Journal of Microbiology

Volume 57(1); January 2019

Reviews

MINIREVIEW] Exopolymeric substances (EPS) from Salmonella enterica: polymers, proteins and their interactions with plants and abiotic surfaces: Rugare Maruzani , Gabriel Sutton , Paola Nocerino , Massimiliano Marvasi; J. Microbiol. 2019;57(1):1-8. Published online September 6, 2018; DOI: https://doi.org/10.1007/s12275-019-8353-y

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When Salmonella enterica is not in a planktonic state, it persists in organised communities encased in extracellular polymeric substances (EPS), defined as biofilms. Environmental conditions ultimately dictate the key properties of the biofilms such as porosity, density, water content, charge, sorption and ion exchange properties, hydrophobicity and mechanical stability. S. enterica has been extensively studied due to its ability to infect the gastrointestinal environment. However, only during the last decades studies on its persistence and replication in soil, plant and abiotic surfaces have been proposed. S. enterica is an environmental bacterium able to effectively persist outside the human host. It does so by using EPS as tools to cope with environmental fluctuations. We therefore address this mini-review to classify those EPS that are produced by Salmonella with focus on the environment (plant, soil, and abiotic surfaces) by using a classification of EPS proposed by Flemming and collaborators in 2007. The EPS are therefore classified as structural, sorptive, surface-active, active, and informative.

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Inhibition of Salmonella Typhimurium biofilm and polysaccharide production via eugenol-glucosyltransferase interactions
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Bacterial extracellular biopolymers: Eco-diversification, biosynthesis, technological development and commercial applications
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Galactosamine and mannosamine are integral parts of bacterial and fungal extracellular polymeric substances
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A novel method using a differential staining fluorescence microscopy (DSFM) to track the location of enteric pathogens within mixed-species biofilms
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Secretion of poly-γ-glutamic acid by Bacillus atrophaeus NX-12 enhanced its root colonization and biocontrol activity
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Differential Survivability of Two Genetically Similar Salmonella Thompson Strains on Pre-harvest Sweet Basil (Ocimum basilicum) Leaves
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Electro-Optical Detection of Phage Antibody Interaction with Complementary Antigens of Herbaspirillum seropedicae Z78 Cells
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Tania Henriquez, Anna Lenzi, Ada Baldi, Massimiliano Marvasi
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MINIREVIEW] Synthetic lethal interaction between oxidative stress response and DNA damage repair in the budding yeast and its application to targeted anticancer therapy: Ji Eun Choi , Woo-Hyun Chung; J. Microbiol. 2019;57(1):9-17. Published online December 29, 2018; DOI: https://doi.org/10.1007/s12275-019-8475-2

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Abstract

Synthetic lethality is an extreme form of negative genetic epistasis that arises when a combination of functional deficiency in two or more genes results in cell death, whereas none of the single genetic perturbations are lethal by themselves. This unconventional genetic interaction is a modification of the concept of essentiality that can be exploited for the purpose of targeted cancer therapy. The yeast Saccharomyces cerevisiae has been pivotally used for early large-scale synthetic lethal screens due to its experimental advantages, but recent advances in gene silencing technology have now made direct high-throughput analysis possible in higher organisms. Identification of tumor-specific alterations and characterization of the mechanistic principles underlying synthetic lethal interaction are the key to applying synthetic lethality to clinical cancer treatment by enabling genome-driven oncological research. Here, we provide emerging ideas on the synthetic lethal interactions in budding yeast, particularly between cellular processes responsible for oxidative stress response and DNA damage repair, and discuss how they can be appropriately utilized for context-dependent cancer therapeutics.

