Journal of Microbiology

Journal Articles

Functional Characterization of DNA N‑Glycosylase Ogg1 and Ntg1 in DNA Damage Stress of Cryptococcus neoformans: Kwang-Woo Jung , Sunhak Kwon , Jong-Hyun Jung , Sangyong Lim , Yong-Sun Bahn; J. Microbiol. 2023;61(11):981-992. Published online December 6, 2023; DOI: https://doi.org/10.1007/s12275-023-00092-y

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Abstract: Reactive oxygen species induce DNA strand breaks and DNA oxidation. DNA oxidation leads to DNA mismatches, resulting in mutations in the genome if not properly repaired. Homologous recombination (HR) and non-homologous end-joining (NHEJ) are required for DNA strand breaks, whereas the base excision repair system mainly repairs oxidized DNAs, such as 8-oxoguanine and thymine glycol, by cleaving the glycosidic bond, inserting correct nucleotides, and sealing the gap. Our previous studies revealed that the Rad53-Bdr1 pathway mainly controls DNA strand breaks through the regulation of HRand NHEJ-related genes. However, the functional roles of genes involved in the base excision repair system remain elusive in Cryptococcus neoformans. In the present study, we identified OGG1 and NTG1 genes in the base excision repair system of C. neoformans, which are involved in DNA oxidation repair. The expression of OGG1 was induced in a Hog1-dependent manner under oxidative stress. On the other hand, the expression of NTG1 was strongly induced by DNA damage stress in a Rad53-independent manner. We demonstrated that the deletion of NTG1, but not OGG1, resulted in elevated susceptibility to DNA damage agents and oxidative stress inducers. Notably, the ntg1Δ mutant showed growth defects upon antifungal drug treatment. Although deletion of OGG1 or NTG1 did not increase mutation rates, the mutation profile of each ogg1Δ and ntg1Δ mutant was different from that of the wild-type strain. Taken together, we found that DNA N-glycosylase Ntg1 is required for oxidative DNA damage stress and antifungal drug resistance in C. neoformans.

Comparative genomics of Lactobacillus species as bee symbionts and description of Lactobacillus bombintestini sp. nov., isolated from the gut of Bombus ignitus: Jun Heo , Soo-Jin Kim , Jeong-Seon Kim , Seung-Beom Hong , Soon-Wo Kwon; J. Microbiol. 2020;58(6):445-455. Published online March 28, 2020; DOI: https://doi.org/10.1007/s12275-020-9596-3

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The Lactobacillus genus is widely used for fermentation of plant materials and dairy products. These species are typically found in highly specialized environments, with the bee gut serving as one of the niche locations in which Lactobacillus is detected. Lactobacillus species isolated from the bee gut and bee-related habitats were phylogenetically classified into three distinct groups, Lactobacillus kunkeei, Firm-4, and Firm-5. The L. kunkeei group was clearly differentiated from other members of the Lactobacillus buchneri group isolated from non-bee habitats. In comparison with non-bee members of the L. buchneri group, three bee-symbiotic Lactobacillus groups had a small-sized genome with low G + C content and showed a sharp reduction in the number of genes involved in energy production, carbohydrate transport and metabolism, and amino acid transport and metabolism. In addition, all three groups lacked the mutY gene, which encodes A/G-specific adenine glycosylase. The phylogenetic dendrogram based on the presence or absence of 1,199 functional genes indicated that these bee-symbiotic groups experienced convergent evolution. The occurrence of convergent evolution is thought to stem from the three bee-symbiotic groups sharing a similar habitat, i.e., the bee gut. The causative factor underlying genomic reduction was postulated to be mutY, which was absent in all three groups. Here, a novel strain, BHWM-4T, isolated from the gut of Bombus ignites was studied using polyphasic taxonomy and classified as a new member of the L. kunkeei group. The strain was Gram-positive, facultative anaerobic, and rod-shaped. The 16S ribosomal RNA gene sequence and genome analysis revealed that strain BHWM-4T was clustered into the L. kunkeei group, forming a compact cluster with L. kunkeei and Lactobacillus apinorum. Biochemical, chemotaxonomic, and genotypic data of strain BHWM-4T supports the proposal of a novel species, Lactobacillus bombintestini sp. nov., whose type strain is BHWM-4T (= KACC 19317T = NBRC 113067T).

