; J. Microbiol. 2015;53(11):776-782. Published online October 28, 2015; DOI: https://doi.org/10.1007/s12275-015-5475-8

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Abstract

Acinetobacter baumannii, which is emerging as a multidrugresistant nosocomial pathogen, causes a number of diseases, including pneumonia, bacteremia, meningitis, and skin infections. With ATP hydrolysis, the D-alanine-D-alanine ligase (DDL) catalyzes the synthesis of D-alanyl-D-alanine, which is an essential component of bacterial peptidoglycan. In this study, we determined the crystal structure of DDL from A. baumannii (AbDDL) at a resolution of 2.2 Å. The asymmetric unit contained six protomers of AbDDL. Five protomers had a closed conformation in the central domain, while one protomer had an open conformation in the central domain. The central domain with an open conformation did not interact with crystallographic symmetry-related protomers and the conformational change of the central domain was not due to crystal packing. The central domain of AbDDL can have an ensemble of the open and closed conformations before the binding of substrate ATP. The conformational change of the central domain is important for the catalytic activity and the detail information will be useful for the development of inhibitors against AbDDL and putative antibacterial agents against A. baumannii. The AbDDL structure was compared with that of other DDLs that were in complex with potent inhibitors and the catalytic activity of AbDDL was confirmed using enzyme kinetics assays.

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Research Support, N.I.H., Extramural

The Mycobacterium tuberculosis relBE toxin:antitoxin genes are stress-responsive modules that regulate growth through translation inhibition: Shaleen B. Korch , Vandana Malhotra , Heidi Contreras , Josephine E. Clark-Curtiss; J. Microbiol. 2015;53(11):783-795. Published online October 28, 2015; DOI: https://doi.org/10.1007/s12275-015-5333-8

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Abstract

Toxin-antitoxin (TA) genes are ubiquitous among bacteria and are associated with persistence and dormancy. Following exposure to unfavorable environmental stimuli, several species (Escherichia coli, Staphylococcus aureus, Myxococcus xanthus) employ toxin proteins such as RelE and MazF to downregulate growth or initiate cell death. Mycobacterium tuberculosis possesses three Rel TA modules (RelMtb): RelBEMtb, RelFGMtb and RelJKMtb (Rv1246c-Rv1247c, Rv2865-Rv2866, and Rv3357-Rv3358, respectively), which inhibit mycobacterial growth when the toxin gene (relE, relG, relK) is expressed independently of the antitoxin gene (relB, relF, relJ). In the present study, we examined the in vivo mechanism of the RelEMtb toxin protein, the impact of RelEMtb on M. tuberculosis physiology and the environmental conditions that regulate all three relMtb modules. RelEMtb negatively impacts growth and the structural integrity of the mycobacterial envelope, generating cells with aberrant forms that are prone to extensive aggregation. At a time coincident with growth defects, RelEMtb mediates mRNA degradation in vivo resulting in significant changes to the proteome. We establish that relMtb modules are stress responsive, as all three operons are transcriptionally activated following mycobacterial exposure to oxidative stress or nitrogen-limiting growth environments. Here we present evidence that the relMtb toxin:antitoxin family is stress-responsive and, through the degradation of mRNA, the RelEMtb toxin influences the growth, proteome and morphology of mycobacterial cells.

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Research Support, Non-U.S. Gov't

Antiviral effects of Lactobacillus ruminis SPM0211 and Bifidobacterium longum SPM1205 and SPM1206 on rotavirus-infected Caco-2 cells and a neonatal mouse model: Joo Yeon Kang , Do Kyung Lee , Nam Joo Ha , Hea Soon Shin; J. Microbiol. 2015;53(11):796-803. Published online October 28, 2015; DOI: https://doi.org/10.1007/s12275-015-5302-2

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Abstract

Rotavirus is worldwide cause of severe gastroenteritis including severe diarrhea and fatal dehydration in infants and young children. There is an available vaccination program for preventing rotavirus infection, but it has limits and restrictions. Probiotics therapy could be an alternative
method
of antiviral prevention and modulation against rotavirus infection. In this study, we screened the antiviral activity of probiotic bacteria such as 3 Lactobacillus spp. and 14 Bifidobacterium spp. isolated from young Korean. Three of the bacteria, Lactobacillus ruminis SPM0211, Bifidobacterium longum SPM1205, and SPM1206, inhibited human strain Wa rotavirus infection in Caco-2 cells. Furthermore, these bacterial strains inhibited rotavirus replication in a rotavirus-infected neonatal mouse model. To clarify the mechanism of inhibition, we investigated gene expression of Interferon (IFN)-signaling components and IFN-inducible antiviral effectors. All 3 probiotics increased IFN-α and IFN- β levels compared with the control. Gene expression of IFNsignaling components and IFN-inducible antiviral effectors also increased. Overall, these results indicate that L. ruminis SPM0211, B. longum SPM1205 and 1206 efficiently inhibit rotavirus replication in vitro and in vivo. Especially, the antiviral effect of Lactobacillus ruminis SPM0211 is worthy of notice. This is the first report of L. ruminis with antiviral activity. Anti-rotaviral effects of the 3 probiotics are likely due to their modulation of the immune response through promoting type I IFNs, which are key regulators in IFN signaling pathway.

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