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Journal Articles

Flavisolibacter aluminii sp. nov., a novel member of the genus Flavisolibacter isolated from an automotive air conditioning system: Hyosun Lee , Dong-Uk Kim , Suyeon Lee , Song-Gun Kim , A-Young Park , Jae-Hyung Ahn , Jong-Ok Ka; J. Microbiol. 2019;57(1):18-22. Published online November 19, 2018; DOI: https://doi.org/10.1007/s12275-019-8219-3

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Abstract

A Gram-stain-negative, aerobic, non-motile, rod-shaped, and yellow-pigmented bacterium, designated strain ID1709T, was isolated from an automotive air conditioning system collected in Korea. Analysis of 16S rRNA gene sequence similarity showed that strain ID1709T had 92.2–94.3% similarities with the type strains of members of the genus Flavisolibacter. The major cellular fatty acids were iso-C15:0, iso-C15:1 G, iso-C17:0 3-OH, and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c). The predominant respiratory quinone was MK-7. The polar lipids comprised phosphatidylethanolamine, aminoglycophospholipid, two unidentified aminolipids, and three unidentified lipids. The DNA G + C content of the strain was 35.6 mol%. Based on phenotypic, chemotaxonomic, and genotypic data, strain ID1709T represents a novel species in the genus Flavisolibacter, for which the name Flavisolibacter aluminii sp. nov. (= KACC 19451T = KCTC 52778T = NBRC 112870T), is proposed.

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Insights into the Response and Evolution of Microbial Communities During Long-Term Natural Remediation of Contaminated Abandoned Shale Gas Wells
Hongyang Ren, Shuangli Chen, Jiajian Shang, Yujia Gao, Yuanpeng Deng, Zhaoyang Wang, Guojun Hu, Bing Wang
Water, Air, & Soil Pollution.2024;[Epub] CrossRef
Metallococcus carri gen. nov., sp. nov., a novel member of the family Dermacoccaceae isolated from an automotive air conditioning system
Jong Sung Lim, Hyosun Lee, Jigwan Son, Song-Gun Kim, Dong-Uk Kim, Jong-Ok Ka
Archives of Microbiology.2021; 203(7): 4073. CrossRef

Gramella fulva sp. nov., isolated from a dry surface of tidal flat: Sae Hyun Hwang , Woon Mo Hwang , Keunsoo Kang , Tae-Young Ahn; J. Microbiol. 2019;57(1):23-29. Published online November 19, 2018; DOI: https://doi.org/10.1007/s12275-019-8370-x

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Abstract

A novel Gram-stain-negative, aerobic, motile by means of gliding, and short rod-shaped bacterium, designated strain SH35T, was isolated from the dry surface of a tidal flat in Hwasung-si, South Korea. Growth occurred at 10–40°C (optimum 30°C), at pH 6.0–8.0 (optimum pH 7.0), in 1–12% NaCl (optimum 2%), and was inhibited in the absence of NaCl and Ca2+ ions. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain SH35T belonged to the genus Gramella and was a member of the family Flavobacteriaceae with highest sequence similarity to Gramella flava JLT2011T (96.1%), followed by Gramella oceani CCAMSZ- TT (95.6%), and 93.0–94.9% to other recognized Gramella species. The major cellular fatty acids (> 5% of the total) of strain SH35T were iso-C15:0, Iso-C16:0, anteiso-C15:0, iso-C17:0 3-OH and summed feature 9 (C16:0 10-methyl and/or C17:1 iso ω9с). The major polar lipids were phosphatidylethanolamine, two unidentified aminolipids and nine unidentified polar lipids. The major respiratory quinone and the predominant polyamine were menaquinone-6 (MK-6) and symhomospermidine, respectively. The DNA G + C content was 40.5 mol% (39.7% based on total genome calculations). Based on phylogenetic analysis and physiological and biochemical characterization, strain SH35T represents a novel species of the genus Gramella, for which the name Gramella fulva sp. nov. is proposed. The type strain is SH35T (= KACC 19447T = JCM 32369T).