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Tiny but mighty? Overview of a decade of research on nectar bacteria
Sergio Quevedo‐Caraballo, Clara de Vega, Bart Lievens, Tadashi Fukami, Sergio Álvarez‐Pérez
New Phytologist.2024;[Epub] CrossRef
Comparative genomic analyses reveal carbohydrates-rich environment adaptability of Lentilactobacillus laojiaonis sp. nov. IM3328
Qiuwei Zhao, Huawei Zhu, Xi Tong, Guanhui Bao, Suping Yang, Songtao Wang, Caihong Shen, Yin Li
Food Bioscience.2023; 53: 102737. CrossRef
International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Bifidobacterium, Lactobacillus and related organisms. Minutes of the closed meeting by videoconference, 3 September 2020
Paola Mattarelli, Giovanna E. Felis, B. Pot, Wilhelm H. Holzapfel, Charles M. A. P. Franz
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Levilactobacillus yiduensis sp. nov., Isolated from Zha-chili in Yidu County, Hubei Province, China
Yun Dong, Yurong Wang, Huijun Zhao, Yan Zhang, Haibo Zhang, Yafang Sun, Zhuang Guo
Current Microbiology.2023;[Epub] CrossRef
Influence of social lifestyles on host–microbe symbioses in the bees
Lauren Mee, Seth M. Barribeau
Ecology and Evolution.2023;[Epub] CrossRef
Effect of Probiotic Microorganisms on Catalase Activity, Fractional Composition of Soluble Proteins, and Intestinal Microbiota of Honey Bee
R.S. Fedoruk, I.I. Kovalchuk, A.Z. Pylypets, M.M. Tsap, Y.V. Lesyk, R.L. Androshulik, O.A. Demchenko, N.O. Tymoshok, L.P. Babenko
Mikrobiolohichnyi Zhurnal.2023; 85(4): 46. CrossRef
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Tomoaki Kouya, Yohei Ishiyama, Shota Ohashi, Ryota Kumakubo, Takeshi Yamazaki, Toshiki Otaki, Guadalupe Virginia Nevárez-Moorillón
PLOS ONE.2023; 18(6): e0286677. CrossRef
cpn60 barcode sequences accurately identify newly defined genera within the Lactobacillaceae
Ishika Shukla, Janet E. Hill
Canadian Journal of Microbiology.2022; 68(6): 457. CrossRef
Lactobacillus huangpiensis sp. nov. and Lactobacillus laiwuensis sp. nov., isolated from the gut of honeybee (Apis mellifera)
Ting Ting Li, Chun Tao Gu
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Seth M. Barribeau, Paul Schmid-Hempel, Jean-Claude Walser, Stefan Zoller, Martina Berchtold, Regula Schmid-Hempel, Niklaus Zemp, Pedro L. Oliveira
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Bombilactobacillus apium sp. nov., isolated from the gut of honeybee (Apis cerana)
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Archives of Microbiology.2021; 203(5): 2193. CrossRef
List of new names and new combinations that have appeared in effective publications outside of the IJSEM and are submitted for valid publication
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International Journal of Systematic and Evolutionary Microbiology .2020; 70(11): 5596. CrossRef
Proposal to reclassify four Lactobacillus species as Apilactobacillus bombintestini, Companilactobacillus suantsaicola, Lactiplantibacillus garii and Levilactobacillus suantsaiihabitans
Paola Mattarelli, Giovanna Felis, Charles M. A. P. Franz, Michael G. Gänzle
International Journal of Systematic and Evolutionary Microbiology .2019;[Epub] CrossRef

Lactobacillus plantarum lipoteichoic acid disrupts mature Enterococcus faecalis biofilm: A Reum Kim , Minji Kang , Yeon-Jee Yoo , Cheol-Heui Yun , Hiran Perinpanayagam , Kee-Yeon Kum , Seung Hyun Han; J. Microbiol. 2020;58(4):314-319. Published online January 28, 2020; DOI: https://doi.org/10.1007/s12275-020-9518-4

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Abstract

Apical periodontitis is caused by biofilm-mediated root canal infection. Early phase oral bacterial biofilms are inhibited by Lactobacillus plantarum lipoteichoic acid (Lp.LTA). However, mature biofilms that develop over 3 weeks are more resistant to traditional endodontic medicaments. Therefore, this study examined the effectiveness of Lp.LTA on disrupting mature Enterococcus faecalis biofilms, and on enhancing the effects of endodontic medicaments. LTA was purified from L. plantarum through butanol extraction followed by hydrophobic and ion-exchange chromatography. E. faecalis biofilms were formed over 3 weeks on glass bottom dishes and in dentin blocks obtained from human single-rooted premolars. These mature biofilms were treated with or without Lp.LTA for 1 h, followed by additional treatment with either chlorhexidine digluconate (CHX), calcium hydroxide (CH), or triple antibiotics for 24 h. Biofilms on glass were live/dead stained and quantified by ZEN through confocal laser microscopy. Biofilms in dentin were fixed, sputter coated and analyzed by ImageJ with scanning electron microscopy. Preformed E. faecalis mature biofilms on the culture dishes were dose-dependently disrupted by Lp.LTA. Lp.LTA potentiated the effects of CHX or CH on the disruption of mature biofilm. Interestingly, CHX-induced disruption of preformed E. faecalis mature biofilms was synergistically enhanced only when pretreated with Lp.LTA. Furthermore, in the dentin block model, Lp.LTA alone reduced E. faecalis mature biofilm and pre-treatment with Lp.LTA promoted the anti-biofilm activity of CHX. Lp.LTA could be an anti-biofilm or supplementary agent that can be effective for E. faecalis-biofilminduced diseases.