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Gramella oceanisediminis sp. nov., isolated from deep-sea sediment of the Indian Ocean
Lin Yang, Haolei Shi, Qian Li, Minggang Zheng, Qiliang Lai, Li Zheng
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Proposal of Christiangramia gen. nov., Neomelitea gen. nov. and Nicoliella gen. nov. as replacement names for the illegitimate prokaryotic generic names Gramella Nedashkovskaya et al. 2005, Melitea Urios et al. 2008 and Nicolia Oliphant et al. 2022, respe
Umakant Bhoopati Deshmukh, Aharon Oren
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Gramella sediminis sp. nov., isolated from a tidal flat of the Yellow Sea
Hui-Jing Niu, Kai-Shi Dong, Li Guan, Li-Ping Sun, Qin Wang, Yan-Jiao Zhang, Yi Li, Cheng-Qiang Xia, Cai-Xia Pei
International Journal of Systematic and Evolutionary Microbiology.2022;[Epub] CrossRef
Pyomelanin-Producing Brevundimonas vitisensis sp. nov., Isolated From Grape (Vitis vinifera L.)
Lingmin Jiang, Doeun Jeon, Jueun Kim, Chul Won Lee, Yuxin Peng, Jiyoon Seo, Ju Huck Lee, Jin Hyub Paik, Cha Young Kim, Jiyoung Lee
Frontiers in Microbiology.2021;[Epub] CrossRef
Saccharibacillus brassicae sp. nov., an endophytic bacterium isolated from kimchi cabbage (Brassica rapa subsp. pekinensis) seeds
Lingmin Jiang, Chan Ju Lim, Song-Gun Kim, Jae Cheol Jeong, Cha Young Kim, Dae-Hyuk Kim, Suk Weon Kim, Jiyoung Lee
Journal of Microbiology.2020; 58(1): 24. CrossRef
Jejubacter calystegiae gen. nov., sp. nov., moderately halophilic, a new member of the family Enterobacteriaceae, isolated from beach morning glory
Lingmin Jiang, Dexin Wang, Jung-Sook Lee, Dae-Hyuk Kim, Jae Cheol Jeong, Cha Young Kim, Suk Weon Kim, Jiyoung Lee
Journal of Microbiology.2020; 58(5): 357. 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(3): 1443. CrossRef
Neobacillus endophyticus sp. nov., an endophytic bacterium isolated from Selaginella involvens roots
Lingmin Jiang, Myoung Hui Lee, Jae Cheol Jeong, Dae-Hyuk Kim, Cha Young Kim, Suk Weon Kim, Jiyoung Lee
International Journal of Systematic and Evolutionary Microbiology .2019;[Epub] CrossRef
Peribacillus faecalis sp. nov., a moderately halophilic bacterium isolated from the faeces of a cow
Lingmin Jiang, Won Yong Jung, Zhun Li, Mi-Kyung Lee, Seung-Hwan Park, Se Won Kang, Jung-Sook Lee, Hyunjung Jung, Tai-Young Hur, Hyeun Bum Kim, Jae-Kyung Kim, Ju-Hoon Lee, Ju Huck Lee, Jiyoung Lee
International Journal of Systematic and Evolutionary Microbiology .2019;[Epub] CrossRef

Community structures and genomic features of undesirable white colony-forming yeasts on fermented vegetables: Joon Yong Kim , Juseok Kim , In-Tae Cha , Min Young Jung , Hye Seon Song , Yeon Bee Kim , Changsu Lee , Seung-Yeon Kang , Jin-Woo Bae , Yoon-E Choi , Tae-Woon Kim , Seong Woon Roh; J. Microbiol. 2019;57(1):30-37. Published online October 25, 2018; DOI: https://doi.org/10.1007/s12275-019-8487-y