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A Systematic Review of the Comparative Efficacy of Lactobacillus Probiotics and Sodium Hypochlorite as Intracanal Irrigants Against Enterococcus faecalis
Mrinalini Mrinalini, Alpa Gupta, Dax Abraham, Arun Kumar Duraisamy, Rajat Sharma
Cureus.2024;[Epub] CrossRef
The role of Lactobacillus plantarum in oral health: a review of current studies
Xinyan Huang, Jianhang Bao, Mingzhen Yang, Yingying Li, Youwen Liu, Yuankun Zhai
Journal of Oral Microbiology.2024;[Epub] CrossRef
Lipoteichoic Acid from Lacticaseibacillus rhamnosus GG as a Novel Intracanal Medicament Targeting Enterococcus faecalis Biofilm Formation
Ji-Young Yoon, Somin Park, Dongwook Lee, Ok-Jin Park, WooCheol Lee, Seung Hyun Han
Journal of Microbiology.2024; 62(10): 897. CrossRef
Isolation, Identification and Antibacterial Characteristics of Lacticaseibacillus rhamnosus YT
Chengran Guan, Feng Li, Peng Yu, Xuan Chen, Yongqi Yin, Dawei Chen, Ruixia Gu, Chenchen Zhang, Bo Pang
Foods.2024; 13(17): 2706. CrossRef
Restriction of growth and biofilm formation of ESKAPE pathogens by caprine gut-derived probiotic bacteria
Prerna Saini, Repally Ayyanna, Rishi Kumar, Sayan Kumar Bhowmick, Vinay Bhaskar, Bappaditya Dey
Frontiers in Microbiology.2024;[Epub] CrossRef
Enterococcus Phage vB_EfaS_HEf13 as an Anti-Biofilm Agent Against Enterococcus faecalis
Dongwook Lee, Jintaek Im, A Reum Kim, Woohyung Jun, Cheol-Heui Yun, Seung Hyun Han
Journal of Microbiology.2024; 62(8): 683. CrossRef
Antibacterial effectiveness of multi-strain probiotics supernatants intracanal medication on Enterococcus faecalis biofilm in a tooth model
Shymaa Shaaban, Salma Genena, Alaaeldin Elraggal, Gamal M. Hamad, Marwa A. Meheissen, Sybel Moussa
BMC Oral Health.2023;[Epub] CrossRef
Antioxidant Effects and Probiotic Properties of Latilactobacillus sakei MS103 Isolated from Sweet Pickled Garlic
Heng Li, Changlin Chen, Yuanxin Li, Zhengqiang Li, Chen Li, Chang Luan
Foods.2023; 12(23): 4276. CrossRef
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Giusy Rita Maria La Rosa, Eugenio Pedullà
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Plantaricin LD1 purified from Lactobacillus plantarum LD1 inhibits biofilm formation of Enterococcus faecalis ATCC 29212 in tooth model
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Letters in Applied Microbiology.2022; 75(3): 623. CrossRef
The Products of Probiotic Bacteria Effectively Treat Persistent Enterococcus faecalis Biofilms
Shatha Safadi, Harsh Maan, Ilana Kolodkin-Gal, Igor Tsesis, Eyal Rosen
Pharmaceutics.2022; 14(4): 751. CrossRef
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Hisham Elnawam, Menatallah Abdelmougod, Ahmed Mobarak, Mai Hussein, Hamdy Aboualmakarem, Michael Girgis, Rania El Backly
Frontiers in Bioengineering and Biotechnology.2022;[Epub] CrossRef
Can Probiotics Emerge as Effective Therapeutic Agents in Apical Periodontitis? A Review
Gaurav Kumar, Sanjay Tewari, John Tagg, Michael Leonidas Chikindas, Igor V Popov, Santosh Kumar Tiwari
Probiotics and Antimicrobial Proteins.2021; 13(2): 299. CrossRef
Interplay between Candida albicans and Lactic Acid Bacteria in the Gastrointestinal Tract: Impact on Colonization Resistance, Microbial Carriage, Opportunistic Infection, and Host Immunity
Karen D. Zeise, Robert J. Woods, Gary B. Huffnagle
Clinical Microbiology Reviews.2021;[Epub] CrossRef
Mucosal Bacteria Modulate Candida albicans Virulence in Oropharyngeal Candidiasis
M. Bertolini, R. Vazquez Munoz, L. Archambault, S. Shah, J. G. S. Souza, R. C. Costa, A. Thompson, Y. Zhou, T. Sobue, A. Dongari-Bagtzoglou, Deborah A. Hogan
mBio.2021;[Epub] CrossRef
Gram Positive Bacterial Lipoteichoic Acid Role in a Root Canal Infection – A Literature Review
Vinoo Subramaniam Ramachandran, Mensudar Rathakrishnan, Malathy Balaraman Ravindrran, Alargarsamy Venkatesh, Vidhya Shankari Shanmugasundaram, Karpagavinayagam Kumaraguru
Journal of Pure and Applied Microbiology.2021; 15(2): 534. CrossRef
Lactobacillus plantarum Lipoteichoic Acids Possess Strain-Specific Regulatory Effects on the Biofilm Formation of Dental Pathogenic Bacteria
Dongwook Lee, Jintaek Im, Dong Hyun Park, Sungho Jeong, Miri Park, Seokmin Yoon, Jaewoong Park, Seung Hyun Han
Frontiers in Microbiology.2021;[Epub] CrossRef
Streptococcus gordonii: Pathogenesis and Host Response to Its Cell Wall Components
Ok-Jin Park, Yeongkag Kwon, Chaeyeon Park, Yoon Ju So, Tae Hwan Park, Sungho Jeong, Jintaek Im, Cheol-Heui Yun, Seung Hyun Han
Microorganisms.2020; 8(12): 1852. CrossRef

Lipoteichoic acids of lactobacilli inhibit Enterococcus faecalis biofilm formation and disrupt the preformed biofilm: Solmin Jung , Ok-Jin Park , A Reum Kim , Ki Bum Ahn , Dongwook Lee , Kee-Yeon Kum , Cheol-Heui Yun , Seung Hyun Han; J. Microbiol. 2019;57(4):310-315. Published online January 22, 2019; DOI: https://doi.org/10.1007/s12275-019-8538-4

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Abstract

Enterococcus faecalis, a Gram-positive bacterium commonly isolated in patients with refractory apical periodontitis, invades dentin tubules easily and forms biofilms. Bacteria in biofilms, which contribute to recurrent and/or chronic inflammatory diseases, are more resistant to antimicrobial agents than planktonic cells and easily avoid phagocytosis. Although Lactobacillus plantarum lipoteichoic acid (Lp.LTA) is associated with biofilm formation, the effect of Lp.LTA on biofilm formation by E. faecalis is not clearly understood. In this study, we investigated whether Lp.LTA inhibits E. faecalis biofilm formation. The degree of biofilm formation was determined by using crystal violet assay and LIVE/DEAD bacteria staining. The quantification of bacterial growth was determined by measuring the optical density at 600 nm with a spectrophotometer. Formation of biofilms on human dentin slices was observed under a scanning electron microscope. E. faecalis biofilm formation was reduced by Lp.LTA treatment in a dose-dependent manner. Lp.LTA inhibited biofilm development of E. faecalis at the early stage without affecting bacterial growth. LTA from other Lactobacillus species such as Lactobacillus acidophilus, Lactobacillus casei, or Lactobacillus rhamnosus GG also inhibited E. faecalis biofilm formation. In particular, among LTAs from various lactobacilli, Lp.LTA showed the highest inhibitory effect on biofilms formed by E. faecalis. Interestingly, LTAs from lactobacilli could remove the biofilm preformed by E. faecalis. These inhibitory effects were also observed on the surface of human dentin slices. In conclusion, Lactobacillus species LTA inhibits biofilm formation caused by E. faecalis and it could be used as an anti-biofilm agent for prevention or treatment against E. faecalis-associated diseases.