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Abstract

White colony-forming yeasts (WCFYs) often appear in fermented foods, depending on the storage method. Despite the ongoing research on fermented foods, the community and genome features of WCFYs have not been well studied. In this study, the community structures of WCFYs on fermented vegetables (kimchi) prepared with various raw materials were investigated using deep sequencing. Only eight operational taxonomic units (OTUs) were detected, indicating that the community structure of WCFYs on kimchi is very simple. The five most abundant OTUs represented Pichia kluyveri, Yarrowia lipolytica, Candida sake, Hanseniaspora uvarum, and Kazachstania servazzii. Using a culture-dependent
method
, 41 strains representing the five major OTUs were isolated from the surface of the food samples. Whole genomes of the five major yeast strains were sequenced and annotated. The total genome length for the strains ranged from 8.97 Mbp to 21.32 Mbp. This is the first study to report genome sequences of the two yeasts Pichia kluyveri and Candida sake. Genome analysis indicated that each yeast strain had core metabolic pathways such as oxidative phosphorylation; purine metabolism; glycolysis/gluconeogenesis; aminoacyl- tRNA biosynthesis; citrate cycle; but strain specific pathways were also found. In addition, no toxin or antimicrobial resistance genes were identified. Our study provides genome information for five WCFY strains that may highlight their potential beneficial or harmful metabolic effects in fermented vegetables.

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Ting Mi, Yao Jin, Yulan Che, Jun Huang, Rongqing Zhou, Chongde Wu
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Joon Yong Kim, Seong-Eun Park, Eun-Ju Kim, Seung-Ho Seo, Tae Woong Whon, Kwang-Moon Cho, Sun Jae Kwon, Seong Woon Roh, Hong-Seok Son
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Safety assessment of white colony-forming yeasts in kimchi
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Chang Hee Jeong, Joon Yong Kim, Young Joon Oh, Hye In Ko, Seong Woon Roh, Sung Wook Hong, Hyuk Cheol Kwon, Sung Gu Han, Tae-Woon Kim
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Non-tandem repeat polymorphisms at microsatellite loci in wine yeast species
María Laura Raymond Eder, Alberto Luis Rosa
Molecular Genetics and Genomics.2020; 295(3): 685. CrossRef
Unraveling microbial fermentation features in kimchi: from classical to meta-omics approaches
Se Hee Lee, Tae Woong Whon, Seong Woon Roh, Che Ok Jeon
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Draft Genome Sequences of Two Isolates of the Yeast Kazachstania servazzii Recovered from Soil in Ireland
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Mediterraneibacter butyricigenes sp. nov., a butyrate-producing bacterium isolated from human faeces: Ji-Sun Kim , Keun Chul Lee , Min Kuk Suh , Kook-Il Han , Mi Kyung Eom , Ju Huck Lee , Seung-Hwan Park , Se Won Kang , Jam-Eon Park , Byeong Seob Oh , Seung Yeob Yu , Seung-Hyeon Choi , Dong Ho Lee , Hyuk Yoon , Byung-Yong Kim , Seung-Jo Yang , Jung-Sook Lee; J. Microbiol. 2019;57(1):38-44. Published online December 29, 2018; DOI: https://doi.org/10.1007/s12275-019-8550-8

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Abstract

A Gram-stain-positive, obligately anaerobic, non-motile, nonspore- forming, and rod-shaped bacterial strain, designated KGMB01110T, was isolated from a faecal sample of a healthy male in South Korea. Phylogenetic analysis based on 16S rRNA gene showed that strain KGMB01110T belonged to Clostridium cluster XIVa and was most closely related to Mediterraneibacter glycyrrhizinilyticus KCTC 5760T (95.9% 16S rRNA gene sequence similarity). The DNA G + C content of strain KGMB01110T based on its whole genome sequence was 44.1 mol%. The major cellular fatty acids (> 10%) of the isolate were C14:0 and C16:0. The strain KGMB01110T was positive for arginine dihydrolase, β-galactosidase-6-phosphatase, and alkaline phosphatase. The strain KGMB01110T also produced acid from D-glucose and D-rhamnose, and hydrolyzed gelatin and aesculin. Furthermore, HPLC analysis and UV-tests of culture supernatant revealed that the strain KGMB01110T produced butyrate as the major end product of glucose fermentation. Based on the phylogenetic and phenotypic characteristics, strain KGMB01110T represent a novel species of the genus Mediterraneibacter in the family Lachnospiraceae. The type strain is KGMB01110T (= KCTC 15684T = CCUG 72830T).

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Increased susceptibility against Cryptococcus neoformans of lupus mouse models (pristane-induction and FcGRIIb deficiency) is associated with activated macrophage, regardless of genetic background: Saowapha Surawut , Jiradej Makjaroen , Arthid Thim-uam , Jutamas Wongphoom , Tanapat Palaga , Prapaporn Pisitkun , Ariya Chindamporn , Asada Leelahavanichkul; J. Microbiol. 2019;57(1):45-53. Published online November 19, 2018; DOI: https://doi.org/10.1007/s12275-019-8311-8

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Abstract

The severity of cryptococcosis in lupus from varying geneticbackgrounds might be different due to the heterogeneity of lupus-pathogenesis. This study explored cryptococcosis in lupus mouse models of pristane-induction (normal geneticbackground) and FcGRIIb deficiency (genetic defect). Because the severity of lupus nephritis, as determined by proteinuria and serum creatinine, between pristane and FcGRIIb-/- mice were similar at 6-month-old, Cryptococcus neoformans was intravenously administered in 6-month-old mice and were age-matched with wild-type. Indeed, the cryptococcosis disease severity, as evaluated by mortality rate, internal-organ fungal burdens and serum cytokines, between pristane and FcGRIIb-/- mice was not different. However, the severity of cryptococcosis in wild-type was less severe than the lupus mice. On the other hand, phagocytosis activity of peritoneal macrophages from lupus mice (pristane and FcGRIIb-/-) was more predominant than the wild-type without the difference in macrophage killing-activity among these groups. In addition, the number of active T helper cells (Th-cell) in the spleen, including Th-cells with intracellular IFN-γ, from lupus mice (pristane and FcGRIIb-/-) was higher than wildtype. Moreover, these active Th-cells were even higher after 2 weeks of cryptococcal infection. These data support enhanced macrophage activation through prominent Th-cells in both lupus models. In conclusion, an increased susceptibility of cryptococcosis in both lupus models was independent to genetic background. This might due to Th-cell enhanced macrophage phagocytosis with the interference of macrophage killing activity from Cryptococcal immune-evasion properties.

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Metabolomic profiling reveals enrichment of cordycepin in senescence process of Cordyceps militaris fruit bodies: Junsang Oh , Deok-Hyo Yoon , Bhushan Shrestha , Hyung-Kyoon Choi , Gi-Ho Sung; J. Microbiol. 2019;57(1):54-63. Published online December 29, 2018; DOI: https://doi.org/10.1007/s12275-019-8486-z

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Abstract

Cordyceps militaris is a species of Cordyceps that is classified in the Cordycipitaceae family and is well known in East Asia as a traditional medicinal mushroom. Its artificial fruit body has been widely cultivated for commercial use in cosmetics, functional food, and medicine. To explore the metabolites associated with fruit body development, we conducted gas chromatography mass spectrometry (GC-MS) analyses based on developmental stage, which was divided into the growth period (stage 1, stage 2, and stage 3) and aging period (stage 4). We detected 39 biochemical metabolites associated with nucleotide, carbohydrate, and amino acid metabolism. Cordycepin, one of the representative bioactive compounds in C. militaris, was significantly enriched in stage 4 of aging period and is associated with glucose accumulation. The accumulation of cordycepin in stage 4 of aging period also seems to be related to the glutamine and glutamic acid pathway. Our
results
also showed enrichment of other bioactive compounds such as mannitol and xylitol in stage 4 of aging period. Our metabolomic profiling based on the developmental stages of C. militaris is useful for exploring bioactive compounds (e.g., cordycepin, mannitol, GABA, and xylitol) that are enriched in stage 4 of aging period and understanding the biosynthetic mechanisms associated with cordycepin production. Through optimization of fruit body cultivation by selecting stage 4 of aging period as a harvesting time, our findings can be utilized in food and medical applications of C. militaris in future.