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Review

MINIREVIEW] Clinical relevance of infections with zoonotic and human oral species of Campylobacter: Soomin Lee , Jeeyeon Lee , Jimyeong Ha , Yukyung Choi , Sejeong Kim , Heeyoung Lee , Yohan Yoon , Kyoung-Hee Choi; J. Microbiol. 2016;54(7):459-467. Published online June 28, 2016; DOI: https://doi.org/10.1007/s12275-016-6254-x

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Abstract

Genus Campylobacter has been recognized as a causative bacterial agent of animal and human diseases. Human Campylobacter infections have caused more concern. Campylobacters can be classified into two groups in terms of their original host: zoonotic and human oral species. The major zoonotic species are Campylobacter jejuni and Campylobacter coli, which mostly reside in the intestines of avian species and are transmitted to humans via consumption of contaminated poultry products, thus causing human gastroenteritis and other diseases as sequelae. The other campylobacters, human oral species, include C. concisus, C. showae, C. gracilis, C. ureolyticus, C. curvus, and C. rectus. These species are isolated from the oral cavity, natural colonization site, but have potential clinical relevance in the periodontal region to varying extent. Two species, C. jejuni and C. coli, are believed to be mainly associated with intestinal diseases, but recent studies suggested that oral Campylobacter species also play a significant role in intestinal diseases. This review offers an outline of the two Campylobacter groups (zoonotic and human oral), their virulence traits, and the associated illnesses including gastroenteritis.

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

Plasminogen Activator Inhibitor Type 1 Expression Induced by Lipopolysaccharide of Porphyromonas gingivalis in Human Gingival Fibroblast: Hee Sam Na , Eun J. Lim , So Y. Jeong , Mi H. Ryu , Mi Hee Park , Jin Chung; J. Microbiol. 2014;52(2):154-160. Published online February 1, 2014; DOI: https://doi.org/10.1007/s12275-014-3022-7

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Abstract

In the gingival tissues of patients with periodontitis, inflammatory responses are mediated by a wide variety of genes. In our previous screening study, plasminogen activator inhibitor type 1 (PAI-1) mRNA binding protein expression was increased in gingiva from periodontitis patients. In this study, we further investigated the signaling pathway involved in PAI-1 expression induced by Porphyromonas gingivalis LPS (Pg LPS) in human gingival fibroblasts (HGF). When HGFs were treated with Pg LPS, both PAI-1 mRNA expression and PAI-1 protein were induced in a dose-dependent manner. Pg LPS induced NF-κB activation and the expressions of PAI-1 mRNA and protein were suppressed by pretreating with a NF-κB inhibitor. Pg LPS also induced ERK, p38, and JNK activation, and Pg LPS-induced PAI-1 expression was inhibited by ERK/p38/JNK inhibitor pretreatment. In conclusion, Pg LPS induced PAI-1 expression through NF-κB and MAP kinases activation in HGF.

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Characterization of Antibiotic Resistance Determinants in Oral Biofilms: Seon-Mi Kim , Hyeong C. Kim , Seok-Woo S. Lee; J. Microbiol. 2011;49(4):595-602. Published online September 2, 2011; DOI: https://doi.org/10.1007/s12275-011-0519-1

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Abstract: Oral biofilms contain numerous antibiotic resistance determinants that can be transferred within or outside of the oral cavity. The aim of this study was to evaluate the prevalence and the relative level of antibiotic resistance determinants from oral biofilms. Oral biofilm samples that were collected from healthy subjects and periodontitis patients were subjected to qualitative and quantitative analyses for selected antibiotic resistance determinants using PCR. The prevalence of tet(Q), tet(M), cfxA, and blaTEM was very high both in the patient and the healthy subject group, with a tendency toward higher values in the patient group, with the exception of erm(F), which was more prevalent in the healthy group. The two extended spectrum β-lactam (ESBL) resistance determinants blaSHV and blaTEM showed a dramatic difference, as blaTEM was present in all of the samples and blaSHV was not found at all. The aacA-aphD, vanA, and mecA genes were rarely detected, suggesting that they are not common in oral bacteria. A quantitative PCR analysis showed that the relative amount of resistance determinants present in oral biofilms of the patient group was much greater than that of the healthy group, exhibiting 17-, 13-, 145-, and 3-fold increases for tet(Q), tet(M), erm(F), and cfxA, respectively. The results of this study suggest that the oral antibiotic resistome is more diverse and abundant in periodontitis patients than in healthy subjects, suggesting that there is a difference in the diversity and distribution of antibiotic resistance in oral biofilms associated with health and disease.

Published Erratum

Erratum] Brevibacterium limosum sp. nov., Brevibacterium pigmenatum sp. nov., and Brevibacterium atlanticum sp. nov., three novel dye decolorizing actinobacteria isolated from ocean sediments: Shengxiang Pei , Siwen Niu , Fuquan Xie , Wenjing Wang , Shuang Zhang , Gaiyun Zhang; J. Microbiol. 2021;59(11):1064-1065.; DOI: https://doi.org/10.1007/s12275-021-0235-4

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