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Effective mucosal live attenuated Salmonella vaccine by deleting phosphotransferase system component genes ptsI and crr: Yong Zhi , Shun Mei Lin , A-Yeung Jang , Ki Bum Ahn , Hyun Jung Ji , Hui-Chen Guo , Sangyong Lim , Ho Seong Seo; J. Microbiol. 2019;57(1):64-73. Published online October 2, 2018; DOI: https://doi.org/10.1007/s12275-019-8416-0

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Abstract

Salmonella enterica is a major human pathogen that causes invasive non-typhoidal Salmonellosis (iNTS), resulting in significant morbidity and mortality. Although a number of pre-clinical and clinical studies have reported on the feasibility of developing a safe and effective vaccine against iNTS, there have been no licensed Salmonella vaccines available to protect against NTS strains. Vaccine formulations of highest priority for NTS are live attenuated vaccines, which can elicit effective induction of intestinal mucosal and intracellular bacteria-specific cell mediated immune responses. Since glucose is crucial for intracellular survival and replication in host cells, we constructed strains with mutations in components of the glucose uptake system, called the phosphotransferase system (PTS), and compared the relative virulence and immune responses in mice. In this study, we found that the strain with mutations in both ptsI and crr (KST0556) was the most attenuated strain among the tested strains, and proved to be highly effective in inducing a mucosal immune response that can protect against NTS infections in mice. Thus, we suggest here that KST0556 (ΔptsIΔcrr) is a potential live vaccine candidate for NTS, and may also be a candidate for a live delivery vector for heterologous antigens. Moreover, since PTS is a well-conserved glucose transporter system in both Gramnegative and Gram-positive bacteria, the ptsI and crr genes may be potential targets for creating live bacterial vectors or vaccine strains.

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Anti-varicella-zoster virus activity of cephalotaxine esters in vitro: Jung-Eun Kim , Yoon-Jae Song; J. Microbiol. 2019;57(1):74-79. Published online November 19, 2018; DOI: https://doi.org/10.1007/s12275-019-8514-z

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Abstract

Harringtonine (HT) and homoharringtonine (HHT), alkaloid esters isolated from the genus Cephalotaxus, exhibit antitumor activity. A semisynthetic HHT has been approved for treatment of chronic myelogenous leukemia. In addition to antileukemic activity, HT and HHT are reported to possess potent antiviral activity. In this study, we investigated the effects of HT and HHT on replication of varicella-zoster virus (VZV) in vitro. HT and HHT, but not their biologically inactive parental alkaloid cephalotaxine (CET), significantly inhibited replication of recombinant VZV-pOka luciferase. Furthermore, HT and HHT, but not CET, strongly induced down-regulation of VZV lytic genes and exerted potent antiviral effects against a VZV clinical isolate. The collective data support the utility of HT and HHT as effective antiviral candidates for treatment of VZV-associated diseases.

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Published Erratum

Erratum] Histone deacetylase-mediated morphological transition in Candida albicans: Jueun Kim , Ji-Eun Lee , Jung-Shin Lee; J. Microbiol. 2019;57(1):80-80.; DOI: https://doi.org/10.1007/s12275-019-8581-1

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Abstract: In the article by Kim et al. published in Journal of Microbiology 2015; 53, 805–811, the first sentence of 2nd paragraph in the section of ‘Rpd31: The repressor of hyphal induction and the activator of hyphal extension interacting with Ssn6’ on page 808 should have read: In C. albicans, there are two proteins as the orthologue of S. cerevisiae Rpd3: Rpd31 (orf19.6801, orf19.14093) and Rpd32 (orf19.2834, orf19.10352) (Hnisz et al., 2009). And the figure 1 should be corrected as below. We apologize for any inconvenience that this may have caused.

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